├── CNAME ├── docs ├── CNAME ├── mouse.rst ├── measure.rst ├── render.rst ├── axes.rst ├── imd.rst ├── material.rst ├── label.rst └── selection.rst ├── vmd ├── plugins │ ├── fmtool │ │ ├── test │ │ │ └── 1.dat │ │ ├── .cvsignore │ │ ├── dmabufalloc.h │ │ ├── cudamgr.h │ │ ├── write_psf.h │ │ └── psf_from_file_xy_to_r.h │ ├── stamp │ │ ├── pdb.directories │ │ └── dssp.directories │ ├── bdtk │ │ ├── database │ │ │ ├── membrane.dat │ │ │ ├── shapes │ │ │ │ ├── shape1.gif │ │ │ │ ├── shape2.gif │ │ │ │ ├── shape2.shp │ │ │ │ └── shape1.shp │ │ │ ├── interactions.dat │ │ │ └── ions.dat │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── psfgen │ │ ├── python │ │ │ └── Psfgen │ │ │ │ └── __init__.py │ │ ├── scripts │ │ │ ├── template.conf │ │ │ └── buildmin.tcl │ │ └── src │ │ │ ├── charmm_file.h │ │ │ ├── charmm_parse_topo_defs.h │ │ │ ├── psf_file_extract.h │ │ │ ├── memarena.h │ │ │ ├── stringhash.h │ │ │ ├── psfgen.h │ │ │ ├── pkgIndex.tcl │ │ │ ├── extract_alias.h │ │ │ └── pdb_file_extract.h │ ├── ilstools │ │ ├── xenon.xyz │ │ ├── nitricoxide.xyz │ │ ├── carbonmonoxide.xyz │ │ ├── hydrogen.xyz │ │ ├── nitrogen.xyz │ │ ├── oxygen.xyz │ │ ├── carbondioxide.xyz │ │ ├── nitrousoxide.xyz │ │ ├── acetylene.xyz │ │ ├── nitrogendioxide.xyz │ │ ├── methane.xyz │ │ ├── ethene.xyz │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── libbiokit │ │ └── src │ │ │ ├── libbiokit │ │ │ ├── alnReader.cpp │ │ │ ├── alnReader.h │ │ │ └── typeConvert.h │ │ │ ├── utils │ │ │ ├── version.h │ │ │ └── qh.h │ │ │ └── interface │ │ │ └── tcl_libbiokit.i │ ├── molefacture │ │ ├── lib │ │ │ ├── fragments │ │ │ │ ├── chloride.mfrag │ │ │ │ ├── carboxyl.mfrag │ │ │ │ ├── thiol.mfrag │ │ │ │ ├── hydroxyl.mfrag │ │ │ │ ├── nitrile.frag │ │ │ │ ├── methyl.pdb │ │ │ │ ├── nitro.frag │ │ │ │ ├── methyl.mfrag │ │ │ │ ├── carboxylate.frag │ │ │ │ ├── amino.mfrag │ │ │ │ ├── formyl.mfrag │ │ │ │ ├── vinyl.mfrag │ │ │ │ ├── phospho.frag │ │ │ │ └── epoxide.frag │ │ │ ├── nucleic_acids │ │ │ │ └── dna_dihedrals.gif │ │ │ ├── basemol │ │ │ │ ├── water.mfrag │ │ │ │ ├── hcn.mfrag │ │ │ │ ├── ammonia.mfrag │ │ │ │ ├── formic_acid.mfrag │ │ │ │ ├── methane.mfrag │ │ │ │ ├── sulfate.mfrag │ │ │ │ ├── oxyrane.mfrag │ │ │ │ ├── benzene.mfrag │ │ │ │ └── cyclopropane.mfrag │ │ │ └── amino_acids │ │ │ │ ├── ALA.mfrag │ │ │ │ ├── CYS.mfrag │ │ │ │ ├── SER.mfrag │ │ │ │ ├── ASP.mfrag │ │ │ │ ├── GLY.mfrag │ │ │ │ ├── GLY-end.mfrag │ │ │ │ ├── ASN.mfrag │ │ │ │ ├── THR.mfrag │ │ │ │ ├── GLU.mfrag │ │ │ │ ├── VAL.mfrag │ │ │ │ ├── GLN.mfrag │ │ │ │ ├── MET.mfrag │ │ │ │ ├── HIS.mfrag │ │ │ │ └── HSE.mfrag │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── remote │ │ ├── mobileapps │ │ │ └── android │ │ │ │ └── VMDMobile │ │ │ │ ├── .cvsignore │ │ │ │ ├── res │ │ │ │ ├── drawable │ │ │ │ │ ├── noimage.png │ │ │ │ │ ├── touchpad.9.png │ │ │ │ │ ├── ic_launcher.png │ │ │ │ │ └── ic_launcher_fullsize.png │ │ │ │ ├── drawable-hdpi │ │ │ │ │ ├── ic_launcher.png │ │ │ │ │ ├── ic_menu_goto.png │ │ │ │ │ ├── ic_menu_stop.png │ │ │ │ │ ├── ic_menu_camera.png │ │ │ │ │ ├── ic_menu_manage.png │ │ │ │ │ ├── ic_menu_revert.png │ │ │ │ │ ├── ic_menu_play_clip.png │ │ │ │ │ └── ic_menu_preferences.png │ │ │ │ ├── drawable-large │ │ │ │ │ └── ic_launcher.png │ │ │ │ ├── drawable-ldpi │ │ │ │ │ ├── ic_launcher.png │ │ │ │ │ ├── ic_menu_goto.png │ │ │ │ │ ├── ic_menu_stop.png │ │ │ │ │ ├── ic_menu_manage.png │ │ │ │ │ ├── ic_menu_revert.png │ │ │ │ │ ├── ic_menu_play_clip.png │ │ │ │ │ └── ic_menu_preferences.png │ │ │ │ ├── drawable-mdpi │ │ │ │ │ ├── ic_launcher.png │ │ │ │ │ ├── ic_menu_goto.png │ │ │ │ │ ├── ic_menu_stop.png │ │ │ │ │ ├── ic_menu_camera.png │ │ │ │ │ ├── ic_menu_manage.png │ │ │ │ │ ├── ic_menu_revert.png │ │ │ │ │ ├── ic_menu_play_clip.png │ │ │ │ │ └── ic_menu_preferences.png │ │ │ │ └── values │ │ │ │ │ └── arrays.xml │ │ │ │ ├── art │ │ │ │ ├── README │ │ │ │ ├── ic_launcher_512x512.png │ │ │ │ ├── ic_launcher_fullsize.png │ │ │ │ └── screenshots │ │ │ │ │ ├── twoFingers.png │ │ │ │ │ ├── oneFingerOff.png │ │ │ │ │ └── settingsScreen.png │ │ │ │ ├── project.properties │ │ │ │ ├── default.properties │ │ │ │ ├── local.properties │ │ │ │ └── local.properties.example │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── blast │ │ ├── blast.tcl │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── phylotree │ │ └── run.tcl │ ├── biocore │ │ ├── locked.gif │ │ ├── unlocked.gif │ │ └── Makefile │ ├── rmsdvt │ │ ├── rmsdvt.tcl │ │ ├── rmsdvt-gui.tcl │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── paratool │ │ ├── paratool.tcl │ │ ├── paratool_charmmcharges.tcl │ │ └── pkgIndex.tcl │ ├── tablelist │ │ ├── demos │ │ │ ├── file.gif │ │ │ ├── open.gif │ │ │ ├── checked.gif │ │ │ ├── clsdFolder.gif │ │ │ ├── openFolder.gif │ │ │ ├── unchecked.gif │ │ │ ├── comp.xbm │ │ │ └── leaf.xbm │ │ ├── scripts │ │ │ └── pencil.cur │ │ ├── COPYRIGHT.txt │ │ └── tablelist.tcl │ ├── intersurf │ │ ├── intersurf_gui.tcl │ │ └── pkgIndex.tcl │ ├── molfile_plugin │ │ ├── msvc │ │ │ ├── vc60.idb │ │ │ └── vc60.pdb │ │ └── src │ │ │ ├── phiplugin.C │ │ │ └── periodic_table.h │ ├── autopsf │ │ └── src │ │ │ ├── psfcheck.h │ │ │ ├── psfcheck.i │ │ │ ├── psftypelist.h │ │ │ ├── psfreslist.h │ │ │ ├── psfbond.h │ │ │ ├── psfatomlist.h │ │ │ └── psftype.h │ ├── mutator │ │ └── src │ │ │ ├── Makefile │ │ │ └── alchemify_tcl.i │ ├── seqdata │ │ └── seqdata_temperature.tcl │ ├── vmdtkcon │ │ ├── tkcon-2.3 │ │ │ └── docs │ │ │ │ └── demopic.gif │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── mdff │ │ ├── load-mdff-results.tcl │ │ ├── resetmaps.sh │ │ └── Makefile │ ├── simpleedit │ │ ├── README │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── seqedit │ │ └── run.tcl │ ├── drugui │ │ ├── probe.xsc │ │ └── pkgIndex.tcl │ ├── cgtools │ │ ├── water.cgc │ │ └── Makefile │ ├── cionize │ │ ├── mgpot_lattice.c │ │ ├── machine.h │ │ ├── energymgrid.h │ │ ├── energythr.h │ │ ├── mgpot_quintic1.c │ │ ├── cudaenergythrsingleion.h │ │ ├── cudaenergythr.h │ │ ├── cionize_grid.h │ │ └── mgpot.h │ ├── nlenergy │ │ └── src │ │ │ └── old │ │ │ ├── hack │ │ │ ├── energy.c │ │ │ ├── test_io.c │ │ │ ├── force.h │ │ │ ├── numeric.h │ │ │ ├── molfiles.h │ │ │ ├── psf.h │ │ │ ├── xplor.h │ │ │ ├── charmm.h │ │ │ ├── nlbase.h │ │ │ ├── mem.h │ │ │ └── test_mem.c │ │ │ ├── moltypes │ │ │ ├── energy.c │ │ │ └── GNUmakefile │ │ │ ├── nlbase │ │ │ ├── test_io.c │ │ │ ├── numeric.h │ │ │ ├── GNUmakefile │ │ │ ├── nlbase.h │ │ │ ├── mem.h │ │ │ └── test_mem.c │ │ │ ├── force │ │ │ ├── force.h │ │ │ └── GNUmakefile │ │ │ ├── molfiles │ │ │ ├── GNUmakefile │ │ │ ├── molfiles.h │ │ │ ├── psf.h │ │ │ ├── xplor.h │ │ │ └── charmm.h │ │ │ └── nlenergy │ │ │ └── GNUmakefile │ ├── navigate │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── volmapgui │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── idatm │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── ramaplot │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── rmsd │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── runante │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── runsqm │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── vdna │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── vmdlite │ │ ├── vmd.rc │ │ ├── centerMolecule.tcl │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── gofrgui │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── ruler │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── bendix │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── bignum │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── hbonds │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── namdplot │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── navfly │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── nmwiz │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── rmsdtt │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── saltbr │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── atomedit │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── cliptool │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── clonerep │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── dipwatch │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── inorganicbuilder │ │ ├── materials │ │ │ ├── au.pdb │ │ │ └── graphite.pdb │ │ └── Makefile │ ├── irspecgui │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── moltoptools │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── parsefep │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── pdbtool │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── propka │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── resptool │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── textview │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── timeline │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── updater │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── vmdmovie │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── vmdprefs │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── zoomseq │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── jmvexport │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── multiplot │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── multitext │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── namdserver │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── plotter │ │ └── Makefile │ ├── stingtool │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── utilities │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── apbsrun │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── contactmap │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── dataimport │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── demomaster │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── dowser │ │ └── Makefile │ ├── heatmapper │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── namdenergy │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── optimization │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── viewmaster │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── vmddebug │ │ └── Makefile │ ├── bossconvert │ │ ├── src │ │ │ ├── Worker.h │ │ │ ├── AtomWeights.h │ │ │ ├── Makefile │ │ │ └── Example.sh │ │ └── pkgIndex.tcl │ ├── colorscalebar │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── exectool │ │ └── Makefile │ ├── extendedpdb │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── imdmenu │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── palettetool │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── psipred │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── symmetrytool │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── aligntool │ │ └── Makefile │ ├── clustalw │ │ └── src │ │ │ └── gcgcheck.c │ ├── mergestructs │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── multimolanim │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── namdgui │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── chirality │ │ └── Makefile │ ├── nanotube │ │ └── Makefile │ ├── autoionize │ │ └── Makefile │ ├── cispeptide │ │ └── Makefile │ ├── solvate │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── structurecheck │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── alascanfep │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── viewchangerender │ │ └── Makefile │ ├── ssrestraints │ │ └── Makefile │ ├── rnaview │ │ ├── BASEPARS │ │ │ └── misc_rna.par │ │ └── pkgIndex.tcl │ ├── pbctools │ │ ├── Makefile │ │ ├── AUTHORS │ │ └── README │ ├── multiseqdialog │ │ └── Makefile │ ├── autoimd │ │ └── Makefile │ ├── networkview │ │ └── Makefile │ ├── qwikmd │ │ └── Makefile │ ├── pmepot │ │ └── src │ │ │ └── pmepot.h │ ├── qmtool │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── membrane │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── signalproc │ │ └── signalproc.tcl │ ├── topotools │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── hesstrans │ │ └── pkgIndex.tcl │ ├── plumed │ │ └── Makefile │ ├── trunctraj │ │ └── pkgIndex.tcl │ ├── readcharmmpar │ │ ├── Makefile │ │ └── pkgIndex.tcl │ ├── volutil │ │ └── pkgIndex.tcl │ ├── fftk │ │ └── pkgIndex.tcl │ ├── mafft │ │ └── pkgIndex.tcl │ ├── torsionplot │ │ └── pkgIndex.tcl │ └── readcharmmtop │ │ └── pkgIndex.tcl └── vmd_src │ └── src │ ├── Makedata.depend │ ├── vmdmac.r │ ├── OptiXShaders.h │ ├── OptiXRenderer.C │ ├── OptiXRenderer.h │ ├── OptiXShaders.cu │ ├── PeriodicTable.C │ ├── macosxvmdstart.h │ ├── OptiXDisplayDevice.C │ ├── OptiXDisplayDevice.h │ ├── fitrms.h │ ├── colvars_version.h │ └── colvarproxy_vmd_version.h ├── .bumpversion.cfg ├── MANIFEST.in ├── .gitignore ├── test ├── test_axes.py └── test_mouse.py └── CHANGELOG.md /CNAME: -------------------------------------------------------------------------------- 1 | vmd.robinbetz.com -------------------------------------------------------------------------------- /docs/CNAME: -------------------------------------------------------------------------------- 1 | vmd.robinbetz.com -------------------------------------------------------------------------------- /vmd/plugins/fmtool/test/1.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /vmd/plugins/fmtool/.cvsignore: -------------------------------------------------------------------------------- 1 | fmtool 2 | *.dat 3 | 4 | -------------------------------------------------------------------------------- /vmd/plugins/stamp/pdb.directories: -------------------------------------------------------------------------------- 1 | /tmp multiseq. .pdb 2 | -------------------------------------------------------------------------------- /vmd/vmd_src/src/Makedata.depend: -------------------------------------------------------------------------------- 1 | ParseTree.o: y.tab.h 2 | -------------------------------------------------------------------------------- /vmd/plugins/bdtk/database/membrane.dat: -------------------------------------------------------------------------------- 1 | Graphene GRAPHENE 2 | -------------------------------------------------------------------------------- /vmd/plugins/stamp/dssp.directories: -------------------------------------------------------------------------------- 1 | /tmp multiseq. .dssp 2 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/python/Psfgen/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | from Psfgen import Psfgen 3 | -------------------------------------------------------------------------------- /vmd/plugins/ilstools/xenon.xyz: -------------------------------------------------------------------------------- 1 | 1 2 | Xenon 3 | Xe 0.00000 0.00000 0.00000 4 | -------------------------------------------------------------------------------- /vmd/plugins/libbiokit/src/libbiokit/alnReader.cpp: -------------------------------------------------------------------------------- 1 | 2 | #include "alnReader.h" 3 | 4 | 5 | 6 | -------------------------------------------------------------------------------- /vmd/plugins/libbiokit/src/utils/version.h: -------------------------------------------------------------------------------- 1 | #ifndef VERSION 2 | #define VERSION "1.13" 3 | #endif 4 | 5 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/chloride.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT CHLORIDE 2 | CL 1.52 0.0 0.0 CL 3 | BONDS 4 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/.cvsignore: -------------------------------------------------------------------------------- 1 | libs 2 | gen 3 | bin 4 | local.properties 5 | -------------------------------------------------------------------------------- /vmd/vmd_src/src/vmdmac.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/vmd_src/src/vmdmac.r -------------------------------------------------------------------------------- /vmd/plugins/blast/blast.tcl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/blast/blast.tcl -------------------------------------------------------------------------------- /vmd/plugins/phylotree/run.tcl: -------------------------------------------------------------------------------- 1 | append auto_path " " "." 2 | package require phylotree 1.1 3 | phylotree_gui 4 | -------------------------------------------------------------------------------- /vmd/plugins/biocore/locked.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/biocore/locked.gif -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/carboxyl.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT CARBOXYL 2 | O 1.40 0.0 0.0 O 3 | BONDS 4 | 0 -1 2.0 5 | -------------------------------------------------------------------------------- /vmd/plugins/rmsdvt/rmsdvt.tcl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/rmsdvt/rmsdvt.tcl -------------------------------------------------------------------------------- /vmd/vmd_src/src/OptiXShaders.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/vmd_src/src/OptiXShaders.h -------------------------------------------------------------------------------- /vmd/plugins/biocore/unlocked.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/biocore/unlocked.gif -------------------------------------------------------------------------------- /vmd/plugins/paratool/paratool.tcl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/paratool/paratool.tcl -------------------------------------------------------------------------------- /vmd/plugins/rmsdvt/rmsdvt-gui.tcl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/rmsdvt/rmsdvt-gui.tcl -------------------------------------------------------------------------------- /vmd/vmd_src/src/OptiXRenderer.C: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/vmd_src/src/OptiXRenderer.C -------------------------------------------------------------------------------- /vmd/vmd_src/src/OptiXRenderer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/vmd_src/src/OptiXRenderer.h -------------------------------------------------------------------------------- /vmd/vmd_src/src/OptiXShaders.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/vmd_src/src/OptiXShaders.cu -------------------------------------------------------------------------------- /vmd/vmd_src/src/PeriodicTable.C: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/vmd_src/src/PeriodicTable.C -------------------------------------------------------------------------------- /vmd/vmd_src/src/macosxvmdstart.h: -------------------------------------------------------------------------------- 1 | /* include file for MacOS X startup code */ 2 | int macosxvmdstart(int argc, char **argv); 3 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/thiol.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT THIOL 2 | S 1.52 0.0 0.0 S 3 | H 2.24 1.24 0.0 H 4 | BONDS 5 | 0 1 1.0 6 | -------------------------------------------------------------------------------- /vmd/plugins/tablelist/demos/file.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/tablelist/demos/file.gif -------------------------------------------------------------------------------- /vmd/plugins/tablelist/demos/open.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/tablelist/demos/open.gif -------------------------------------------------------------------------------- /vmd/vmd_src/src/OptiXDisplayDevice.C: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/vmd_src/src/OptiXDisplayDevice.C -------------------------------------------------------------------------------- /vmd/vmd_src/src/OptiXDisplayDevice.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/vmd_src/src/OptiXDisplayDevice.h -------------------------------------------------------------------------------- /vmd/plugins/fmtool/dmabufalloc.h: -------------------------------------------------------------------------------- 1 | void * DMABufAlloc(size_t sz, int pagelocked); 2 | void DMABufFree(void *mem, int pagelocked); 3 | 4 | -------------------------------------------------------------------------------- /vmd/plugins/intersurf/intersurf_gui.tcl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/intersurf/intersurf_gui.tcl -------------------------------------------------------------------------------- /vmd/plugins/molfile_plugin/msvc/vc60.idb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/molfile_plugin/msvc/vc60.idb -------------------------------------------------------------------------------- /vmd/plugins/molfile_plugin/msvc/vc60.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/molfile_plugin/msvc/vc60.pdb -------------------------------------------------------------------------------- /vmd/plugins/tablelist/demos/checked.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/tablelist/demos/checked.gif -------------------------------------------------------------------------------- /vmd/plugins/tablelist/scripts/pencil.cur: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/tablelist/scripts/pencil.cur -------------------------------------------------------------------------------- /vmd/plugins/autopsf/src/psfcheck.h: -------------------------------------------------------------------------------- 1 | #ifndef _PSFCHECK 2 | #define _PSFCHECK 3 | 4 | int psfupdate(char*, char*, char*); 5 | 6 | #endif 7 | -------------------------------------------------------------------------------- /vmd/plugins/bdtk/database/shapes/shape1.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/bdtk/database/shapes/shape1.gif -------------------------------------------------------------------------------- /vmd/plugins/bdtk/database/shapes/shape2.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/bdtk/database/shapes/shape2.gif -------------------------------------------------------------------------------- /vmd/plugins/ilstools/nitricoxide.xyz: -------------------------------------------------------------------------------- 1 | 2 2 | nitric oxide 3 | N 0.00000 0.00000 0.00000 4 | O 0.00000 1.15000 0.00000 5 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/hydroxyl.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT HYDROXYL 2 | O 1.52 0.0 0.0 O 3 | H 2.24 1.24 0.0 H 4 | BONDS 5 | 0 1 1.0 6 | -------------------------------------------------------------------------------- /vmd/plugins/molfile_plugin/src/phiplugin.C: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/molfile_plugin/src/phiplugin.C -------------------------------------------------------------------------------- /vmd/plugins/mutator/src/Makefile: -------------------------------------------------------------------------------- 1 | libalchemify_wrap.c : alchemify_tcl.i 2 | swig -tcl8 -o alchemify_tcl_wrap.c alchemify_tcl.i 3 | 4 | 5 | -------------------------------------------------------------------------------- /vmd/plugins/seqdata/seqdata_temperature.tcl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/seqdata/seqdata_temperature.tcl -------------------------------------------------------------------------------- /vmd/plugins/tablelist/demos/clsdFolder.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/tablelist/demos/clsdFolder.gif -------------------------------------------------------------------------------- /vmd/plugins/tablelist/demos/openFolder.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/tablelist/demos/openFolder.gif -------------------------------------------------------------------------------- /vmd/plugins/tablelist/demos/unchecked.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/tablelist/demos/unchecked.gif -------------------------------------------------------------------------------- /vmd/plugins/ilstools/carbonmonoxide.xyz: -------------------------------------------------------------------------------- 1 | 2 2 | carbon monoxide 3 | C 0.00000 0.00000 0.00000 4 | O 0.00000 1.00350 0.00000 5 | -------------------------------------------------------------------------------- /vmd/plugins/molfile_plugin/src/periodic_table.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/molfile_plugin/src/periodic_table.h -------------------------------------------------------------------------------- /vmd/plugins/paratool/paratool_charmmcharges.tcl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/paratool/paratool_charmmcharges.tcl -------------------------------------------------------------------------------- /vmd/plugins/vmdtkcon/tkcon-2.3/docs/demopic.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/vmdtkcon/tkcon-2.3/docs/demopic.gif -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/nitrile.frag: -------------------------------------------------------------------------------- 1 | FRAGMENT NITRILE 2 | C 1.0 0.0 0.0 C 3 | N 3.22769999504 0.0 0.0 N 4 | BONDS 5 | 0 1 3.0 6 | 1 0 3.0 7 | -------------------------------------------------------------------------------- /vmd/plugins/autopsf/src/psfcheck.i: -------------------------------------------------------------------------------- 1 | %module psfcheck 2 | %{ 3 | #include "psfcheck.h" 4 | %} 5 | 6 | int psfupdate(char* topin, char* inpdb, char* psfout); 7 | -------------------------------------------------------------------------------- /vmd/plugins/bdtk/database/shapes/shape2.shp: -------------------------------------------------------------------------------- 1 | Cylindrical 2 | CylinderPoreSurf 3 | Nanopore thickness 4 | Pore diameter X 5 | Pore diameter Y 6 | Corner radius 7 | -------------------------------------------------------------------------------- /vmd/plugins/mdff/load-mdff-results.tcl: -------------------------------------------------------------------------------- 1 | #pass ".sort" to load sorted 2 | set ::sort [lindex $argv 0] 3 | source remdff.namd 4 | source show_replicas_mdff.vmd 5 | -------------------------------------------------------------------------------- /vmd/plugins/ilstools/hydrogen.xyz: -------------------------------------------------------------------------------- 1 | 2 2 | hydrogen 3 | H2 0.000000 0.000000 0.000000 4 | H2 0.741300 0.000000 0.000000 5 | -------------------------------------------------------------------------------- /vmd/plugins/ilstools/nitrogen.xyz: -------------------------------------------------------------------------------- 1 | 2 2 | nitrogen 3 | N2 0.000000 0.000000 0.000000 4 | N2 1.097600 0.000000 0.000000 5 | -------------------------------------------------------------------------------- /vmd/plugins/ilstools/oxygen.xyz: -------------------------------------------------------------------------------- 1 | 2 2 | generated by VMD 3 | O2 0.000000 0.000000 0.000000 4 | O2 0.000000 1.230000 0.000000 5 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/nucleic_acids/dna_dihedrals.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/molefacture/lib/nucleic_acids/dna_dihedrals.gif -------------------------------------------------------------------------------- /vmd/plugins/ilstools/carbondioxide.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | carbon dioxide 3 | C -0.01430 1.20380 0.00870 4 | O 0.00210 -0.00410 0.00200 5 | O -0.03070 2.41170 0.01530 6 | -------------------------------------------------------------------------------- /vmd/plugins/ilstools/nitrousoxide.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | nitrous oxide 3 | N -1.18600 0.00000 0.00000 4 | N 0.00000 0.00000 0.00000 5 | O 1.12600 0.00000 0.00000 6 | -------------------------------------------------------------------------------- /vmd/plugins/bdtk/database/shapes/shape1.shp: -------------------------------------------------------------------------------- 1 | Double Cone 2 | DoubleconePoreSurf 3 | Nanopore thickness 4 | Inner diameter X 5 | Inner diameter Y 6 | Outer diameter X 7 | Outer diameter Y 8 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/basemol/water.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT WATER HOH 2 | O 0.0 0.0 0.0 O 3 | H 1.0 0.0 0.0 H 4 | H -0.325568139553 0.945518553257 -2.71878575209e-10 H 5 | BONDS 6 | 0 1 1 7 | 0 2 1 8 | -------------------------------------------------------------------------------- /vmd/plugins/simpleedit/README: -------------------------------------------------------------------------------- 1 | Simple editor module for multiseq. This glues stuff together to export seq into a 2 | text file, invoke editor, and re-import the data when the editor exits. 3 | 4 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable/noimage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable/noimage.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/art/README: -------------------------------------------------------------------------------- 1 | launcher icon is the launcher_fullsize reduced to proper sizes. This 2 | isn't the best way to get the absolute best look, but it works for now. 3 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/art/ic_launcher_512x512.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/art/ic_launcher_512x512.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable/touchpad.9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable/touchpad.9.png -------------------------------------------------------------------------------- /vmd/plugins/mdff/resetmaps.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | rm -rf output/ 3 | mkdir output 4 | for i in `seq 0 5`; 5 | do 6 | mkdir output/$i 7 | rm -f $i.dx 8 | ln -s initialmaps/$i.dx $i.dx 9 | done 10 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/art/ic_launcher_fullsize.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/art/ic_launcher_fullsize.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/art/screenshots/twoFingers.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/art/screenshots/twoFingers.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable/ic_launcher.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable/ic_launcher.png -------------------------------------------------------------------------------- /vmd/plugins/ilstools/acetylene.xyz: -------------------------------------------------------------------------------- 1 | 4 2 | acetylene 3 | C 0.00210 -0.00410 0.00200 4 | C -0.01380 1.16980 0.00850 5 | H 0.01630 -1.05400 -0.00380 6 | H -0.02810 2.21970 0.01420 7 | -------------------------------------------------------------------------------- /vmd/plugins/mutator/src/alchemify_tcl.i: -------------------------------------------------------------------------------- 1 | %module alchemify 2 | 3 | %{ 4 | extern int alchemify(char *inPSF, char *outPSF, char *inFEP); 5 | %} 6 | 7 | extern int alchemify(char *inPSF, char *outPSF, char *inFEP); 8 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/art/screenshots/oneFingerOff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/art/screenshots/oneFingerOff.png -------------------------------------------------------------------------------- /vmd/vmd_src/src/fitrms.h: -------------------------------------------------------------------------------- 1 | #ifdef __cplusplus 2 | extern "C" { 3 | #endif 4 | 5 | void MatrixFitRMS(int n, float *v1, float *v2, const float *wt, float *ttt); 6 | 7 | #ifdef __cplusplus 8 | } 9 | #endif 10 | -------------------------------------------------------------------------------- /vmd/plugins/fmtool/cudamgr.h: -------------------------------------------------------------------------------- 1 | 2 | 3 | #if defined(__cplusplus) 4 | extern "C" { 5 | #endif 6 | 7 | int open_cuda_dev(int cudadev); 8 | 9 | 10 | #if defined(__cplusplus) 11 | } 12 | #endif 13 | 14 | 15 | 16 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/art/screenshots/settingsScreen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/art/screenshots/settingsScreen.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_launcher.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_launcher.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_goto.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_goto.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_stop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_stop.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-large/ic_launcher.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-large/ic_launcher.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_launcher.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_launcher.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_goto.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_goto.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_stop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_stop.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_launcher.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_launcher.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_goto.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_goto.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_stop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_stop.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_camera.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_camera.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_manage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_manage.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_revert.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_revert.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_manage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_manage.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_revert.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_revert.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_camera.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_camera.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_manage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_manage.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_revert.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_revert.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable/ic_launcher_fullsize.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable/ic_launcher_fullsize.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_play_clip.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_play_clip.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_play_clip.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_play_clip.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_play_clip.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_play_clip.png -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/methyl.pdb: -------------------------------------------------------------------------------- 1 | FRAGMENT METHYL 2 | C 1.500 0.000 0.000 C 3 | H 1.872 -0.103 1.042 H 4 | H 1.899 -0.852 -0.592 H 5 | H 1.909 0.945 -0.419 H 6 | BONDS 7 | 0 1 1 8 | 0 2 1 9 | 0 3 1 10 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/nitro.frag: -------------------------------------------------------------------------------- 1 | FRAGMENT NITRO 2 | N 1.0 0.0 0.0 N 3 | O 1.67499995232 -1.16912996769 0.0 O 4 | O 1.67499995232 1.16912996769 0.0 O 5 | BONDS 6 | 0 1 2.0 7 | 0 2 1.0 8 | 1 0 2.0 9 | 2 0 1.0 10 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_preferences.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-hdpi/ic_menu_preferences.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_preferences.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-ldpi/ic_menu_preferences.png -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_preferences.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eigenstate/vmd-python/HEAD/vmd/plugins/remote/mobileapps/android/VMDMobile/res/drawable-mdpi/ic_menu_preferences.png -------------------------------------------------------------------------------- /vmd/plugins/ilstools/nitrogendioxide.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | nitrogen dioxide 3 | N -0.014300 1.203820 0.004390 4 | O 0.000450 0.104670 -0.469370 5 | O -0.029470 2.308120 -0.457240 6 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/basemol/hcn.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT HYDROGEN_CYANIDE HCN 2 | C -1.11727643013 -0.0 -0.0 C 3 | H -2.11727643013 0.0 0.0 H 4 | N 1.11042356491 -0.0 0.0 N 5 | BONDS 6 | 0 1 1.0 7 | 0 2 1.0 8 | 1 0 1.0 9 | 2 0 1.0 10 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/methyl.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT METHYL 2 | C 1.500 0.000 0.000 C 3 | H 1.872 -0.103 1.042 H 4 | H 1.899 -0.852 -0.592 H 5 | H 1.909 0.945 -0.419 H 6 | BONDS 7 | 0 1 1 8 | 0 2 1 9 | 0 3 1 10 | -------------------------------------------------------------------------------- /vmd/plugins/seqedit/run.tcl: -------------------------------------------------------------------------------- 1 | append auto_path " " "." " " "../seqdata" " " "../clustalw" 2 | package require seqdata 1.1 3 | package require seqedit_widget 1.1 4 | package require seqedit 1.1 5 | package require clustalw 1.1 6 | seqedit_gui 7 | -------------------------------------------------------------------------------- /vmd/plugins/libbiokit/src/libbiokit/alnReader.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef ALNREADER_H 3 | #define ALNREADER_H 4 | 5 | #include 6 | 7 | class ALNReader { 8 | 9 | public: 10 | 11 | 12 | private: 13 | 14 | 15 | }; 16 | 17 | #endif 18 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/carboxylate.frag: -------------------------------------------------------------------------------- 1 | FRAGMENT CARBOXYLATE 2 | C 1.0 0.0 0.0 C 3 | O 1.70000004768 -1.21244001389 0.0 O 4 | O 1.70000004768 1.21244001389 0.0 O 5 | BONDS 6 | 0 1 1.0 7 | 0 2 2.0 8 | 1 0 1.0 9 | 2 0 2.0 10 | -------------------------------------------------------------------------------- /vmd/plugins/drugui/probe.xsc: -------------------------------------------------------------------------------- 1 | # NAMD extended system configuration output file 2 | #$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w 3 | 0 62.3572 0 0 0 62.3572 0 0 0 62.3572 31.1786 31.1786 31.1786 0 0 0 0 0 0 4 | -------------------------------------------------------------------------------- /.bumpversion.cfg: -------------------------------------------------------------------------------- 1 | [bumpversion] 2 | current_version = 3.1.7 3 | tag = True 4 | commit = True 5 | allow_dirty = True 6 | 7 | [bumpversion:file:setup.py] 8 | 9 | [bumpversion:file:meta.yaml] 10 | 11 | [bumpversion:file:vmd/vmd_src/__init__.py] 12 | -------------------------------------------------------------------------------- /vmd/plugins/ilstools/methane.xyz: -------------------------------------------------------------------------------- 1 | 5 2 | methane 3 | C -0.01270 1.08580 0.00800 4 | H 0.00210 -0.00410 0.00200 5 | H 1.00990 1.46310 0.00030 6 | H -0.53990 1.44690 -0.87510 7 | H -0.52290 1.43730 0.90480 8 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include bld.bat 2 | include build.sh 3 | include LICENSE 4 | include meta.yaml 5 | include README.md 6 | include setup.py 7 | 8 | graft vmd 9 | graft test 10 | 11 | prune vmd/vmd_src/LINUXAMD64 12 | prune vmd/plugins/build 13 | 14 | 15 | -------------------------------------------------------------------------------- /vmd/plugins/cgtools/water.cgc: -------------------------------------------------------------------------------- 1 | CGBEGIN 2 | TIP3 H2O 0 3 | TIP3 OH2 0 4 | TIP3 H1 0 5 | TIP3 H2 0 6 | TIP3 OH2 1 7 | TIP3 H1 1 8 | TIP3 H2 1 9 | TIP3 OH2 2 10 | TIP3 H1 2 11 | TIP3 H2 2 12 | TIP3 OH2 3 13 | TIP3 H1 3 14 | TIP3 H2 3 15 | CGEND 16 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/amino.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT AMINO 2 | N 1.39999997616 0.0 0.0 N 3 | H 1.72556781769 0.945518672466 0.0 H 4 | H 1.7410081625 -0.461746007204 0.818843126297 H 5 | BONDS 6 | 0 1 1.0 7 | 0 2 1.0 8 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/formyl.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT FORMYL 2 | C 1.39999985695 2.24040164198e-07 3.27825546265e-07 C 3 | O 2.13041114807 1.30846273899 -0.0658376216888 O 4 | H 1.9126765728 -0.856054604053 0.0658156275749 H 5 | BONDS 6 | 0 1 2.0 7 | 0 2 1.0 8 | -------------------------------------------------------------------------------- /docs/mouse.rst: -------------------------------------------------------------------------------- 1 | .. _mouse: 2 | .. currentmodule:: vmd.mouse 3 | .. highlight:: python 4 | 5 | Mouse 6 | ===== 7 | 8 | Control the behavior of the mouse in the render window. 9 | 10 | 11 | .. autosummary:: 12 | :toctree: api/generated/ 13 | 14 | mode 15 | -------------------------------------------------------------------------------- /vmd/plugins/cionize/mgpot_lattice.c: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | * 4 | * mgpot_lattice.c 5 | * 6 | * Expand lattice class methods. 7 | */ 8 | 9 | #include "mgpot_lattice.h" 10 | 11 | LATTICE_CLASS_METHODS(float) 12 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/basemol/ammonia.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT AMMONIA NH3 2 | N 0.0 0.0 0.0 N 3 | H 1.0 0.0 0.0 H 4 | H -0.325568139553 0.945518553257 -2.71878575209e-10 H 5 | H -0.325568139553 -0.472759306431 0.818843126297 H 6 | BONDS 7 | 0 1 1 8 | 0 2 1 9 | 0 3 1 10 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/ALA.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT ALA 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.900000 -0.997000 0.284000 H 4 | HB2 1.892000 0.251000 -1.010000 H 5 | HB3 1.890000 0.746000 0.726000 H 6 | BONDS 7 | 0 1 1 8 | 0 2 1 9 | 0 3 1 10 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/scripts/template.conf: -------------------------------------------------------------------------------- 1 | 2 | dcdFreq 1 3 | timestep 1 4 | nonbondedFreq 2 5 | stepsPerCycle 20 6 | binaryRestart no 7 | 8 | switching on 9 | switchDist 10.5 10 | cutoff 12 11 | pairlistdist 13.5 12 | 13 | exclude scaled1-4 14 | 1-4scaling 1.0 15 | 16 | -------------------------------------------------------------------------------- /vmd/plugins/cionize/machine.h: -------------------------------------------------------------------------------- 1 | /* 2 | * machine.h - This is the machine specific include file 3 | * 4 | * $Id: machine.h,v 1.1 2006/11/14 19:37:10 petefred Exp $ 5 | */ 6 | 7 | #include 8 | #include 9 | #include 10 | #include 11 | 12 | -------------------------------------------------------------------------------- /vmd/plugins/tablelist/demos/comp.xbm: -------------------------------------------------------------------------------- 1 | #define comp_width 14 2 | #define comp_height 12 3 | static unsigned char comp_bits[] = { 4 | 0xff, 0x3f, 0x01, 0x20, 0xfd, 0x3f, 0x05, 0x20, 0xf5, 0x3f, 0x15, 0x20, 5 | 0xd5, 0x3f, 0x55, 0x20, 0x55, 0x3f, 0x55, 0x21, 0x55, 0x21, 0xff, 0x3f}; 6 | -------------------------------------------------------------------------------- /vmd/plugins/tablelist/demos/leaf.xbm: -------------------------------------------------------------------------------- 1 | #define leaf_width 14 2 | #define leaf_height 12 3 | static unsigned char leaf_bits[] = { 4 | 0xff, 0x3f, 0x01, 0x20, 0x01, 0x20, 0x01, 0x20, 0x01, 0x20, 0x01, 0x20, 5 | 0x01, 0x20, 0x01, 0x20, 0x01, 0x20, 0x01, 0x20, 0x01, 0x20, 0xff, 0x3f}; 6 | -------------------------------------------------------------------------------- /vmd/plugins/ilstools/ethene.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | 4916108 3 | C -0.01570 1.30580 0.00920 4 | C 0.00210 -0.00410 0.00200 5 | H 0.91220 1.85850 0.00330 6 | H -0.95820 1.83300 0.01660 7 | H -0.92580 -0.55670 0.00790 8 | H 0.94460 -0.53130 -0.00980 9 | -------------------------------------------------------------------------------- /docs/measure.rst: -------------------------------------------------------------------------------- 1 | .. _measure: 2 | .. currentmodule:: vmd.measure 3 | .. highlight:: python 4 | 5 | Measure 6 | ======= 7 | 8 | Measure distances or angles in loaded trajectories. 9 | 10 | .. autosummary:: 11 | :toctree: api/generated/ 12 | 13 | bond 14 | angle 15 | dihedral 16 | -------------------------------------------------------------------------------- /vmd/plugins/bdtk/database/interactions.dat: -------------------------------------------------------------------------------- 1 | GRAPHENE POT potentials/graphene_pot.dat 2 | GRAPHENE CLA potentials/graphene_cla.dat 3 | POT POT potentials/extend114_pot-pot.dat 4 | POT CLA potentials/extend114_pot-chl.dat 5 | CLA CLA potentials/extend114_chl-chl.dat 6 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/energy.c: -------------------------------------------------------------------------------- 1 | /* energy.c */ 2 | 3 | #include 4 | #include "moltypes/energy.h" 5 | 6 | 7 | int Energy_init(Energy *e) { 8 | memset(e, 0, sizeof(Energy)); 9 | return OK; 10 | } 11 | 12 | void Energy_done(Energy *e) { 13 | /* nothing to do! */ 14 | } 15 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/src/charmm_file.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef CHARMM_FILE_H 3 | #define CHARMM_FILE_H 4 | 5 | #include 6 | 7 | int charmm_get_tokens(char **tok, int toklen, 8 | char *sbuf, int sbuflen, 9 | char *lbuf, int *lineno, 10 | FILE *stream, int all_caps); 11 | 12 | #endif 13 | 14 | -------------------------------------------------------------------------------- /vmd/plugins/cionize/energymgrid.h: -------------------------------------------------------------------------------- 1 | #ifndef CIONIZE_ENERMGRID 2 | #define CIONIZE_ENERMGRID 3 | 4 | int calc_grid_energies_excl_mgrid(float* atoms, float* grideners, long int numplane, long int numcol, long int numpt, long int natoms, float gridspacing, unsigned char* excludepos, int maxnumprocs); 5 | 6 | #endif 7 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/moltypes/energy.c: -------------------------------------------------------------------------------- 1 | /* energy.c */ 2 | 3 | #include 4 | #include "moltypes/energy.h" 5 | 6 | 7 | int Energy_init(Energy *e) { 8 | memset(e, 0, sizeof(Energy)); 9 | return OK; 10 | } 11 | 12 | void Energy_done(Energy *e) { 13 | /* nothing to do! */ 14 | } 15 | -------------------------------------------------------------------------------- /vmd/plugins/cionize/energythr.h: -------------------------------------------------------------------------------- 1 | #ifndef CIONIZE_ENERTHR 2 | #define CIONIZE_ENERTHR 3 | 4 | int calc_grid_energies(float* atoms, float* grideners, long int numplane, long int numcol, long int numpt, long int natoms, float gridspacing, unsigned char* excludepos, int maxnumprocs, int calctype, float ddd); 5 | 6 | #endif 7 | -------------------------------------------------------------------------------- /vmd/plugins/cionize/mgpot_quintic1.c: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | * 4 | * mgpot_quintic1.c - smooth quintic C1 interpolant 5 | */ 6 | 7 | #include "mgpot_defn.h" 8 | 9 | int mgpot_longrng_quintic1(Mgpot *mg) { 10 | return ERROR("not yet implemented\n"); 11 | } 12 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/basemol/formic_acid.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT FORMIC_ACID FMA 2 | C -0.475176334381 0.0 -0.0 C 3 | O 0.224823713303 -1.21244001389 -0.0 O 4 | O 0.224823713303 1.21244001389 -0.0 O 5 | H -1.47517633438 0.0 0.0 H 6 | BONDS 7 | 0 1 1.0 8 | 0 2 2.0 9 | 0 3 1.0 10 | 1 0 1.0 11 | 2 0 2.0 12 | 3 0 1.0 13 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/test_io.c: -------------------------------------------------------------------------------- 1 | #include "nlbase/nlbase.h" 2 | 3 | int main() { 4 | INFO("\nThe meaning of %s, %s, and %s is %d.\n\n", 5 | "life", "the universe", "everything", 42); 6 | /* WARN("Look out, %s.", "something is wrong"); */ 7 | (void) ERROR(ERR_MEMALLOC); 8 | return OK; 9 | } 10 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/nlbase/test_io.c: -------------------------------------------------------------------------------- 1 | #include "nlbase/nlbase.h" 2 | 3 | int main() { 4 | INFO("\nThe meaning of %s, %s, and %s is %d.\n\n", 5 | "life", "the universe", "everything", 42); 6 | /* WARN("Look out, %s.", "something is wrong"); */ 7 | (void) ERROR(ERR_MEMALLOC); 8 | return OK; 9 | } 10 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/CYS.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT CYS 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.618000 -1.072000 -0.277000 H 4 | HB2 1.545000 0.571000 -0.954000 H 5 | SG 2.744000 0.501000 1.231000 S 6 | HG1 3.824000 0.221000 0.499000 H 7 | BONDS 8 | 0 1 1 9 | 0 2 1 10 | 0 3 1 11 | 3 4 1 12 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/SER.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT SER 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.784000 -0.898000 -0.596000 H 4 | HB2 1.731000 0.893000 -0.624000 H 5 | OG 2.226000 0.005000 1.220000 O 6 | HG1 3.150000 -0.172000 1.001000 H 7 | BONDS 8 | 0 1 1 9 | 0 2 1 10 | 0 3 1 11 | 3 4 1 12 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/basemol/methane.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT METHANE MET 2 | C 0.0 0.0 0.0 C 3 | H -0.325568139553 0.945518553257 -2.71878575209e-10 H 4 | H -0.325568139553 -0.472759306431 0.818843126297 H 5 | H -0.325568139553 -0.472759306431 -0.818843126297 H 6 | H 1.0 0.0 0.0 H 7 | BONDS 8 | 0 1 9 | 0 2 10 | 0 3 11 | 0 4 12 | -------------------------------------------------------------------------------- /docs/render.rst: -------------------------------------------------------------------------------- 1 | .. _render: 2 | .. currentmodule:: vmd.render 3 | .. highlight:: python 4 | 5 | Render 6 | ====== 7 | 8 | Render the current scene in the GUI with an external rendering engine or a 9 | snapshot (requires EGL) 10 | 11 | .. autosummary:: 12 | :toctree: api/generated/ 13 | 14 | listall 15 | render 16 | -------------------------------------------------------------------------------- /vmd/plugins/bdtk/database/ions.dat: -------------------------------------------------------------------------------- 1 | # Ions 2 | # Format: FULL NAME - CODE - CHARGE - DIFFUSION - RADIUS - EPSILON 3 | # CODE will be used in BD software package 4 | # RADIUS and EPSILON are from CHARMM 5 | 6 | Potassium POT 1.0 238.0 1.76375 0.087 7 | Chloride CLA -1.0 231.0 2.27 0.150 8 | -------------------------------------------------------------------------------- /vmd/plugins/navigate/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | COPYFILES = navigate.tcl pkgIndex.tcl 4 | DIR = $(PLUGINDIR)/noarch/tcl/navigate1.0 5 | 6 | bins: 7 | win32bins: 8 | dynlibs: 9 | staticlibs: 10 | win32staticlibs: 11 | 12 | distrib: 13 | @echo "Copying navigate 1.0 files to $(DIR)" 14 | mkdir -p $(DIR) 15 | cp -rf $(COPYFILES) $(DIR) 16 | -------------------------------------------------------------------------------- /vmd/plugins/libbiokit/src/libbiokit/typeConvert.h: -------------------------------------------------------------------------------- 1 | #ifndef TYPECONVERT_H 2 | #define TYPECONVERT_H 3 | 4 | #include 5 | #include 6 | 7 | // convert between types 8 | float charToFloat(char *); 9 | int charToInt(char *); 10 | char* intToString(int, int); 11 | char* charToString(char); 12 | char* lower(char*); 13 | 14 | #endif 15 | -------------------------------------------------------------------------------- /vmd/plugins/volmapgui/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | COPYFILES = volmapgui.tcl pkgIndex.tcl 4 | DIR = $(PLUGINDIR)/noarch/tcl/volmapgui1.1 5 | 6 | bins: 7 | win32bins: 8 | dynlibs: 9 | staticlibs: 10 | win32staticlibs: 11 | 12 | distrib: 13 | @echo "Copying volmapgui 1.1 files to $(DIR)" 14 | mkdir -p $(DIR) 15 | cp -rf $(COPYFILES) $(DIR) 16 | -------------------------------------------------------------------------------- /vmd/plugins/idatm/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = idatm.tcl pkgIndex.tcl 4 | VMVERSION = 0.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/idatm$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying idatm $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | -------------------------------------------------------------------------------- /docs/axes.rst: -------------------------------------------------------------------------------- 1 | .. _axes: 2 | .. currentmodule:: vmd.axes 3 | .. highlight:: python 4 | 5 | Axes 6 | ==== 7 | 8 | Axes displayes how the axes are displayed in the view window. 9 | This module is pretty useless in vmd-python unless doing rendering. 10 | 11 | .. autosummary:: 12 | :toctree: api/generated/ 13 | 14 | get_location 15 | set_location 16 | 17 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/src/charmm_parse_topo_defs.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef CHARMM_PARSE_TOPO_DEFS_H 3 | #define CHARMM_PARSE_TOPO_DEFS_H 4 | 5 | #include 6 | #include "topo_defs.h" 7 | 8 | int charmm_parse_topo_defs(topo_defs *defs, FILE *file, int all_caps, void *v, 9 | void (*print_msg)(void *,const char *)); 10 | 11 | #endif 12 | 13 | -------------------------------------------------------------------------------- /vmd/plugins/ramaplot/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | FILES = ramaplot.tcl pkgIndex.tcl 4 | VERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/ramaplot$(VERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying ramaplot $(VERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(FILES) $(DIR) 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/rmsd/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = rmsd.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/rmsd$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying rmsd $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/runante/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = runante.tcl pkgIndex.tcl 4 | VMVERSION = 0.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/runante$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying runante $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | -------------------------------------------------------------------------------- /vmd/plugins/runsqm/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = runsqm.tcl pkgIndex.tcl 4 | VMVERSION = 0.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/runsqm$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying runsqm $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/vdna/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = vdna.tcl pkgIndex.tcl 4 | VMVERSION = 2.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/vdna$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying vdna $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/vmdlite/vmd.rc: -------------------------------------------------------------------------------- 1 | # turn on lights 0 and 1 2 | light 0 on 3 | light 1 on 4 | light 2 off 5 | light 3 off 6 | 7 | # position the stage and axes 8 | axes location lowerleft 9 | stage location off 10 | 11 | menu main off 12 | menu graphics off 13 | 14 | ## FOR VMDLITE ## 15 | menu main off 16 | menu graphics off 17 | package require vmdlite 18 | vmdlite 19 | -------------------------------------------------------------------------------- /vmd/plugins/gofrgui/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = gofrgui.tcl pkgIndex.tcl 4 | VMVERSION = 1.3 5 | DIR = $(PLUGINDIR)/noarch/tcl/gofrgui$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying gofrgui $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/libbiokit/src/interface/tcl_libbiokit.i: -------------------------------------------------------------------------------- 1 | %module TCL_Libbiokit 2 | %{ 3 | #include "ShortIntList.h" 4 | #include "alphabet.h" 5 | #include "alignedSequence.h" 6 | #include "tcl_libbiokit.h" 7 | %} 8 | 9 | const char* seq(const char *arg1=NULL, const char *arg2=NULL, const char *arg3=NULL, const char *arg4=NULL, const char *arg5=NULL, const char *arg6=NULL); 10 | -------------------------------------------------------------------------------- /vmd/plugins/ruler/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = ruler.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/ruler$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying ruler $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/vmdlite/centerMolecule.tcl: -------------------------------------------------------------------------------- 1 | mol new cg_POPE.psf 2 | mol addfile POPE-noSolv.dcd waitfor all 3 | 4 | set nf [molinfo top get numframes] 5 | 6 | for {set i 0 } {$i < $nf} {incr i} { 7 | 8 | animate goto ${i} 9 | set all [atomselect top all] 10 | ${all} moveby [vecinvert [measure center ${all}]] 11 | 12 | $all writepdb ./dcdNew/frame${i}.pdb 13 | 14 | } 15 | -------------------------------------------------------------------------------- /vmd/plugins/bendix/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = bendix.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/bendix$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying bendix $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/bignum/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = bignum.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/bignum$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying bignum $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/hbonds/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = hbonds.tcl pkgIndex.tcl 4 | VMVERSION = 1.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/hbonds$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying hbonds $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/ASP.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT ASP 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.741000 -0.358000 -1.021000 H 4 | HB2 1.719000 1.085000 0.050000 H 5 | CG 2.426000 -0.727000 0.971000 C 6 | OD1 2.107000 -0.808000 2.218000 O 7 | OD2 3.519000 -1.260000 0.546000 O 8 | BONDS 9 | 0 1 1 10 | 0 2 1 11 | 0 3 1 12 | 3 5 2 13 | 3 4 1 14 | -------------------------------------------------------------------------------- /vmd/plugins/namdplot/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = namdplot.tcl pkgIndex.tcl 4 | VMVERSION = 1.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/namdplot$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying namdplot $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/navfly/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = navfly.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/navfly$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying navfly $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/nmwiz/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = nmwiz.tcl pkgIndex.tcl 4 | 5 | VMVERSION = 1.2 6 | DIR = $(PLUGINDIR)/noarch/tcl/nmwiz$(VMVERSION) 7 | 8 | bins: 9 | win32bins: 10 | dynlibs: 11 | staticlibs: 12 | win32staticlibs: 13 | 14 | distrib: 15 | @echo "Copying nmwiz $(VMVERSION) files to $(DIR)" 16 | mkdir -p $(DIR) 17 | cp $(VMFILES) $(DIR) 18 | 19 | 20 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/src/psf_file_extract.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef PSF_FILE_READ_H 3 | #define PSF_FILE_READ_H 4 | 5 | #include 6 | #include "topo_mol.h" 7 | 8 | int psf_file_extract(topo_mol *mol, FILE *file, FILE *pdbfile, FILE *namdbinfile, FILE *velnamdbinfile, 9 | void *, void (*print_msg)(void *, const char *)); 10 | 11 | #endif 12 | 13 | -------------------------------------------------------------------------------- /vmd/plugins/remote/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = remote.tcl pkgIndex.tcl 4 | VMVERSION = 0.6 5 | DIR = $(PLUGINDIR)/noarch/tcl/remote$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying remote $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/rmsdtt/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = rmsdtt.tcl pkgIndex.tcl 4 | VMVERSION = 3.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/rmsdtt$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying rmsdtt $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/saltbr/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = saltbr.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/saltbr$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying saltbr $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/vmdtkcon/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | TKCONFILES = vmdtkcon.tcl tkcon-modified.tcl pkgIndex.tcl tkcon-2.3 README 4 | DIR = $(PLUGINDIR)/noarch/tcl/vmdtkcon1.1 5 | 6 | bins: 7 | win32bins: 8 | dynlibs: 9 | staticlibs: 10 | win32staticlibs: 11 | 12 | distrib: 13 | @echo "Copying vmdtkcon 1.1 files to $(DIR)" 14 | mkdir -p $(DIR) 15 | cp -rf $(TKCONFILES) $(DIR) 16 | -------------------------------------------------------------------------------- /docs/imd.rst: -------------------------------------------------------------------------------- 1 | .. _imd: 2 | .. currentmodule:: vmd.imd 3 | .. highlight:: python 4 | 5 | IMD 6 | === 7 | 8 | Connect to and control interactive molecular dynamics simulations 9 | 10 | .. autosummary:: 11 | :toctree: api/generated/ 12 | 13 | connect 14 | connected 15 | copyunitcell 16 | detach 17 | keep 18 | kill 19 | pause 20 | transfer 21 | 22 | -------------------------------------------------------------------------------- /vmd/plugins/atomedit/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = atomedit.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/atomedit$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying atomedit $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/cliptool/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = cliptool.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/cliptool$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying cliptool $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/clonerep/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = clonerep.tcl pkgIndex.tcl 4 | VMVERSION = 1.3 5 | DIR = $(PLUGINDIR)/noarch/tcl/clonerep$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying clonerep $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/dipwatch/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = dipwatch.tcl pkgIndex.tcl 4 | VMVERSION = 1.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/dipwatch$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying dipwatch $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/inorganicbuilder/materials/au.pdb: -------------------------------------------------------------------------------- 1 | ATOM 1 AU1 AU X 1 0.000 0.000 0.000 1.00 0.00 UC1 AU 0 2 | ATOM 2 AU2 AU X 1 0.000 2.039 2.039 1.00 0.00 UC1 AU 0 3 | ATOM 3 AU3 AU X 1 2.039 0.000 2.039 1.00 0.00 UC1 AU 0 4 | ATOM 4 AU4 AU X 1 2.039 2.039 0.000 1.00 0.00 UC1 AU 0 5 | END 6 | -------------------------------------------------------------------------------- /vmd/plugins/irspecgui/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = irspecgui.tcl pkgIndex.tcl 4 | VMVERSION = 1.3 5 | DIR = $(PLUGINDIR)/noarch/tcl/irspecgui$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying irspecgui $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/moltoptools/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = moltoptools.tcl pkgIndex.tcl 4 | VMVERSION = 0.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/moltoptools$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying moltoptools $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | -------------------------------------------------------------------------------- /vmd/plugins/parsefep/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = parseFEP.tcl pkgIndex.tcl 4 | VMVERSION = 2.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/parsefep$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying parsefep $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/pdbtool/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = pdbtool.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/pdbtool$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying pdbtool $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/propka/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = propka.tcl pkgIndex.tcl 4 | 5 | VMVERSION = 1.1 6 | DIR = $(PLUGINDIR)/noarch/tcl/propka$(VMVERSION) 7 | 8 | bins: 9 | win32bins: 10 | dynlibs: 11 | staticlibs: 12 | win32staticlibs: 13 | 14 | distrib: 15 | @echo "Copying propka $(VMVERSION) files to $(DIR)" 16 | mkdir -p $(DIR) 17 | cp $(VMFILES) $(DIR) 18 | 19 | 20 | -------------------------------------------------------------------------------- /vmd/plugins/resptool/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = resptool.tcl pkgIndex.tcl 4 | VMVERSION = 1.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/resptool$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying resptool $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/textview/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = textview.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/textview$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying textview $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/timeline/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = timeline.tcl pkgIndex.tcl 4 | VMVERSION = 2.3 5 | DIR = $(PLUGINDIR)/noarch/tcl/timeline$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying timeline $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/updater/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = updater.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/updater$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying updater $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/vmdmovie/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = vmdmovie.tcl pkgIndex.tcl 4 | VMVERSION = 1.9 5 | DIR = $(PLUGINDIR)/noarch/tcl/vmdmovie$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying vmdmovie $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/vmdprefs/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = vmdprefs.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/vmdprefs$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying vmdprefs $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/zoomseq/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = zoomseq.tcl pkgIndex.tcl 4 | VMVERSION = 1.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/zoomseq$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying zoomseq $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/inorganicbuilder/materials/graphite.pdb: -------------------------------------------------------------------------------- 1 | ATOM 1 C1 C X 1 0.000 0.000 1.674 1.00 0.00 UC1 C 0 2 | ATOM 2 C2 C X 1 0.000 0.000 5.022 1.00 0.00 UC1 C 0 3 | ATOM 3 C3 C X 1 1.228 0.709 1.674 1.00 0.00 UC1 C 0 4 | ATOM 4 C4 C X 1 1.228 -0.709 5.022 1.00 0.00 UC1 C 0 5 | END 6 | -------------------------------------------------------------------------------- /vmd/plugins/jmvexport/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = jmvexport.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/jmvexport$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying jmvexport $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/multiplot/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = multiplot.tcl pkgIndex.tcl 4 | VMVERSION = 1.7 5 | DIR = $(PLUGINDIR)/noarch/tcl/multiplot$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying multiplot $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/multitext/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = multitext.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/multitext$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying multitext $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/namdserver/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = namdserver.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/namdserver$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying namdserver $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/plotter/Makefile: -------------------------------------------------------------------------------- 1 | 2 | VMFILES = plotter.tcl pkgIndex.tcl 3 | VMVERSION = 1.2 4 | DIR = $(PLUGINDIR)/noarch/tcl/plotter$(VMVERSION) 5 | 6 | # 7 | # Rules 8 | # 9 | bins: 10 | win32bins: 11 | dynlibs: 12 | staticlibs: 13 | win32staticlibs: 14 | 15 | distrib: 16 | echo "Copying plotter $(VMVERSION) files to $(DIR)" 17 | mkdir -p $(DIR) 18 | cp $(VMFILES) $(DIR) 19 | 20 | -------------------------------------------------------------------------------- /vmd/plugins/stingtool/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = stingtool.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/stingtool$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying stingtool $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/utilities/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = utilities.tcl pkgIndex.tcl 4 | VMVERSION = 1.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/utilities$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying utilities $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/apbsrun/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = apbsrun.tcl pkgIndex.tcl radii.dat 4 | VMVERSION = 1.3 5 | DIR = $(PLUGINDIR)/noarch/tcl/apbsrun$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying apbsrun $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/contactmap/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = contactmap.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/contactmap$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying contactmap $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/dataimport/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = dataimport.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/dataimport$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying dataimport $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/demomaster/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = demomaster.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/demomaster$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying demomaster $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/dowser/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = dowser.tcl dowser_gui.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/dowser$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying dowser $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/heatmapper/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = heatmapper.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/heatmapper$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying heatmapper $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/vinyl.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT VINYL 2 | C 1.39999985695 2.24040164198e-07 3.27825546265e-07 C 3 | C 2.13041114807 1.30846273899 -0.0658376216888 C 4 | H 1.9126765728 -0.856054604053 0.0658156275749 H 5 | H 1.63041114807 2.17448806763 -0.0658376216888 H 6 | H 3.13041114807 1.30846273899 -0.0658376216888 H 7 | BONDS 8 | 0 1 2.0 9 | 0 2 1.0 10 | 1 3 1.0 11 | 1 4 1.0 12 | -------------------------------------------------------------------------------- /vmd/plugins/namdenergy/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = namdenergy.tcl pkgIndex.tcl 4 | VMVERSION = 1.4 5 | DIR = $(PLUGINDIR)/noarch/tcl/namdenergy$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying namdenergy $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/optimization/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = optimization.tcl pkgIndex.tcl 4 | VMVERSION = 1.3 5 | DIR = $(PLUGINDIR)/noarch/tcl/optimization$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying optimization $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/viewmaster/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = viewmaster.tcl pkgIndex.tcl 4 | VMVERSION = 2.6 5 | DIR = $(PLUGINDIR)/noarch/tcl/viewmaster$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying viewmaster $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/vmddebug/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = vmddebug.tcl debugatomsel.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/vmddebug$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying vmddebug $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/bossconvert/src/Worker.h: -------------------------------------------------------------------------------- 1 | #ifndef _WORKER_H_ 2 | #define _WORKER_H_ 3 | #include 4 | #include 5 | #include 6 | #include 7 | #include 8 | using namespace std; 9 | 10 | int writeRTFFile(string); 11 | int writePRMFile(string); 12 | bool contains(list, string); 13 | int writeAliasParameters(); 14 | //void clean(); 15 | 16 | #endif 17 | -------------------------------------------------------------------------------- /vmd/plugins/colorscalebar/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = colorscalebar.tcl pkgIndex.tcl 4 | VMVERSION = 3.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/colorscalebar$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying colorscalebar $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/exectool/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = exectool.tcl jobmanager.tcl pkgIndex.tcl 4 | VMVERSION = 1.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/exectool$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying exectool $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/extendedpdb/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = extendedpdb.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/extendedpdb$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying extendedpdb $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/imdmenu/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | IMDMENUFILES = imdmenu.tcl pkgIndex.tcl 4 | IMDMENUVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/imdmenu$(IMDMENUVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying imdmenu $(IMDMENUVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp -f $(IMDMENUFILES) $(DIR) 17 | -------------------------------------------------------------------------------- /vmd/plugins/palettetool/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = palettetool.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/palettetool$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying palettetool $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/psipred/Makefile: -------------------------------------------------------------------------------- 1 | 2 | TCLFILES = psipred.tcl pkgIndex.tcl 3 | PKGVERSION = 1.1 4 | DIR = $(PLUGINDIR)/noarch/tcl/psipred$(PKGVERSION) 5 | 6 | # 7 | # Rules 8 | # 9 | bins: 10 | win32bins: 11 | dynlibs: 12 | staticlibs: 13 | win32staticlibs: 14 | 15 | distrib: 16 | echo "Copying psipred $(PKGVERSION) files to $(DIR)" 17 | mkdir -p $(DIR) 18 | cp $(TCLFILES) $(DIR) 19 | 20 | 21 | -------------------------------------------------------------------------------- /vmd/plugins/symmetrytool/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = symmetry.tcl pkgIndex.tcl 4 | VMVERSION = 1.3 5 | DIR = $(PLUGINDIR)/noarch/tcl/symmetrytool$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying symmetrytool $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Object files 2 | *.o 3 | *.ko 4 | *.obj 5 | *.elf 6 | 7 | # Precompiled Headers 8 | *.gch 9 | *.pch 10 | 11 | # Libraries 12 | *.lib 13 | *.a 14 | *.la 15 | *.lo 16 | 17 | # Shared objects (inc. Windows DLLs) 18 | *.dll 19 | *.so 20 | *.so.* 21 | *.dylib 22 | 23 | # Executables 24 | *.exe 25 | *.out 26 | *.app 27 | *.i*86 28 | *.x86_64 29 | *.hex 30 | 31 | # Debug files 32 | *.dSYM/ 33 | -------------------------------------------------------------------------------- /vmd/plugins/aligntool/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = aligntool.tcl cealign.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/aligntool$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying aligntool $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/clustalw/src/gcgcheck.c: -------------------------------------------------------------------------------- 1 | #include /* because of toupper() */ 2 | int SeqGCGCheckSum(char *seq, int len); 3 | 4 | int SeqGCGCheckSum(char *seq, int len) 5 | { 6 | int i; 7 | long check; 8 | 9 | for( i=0, check=0; i< len; i++,seq++) 10 | check += ((i % 57)+1) * toupper(*seq); 11 | 12 | return(check % 10000); 13 | } 14 | 15 | 16 | -------------------------------------------------------------------------------- /vmd/plugins/mergestructs/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = mergestructs.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/mergestructs$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying mergestructs $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/multimolanim/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = multimolanim.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/multimolanim$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying multimolanim $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/namdgui/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = namdgui.tcl namdgui_tclforces.tcl pkgIndex.tcl 4 | VMVERSION = 1.4 5 | DIR = $(PLUGINDIR)/noarch/tcl/namdgui$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying namdgui $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/rmsdvt/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = modal.tcl rmsdvt-gui.tcl rmsdvt.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/rmsdvt$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying rmsdvt $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/chirality/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = chirality.tcl chirality_gui.tcl pkgIndex.tcl 4 | VMVERSION = 1.2 5 | DIR = $(PLUGINDIR)/noarch/tcl/chirality$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying chirality $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/nanotube/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = gui.tcl graphene.tcl nanotube.tcl pkgIndex.tcl 4 | VMVERSION = 1.6 5 | DIR = $(PLUGINDIR)/noarch/tcl/nanotube$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying nanotube $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/simpleedit/Makefile: -------------------------------------------------------------------------------- 1 | 2 | VMFILES = simpleedit.tcl pkgIndex.tcl 3 | VMVERSION = 1.0 4 | DIR = $(PLUGINDIR)/noarch/tcl/simpleedit$(VMVERSION) 5 | 6 | # 7 | # Rules 8 | # 9 | bins: 10 | win32bins: 11 | dynlibs: 12 | staticlibs: 13 | win32staticlibs: 14 | 15 | distrib: 16 | echo "Copying simpleedit $(VMVERSION) files to $(DIR)" 17 | mkdir -p $(DIR) 18 | cp $(VMFILES) $(DIR) 19 | 20 | 21 | -------------------------------------------------------------------------------- /vmd/plugins/autoionize/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = autoionize.tcl autoionizegui.tcl pkgIndex.tcl 4 | VMVERSION = 1.5 5 | DIR = $(PLUGINDIR)/noarch/tcl/autoionize$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying autoionize $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/cispeptide/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = cispeptide.tcl cispeptide_gui.tcl pkgIndex.tcl 4 | VMVERSION = 1.3 5 | DIR = $(PLUGINDIR)/noarch/tcl/cispeptide$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying cispeptide $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/solvate/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | SOLVFILES = wat.top wat.pdb wat.psf solvate.tcl pkgIndex.tcl 4 | SOLVVERSION = 1.7 5 | DIR = $(PLUGINDIR)/noarch/tcl/solvate$(SOLVVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying solvate $(SOLVVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(SOLVFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/structurecheck/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = pkgIndex.tcl structurecheck.tcl 4 | 5 | VMVERSION = 1.1 6 | DIR = $(PLUGINDIR)/noarch/tcl/structurecheck$(VMVERSION) 7 | 8 | bins: 9 | win32bins: 10 | dynlibs: 11 | staticlibs: 12 | win32staticlibs: 13 | 14 | distrib: 15 | @echo "Copying structurecheck $(VMVERSION) files to $(DIR)" 16 | mkdir -p $(DIR) 17 | cp $(VMFILES) $(DIR) 18 | 19 | 20 | -------------------------------------------------------------------------------- /vmd/plugins/alascanfep/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = alascan.tcl alascan_analysis.tcl fep.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/alascanfep$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying alascanfep $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/bdtk/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = bdtk.tcl bdtk_gui.tcl bdtk_procs.tcl pkgIndex.tcl 4 | VMVERSION = 1.0 5 | DIR = $(PLUGINDIR)/noarch/tcl/bdtk$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying bdtk $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | cp -r database $(DIR) 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/blast/Makefile: -------------------------------------------------------------------------------- 1 | 2 | TCLFILES = blast.tcl blast_resultviewer.tcl pkgIndex.tcl 3 | PKGVERSION = 1.11 4 | DIR = $(PLUGINDIR)/noarch/tcl/blast$(PKGVERSION) 5 | 6 | # 7 | # Rules 8 | # 9 | bins: 10 | win32bins: 11 | dynlibs: 12 | staticlibs: 13 | win32staticlibs: 14 | 15 | distrib: 16 | echo "Copying blast $(PKGVERSION) files to $(DIR)" 17 | mkdir -p $(DIR) 18 | cp $(TCLFILES) $(DIR) 19 | 20 | 21 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/res/values/arrays.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Latest 5 | 9 6 | 8 7 | 8 | 9 | 10 | Latest 11 | 9 12 | 8 13 | 14 | 15 | -------------------------------------------------------------------------------- /vmd/plugins/viewchangerender/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = vcr.tcl vcr_gui.tcl pkgIndex.tcl 4 | VMVERSION = 1.8 5 | DIR = $(PLUGINDIR)/noarch/tcl/viewchangerender$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying viewchangerender $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/ssrestraints/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = ssrestraints.tcl ssrestraints_stride.tcl pkgIndex.tcl 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/ssrestraints$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying ssrestraints $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/cionize/cudaenergythrsingleion.h: -------------------------------------------------------------------------------- 1 | #ifndef CIONIZE_CUDAENERTHR 2 | #define CIONIZE_CUDAENERTHR 3 | 4 | #ifdef __cplusplus 5 | extern "C" { 6 | #endif 7 | 8 | int calc_grid_energies_cuda_thr_singleion(float* atom, float* grideners, long int numplane, long int numcol, long int numpt, float gridspacing, unsigned char* excludepos, int maxnumprocs); 9 | 10 | #ifdef __cplusplus 11 | } 12 | #endif 13 | 14 | #endif 15 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/GLY.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT GLY 2 | N 1.300 0.000 0.000 N 3 | C 1.667 -1.378 2.005 C 4 | O 1.404 -2.508 2.411 O 5 | CA 2.055 -1.125 0.558 C 6 | HA2 1.850 -1.931 0.002 H 7 | HA1 3.032 -0.926 0.494 H 8 | HC1 1.635 -0.566 2.638 H 9 | HN 1.819 0.760 -0.376 H 10 | BONDS 11 | 1 3 1 12 | 1 2 2 13 | 1 6 1 14 | 0 3 1 15 | 0 7 1 16 | 3 1 2 17 | 3 5 1 18 | 3 4 1 19 | -------------------------------------------------------------------------------- /vmd/plugins/cionize/cudaenergythr.h: -------------------------------------------------------------------------------- 1 | #ifndef CIONIZE_CUDAENERTHR 2 | #define CIONIZE_CUDAENERTHR 3 | 4 | #ifdef __cplusplus 5 | extern "C" { 6 | #endif 7 | 8 | int calc_grid_energies_cuda_thr(float* atoms, float* grideners, long int numplane, long int numcol, long int numpt, long int natoms, float gridspacing, unsigned char* excludepos, int maxnumprocs); 9 | 10 | 11 | #ifdef __cplusplus 12 | } 13 | #endif 14 | 15 | #endif 16 | -------------------------------------------------------------------------------- /docs/material.rst: -------------------------------------------------------------------------------- 1 | .. _material: 2 | .. currentmodule:: vmd.material 3 | .. highlight:: python 4 | 5 | Material 6 | ======== 7 | 8 | Control the materials used to render molecules or graphics objects. Not useful 9 | without EGL or another way to render. 10 | 11 | .. autosummary:: 12 | :toctree: api/generated/ 13 | 14 | add 15 | change 16 | default 17 | delete 18 | listall 19 | rename 20 | settings 21 | -------------------------------------------------------------------------------- /vmd/plugins/inorganicbuilder/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = inorganicbuilder.tcl pkgIndex.tcl 4 | VMVERSION = 0.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/inorganicbuilder$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying inorganicbuilder $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | cp -r materials $(DIR) 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/src/memarena.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef MEMARENA_H 3 | #define MEMARENA_H 4 | 5 | struct memarena; 6 | typedef struct memarena memarena; 7 | 8 | memarena * memarena_create(void); 9 | void memarena_destroy(memarena *a); 10 | 11 | void memarena_blocksize(memarena *a, int blocksize); 12 | void * memarena_alloc(memarena *a, int size); 13 | void * memarena_alloc_aligned(memarena *a, int size, int alignment); 14 | 15 | #endif 16 | 17 | -------------------------------------------------------------------------------- /vmd/plugins/autopsf/src/psftypelist.h: -------------------------------------------------------------------------------- 1 | #ifndef PSFTYPELIST 2 | #define PSFTYPELIST 3 | 4 | class PsfTypeList { 5 | public: 6 | PsfTypeList() { 7 | head=NULL; 8 | } 9 | 10 | ~PsfTypeList() { 11 | delete head; 12 | } 13 | 14 | bool search(PsfType*); 15 | 16 | void addtype(PsfType*); 17 | 18 | PsfType* lookForType(PsfType*); 19 | 20 | void print(FILE*); 21 | 22 | private: 23 | PsfType* head; 24 | }; 25 | 26 | #endif 27 | -------------------------------------------------------------------------------- /vmd/plugins/rnaview/BASEPARS/misc_rna.par: -------------------------------------------------------------------------------- 1 | 3.4 0.0 ON A1 # upper H-bond length limits/atoms, alternative location 2 | 26.0 # max. distance between paired base origins (10.0) 3 | 2.5 # max. vertical distance between paired base origins (2.0) 4 | 65.0 # max. angle between paired bases [0-90] (60.0) 5 | 5.4 # MIN. distance between RN9/YN1 atoms (6.0) 6 | 8.0 # max. distance criterion for helix break [0-12] (8.0) 7 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/force.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file force/force.h 6 | * @brief Primary header file for force library. 7 | * @author David J. Hardy 8 | * @date Aug. 2007 9 | */ 10 | 11 | #ifndef FORCE_H 12 | #define FORCE_H 13 | 14 | #include "force/fbonded.h" 15 | #include "force/fnbcut.h" 16 | #include "force/nbpair.h" 17 | 18 | #endif /* FORCE_H */ 19 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/basemol/sulfate.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT SULFATE SUL 2 | S -0.0128062963486 0.00463346531615 -0.0182707197964 S 3 | O 0.481653690338 1.17103338242 0.687089264393 O 4 | O -1.36280632019 0.00463346531615 -0.0182707197964 O 5 | O 0.447553634644 0.00463346531615 -1.28735077381 O 6 | O 0.459263682365 -1.1895865202 0.655149281025 O 7 | BONDS 8 | 0 1 2.0 9 | 0 2 1.0 10 | 0 3 1.0 11 | 0 4 2.0 12 | 1 0 2.0 13 | 2 0 1.0 14 | 3 0 1.0 15 | 4 0 2.0 16 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/force/force.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file force/force.h 6 | * @brief Primary header file for force library. 7 | * @author David J. Hardy 8 | * @date Aug. 2007 9 | */ 10 | 11 | #ifndef FORCE_H 12 | #define FORCE_H 13 | 14 | #include "force/fbonded.h" 15 | #include "force/fnbcut.h" 16 | #include "force/nbpair.h" 17 | 18 | #endif /* FORCE_H */ 19 | -------------------------------------------------------------------------------- /vmd/plugins/pbctools/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = pbcbox.tcl pbcgui.tcl pbcjoin.tcl pbcset.tcl pbctools.tcl \ 4 | pbcunwrap.tcl pbcwrap.tcl pkgIndex.tcl 5 | 6 | VMVERSION = 2.8 7 | DIR = $(PLUGINDIR)/noarch/tcl/pbctools$(VMVERSION) 8 | 9 | bins: 10 | win32bins: 11 | dynlibs: 12 | staticlibs: 13 | win32staticlibs: 14 | 15 | distrib: 16 | @echo "Copying pbctools $(VMVERSION) files to $(DIR)" 17 | mkdir -p $(DIR) 18 | cp $(VMFILES) $(DIR) 19 | 20 | 21 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/project.properties: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by Android Tools. 2 | # Do not modify this file -- YOUR CHANGES WILL BE ERASED! 3 | # 4 | # This file must be checked in Version Control Systems. 5 | # 6 | # To customize properties used by the Ant build system use, 7 | # "ant.properties", and override values to adapt the script to your 8 | # project structure. 9 | 10 | # Project target. 11 | target=android-10 12 | -------------------------------------------------------------------------------- /docs/label.rst: -------------------------------------------------------------------------------- 1 | .. _label: 2 | .. currentmodule:: vmd.label 3 | .. highlight:: python 4 | 5 | Label 6 | ===== 7 | 8 | Control the visibility and style of labels applied to the molecule. Again, 9 | not super useful without EGL rendering as labels appear in the render window. 10 | 11 | .. autosummary:: 12 | :toctree: api/generated/ 13 | 14 | add 15 | delete 16 | get_values 17 | listall 18 | set_visible 19 | text_size 20 | text_thickness 21 | -------------------------------------------------------------------------------- /vmd/plugins/cgtools/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = cggui.tcl cgtools.tcl cgnetworking.tcl pkgIndex.tcl \ 4 | protein.cgc water.cgc rbcg-2007.par rbcg-2007.top 5 | VMVERSION = 1.2 6 | DIR = $(PLUGINDIR)/noarch/tcl/cgtools$(VMVERSION) 7 | 8 | bins: 9 | win32bins: 10 | dynlibs: 11 | staticlibs: 12 | win32staticlibs: 13 | 14 | distrib: 15 | @echo "Copying cgtools $(VMVERSION) files to $(DIR)" 16 | mkdir -p $(DIR) 17 | cp $(VMFILES) $(DIR) 18 | 19 | 20 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/default.properties: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by Android Tools. 2 | # Do not modify this file -- YOUR CHANGES WILL BE ERASED! 3 | # 4 | # This file must be checked in Version Control Systems. 5 | # 6 | # To customize properties used by the Ant build system use, 7 | # "build.properties", and override values to adapt the script to your 8 | # project structure. 9 | 10 | # Project target. 11 | target=android-10 12 | -------------------------------------------------------------------------------- /vmd/plugins/autopsf/src/psfreslist.h: -------------------------------------------------------------------------------- 1 | #ifndef PSFRESLIST 2 | #define PSFRESLIST 3 | 4 | class PsfResList { 5 | public: 6 | PsfResList() { 7 | head=NULL; 8 | tail=NULL; 9 | } 10 | 11 | ~PsfResList() { 12 | delete head; 13 | } 14 | 15 | bool search(PsfAtom*); 16 | 17 | void addres(PsfRes*); 18 | 19 | PsfRes* lookForRes(PsfAtom*); 20 | 21 | void print(FILE*); 22 | 23 | private: 24 | PsfRes* head; 25 | PsfRes* tail; 26 | }; 27 | 28 | #endif 29 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/GLY-end.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT GLY GLY 2 | N -0.132 2.450 -0.112 N 3 | C 0.000 0.000 0.000 C 4 | O -0.632 -0.944 0.468 O 5 | CA -0.701 1.208 -0.598 C 6 | HA1 -0.614 1.196 -1.594 H 7 | HA2 -1.671 1.196 -0.355 H 8 | HC1 1.000 0.000 0.000 H 9 | HT1 0.220 3.108 -0.747 H 10 | HT2 -0.767 3.067 0.352 H 11 | BONDS 12 | 1 3 1 13 | 1 2 2 14 | 1 6 1 15 | 0 3 1 16 | 0 7 1 17 | 0 8 1 18 | 3 1 2 19 | 3 5 1 20 | 3 4 1 21 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/phospho.frag: -------------------------------------------------------------------------------- 1 | FRAGMENT PHOSPHO 2 | P 1.0 0.0 0.0 P 3 | O 1.4603600502 1.08596003056 -0.656710028648 O 4 | O 1.4603600502 0.0 1.26908004284 O 5 | O 1.43952000141 -1.11186003685 -0.626980006695 O 6 | HM6 2.11048007011 -0.751760005951 1.3795800209 H 7 | HM7 2.4395198822 -1.11186003685 -0.626980006695 H 8 | BONDS 9 | 0 1 2.0 10 | 0 2 1.0 11 | 0 3 1.0 12 | 1 0 2.0 13 | 2 0 1.0 14 | 2 4 -1.0 15 | 3 0 1.0 16 | 3 5 -1.0 17 | 4 2 -1.0 18 | 5 3 -1.0 19 | -------------------------------------------------------------------------------- /vmd/plugins/multiseqdialog/Makefile: -------------------------------------------------------------------------------- 1 | 2 | VMFILES = download_updates.tcl multiseqdialog.tcl pkgIndex.tcl scrolledframe.tcl wait_dialog.tcl 3 | 4 | VMVERSION = 1.1 5 | DIR = $(PLUGINDIR)/noarch/tcl/multiseqdialog$(VMVERSION) 6 | 7 | # 8 | # Rules 9 | # 10 | bins: 11 | win32bins: 12 | dynlibs: 13 | staticlibs: 14 | win32staticlibs: 15 | 16 | distrib: 17 | echo "Copying multiseqdialog $(VMVERSION) files to $(DIR)" 18 | mkdir -p $(DIR) 19 | cp $(VMFILES) $(DIR) 20 | 21 | 22 | -------------------------------------------------------------------------------- /vmd/vmd_src/src/colvars_version.h: -------------------------------------------------------------------------------- 1 | #ifndef COLVARS_VERSION 2 | #define COLVARS_VERSION "2018-11-16" 3 | // This file is part of the Collective Variables module (Colvars). 4 | // The original version of Colvars and its updates are located at: 5 | // https://github.com/colvars/colvars 6 | // Please update all Colvars source files before making any changes. 7 | // If you wish to distribute your changes, please submit them to the 8 | // Colvars repository at GitHub. 9 | 10 | #endif 11 | -------------------------------------------------------------------------------- /vmd/plugins/bossconvert/src/AtomWeights.h: -------------------------------------------------------------------------------- 1 | #ifndef _ATOMWEIGHTS_H_ 2 | #define _ATOMWEIGHTS_H_ 3 | 4 | const float C = 12.01070f; 5 | const float H = 1.0079f; 6 | const float N = 14.0067f; 7 | const float O = 15.9994f; 8 | const float S = 32.0666f; 9 | const float F = 18.9984f; 10 | const float Cl = 34.4528f; 11 | const float Br = 79.9041f; 12 | const float B = 10.8117f; 13 | const float Si = 28.0855f; 14 | const float P = 30.9738f; 15 | const float I = 126.9045f; 16 | 17 | #endif 18 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/ASN.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT ASN 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.728000 -0.587000 -0.916000 H 4 | HB2 1.668000 1.070000 -0.239000 H 5 | CG 2.334000 -0.483000 1.155000 C 6 | OD1 1.907000 -0.388000 2.337000 O 7 | ND2 3.483000 -1.052000 0.778000 N 8 | HD21 4.077000 -1.404000 1.496000 H 9 | HD22 3.703000 -1.138000 -0.189000 H 10 | BONDS 11 | 0 1 1 12 | 0 2 1 13 | 0 3 1 14 | 3 5 1 15 | 3 4 2 16 | 5 7 1 17 | 5 6 1 18 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/THR.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT THR 2 | CB 1.500000 0.000000 0.000000 C 3 | HB 1.564000 -0.579000 0.954000 H 4 | OG1 2.119000 1.259000 0.210000 O 5 | HG1 3.049000 1.065000 0.366000 H 6 | CG2 2.229000 -0.680000 -1.164000 C 7 | HG21 3.280000 -0.913000 -0.890000 H 8 | HG22 1.727000 -1.634000 -1.431000 H 9 | HG23 2.241000 -0.028000 -2.064000 H 10 | BONDS 11 | 0 4 1 12 | 0 1 1 13 | 0 2 1 14 | 2 3 1 15 | 4 5 1 16 | 4 6 1 17 | 4 7 1 18 | -------------------------------------------------------------------------------- /vmd/plugins/pbctools/AUTHORS: -------------------------------------------------------------------------------- 1 | CREDITS 2 | ------- 3 | 4 | The PBCTools plugin has been written by (in alphabetical order) 5 | * Toni Giorgino 6 | * Jerome Henin 7 | * Olaf Lenz (maintainer) 8 | * Cameron Mura 9 | * Jan Saam 10 | 11 | The "pbcbox" procedure copies a lot of the ideas of Axel Kohlmeyer's 12 | script "vmd_draw_unitcell". 13 | -------------------------------------------------------------------------------- /vmd/plugins/autoimd/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | AUTOIMDFILES = autoimd.tcl autoimd-settings.tcl autoimd-api.tcl autoimd-gui.tcl pkgIndex.tcl autoimd-template.namd namdrun.tcl 4 | AUTOIMDVERSION = 1.7 5 | DIR = $(PLUGINDIR)/noarch/tcl/autoimd$(AUTOIMDVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | 14 | distrib: 15 | @echo "Copying autoimd $(AUTOIMDVERSION) files to $(DIR)" 16 | mkdir -p $(DIR) 17 | cp -f $(AUTOIMDFILES) $(DIR) 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/networkview/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = networkView.tcl networkViewGui.tcl communityNetwork.tcl suboptimalPaths.tcl networkSetup.tcl adjacencyMatrix.tcl pkgIndex.tcl 4 | 5 | VMVERSION = 1.41 6 | DIR = $(PLUGINDIR)/noarch/tcl/networkview$(VMVERSION) 7 | 8 | bins: 9 | win32bins: 10 | dynlibs: 11 | staticlibs: 12 | win32staticlibs: 13 | 14 | distrib: 15 | @echo "Copying networkview $(VMVERSION) files to $(DIR)" 16 | mkdir -p $(DIR) 17 | cp $(VMFILES) $(DIR) 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/biocore/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = biocore.tcl biocorechat.tcl biocorelogin.tcl biocorepubsync.tcl pkgIndex.tcl locked.gif unlocked.gif biocoreHelper.tcl biocoreutil.tcl 4 | 5 | VMVERSION = 1.1 6 | DIR = $(PLUGINDIR)/noarch/tcl/biocore$(VMVERSION) 7 | 8 | bins: 9 | win32bins: 10 | dynlibs: 11 | staticlibs: 12 | win32staticlibs: 13 | 14 | distrib: 15 | @echo "Copying biocore $(VMVERSION) files to $(DIR)" 16 | mkdir -p $(DIR) 17 | cp $(VMFILES) $(DIR) 18 | 19 | 20 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/force/GNUmakefile: -------------------------------------------------------------------------------- 1 | # GNUmakefile 2 | # definitions for building "force" 3 | 4 | TOP = ../.. 5 | NAME = force 6 | TYPE = lib 7 | OBJ = fbonded angle bond dihedral improper fnbcut fnbcut_eval nbpair 8 | LIB = moltypes nlbase m 9 | LINKCPP = no 10 | HEADER = force fbonded fnbcut nbpair 11 | DEMO = 12 | DEMOOBJ = 13 | DEMOLIB = 14 | DEMOLINKCPP = 15 | 16 | ifeq (0,$(MAKELEVEL)) 17 | .PHONY : src clean 18 | src clean : ; $(MAKE) -C $(TOP) SRC="$(NAME)" $@ 19 | endif 20 | -------------------------------------------------------------------------------- /vmd/vmd_src/src/colvarproxy_vmd_version.h: -------------------------------------------------------------------------------- 1 | #ifndef COLVARPROXY_VERSION 2 | #define COLVARPROXY_VERSION "2018-08-29" 3 | // This file is part of the Collective Variables module (Colvars). 4 | // The original version of Colvars and its updates are located at: 5 | // https://github.com/colvars/colvars 6 | // Please update all Colvars source files before making any changes. 7 | // If you wish to distribute your changes, please submit them to the 8 | // Colvars repository at GitHub. 9 | 10 | #endif 11 | -------------------------------------------------------------------------------- /vmd/plugins/cionize/cionize_grid.h: -------------------------------------------------------------------------------- 1 | #ifndef CIONIZE_GRID 2 | #define CIONIZE_GRID 3 | 4 | /* electrostatic grid information */ 5 | typedef struct { 6 | long int numplane, numcol, numpt; 7 | float minx, miny, minz; 8 | float maxx, maxy, maxz; 9 | float gridspacing; 10 | 11 | /* Array for energies at grid nodes */ 12 | float* eners; 13 | /* Array for excluded grid positions; if it is != 0, the point is excluded */ 14 | unsigned char *excludepos; 15 | } cionize_grid; 16 | 17 | #endif 18 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/fragments/epoxide.frag: -------------------------------------------------------------------------------- 1 | FRAGMENT EPOXIDE 2 | C 1.00011003017 0.0 0.0 C 3 | O 1.76616001129 -0.71442002058 -1.07315003872 O 4 | C 2.02735996246 0.716600000858 -1.43904995918 C 5 | H 1.3250399828 0.0 0.945860028267 H 6 | H 1.60757994652 1.12059998512 -2.25202989578 H 7 | H 2.93262004852 1.12059998512 -1.30616998672 H 8 | BONDS 9 | 0 1 1.0 10 | 0 3 1.0 11 | 0 2 1.0 12 | 1 0 1.0 13 | 1 2 1.0 14 | 2 0 1.0 15 | 2 1 1.0 16 | 2 4 1.0 17 | 2 5 1.0 18 | 3 0 1.0 19 | 4 2 1.0 20 | 5 2 1.0 21 | -------------------------------------------------------------------------------- /vmd/plugins/bossconvert/src/Makefile: -------------------------------------------------------------------------------- 1 | CXX=g++ 2 | CXXFLAGS= -Wall 3 | 4 | all: Topology 5 | 6 | Topology: Parser.o Worker.o Atom.o Main.o 7 | $(CXX) $(CXXFLAGS) Parser.o Worker.o Atom.o Main.o -o Topology 8 | 9 | Parser.o: Parser.cpp 10 | $(CXX) $(CXXFLAGS) -c Parser.cpp 11 | 12 | Worker.o: Worker.cpp 13 | $(CXX) $(CXXFLAGS) -c Worker.cpp 14 | 15 | Atom.o: Atom.cpp 16 | $(CXX) $(CXXFLAGS) -c Atom.cpp 17 | 18 | Main.o: Main.cpp 19 | 20 | clean: 21 | rm -rf *o Topology 22 | -------------------------------------------------------------------------------- /vmd/plugins/fmtool/write_psf.h: -------------------------------------------------------------------------------- 1 | #ifndef _WRITE_PSF_H_ 2 | #define _WRITE_PSF_H_ 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | #include 12 | 13 | void write_psf(int &, int &, double *, double *, double &, double &, double &, 14 | double &, double &, double &, double &, double &, int &, int &, 15 | int &, int &, 16 | int &PSF_write_dx); 17 | 18 | #endif 19 | -------------------------------------------------------------------------------- /vmd/plugins/qwikmd/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = pkgIndex.tcl qwikmd_ballon.tcl qwikmd_func.tcl qwikmd_info.tcl qwikmd.tcl qwikmd_logText.tcl Annealing.conf Equilibration.conf MD.conf Minimization.conf SMD.conf 4 | 5 | VMVERSION = 1.1 6 | DIR = $(PLUGINDIR)/noarch/tcl/qwikmd$(VMVERSION) 7 | 8 | bins: 9 | win32bins: 10 | dynlibs: 11 | staticlibs: 12 | win32staticlibs: 13 | 14 | distrib: 15 | @echo "Copying qwikmd $(VMVERSION) files to $(DIR)" 16 | mkdir -p $(DIR) 17 | cp $(VMFILES) $(DIR) 18 | 19 | 20 | -------------------------------------------------------------------------------- /test/test_axes.py: -------------------------------------------------------------------------------- 1 | """ 2 | Tests the axes module 3 | """ 4 | 5 | import pytest 6 | from vmd import axes 7 | 8 | def test_locations(): 9 | 10 | axes.set_location(axes.OFF) 11 | assert axes.get_location() == "Off" 12 | 13 | with pytest.raises(ValueError): 14 | axes.set_location("invalid") 15 | 16 | axes.set_location(axes.ORIGIN) 17 | assert axes.get_location() == axes.ORIGIN 18 | 19 | axes.set_location("LowerLeft") 20 | assert axes.get_location() == axes.LOWERLEFT 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/molfiles/GNUmakefile: -------------------------------------------------------------------------------- 1 | # GNUmakefile 2 | # definitions for building "molfiles" 3 | 4 | TOP = ../.. 5 | NAME = molfiles 6 | TYPE = lib 7 | OBJ = xplor charmm psf pdbatom bincoord config 8 | LIB = moltypes nlbase m 9 | LINKCPP = no 10 | HEADER = molfiles xplor charmm psf pdbatom bincoord config 11 | DEMO = 12 | DEMOOBJ = 13 | DEMOLIB = molfiles moltypes nlbase 14 | DEMOLINKCPP = 15 | 16 | ifeq (0,$(MAKELEVEL)) 17 | .PHONY : src clean 18 | src clean : ; $(MAKE) -C $(TOP) SRC="$(NAME)" $@ 19 | endif 20 | -------------------------------------------------------------------------------- /vmd/plugins/pmepot/src/pmepot.h: -------------------------------------------------------------------------------- 1 | /* 2 | * $Id: pmepot.h,v 1.2 2005/07/20 15:37:39 johns Exp $ 3 | * 4 | */ 5 | 6 | #ifndef PMEPOT_H 7 | #define PMEPOT_H 8 | 9 | typedef struct pmepot_data_struct pmepot_data; 10 | 11 | pmepot_data* pmepot_create(int *dims, float ewald_factor); 12 | 13 | void pmepot_destroy(pmepot_data *data); 14 | 15 | int pmepot_add(pmepot_data *data, const float *cell, 16 | int natoms, const float *atoms); 17 | 18 | int pmepot_writedx(pmepot_data *data, const char *filename); 19 | 20 | #endif 21 | 22 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/numeric.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2008 by David J. Hardy. All rights reserved. 3 | * 4 | * numeric.h - NAMD-Lite semi-numeric functions. 5 | */ 6 | 7 | #ifndef NLBASE_NUMERIC_H 8 | #define NLBASE_NUMERIC_H 9 | 10 | #include "nlbase/types.h" 11 | 12 | #ifdef __cplusplus 13 | extern "C" { 14 | #endif 15 | 16 | /**@brief Return greatest common divisor. */ 17 | uint32 Numeric_gcd(uint32 a, uint32 b); 18 | 19 | #ifdef __cplusplus 20 | } 21 | #endif 22 | 23 | #endif /* NLBASE_NUMERIC_H */ 24 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/nlbase/numeric.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2008 by David J. Hardy. All rights reserved. 3 | * 4 | * numeric.h - NAMD-Lite semi-numeric functions. 5 | */ 6 | 7 | #ifndef NLBASE_NUMERIC_H 8 | #define NLBASE_NUMERIC_H 9 | 10 | #include "nlbase/types.h" 11 | 12 | #ifdef __cplusplus 13 | extern "C" { 14 | #endif 15 | 16 | /**@brief Return greatest common divisor. */ 17 | uint32 Numeric_gcd(uint32 a, uint32 b); 18 | 19 | #ifdef __cplusplus 20 | } 21 | #endif 22 | 23 | #endif /* NLBASE_NUMERIC_H */ 24 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/GLU.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT GLU 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.736000 0.872000 0.653000 H 4 | HB2 1.712000 -0.906000 0.611000 H 5 | CG 2.370000 0.034000 -1.264000 C 6 | HG1 2.247000 -0.912000 -1.822000 H 7 | HG2 2.087000 0.883000 -1.918000 H 8 | CD 3.839000 0.136000 -0.985000 C 9 | OE1 4.247000 1.119000 -0.316000 O 10 | OE2 4.555000 -0.810000 -1.412000 O 11 | BONDS 12 | 0 3 1 13 | 0 1 1 14 | 0 2 1 15 | 3 4 1 16 | 3 5 1 17 | 3 6 1 18 | 6 8 2 19 | 6 7 1 20 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/local.properties: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by Android Tools. 2 | # Do not modify this file -- YOUR CHANGES WILL BE ERASED! 3 | # 4 | # This file must *NOT* be checked in Version Control Systems, 5 | # as it contains information specific to your local configuration. 6 | 7 | # location of the SDK. This is only used by Ant 8 | # For customization when using a Version Control System, please read the 9 | # header note. 10 | sdk.dir=/home/kvandivo/Proj/android-sdk-linux_86 11 | 12 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/src/stringhash.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef STRINGHASH_H 3 | #define STRINGHASH_H 4 | 5 | struct stringhash; 6 | typedef struct stringhash stringhash; 7 | 8 | stringhash * stringhash_create(void); 9 | void stringhash_destroy(stringhash *h); 10 | 11 | const char* stringhash_insert(stringhash *h, const char *key, const char *data); 12 | 13 | #define STRINGHASH_FAIL 0 14 | 15 | const char* stringhash_lookup(stringhash *h, const char *key); 16 | 17 | const char* stringhash_delete(stringhash *h, const char *key); 18 | 19 | #endif 20 | 21 | -------------------------------------------------------------------------------- /vmd/plugins/qmtool/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = qmtool.tcl qmtool_analysis.tcl qmtool_atomedit.tcl \ 4 | qmtool_aux.tcl qmtool_charges.tcl qmtool_intcoor.tcl \ 5 | qmtool_readwrite.tcl qmtool_setup.tcl pkgIndex.tcl 6 | 7 | VMVERSION = 1.3 8 | DIR = $(PLUGINDIR)/noarch/tcl/qmtool$(VMVERSION) 9 | 10 | bins: 11 | win32bins: 12 | dynlibs: 13 | staticlibs: 14 | win32staticlibs: 15 | 16 | distrib: 17 | @echo "Copying qmtool $(VMVERSION) files to $(DIR)" 18 | mkdir -p $(DIR) 19 | cp $(VMFILES) $(DIR) 20 | 21 | 22 | -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- 1 | ## [3.1.6] - 2025-01-28 2 | 3 | ### Changed 4 | 5 | - Don't build dynamic plugins for molfile since they are all build statically 6 | as well. This removes a lot of spurious warnings. 7 | 8 | ### Fixed 9 | 10 | - Build with Clang. 11 | 12 | 13 | ## [3.1.5] - 2025-01-27 14 | 15 | ### Fixed 16 | 17 | - Support for Python <= 3.12. 18 | - Initialize atomsel type with the spec-based initializer 19 | instead of manually creating the type struct. This is part of 20 | the Limited ABI so should be a lot more future proof. 21 | 22 | 23 | -------------------------------------------------------------------------------- /test/test_mouse.py: -------------------------------------------------------------------------------- 1 | """ 2 | Tests the mouse module 3 | """ 4 | 5 | import pytest 6 | from vmd import mouse 7 | 8 | def test_mouse(): 9 | 10 | mouse.mode(mode=mouse.ROTATE) 11 | mouse.mode(mode=mouse.QUERY) 12 | mouse.mode(mouse.LIGHT, 0) 13 | 14 | with pytest.raises(ValueError): 15 | mouse.mode(mode=mouse.ROTATE, lightnum=mouse.LABELATOM) 16 | 17 | with pytest.raises(ValueError): 18 | mouse.mode(mode=mouse.LIGHT) 19 | 20 | with pytest.raises(ValueError): 21 | mouse.mode(mouse.LIGHT, lightnum=3599) 22 | 23 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = molefacture.tcl molefacture_builder.tcl \ 4 | molefacture_edit.tcl molefacture_geometry.tcl molefacture_gui.tcl \ 5 | molefacture_internals.tcl molefacture_state.tcl pkgIndex.tcl 6 | VMVERSION = 1.4 7 | DIR = $(PLUGINDIR)/noarch/tcl/molefacture$(VMVERSION) 8 | 9 | bins: 10 | win32bins: 11 | dynlibs: 12 | staticlibs: 13 | win32staticlibs: 14 | 15 | distrib: 16 | @echo "Copying molefacture $(VMVERSION) files to $(DIR)" 17 | mkdir -p $(DIR) 18 | cp $(VMFILES) $(DIR) 19 | cp -r lib $(DIR) 20 | -------------------------------------------------------------------------------- /vmd/plugins/membrane/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = membrane.tcl pkgIndex.tcl \ 4 | popc_box.pdb popc_box.psf \ 5 | popc36_box.pdb popc36_box.psf \ 6 | pope36_box.pdb pope36_box.psf \ 7 | pope_box.pdb pope_box.psf \ 8 | top_all27_prot_lipid.inp 9 | 10 | VMVERSION = 1.2 11 | DIR = $(PLUGINDIR)/noarch/tcl/membrane$(VMVERSION) 12 | 13 | bins: 14 | win32bins: 15 | dynlibs: 16 | staticlibs: 17 | win32staticlibs: 18 | 19 | distrib: 20 | @echo "Copying membrane $(VMVERSION) files to $(DIR)" 21 | mkdir -p $(DIR) 22 | cp $(VMFILES) $(DIR) 23 | 24 | 25 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/moltypes/GNUmakefile: -------------------------------------------------------------------------------- 1 | # GNUmakefile 2 | # definitions for building "moltypes" 3 | 4 | TOP = ../.. 5 | NAME = moltypes 6 | TYPE = lib 7 | OBJ = forceprm forceprm_init forceprm_nonb topology topology_init \ 8 | domain coord simprm energy exclude 9 | LIB = nlbase m 10 | LINKCPP = no 11 | HEADER = moltypes forceprm topology domain coord simprm energy 12 | DEMO = 13 | DEMOOBJ = 14 | DEMOLIB = 15 | DEMOLINKCPP = 16 | 17 | ifeq (0,$(MAKELEVEL)) 18 | .PHONY : src clean 19 | src clean : ; $(MAKE) -C $(TOP) SRC="$(NAME)" $@ 20 | endif 21 | -------------------------------------------------------------------------------- /vmd/plugins/pbctools/README: -------------------------------------------------------------------------------- 1 | ------------------- 2 | VMD PBCTools plugin 3 | ------------------- 4 | 5 | For documentation of the plugin, please refer to the docs in either of 6 | the following files 7 | 8 | doc/pbctools.tex 9 | doc/pbctools.html 10 | doc/pbctools.pdf 11 | 12 | (the latter two only exist if you downloaded a tarball). 13 | 14 | or to the plugin's home page at 15 | 16 | http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/ 17 | 18 | The plugin's development page can be found at 19 | 20 | http://github.com/olenz/pbctools 21 | -------------------------------------------------------------------------------- /vmd/plugins/signalproc/signalproc.tcl: -------------------------------------------------------------------------------- 1 | # hello emacs this is -*- tcl -*- 2 | # 3 | # convenience package that pulls in all individual package in signalproc 4 | # 5 | # (c) 2008-2009 by Axel Kohlmeyer 6 | ######################################################################## 7 | # 8 | # $Id: signalproc.tcl,v 1.2 2013/04/15 17:41:23 johns Exp $ 9 | # 10 | package require fftcmds 1.1 11 | package require fftpack 1.1 12 | package require sgsmooth 1.1 13 | package require data_io_lib 1.1 14 | package provide signalproc 1.1 15 | 16 | -------------------------------------------------------------------------------- /vmd/plugins/autopsf/src/psfbond.h: -------------------------------------------------------------------------------- 1 | #ifndef _PSFBOND 2 | #define _PSFBOND 3 | 4 | #include "psfatomlist.h" 5 | 6 | 7 | class PsfBond { 8 | public: 9 | PsfBond(int); 10 | 11 | PsfBond(char*, char*); 12 | 13 | ~PsfBond(); 14 | 15 | bool equals(PsfBond); 16 | 17 | void setnext(PsfBond*); 18 | 19 | bool search(PsfBond*); 20 | 21 | char* name0(); 22 | char* name1(); 23 | 24 | void print(FILE*); 25 | 26 | private: 27 | char atomname0[5]; 28 | char atomname1[5]; 29 | PsfBond* next; 30 | }; 31 | 32 | char *eatwhite(char *s); 33 | 34 | #endif 35 | -------------------------------------------------------------------------------- /vmd/plugins/vmdlite/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = pkgIndex.tcl centerMolecule.tcl vmdlite_analysis.tcl \ 4 | vmdlite_graphics.tcl vmdlite_guiProcs.tcl vmdlite_main.tcl \ 5 | vmdlite_sandbox.tcl vmdlite_system.tcl vmdlite.tcl vmd.rc 6 | 7 | VMVERSION = 1.1 8 | DIR = $(PLUGINDIR)/noarch/tcl/vmdlite$(VMVERSION) 9 | 10 | bins: 11 | win32bins: 12 | dynlibs: 13 | staticlibs: 14 | win32staticlibs: 15 | 16 | distrib: 17 | @echo "Copying vmdlite $(VMVERSION) files to $(DIR)" 18 | mkdir -p $(DIR) 19 | cp $(VMFILES) $(DIR) 20 | cp -r sandboxMolecules $(DIR) 21 | 22 | -------------------------------------------------------------------------------- /vmd/plugins/autopsf/src/psfatomlist.h: -------------------------------------------------------------------------------- 1 | #ifndef PSFATOMLIST 2 | #define PSFATOMLIST 3 | 4 | #include "psfatom.h" 5 | 6 | class PsfAtomList { 7 | public: 8 | PsfAtomList() { 9 | head=NULL; 10 | } 11 | 12 | ~PsfAtomList() { 13 | while (head != NULL) { 14 | PsfAtom* curr = head; 15 | head = head->getnext(); 16 | delete curr; 17 | } 18 | } 19 | 20 | PsfAtom* find_index(int); 21 | 22 | void addatom(PsfAtom*); 23 | 24 | void print(FILE*); 25 | 26 | private: 27 | PsfAtom* head; 28 | }; 29 | 30 | #endif 31 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/molfiles.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file molfiles/molfiles.h 6 | * @brief Main header file for molfiles library. 7 | * @author David J. Hardy 8 | * @date Aug. 2007 9 | */ 10 | 11 | #ifndef MOLFILES_H 12 | #define MOLFILES_H 13 | 14 | #include "molfiles/xplor.h" 15 | #include "molfiles/charmm.h" 16 | #include "molfiles/psf.h" 17 | #include "molfiles/pdbatom.h" 18 | #include "molfiles/bincoord.h" 19 | #include "molfiles/config.h" 20 | 21 | #endif /* MOLFILES_H */ 22 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/nlenergy/GNUmakefile: -------------------------------------------------------------------------------- 1 | # GNUmakefile 2 | # definitions for building "nlenergy" 3 | 4 | TOP = ../.. 5 | NAME = nlenergy 6 | TYPE = plugin 7 | OBJ = tcl_nlenergy nlenergy parse get set add remove fileio eval tclwrap 8 | LIB = force molfiles moltypes nlbase $(darwin_tcl) m 9 | LINKCPP = 10 | HEADER = 11 | DEMO = 12 | DEMOOBJ = 13 | DEMOLIB = 14 | DEMOLINKCPP = 15 | 16 | ifeq (0,$(MAKELEVEL)) 17 | .PHONY : src clean 18 | src clean : ; $(MAKE) -C $(TOP) SRC="$(NAME)" $@ 19 | endif 20 | 21 | CPPFLAGS := -I/Projects/vmd/vmd/lib/tcl/include $(CPPFLAGS) 22 | -------------------------------------------------------------------------------- /vmd/plugins/tablelist/COPYRIGHT.txt: -------------------------------------------------------------------------------- 1 | Multi-column listbox and tree widget package Tablelist, version 5.13 2 | Copyright (c) 2000-2015 Csaba Nemethi (E-mail: csaba.nemethi@t-online.de) 3 | 4 | This library is free software; you can use, modify, and redistribute it 5 | for any purpose, provided that existing copyright notices are retained 6 | in all copies and that this notice is included verbatim in any 7 | distributions. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even the 10 | implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 11 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/molfiles/molfiles.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file molfiles/molfiles.h 6 | * @brief Main header file for molfiles library. 7 | * @author David J. Hardy 8 | * @date Aug. 2007 9 | */ 10 | 11 | #ifndef MOLFILES_H 12 | #define MOLFILES_H 13 | 14 | #include "molfiles/xplor.h" 15 | #include "molfiles/charmm.h" 16 | #include "molfiles/psf.h" 17 | #include "molfiles/pdbatom.h" 18 | #include "molfiles/bincoord.h" 19 | #include "molfiles/config.h" 20 | 21 | #endif /* MOLFILES_H */ 22 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/VAL.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT VAL 2 | CB 1.500000 0.000000 0.000000 C 3 | HB 1.681000 1.097000 -0.112000 H 4 | CG1 2.140000 -0.461000 1.314000 C 5 | HG11 3.241000 -0.319000 1.276000 H 6 | HG12 1.760000 0.118000 2.180000 H 7 | HG13 1.938000 -1.539000 1.491000 H 8 | CG2 2.188000 -0.636000 -1.201000 C 9 | HG21 3.288000 -0.495000 -1.144000 H 10 | HG22 1.977000 -1.727000 -1.240000 H 11 | HG23 1.842000 -0.180000 -2.151000 H 12 | BONDS 13 | 0 6 1 14 | 0 2 1 15 | 0 1 1 16 | 2 3 1 17 | 2 5 1 18 | 2 4 1 19 | 6 7 1 20 | 6 8 1 21 | 6 9 1 22 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/psf.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2008 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file molfiles/psf.h 6 | * @brief Read PSF into Topology data container. 7 | * @author David J. Hardy 8 | * @date Aug. 2007 9 | */ 10 | 11 | #ifndef MOLFILES_PSF_H 12 | #define MOLFILES_PSF_H 13 | 14 | #include "moltypes/moltypes.h" 15 | 16 | #ifdef __cplusplus 17 | extern "C" { 18 | #endif 19 | 20 | int Topology_read_psf(Topology *, const char *fname); 21 | 22 | #ifdef __cplusplus 23 | } 24 | #endif 25 | 26 | #endif /* MOLFILES_PSF_H */ 27 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/basemol/oxyrane.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT OXYRANE EOX 2 | O -0.265105366707 -0.709054172039 0.0 O 3 | C -0.753455400467 0.709225833416 -0.0 C 4 | C 1.0339345932 0.040945827961 0.0 C 5 | H -1.18148541451 1.10166573524 0.81411999464 H 6 | H -1.18148541451 1.10166573524 -0.81411999464 H 7 | H 1.61443459988 0.0563158392906 -0.81411999464 H 8 | H 1.61443459988 0.0563158392906 0.81411999464 H 9 | BONDS 10 | 0 1 1.0 11 | 0 2 1.0 12 | 1 0 1.0 13 | 1 3 1.0 14 | 1 4 1.0 15 | 1 2 1.0 16 | 2 0 1.0 17 | 2 1 1.0 18 | 2 5 1.0 19 | 2 6 1.0 20 | 3 1 1.0 21 | 4 1 1.0 22 | 5 2 1.0 23 | 6 2 1.0 24 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/molfiles/psf.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2008 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file molfiles/psf.h 6 | * @brief Read PSF into Topology data container. 7 | * @author David J. Hardy 8 | * @date Aug. 2007 9 | */ 10 | 11 | #ifndef MOLFILES_PSF_H 12 | #define MOLFILES_PSF_H 13 | 14 | #include "moltypes/moltypes.h" 15 | 16 | #ifdef __cplusplus 17 | extern "C" { 18 | #endif 19 | 20 | int Topology_read_psf(Topology *, const char *fname); 21 | 22 | #ifdef __cplusplus 23 | } 24 | #endif 25 | 26 | #endif /* MOLFILES_PSF_H */ 27 | -------------------------------------------------------------------------------- /vmd/plugins/ilstools/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = ilstools.tcl pkgIndex.tcl oxygen.xyz nitricoxide.xyz \ 4 | carbonmonoxide.xyz carbondioxide.xyz ethene.xyz methane.xyz \ 5 | nitrousoxide.xyz nitrogendioxide.xyz nitrogen.xyz \ 6 | acetylene.xyz hydrogen.xyz 7 | VMVERSION = 1.5 8 | 9 | DIR = $(PLUGINDIR)/noarch/tcl/ilstools$(VMVERSION) 10 | 11 | bins: 12 | win32bins: 13 | dynlibs: 14 | staticlibs: 15 | win32staticlibs: 16 | 17 | distrib: 18 | @echo "Copying ilstools $(VMVERSION) files to $(DIR)" 19 | mkdir -p $(DIR) 20 | cp -rf $(VMFILES) $(DIR) 21 | -------------------------------------------------------------------------------- /vmd/plugins/vdna/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded vdna 2.2 [list source [file join $dir vdna.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/bignum/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded bignum 1.0 [list source [file join $dir bignum.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/hbonds/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded hbonds 1.2 [list source [file join $dir hbonds.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/navfly/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded navfly 1.0 [list source [file join $dir navfly.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/nmwiz/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded nmwiz 1.2 [list source [file join $dir nmwiz.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/propka/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded propka 1.1 [list source [file join $dir propka.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/src/psfgen.h: -------------------------------------------------------------------------------- 1 | 2 | /* psfgen.h 3 | * Defines set of data structures used in creation of molecule structures 4 | * Exported here so that new modules can be written to interface with psfgen 5 | */ 6 | 7 | #ifndef PSFGEN_H 8 | #define PSFGEN_H 9 | 10 | #include "topo_defs.h" 11 | #include "topo_mol.h" 12 | #include "stringhash.h" 13 | 14 | /* psfgen-specific data */ 15 | struct psfgen_data { 16 | int id, in_use, all_caps; 17 | topo_defs *defs; 18 | topo_mol *mol; 19 | stringhash *aliases; 20 | }; 21 | typedef struct psfgen_data psfgen_data; 22 | 23 | #endif /* PSFGEN_H */ 24 | -------------------------------------------------------------------------------- /vmd/plugins/rmsd/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded rmsdtool 1.0 [list source [file join $dir rmsd.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/ruler/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded ruler 1.0 [list source [file join $dir ruler.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/saltbr/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded saltbr 1.1 [list source [file join $dir saltbr.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/tablelist/tablelist.tcl: -------------------------------------------------------------------------------- 1 | #============================================================================== 2 | # Main Tablelist package module. 3 | # 4 | # Copyright (c) 2000-2015 Csaba Nemethi (E-mail: csaba.nemethi@t-online.de) 5 | #============================================================================== 6 | 7 | package require Tcl 8 8 | package require Tk 8 9 | package require -exact tablelist::common 5.13 10 | 11 | package provide tablelist $::tablelist::version 12 | package provide Tablelist $::tablelist::version 13 | 14 | ::tablelist::useTile 0 15 | ::tablelist::createBindings 16 | -------------------------------------------------------------------------------- /vmd/plugins/topotools/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = pkgIndex.tcl README topotools.tcl topoatoms.tcl \ 4 | topobonds.tcl topoangles.tcl topodihedrals.tcl topoimpropers.tcl \ 5 | topocrossterms.tcl topolammps.tcl topoutils.tcl topohelpers.tcl \ 6 | topogromacs.tcl topovarxyz.tcl 7 | 8 | VMVERSION = 1.7 9 | DIR = $(PLUGINDIR)/noarch/tcl/topotools$(VMVERSION) 10 | 11 | bins: 12 | win32bins: 13 | dynlibs: 14 | staticlibs: 15 | win32staticlibs: 16 | 17 | distrib: 18 | @echo "Copying topotools $(VMVERSION) files to $(DIR)" 19 | mkdir -p $(DIR) 20 | cp $(VMFILES) $(DIR) 21 | 22 | 23 | -------------------------------------------------------------------------------- /docs/selection.rst: -------------------------------------------------------------------------------- 1 | .. _selection: 2 | .. currentmodule:: vmd.selection 3 | .. highlight:: python 4 | 5 | Selection 6 | ========= 7 | 8 | Methods for creating, modifying, or deleting macros for atom selections. 9 | Often you'll want to create a short word that expands to mean more in an 10 | atom selection context: for example, the built-in macro `noh` expands to 11 | `not hydrogen`. 12 | 13 | .. autosummary:: 14 | :toctree: api/generated/ 15 | 16 | add_macro 17 | all_macros 18 | booleans 19 | del_macro 20 | functions 21 | get_macro 22 | keywords 23 | stringfunctions 24 | -------------------------------------------------------------------------------- /vmd/plugins/gofrgui/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded gofrgui 1.3 [list source [file join $dir gofrgui.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/imdmenu/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded imdmenu 1.0 [list source [file join $dir imdmenu.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/pdbtool/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded pdbtool 1.1 [list source [file join $dir pdbtool.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/remote/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 0.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded remote 0.6 "source [list [file join $dir remote.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/zoomseq/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded zoomseq 1.2 [list source [file join $dir zoomseq.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/atomedit/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded atomedit 1.0 [list source [file join $dir atomedit.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/cliptool/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded cliptool 1.0 [list source [file join $dir cliptool.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/clonerep/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded clonerep 1.3 [list source [file join $dir clonerep.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/dipwatch/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded dipwatch 1.3 [list source [file join $dir dipwatch.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/irspecgui/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded irspecgui 1.3 [list source [file join $dir irspecgui.tcl] ] 12 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/basemol/benzene.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT BENZENE BEN 2 | C 1.230 0.710 0.000 C 3 | H 2.162 1.249 0.000 H 4 | C 0.000 1.420 0.000 C 5 | H 0.000 2.497 0.000 H 6 | C -1.230 0.710 0.000 C 7 | H -2.162 1.249 0.000 H 8 | C -1.230 -0.710 0.000 C 9 | H -2.162 -1.249 0.000 H 10 | C -0.000 -1.420 0.000 C 11 | H -0.000 -2.497 0.000 H 12 | C 1.230 -0.710 0.000 C 13 | H 2.162 -1.249 0.000 H 14 | BONDS 15 | 0 1 1 16 | 0 2 2 17 | 0 10 1 18 | 2 3 1 19 | 2 4 1 20 | 4 5 1 21 | 4 6 2 22 | 6 7 1 23 | 6 8 1 24 | 8 9 1 25 | 8 10 2 26 | 10 11 1 27 | -------------------------------------------------------------------------------- /vmd/plugins/multiplot/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded multiplot 1.7 [list source [file join $dir multiplot.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/multitext/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded multitext 1.1 [list source [file join $dir multitext.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/namdplot/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded namdplot 1.2 [list source [file join $dir namdplot.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/navigate/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded navigate 1.0 [list source [file join $dir navigate.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/parsefep/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded parsefep 2.1 [list source [file join $dir parseFEP.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/ramaplot/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.0 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded ramaplot 1.1 [list source [file join $dir ramaplot.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/resptool/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.2 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded resptool 1.2 [list source [file join $dir resptool.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/stingtool/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded stingtool 1.0 [list source [file join $dir stingtool.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/textview/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded textview 1.1 [list source [file join $dir textview.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/timeline/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded timeline 2.3 "source [list [file join $dir timeline.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/utilities/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded utilities 1.2 [list source [file join $dir utilities.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/vmdmovie/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded vmdmovie 1.9 [list source [file join $dir vmdmovie.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/vmdprefs/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded vmdprefs 1.1 [list source [file join $dir vmdprefs.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/volmapgui/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded volmapgui 1.1 [list source [file join $dir volmapgui.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/autopsf/src/psftype.h: -------------------------------------------------------------------------------- 1 | #ifndef _PSFTYPE 2 | #define _PSFTYPE 3 | 4 | class PsfType { 5 | public: 6 | PsfType(char*); 7 | 8 | PsfType(char*, float, char*); 9 | 10 | ~PsfType(); 11 | 12 | bool equals(PsfType); 13 | 14 | void setnext(PsfType*); 15 | 16 | bool search(PsfType*); 17 | 18 | char* type(); 19 | 20 | float mass(); 21 | 22 | char* elem(); 23 | 24 | void print(FILE*); 25 | 26 | private: 27 | char atomtype[10]; 28 | int index; 29 | float atommass; 30 | char element[10]; 31 | PsfType* next; 32 | }; 33 | 34 | char *eatwhite(char *s); 35 | 36 | #endif 37 | -------------------------------------------------------------------------------- /vmd/plugins/bossconvert/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded bossconvert 1.0 [list source [file join $dir bossconvert.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/bossconvert/src/Example.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | if [ -x Topology ]; then 4 | mkdir -p ExampleOutput 5 | cd ExampleOutput 6 | cp ../ExampleInput/* . 7 | echo "Running ../Topology -oplssb ../../oplsaa.sb -oplspar ../../oplsaa.par -imprlist ../../imprlist -bossout out test.z" 8 | echo "" 9 | ../Topology -oplssb ../../oplsaa.sb -oplspar ../../oplsaa.par -imprlist ../../imprlist -bossout out test.z 10 | rm -f test.z out 11 | echo "Output written to ExampleOutput/" 12 | echo "" 13 | else 14 | echo "Topology executable not compiled... run make and then Example.sh" 15 | fi 16 | -------------------------------------------------------------------------------- /vmd/plugins/contactmap/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded contactmap 1.0 "source [list [file join $dir contactmap.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/dataimport/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded dataimport 1.0 [list source [file join $dir dataimport.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/demomaster/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded demomaster 0.1 [list source [file join $dir demomaster.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/extendedpdb/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded extendedpdb 1.0 [list source [file join $dir extendedpdb.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/hesstrans/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded hesstrans 1.1 [list load [file join $dir hesstrans.so]] 12 | 13 | -------------------------------------------------------------------------------- /vmd/plugins/libbiokit/src/utils/qh.h: -------------------------------------------------------------------------------- 1 | /***************************************************************************** 2 | * 3 | * (C) Copyright 1995-2005 The Board of Trustees of the 4 | * University of Illinois 5 | * All Rights Reserved 6 | * 7 | ******************************************************************************/ 8 | 9 | 10 | #ifndef QH_H 11 | #define QH_H 12 | 13 | #include "version.h" 14 | 15 | int parseArgs(int argc, char** argv); 16 | void printUsage(int argc, char** argv); 17 | void printCopyright(int argc, char** argv); 18 | 19 | #endif 20 | -------------------------------------------------------------------------------- /vmd/plugins/namdserver/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded namdserver 1.1 [list source [file join $dir namdserver.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/palettetool/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded palettetool 1.0 [list source [file join $dir palettetool.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/plumed/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = vmdplumed.tcl pkgIndex.tcl \ 4 | templates_list_v1.tcl templates_list_v2.tcl templates_list_vmdcv.tcl 5 | VMVERSION = 2.7 6 | DIR = $(PLUGINDIR)/noarch/tcl/plumed$(VMVERSION) 7 | 8 | 9 | bins: 10 | win32bins: 11 | dynlibs: 12 | staticlibs: 13 | win32staticlibs: 14 | 15 | 16 | # The first targets are used by VMD's builds. 17 | distrib: 18 | @echo "Copying plumed $(VMVERSION) files to $(DIR)" 19 | mkdir -p $(DIR) 20 | cp $(VMFILES) $(DIR) 21 | 22 | 23 | 24 | # export 25 | # .PHONY: 26 | # autogen: 27 | # make -f maintainer/Makefile 28 | 29 | 30 | -------------------------------------------------------------------------------- /vmd/plugins/psipred/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded psipred 1.1 "[list source [file join $dir psipred.tcl]]" 12 | 13 | -------------------------------------------------------------------------------- /vmd/plugins/remote/mobileapps/android/VMDMobile/local.properties.example: -------------------------------------------------------------------------------- 1 | # This is an example file. Copy it to local.properties and modify appropriately 2 | # This file is automatically generated by Android Tools. 3 | # Do not modify this file -- YOUR CHANGES WILL BE ERASED! 4 | # 5 | # This file must *NOT* be checked in Version Control Systems, 6 | # as it contains information specific to your local configuration. 7 | 8 | # location of the SDK. This is only used by Ant 9 | # For customization when using a Version Control System, please read the 10 | # header note. 11 | sdk.dir=/Users/kvandivo/android-sdk-mac_x86 12 | -------------------------------------------------------------------------------- /vmd/plugins/simpleedit/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded simpleedit 1.0 [list source [file join $dir simpleedit.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/symmetrytool/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded symmetrytool 1.3 [list source [file join $dir symmetry.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/viewmaster/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded ViewMaster 2.6 "source [list [file join $dir viewmaster.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/mergestructs/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded mergestructs 1.1 [list source [file join $dir mergestructs.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/multimolanim/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded multimolanim 1.0 [list source [file join $dir multimolanim.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/optimization/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded optimization 1.3 [list source [file join $dir optimization.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/src/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | 2 | # Tcl package index file, version 1.4.2 3 | # This file is generated by the "pkg_mkIndex" command 4 | # and sourced either when an application starts up or 5 | # by a "package unknown" script. It invokes the 6 | # "package ifneeded" command to set up package-related 7 | # information so that packages will be loaded automatically 8 | # in response to "package require" commands. When this 9 | # script is sourced, the variable $dir must contain the 10 | # full path name of this file's directory. 11 | 12 | package ifneeded psfgen 1.7 [list load [file join $dir libpsfgen.so]] 13 | 14 | -------------------------------------------------------------------------------- /vmd/plugins/trunctraj/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded truncate_trajectory 1.5 [list source [file join $dir trunctraj.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/colorscalebar/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded colorscalebar 3.0 [list source [file join $dir colorscalebar.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/mdff/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = mdff.tcl mdff_check.tcl mdff_map.tcl mdff_sim.tcl mdff_correlation.tcl mdff_setup.tcl pkgIndex.tcl mdff_template.namd mdff_tmp.tcl xmdff_phenix.tcl xmdff_template.namd mdff_gui.tcl remdff_template.namd replica-mdff.namd load-mdff-results.tcl show_replicas_mdff.vmd resetmaps.sh 4 | 5 | VMVERSION = 0.5 6 | DIR = $(PLUGINDIR)/noarch/tcl/mdff$(VMVERSION) 7 | 8 | bins: 9 | win32bins: 10 | dynlibs: 11 | staticlibs: 12 | win32staticlibs: 13 | 14 | distrib: 15 | @echo "Copying mdff $(VMVERSION) files to $(DIR)" 16 | mkdir -p $(DIR) 17 | cp $(VMFILES) $(DIR) 18 | 19 | 20 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/xplor.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2008 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file molfiles/xplor.h 6 | * @brief Read X-Plor force field parameters file into ForcePrm container. 7 | * @author David J. Hardy 8 | * @date Apr. 2008 9 | */ 10 | 11 | #ifndef MOLFILES_XPLOR_H 12 | #define MOLFILES_XPLOR_H 13 | 14 | #include "moltypes/moltypes.h" 15 | 16 | #ifdef __cplusplus 17 | extern "C" { 18 | #endif 19 | 20 | int ForcePrm_read_xplor(ForcePrm *, const char *fname); 21 | 22 | #ifdef __cplusplus 23 | } 24 | #endif 25 | 26 | #endif /* MOLFILES_XPLOR_H */ 27 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/molfiles/xplor.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2008 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file molfiles/xplor.h 6 | * @brief Read X-Plor force field parameters file into ForcePrm container. 7 | * @author David J. Hardy 8 | * @date Apr. 2008 9 | */ 10 | 11 | #ifndef MOLFILES_XPLOR_H 12 | #define MOLFILES_XPLOR_H 13 | 14 | #include "moltypes/moltypes.h" 15 | 16 | #ifdef __cplusplus 17 | extern "C" { 18 | #endif 19 | 20 | int ForcePrm_read_xplor(ForcePrm *, const char *fname); 21 | 22 | #ifdef __cplusplus 23 | } 24 | #endif 25 | 26 | #endif /* MOLFILES_XPLOR_H */ 27 | -------------------------------------------------------------------------------- /vmd/plugins/readcharmmpar/Makefile: -------------------------------------------------------------------------------- 1 | .SILENT: 2 | 3 | VMFILES = readcharmmpar.tcl par_all27_prot_lipid_na.inp pkgIndex.tcl par_amber2charmm.inp par_all36_lipid.prm toppar_all36_carb_glycopeptide.str toppar_water_ions_namd.str par_all22_prot.prm par_all36_carb.prm par_all36_cgenff.prm par_all36_na.prm par_all36_prot.prm 4 | VMVERSION = 1.4 5 | DIR = $(PLUGINDIR)/noarch/tcl/readcharmmpar$(VMVERSION) 6 | 7 | bins: 8 | win32bins: 9 | dynlibs: 10 | staticlibs: 11 | win32staticlibs: 12 | 13 | distrib: 14 | @echo "Copying readcharmmpar $(VMVERSION) files to $(DIR)" 15 | mkdir -p $(DIR) 16 | cp $(VMFILES) $(DIR) 17 | 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/cionize/mgpot.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | * 4 | * mgpot.h 5 | */ 6 | 7 | #ifndef MGPOT_H 8 | #define MGPOT_H 9 | 10 | #ifdef __cplusplus 11 | extern "C" { 12 | #endif 13 | 14 | /* entry point for computing grid energies using mgpot */ 15 | int calc_grid_energies_excl_mgpot(float* atoms, float* grideners, 16 | long int numplane, long int numcol, long int numpt, long int natoms, 17 | float gridspacing, unsigned char* excludepos, int maxnumprocs, 18 | int emethod); 19 | 20 | #ifdef __cplusplus 21 | } 22 | #endif 23 | 24 | #endif /* MGPOT_H */ 25 | -------------------------------------------------------------------------------- /vmd/plugins/fmtool/psf_from_file_xy_to_r.h: -------------------------------------------------------------------------------- 1 | #ifndef _PSF_FROM_FILE_XY_TO_R_ 2 | #define _PSF_FROM_FILE_XY_TO_R_ 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | #include 12 | 13 | void psf_from_file_xy_to_r(int &, int &, double &, double &, double &, 14 | double &, double &, double &, double &, string &, 15 | string &, int &, double *, double *, double &, 16 | double &, double &, double &, int &, int &); 17 | #endif 18 | 19 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/charmm.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2008 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file molfiles/charmm.h 6 | * @brief Read CHARMM force field parameters file into ForcePrm container. 7 | * @author David J. Hardy 8 | * @date Apr. 2008 9 | */ 10 | 11 | #ifndef MOLFILES_CHARMM_H 12 | #define MOLFILES_CHARMM_H 13 | 14 | #include "moltypes/moltypes.h" 15 | 16 | #ifdef __cplusplus 17 | extern "C" { 18 | #endif 19 | 20 | int ForcePrm_read_charmm(ForcePrm *, const char *fname); 21 | 22 | #ifdef __cplusplus 23 | } 24 | #endif 25 | 26 | #endif /* MOLFILES_CHARMM_H */ 27 | -------------------------------------------------------------------------------- /vmd/plugins/rnaview/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded rnaview 1.1 "set env(RNAVIEW) {$dir}; [list source [file join $dir rnaview.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/bdtk/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded bdtoolkit 1.0 "set env(BDTKDIR) [list $dir]; [list source [file join $dir bdtk.tcl]] ; " 12 | -------------------------------------------------------------------------------- /vmd/plugins/idatm/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded idatm 0.1 "set env(IDATMDIR) [list $dir] ; source [list [file join $dir idatm.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/molfiles/charmm.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2008 by David J. Hardy. All rights reserved. 3 | */ 4 | 5 | /**@file molfiles/charmm.h 6 | * @brief Read CHARMM force field parameters file into ForcePrm container. 7 | * @author David J. Hardy 8 | * @date Apr. 2008 9 | */ 10 | 11 | #ifndef MOLFILES_CHARMM_H 12 | #define MOLFILES_CHARMM_H 13 | 14 | #include "moltypes/moltypes.h" 15 | 16 | #ifdef __cplusplus 17 | extern "C" { 18 | #endif 19 | 20 | int ForcePrm_read_charmm(ForcePrm *, const char *fname); 21 | 22 | #ifdef __cplusplus 23 | } 24 | #endif 25 | 26 | #endif /* MOLFILES_CHARMM_H */ 27 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/src/extract_alias.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef EXTRACT_ALIAS_H 3 | #define EXTRACT_ALIAS_H 4 | 5 | #include "stringhash.h" 6 | 7 | #define EXTRACT_ALIAS_FAIL -1 8 | 9 | int extract_alias_residue_define(stringhash *h, 10 | const char *altres, const char *realres); 11 | 12 | int extract_alias_atom_define(stringhash *h, const char *resname, 13 | const char *altatom, const char *realatom); 14 | 15 | const char * extract_alias_residue_check(stringhash *h, 16 | const char *resname); 17 | 18 | const char * extract_alias_atom_check(stringhash *h, 19 | const char *resname, const char *atomname); 20 | 21 | #endif 22 | 23 | -------------------------------------------------------------------------------- /vmd/plugins/qmtool/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded qmtool 1.3 "set env(QMTOOLDIR) [list $dir]; [list source [file join $dir qmtool.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/runsqm/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded runsqm 0.2 "set env(VMDSQMDIR) [list $dir] ; source [list [file join $dir runsqm.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/updater/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded updater 1.0 [list tclPkgSetup $dir updater 1.0 {{updater.tcl source pluginupdater}}] 12 | -------------------------------------------------------------------------------- /vmd/plugins/volutil/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded volutil 1.3 "set env(VOLUTILDIR) {$dir}; [list source [file join $dir volutil.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/apbsrun/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded apbsrun 1.3 "set env(APBSRUNDIR) [list $dir] ; [list source [file join $dir apbsrun.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/bendix/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.0 2 | # This file is generated by the "pkg_mkIndex" 3 | 4 | # This code makes Bendix into a package. 5 | # VMD startup code executes 'package require', 6 | # looks for this file and uses the one-liner to create an index of Bendix (specifying what version to use, where appropriate) 7 | # where available packages are listed, so that Tcl can use this index to load Bendix by the path provided below. 8 | # 'Package provide' in the main bendix code, checks that the package exists. 9 | 10 | 11 | package ifneeded bendix 1.1 [list source [file join $dir bendix.tcl]] 12 | -------------------------------------------------------------------------------- /vmd/plugins/fftk/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded forcefieldtoolkit 1.2 "set env(FFTKDIR) [list $dir]; [list source [file join $dir fftk.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/ilstools/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded ilstools 1.5 "set env(ILSTOOLSDIR) {$dir}; [list source [file join $dir ilstools.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/jmvexport/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded jmvexport 1.0 [list tclPkgSetup $dir jmvexport 1.0 {{jmvexport.tcl source jmvexport}}] 12 | -------------------------------------------------------------------------------- /vmd/plugins/mafft/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded mafft 1.1 "set env(MAFFTRUNDIR) [list $dir] ; [list source [file join $dir mafft.tcl]]" 12 | 13 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/GLN.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT GLN 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.750000 -0.433000 0.997000 H 4 | HB2 1.721000 -0.795000 -0.748000 H 5 | CG 2.388000 1.228000 -0.249000 C 6 | HG1 1.995000 1.825000 -1.100000 H 7 | HG2 2.410000 1.884000 0.645000 H 8 | CD 3.819000 0.798000 -0.612000 C 9 | OE1 4.131000 -0.358000 -0.916000 O 10 | NE2 4.750000 1.713000 -0.557000 N 11 | HE21 5.674000 1.430000 -0.797000 H 12 | HE22 4.520000 2.636000 -0.268000 H 13 | BONDS 14 | 0 2 1 15 | 0 3 1 16 | 0 1 1 17 | 3 4 1 18 | 3 5 1 19 | 3 6 1 20 | 6 7 2 21 | 6 8 1 22 | 8 10 1 23 | 8 9 1 24 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/MET.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT MET 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.763000 -1.027000 -0.345000 H 4 | HB2 1.723000 0.681000 -0.851000 H 5 | CG 2.379000 0.346000 1.196000 C 6 | HG1 3.438000 0.451000 0.879000 H 7 | HG2 2.058000 1.320000 1.626000 H 8 | SD 2.281000 -0.938000 2.468000 S 9 | CE 3.828000 -0.644000 3.379000 C 10 | HE1 3.942000 -1.370000 4.212000 H 11 | HE2 4.711000 -0.750000 2.711000 H 12 | HE3 3.849000 0.379000 3.811000 H 13 | BONDS 14 | 0 1 1 15 | 0 2 1 16 | 0 3 1 17 | 3 4 1 18 | 3 6 1 19 | 3 5 1 20 | 6 7 1 21 | 7 9 1 22 | 7 8 1 23 | 7 10 1 24 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/nlbase.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | * 4 | * nlbase.h - NAMD-Lite basic routines and data structures. 5 | */ 6 | 7 | #ifndef NLBASE_H 8 | #define NLBASE_H 9 | 10 | #include "nlbase/types.h" 11 | #include "nlbase/error.h" 12 | #include "nlbase/io.h" 13 | #include "nlbase/mem.h" 14 | #include "nlbase/array.h" 15 | #include "nlbase/strmap.h" 16 | #include "nlbase/arrmap.h" 17 | #include "nlbase/idlist.h" 18 | #include "nlbase/string.h" 19 | #include "nlbase/random.h" 20 | #include "nlbase/sort.h" 21 | #include "nlbase/numeric.h" 22 | 23 | #endif /* NLBASE_H */ 24 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/nlbase/GNUmakefile: -------------------------------------------------------------------------------- 1 | # GNUmakefile 2 | # definitions for building "nlbase" 3 | 4 | TOP = ../.. 5 | NAME = nlbase 6 | TYPE = lib 7 | OBJ = error io mem array strmap arrmap idlist string random sort numeric 8 | LIB = m 9 | LINKCPP = no 10 | HEADER = nlbase \ 11 | error io mem array strmap arrmap idlist string random sort numeric 12 | DEMO = test_io test_mem test_array test_strmap test_strmap2 test_arrmap \ 13 | test_idlist test_sort 14 | DEMOOBJ = 15 | DEMOLIB = nlbase 16 | DEMOLINKCPP = 17 | 18 | ifeq (0,$(MAKELEVEL)) 19 | .PHONY : src clean 20 | src clean : ; $(MAKE) -C $(TOP) SRC="$(NAME)" $@ 21 | endif 22 | -------------------------------------------------------------------------------- /vmd/plugins/rmsdtt/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded rmsdtt 3.0 "set env(RMSDTTDIR) [list $dir]; [list source [file join $dir rmsdtt.tcl]]" 12 | 13 | -------------------------------------------------------------------------------- /vmd/plugins/runante/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded runante 0.2 "set env(VMDANTEDIR) [list $dir] ; source [list [file join $dir runante.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/solvate/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded solvate 1.7 "source [list [file join $dir solvate.tcl]] ; set env(SOLVATEDIR) [list $dir]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/structurecheck/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded structurecheck 1.0 [list source [file join $dir structurecheck.tcl]] 12 | 13 | 14 | -------------------------------------------------------------------------------- /vmd/plugins/vmdlite/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded vmdlite 1.1 "set env(VMDLITEDIR) [list $dir]; [list source [file join $dir vmdlite.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/membrane/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded membrane 1.2 "set env(MEMBRANEDIR) [list $dir]; [list source [file join $dir membrane.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/namdgui/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded namdgui 1.4 "set env(NAMDGUIDIR) [list $dir]; source [list [file join $dir namdgui.tcl]]" 12 | 13 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/nlbase/nlbase.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | * 4 | * nlbase.h - NAMD-Lite basic routines and data structures. 5 | */ 6 | 7 | #ifndef NLBASE_H 8 | #define NLBASE_H 9 | 10 | #include "nlbase/types.h" 11 | #include "nlbase/error.h" 12 | #include "nlbase/io.h" 13 | #include "nlbase/mem.h" 14 | #include "nlbase/array.h" 15 | #include "nlbase/strmap.h" 16 | #include "nlbase/arrmap.h" 17 | #include "nlbase/idlist.h" 18 | #include "nlbase/string.h" 19 | #include "nlbase/random.h" 20 | #include "nlbase/sort.h" 21 | #include "nlbase/numeric.h" 22 | 23 | #endif /* NLBASE_H */ 24 | -------------------------------------------------------------------------------- /vmd/plugins/paratool/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded paratool 1.5 "set env(PARATOOLDIR) [list $dir]; [list source [file join $dir paratool.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/src/pdb_file_extract.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef PDB_FILE_EXTRACT_H 3 | #define PDB_FILE_EXTRACT_H 4 | 5 | #include 6 | #include "stringhash.h" 7 | #include "topo_mol.h" 8 | 9 | int pdb_file_extract_residues(topo_mol *mol, FILE *file, stringhash *h, int all_caps, 10 | void *, void (*print_msg)(void *,const char *)); 11 | 12 | int pdb_file_extract_coordinates(topo_mol *mol, FILE *file, FILE *namdbinfile, 13 | const char *segid, stringhash *h, int all_caps, 14 | void *,void (*print_msg)(void *,const char *)); 15 | 16 | #endif 17 | 18 | -------------------------------------------------------------------------------- /vmd/plugins/rmsdvt/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded rmsdvt 1.0 "set env(RMSDVTDIR) [list $dir]; [list source [file join $dir rmsdvt.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/topotools/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded topotools 1.7 "set env(TOPOTOOLSDIR) {$dir}; [list source [file join $dir topotools.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/torsionplot/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.0 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded torsionplot 1.1 "set env(TORPLOTDIR) {$dir}; [list source [file join $dir torsionplot.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/vmdtkcon/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded vmdtkcon 1.1 "source [list [file join $dir vmdtkcon.tcl]] ; set env(TKCONDIR) [list $dir]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/intersurf/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded intersurf 1.1 "set env(INTERSURFDIR) [list $dir]; source [list [file join $dir intersurf_gui.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/drugui/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded drugui 1.0 [list source [file join $dir drugui.tcl]] 12 | global env 13 | set env(DRUGGABILITY_PATH) $dir 14 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/HIS.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT HIS 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.751000 -0.251000 1.053000 H 4 | HB2 1.699000 -0.908000 -0.607000 H 5 | ND1 3.636000 0.934000 -1.056000 N 6 | CG 2.405000 1.159000 -0.446000 C 7 | CE1 4.187000 2.104000 -1.325000 C 8 | HE1 5.162000 2.236000 -1.802000 H 9 | NE2 3.384000 3.057000 -0.925000 N 10 | HE2 3.585000 4.034000 -1.000000 H 11 | CD2 2.265000 2.514000 -0.374000 C 12 | HD2 1.460000 3.107000 0.036000 H 13 | BONDS 14 | 0 2 1 15 | 0 4 1 16 | 0 1 1 17 | 3 4 1 18 | 3 5 2 19 | 4 9 2 20 | 5 6 1 21 | 5 7 1 22 | 7 9 1 23 | 7 8 1 24 | 9 10 1 25 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/amino_acids/HSE.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT HIS 2 | CB 1.500000 0.000000 0.000000 C 3 | HB1 1.751000 -0.251000 1.053000 H 4 | HB2 1.699000 -0.908000 -0.607000 H 5 | ND1 3.636000 0.934000 -1.056000 N 6 | CG 2.405000 1.159000 -0.446000 C 7 | CE1 4.187000 2.104000 -1.325000 C 8 | HE1 5.162000 2.236000 -1.802000 H 9 | NE2 3.384000 3.057000 -0.925000 N 10 | HE2 3.585000 4.034000 -1.000000 H 11 | CD2 2.265000 2.514000 -0.374000 C 12 | HD2 1.460000 3.107000 0.036000 H 13 | BONDS 14 | 0 2 1 15 | 0 4 1 16 | 0 1 1 17 | 3 4 1 18 | 3 5 2 19 | 4 9 2 20 | 5 6 1 21 | 5 7 1 22 | 7 9 1 23 | 7 8 1 24 | 9 10 1 25 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/lib/basemol/cyclopropane.mfrag: -------------------------------------------------------------------------------- 1 | FRAGMENT CYCLOPROPANE CPRO 2 | C 0.936 0.389 -0.452 C 3 | C -0.415 -0.036 -0.982 C 4 | C 0.485 0.850 -1.784 C 5 | H 0.921 0.498 -2.613 H 6 | H 0.241 1.809 -1.928 H 7 | H 1.674 -0.280 -0.374 H 8 | H 0.994 1.031 0.311 H 9 | H -1.246 0.326 -0.567 H 10 | H -0.566 -0.985 -1.252 H 11 | BONDS 12 | 0 1 1.0 13 | 0 2 1.0 14 | 0 5 1.0 15 | 0 6 1.0 16 | 1 0 1.0 17 | 1 2 1.0 18 | 1 7 1.0 19 | 1 8 1.0 20 | 2 0 1.0 21 | 2 1 1.0 22 | 2 3 1.0 23 | 2 4 1.0 24 | 3 2 1.0 25 | 4 2 1.0 26 | 5 0 1.0 27 | 6 0 1.0 28 | 7 1 1.0 29 | 8 1 1.0 30 | -------------------------------------------------------------------------------- /vmd/plugins/molefacture/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded molefacture 1.4 "set env(MOLEFACTUREDIR) [list $dir] ; source [list [file join $dir molefacture.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/moltoptools/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded moltoptools 0.1 "set env(MOLTOPTOOLDIR) [list $dir] ; source [list [file join $dir moltoptools.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/namdenergy/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded namdenergy 1.4 "source [list [file join $dir namdenergy.tcl]] ; set env(NAMDENERGYDIR) [list $dir]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/mem.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | * 4 | * mem.h - NAMD-Lite low-level memory management routines. 5 | */ 6 | 7 | #ifndef NLBASE_MEM_H 8 | #define NLBASE_MEM_H 9 | 10 | #ifdef __cplusplus 11 | extern "C" { 12 | #endif 13 | 14 | /* Similar semantics to the C library routines. */ 15 | void *NL_malloc(size_t size); 16 | void *NL_calloc(size_t nelem, size_t elsize); 17 | void NL_free(void *ptr); 18 | void *NL_realloc(void *ptr, size_t size); 19 | char *NL_strdup(const char *s1); 20 | 21 | #ifdef __cplusplus 22 | } 23 | #endif 24 | 25 | #endif /* NLBASE_MEM_H */ 26 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/hack/test_mem.c: -------------------------------------------------------------------------------- 1 | #include "nlbase/nlbase.h" 2 | 3 | int main() { 4 | int *pn; 5 | int i; 6 | if ((pn = NL_calloc(10, sizeof(int)))==NULL) { 7 | return ERROR(ERR_MEMALLOC); 8 | } 9 | pn[0] = 1; 10 | for (i = 1; i < 10; i++) { 11 | pn[i] = pn[i-1] + 1; 12 | } 13 | if ((pn = NL_realloc(pn, 20*sizeof(int)))==NULL) { 14 | return ERROR(ERR_MEMALLOC); 15 | } 16 | for (i = 10; i < 20; i++) { 17 | pn[i] = pn[i-1] + 1; 18 | } 19 | NL_printf("array: "); 20 | for (i = 0; i < 20; i++) { 21 | NL_printf("%d ", i); 22 | } 23 | NL_printf("\n"); 24 | NL_free(pn); 25 | return OK; 26 | } 27 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/nlbase/mem.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2007 by David J. Hardy. All rights reserved. 3 | * 4 | * mem.h - NAMD-Lite low-level memory management routines. 5 | */ 6 | 7 | #ifndef NLBASE_MEM_H 8 | #define NLBASE_MEM_H 9 | 10 | #ifdef __cplusplus 11 | extern "C" { 12 | #endif 13 | 14 | /* Similar semantics to the C library routines. */ 15 | void *NL_malloc(size_t size); 16 | void *NL_calloc(size_t nelem, size_t elsize); 17 | void NL_free(void *ptr); 18 | void *NL_realloc(void *ptr, size_t size); 19 | char *NL_strdup(const char *s1); 20 | 21 | #ifdef __cplusplus 22 | } 23 | #endif 24 | 25 | #endif /* NLBASE_MEM_H */ 26 | -------------------------------------------------------------------------------- /vmd/plugins/psfgen/scripts/buildmin.tcl: -------------------------------------------------------------------------------- 1 | 2 | # Set SCRIPTDIR to wherever you install this package 3 | set SCRIPTDIR /home/justin/projects/psfgen/scripts 4 | source $SCRIPTDIR/build.tcl 5 | source $SCRIPTDIR/minimize.tcl 6 | 7 | proc buildmin { pdb { buildname NONE } { outputname NONE } } { 8 | if { ![string compare $buildname NONE]} { 9 | set buildname "[lindex [split $pdb '.'] 0]_build" 10 | } 11 | 12 | build $pdb $buildname 13 | 14 | if { ![string compare $outputname NONE]} { 15 | set outputname "[lindex [split $pdb '.'] 0]_min" 16 | } 17 | 18 | minimize "${buildname}.psf" "${buildname}.pdb" $outputname 100 19 | } 20 | 21 | 22 | -------------------------------------------------------------------------------- /vmd/plugins/readcharmmpar/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded readcharmmpar 1.4 "set env(CHARMMPARDIR) {$dir}; [list source [file join $dir readcharmmpar.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/readcharmmtop/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded readcharmmtop 1.2 "set env(CHARMMTOPDIR) {$dir}; [list source [file join $dir readcharmmtop.tcl]]" 12 | -------------------------------------------------------------------------------- /vmd/plugins/nlenergy/src/old/nlbase/test_mem.c: -------------------------------------------------------------------------------- 1 | #include "nlbase/nlbase.h" 2 | 3 | int main() { 4 | int *pn; 5 | int i; 6 | if ((pn = NL_calloc(10, sizeof(int)))==NULL) { 7 | return ERROR(ERR_MEMALLOC); 8 | } 9 | pn[0] = 1; 10 | for (i = 1; i < 10; i++) { 11 | pn[i] = pn[i-1] + 1; 12 | } 13 | if ((pn = NL_realloc(pn, 20*sizeof(int)))==NULL) { 14 | return ERROR(ERR_MEMALLOC); 15 | } 16 | for (i = 10; i < 20; i++) { 17 | pn[i] = pn[i-1] + 1; 18 | } 19 | NL_printf("array: "); 20 | for (i = 0; i < 20; i++) { 21 | NL_printf("%d ", i); 22 | } 23 | NL_printf("\n"); 24 | NL_free(pn); 25 | return OK; 26 | } 27 | -------------------------------------------------------------------------------- /vmd/plugins/alascanfep/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded alascan 1.0 "set env(ALASCANFEPDIR) [list $dir] ; [list source [file join $dir alascan.tcl]]" 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /vmd/plugins/blast/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded blast 1.11 "[list source [file join $dir blast.tcl]]\n[list source [file join $dir blast_resultviewer.tcl]]" 12 | 13 | -------------------------------------------------------------------------------- /vmd/plugins/heatmapper/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded heatmapper 1.1 "set env(HEATMAPPERDIR) [list $dir]; [list source [file join $dir heatmapper.tcl]]" 12 | --------------------------------------------------------------------------------