├── .gitattributes ├── .gitignore ├── .travis.yml ├── CHANGELOG.md ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── bin ├── install_spglib.sh ├── iqmpy ├── oqmd └── qmpy ├── docs ├── Makefile ├── _static │ ├── css │ │ └── custom.css │ ├── oqmd_logo.png │ └── rester.gif ├── analysis.rst ├── calculations.rst ├── conf.py ├── examples.rst ├── faqs.rst ├── getting_started.rst ├── index.rst ├── materials.rst ├── models.rst ├── resources.rst ├── restful.rst └── tutorials.rst ├── examples ├── analysis │ ├── chem_pots.py │ ├── get_formations.py │ └── pot_fitting.py ├── database │ ├── Li-M-O_screen.py │ ├── discovery_rate.py │ ├── oqmd_vs_expt.py │ └── precipitates.py ├── sklearn │ └── build_model.py └── structures │ ├── CNPbI3.cif │ ├── POSCAR │ ├── bond_lengths.py │ ├── find_layered.py │ ├── modify_CNPbI3.py │ └── prototype_constructor.py ├── qmpy ├── VERSION.txt ├── __init__.py ├── analysis │ ├── __init__.py │ ├── bond_valence.py │ ├── database.py │ ├── debye │ │ ├── debye_model.py │ │ ├── exp_PbS │ │ │ ├── PbS_answers │ │ │ ├── PbS_debye │ │ │ ├── PbS_density │ │ │ └── PbS_exp_C │ │ ├── exp_PbTe │ │ │ ├── PbTe_density │ │ │ ├── PbTe_exp_C │ │ │ └── PbTe_model_VII_C │ │ ├── lead │ │ │ ├── Pb_answers │ │ │ ├── Pb_debey_temp │ │ │ ├── Pb_density │ │ │ └── Pb_exp_C │ │ ├── quasi_harmonic.py │ │ ├── read_file.py │ │ ├── sound_waves.py │ │ └── wolfram_tungsten │ │ │ ├── W_density │ │ │ └── W_exp_C │ ├── elastic.py │ ├── griddata.py │ ├── interface_finder.py │ ├── miedema.py │ ├── mining.py │ ├── nearest_neighbors.py │ ├── network.py │ ├── nn.pyx │ ├── pdf.py │ ├── symmetry │ │ ├── __init__.py │ │ ├── routines.py │ │ ├── spacegroup.py │ │ └── tests.py │ ├── test │ │ ├── bond_valence_test.py │ │ ├── dists.txt │ │ ├── ising_test.py │ │ ├── nn_test.py │ │ ├── pdf_test.py │ │ ├── peaks.txt │ │ └── xrd_test.py │ ├── tests.py │ ├── thermodynamics │ │ ├── __init__.py │ │ ├── chemical_potential_fitting.py │ │ ├── convex_hull.py │ │ ├── equilibrium.py │ │ ├── phase.py │ │ ├── reaction.py │ │ ├── setup.py │ │ ├── space.py │ │ └── tests.py │ ├── vasp │ │ ├── __init__.py │ │ ├── calculation.py │ │ ├── dos.py │ │ ├── files │ │ │ ├── convergence │ │ │ │ ├── CHG │ │ │ │ ├── CHGCAR │ │ │ │ ├── CHGCAR.gz │ │ │ │ ├── CONTCAR │ │ │ │ ├── DOSCAR │ │ │ │ ├── EIGENVAL │ │ │ │ ├── IBZKPT │ │ │ │ ├── INCAR │ │ │ │ ├── KPOINTS │ │ │ │ ├── OSZICAR │ │ │ │ ├── OUTCAR │ │ │ │ ├── PCDAT │ │ │ │ ├── POSCAR │ │ │ │ ├── POTCAR │ │ │ │ ├── WAVECAR │ │ │ │ ├── XDATCAR │ │ │ │ ├── auto.q │ │ │ │ ├── joberr.txt │ │ │ │ ├── jobout.txt │ │ │ │ ├── stderr.txt │ │ │ │ ├── stdout.txt │ │ │ │ └── vasprun.xml │ │ │ └── relaxation │ │ │ │ ├── CHGCAR.gz │ │ │ │ ├── CONTCAR │ │ │ │ ├── DOSCAR │ │ │ │ ├── EIGENVAL │ │ │ │ ├── IBZKPT │ │ │ │ ├── INCAR │ │ │ │ ├── KPOINTS │ │ │ │ ├── OSZICAR │ │ │ │ ├── OUTCAR.gz │ │ │ │ ├── PCDAT │ │ │ │ ├── POSCAR │ │ │ │ ├── PROCAR.gz │ │ │ │ ├── XDATCAR │ │ │ │ ├── auto.q │ │ │ │ ├── joberr.txt │ │ │ │ ├── jobout.txt │ │ │ │ ├── stderr.txt │ │ │ │ ├── stdout.txt │ │ │ │ └── vasprun.xml.gz │ │ ├── potential.py │ │ └── test │ │ │ └── dos_test.py │ └── xrd.py ├── computing │ ├── __init__.py │ ├── manager.py │ ├── queue.py │ ├── resources.py │ ├── scripts.py │ └── tests.py ├── configuration │ ├── __init__.py │ ├── qfiles │ │ ├── __init__.py │ │ ├── bebop.q │ │ ├── local.q │ │ ├── quest.q │ │ ├── stampede.q │ │ └── xsede.q │ ├── resources │ │ ├── __init__.py │ │ ├── allocations.yml │ │ ├── hosts.yml │ │ ├── projects.yml │ │ └── users.yml │ ├── site.cfg │ └── vasp_settings │ │ ├── __init__.py │ │ ├── hubbards.yml │ │ ├── inputs │ │ ├── __init__.py │ │ ├── b3lyp.yml │ │ ├── coarse_relax.yml │ │ ├── fine_relax.yml │ │ ├── hf.yml │ │ ├── hse06.yml │ │ ├── initialize.yml │ │ ├── pbe0.yml │ │ ├── relax_fix_vol.yml │ │ ├── relaxation.yml │ │ ├── relaxation_lda.yml │ │ ├── standard.yml │ │ ├── static.yml │ │ ├── static_lda.yml │ │ └── vdw.yml │ │ └── potentials.yml ├── data │ ├── __init__.py │ ├── bond_valence │ │ ├── bond_valence_parameters.yml │ │ └── bond_valence_references.yml │ ├── elements │ │ ├── chemical_potentials.yml │ │ ├── data.yml │ │ └── groups.yml │ ├── meta_data.py │ ├── miedema.yml │ ├── reference.py │ ├── spacegroups.yml │ └── thermodata │ │ ├── README.txt │ │ ├── corrections.dat │ │ ├── iit.dat │ │ ├── konigs.dat │ │ ├── legacy.dat │ │ ├── mat_proj.dat │ │ └── ssub.dat ├── db │ ├── __init__.py │ ├── custom.py │ ├── manage.py │ ├── settings.py │ └── wsgi.py ├── io │ ├── __init__.py │ ├── ase_mapper.py │ ├── cif.py │ ├── files │ │ ├── POSCAR_BCC │ │ ├── POSCAR_BeCl │ │ ├── POSCAR_CsCl │ │ ├── POSCAR_FCC │ │ ├── POSCAR_FCC2 │ │ ├── POSCAR_FCC_prim │ │ ├── POSCAR_HCP │ │ ├── POSCAR_KCl │ │ ├── POSCAR_NaCl │ │ ├── POSCAR_SC │ │ ├── POSCAR_ZnS │ │ ├── POSCAR_trans │ │ ├── POSCAR_vasp4 │ │ ├── POSCAR_vasp5 │ │ ├── fe3o4.cif │ │ ├── joggle.cif │ │ ├── partial.cif │ │ ├── partial_mix.cif │ │ ├── partial_perfect.cif │ │ ├── partial_vac.cif │ │ ├── perfect.cif │ │ └── test.cif │ ├── poscar.py │ └── tests.py ├── logs │ └── __init__.py ├── materials │ ├── __init__.py │ ├── atom.py │ ├── composition.py │ ├── element.py │ ├── entry.py │ ├── formation_energy.py │ ├── structure.py │ └── tests.py ├── models.py ├── rester │ ├── __init__.py │ └── qmpy_rester.py ├── templatetags │ ├── __init__.py │ └── custom_filters.py ├── tests.py ├── utils │ ├── __init__.py │ ├── daemon.py │ ├── folder_management.py │ ├── importer.py │ ├── math.py │ ├── oqmd_optimade │ │ ├── QueryLarkDjangoParser.py │ │ ├── __init__.py │ │ ├── grammar │ │ │ ├── __init__.py │ │ │ ├── optimade_info.json │ │ │ ├── optimade_info_structures.json │ │ │ ├── optimade_links.json │ │ │ ├── v0.1.0.oqmd │ │ │ ├── v0.9.5.g │ │ │ ├── v0.9.6.g │ │ │ ├── v0.9.7.g │ │ │ ├── v1.0.0.g │ │ │ └── v1.0.0.oqmd │ │ ├── optimade_spec_data.py │ │ ├── renderers.py │ │ └── tests.py │ ├── rendering │ │ ├── __init__.py │ │ ├── axis.py │ │ ├── line.py │ │ ├── point.py │ │ ├── renderable.py │ │ ├── renderer.py │ │ └── text.py │ ├── rest_query_parser.py │ ├── strings.py │ ├── test │ │ ├── daemon_test.py │ │ ├── math_test.py │ │ ├── miedema_test.py │ │ └── strings_test.py │ └── test_math.pyx └── web │ ├── __init__.py │ ├── serializers │ ├── __init__.py │ ├── calculation.py │ ├── composition.py │ ├── entry.py │ ├── formationenergy.py │ ├── optimade.py │ └── structure.py │ ├── static │ ├── css │ │ ├── animation.css │ │ ├── base.css │ │ ├── bokeh-0.12.11.min.css │ │ ├── bokeh-0.12.15.min.css │ │ ├── bootstrap-responsive.css │ │ ├── bootstrap-responsive.min.css │ │ ├── bootstrap.css │ │ ├── bootstrap.min.css │ │ ├── flot.css │ │ └── old.css │ ├── docs │ ├── img │ │ ├── AlFe_pd.png │ │ ├── Explanation_Chull.png │ │ ├── NiTiAl_pd.png │ │ ├── crystStruct.png │ │ ├── favicon.ico │ │ ├── grid-minus.gif │ │ ├── grid-plus.gif │ │ ├── logo.png │ │ ├── new_logo_oqmd.png │ │ ├── twitter_composition.png │ │ └── twitter_pd.png │ ├── js │ │ ├── bokeh-0.12.11.min.js │ │ ├── bokeh-0.12.15.min.js │ │ ├── bootstrap-tab.js │ │ ├── bootstrap.js │ │ ├── bootstrap.min.js │ │ ├── jquery-3.5.1.min.js │ │ ├── jquery.base-oqmd.combined.min.js │ │ ├── jquery.flot.axislabels.js │ │ ├── jquery.flot.axislabels.js.alt │ │ ├── jquery.flot.axislabels.min.js │ │ ├── jquery.flot.labels.js │ │ ├── jquery.flot.labels.min.js │ │ ├── jquery.flot.min.js │ │ ├── jquery.flot.pie.js │ │ ├── jquery.flot.pie.min.js │ │ ├── jquery.flot.tooltip.js │ │ ├── jquery.flot.tooltip.min.js │ │ ├── jsmol │ │ │ ├── JSmol.min.js │ │ │ ├── idioma │ │ │ │ ├── ar.po │ │ │ │ ├── bs.po │ │ │ │ ├── ca.po │ │ │ │ ├── ca@valencia.po │ │ │ │ ├── cs.po │ │ │ │ ├── da.po │ │ │ │ ├── de.po │ │ │ │ ├── el.po │ │ │ │ ├── en_GB.po │ │ │ │ ├── es.po │ │ │ │ ├── et.po │ │ │ │ ├── eu.po │ │ │ │ ├── fi.po │ │ │ │ ├── fr.po │ │ │ │ ├── fy.po │ │ │ │ ├── hu.po │ │ │ │ ├── hy.po │ │ │ │ ├── id.po │ │ │ │ ├── it.po │ │ │ │ ├── ja.po │ │ │ │ ├── jv.po │ │ │ │ ├── ko.po │ │ │ │ ├── ms.po │ │ │ │ ├── nb.po │ │ │ │ ├── nl.po │ │ │ │ ├── oc.po │ │ │ │ ├── pl.po │ │ │ │ ├── pt.po │ │ │ │ ├── pt_BR.po │ │ │ │ ├── ru.po │ │ │ │ ├── sl.po │ │ │ │ ├── sv.po │ │ │ │ ├── ta.po │ │ │ │ ├── te.po │ │ │ │ ├── tr.po │ │ │ │ ├── ug.po │ │ │ │ ├── uk.po │ │ │ │ ├── uz.po │ │ │ │ ├── zh_CN.po │ │ │ │ └── zh_TW.po │ │ │ ├── j2s │ │ │ │ ├── J │ │ │ │ │ ├── Jmol.properties │ │ │ │ │ ├── adapter │ │ │ │ │ │ ├── readers │ │ │ │ │ │ │ ├── cif │ │ │ │ │ │ │ │ ├── Cif2DataParser.js │ │ │ │ │ │ │ │ ├── Cif2Reader.js │ │ │ │ │ │ │ │ ├── CifReader.js │ │ │ │ │ │ │ │ ├── MMCifReader.js │ │ │ │ │ │ │ │ ├── MMCifValidationParser.js │ │ │ │ │ │ │ │ ├── MMTFReader.js │ │ │ │ │ │ │ │ ├── MSCifParser.js │ │ │ │ │ │ │ │ ├── MSRdr.js │ │ │ │ │ │ │ │ └── Subsystem.js │ │ │ │ │ │ │ ├── molxyz │ │ │ │ │ │ │ │ ├── Mol3DReader.js │ │ │ │ │ │ │ │ ├── MolReader.js │ │ │ │ │ │ │ │ ├── V3000Rdr.js │ │ │ │ │ │ │ │ └── XyzReader.js │ │ │ │ │ │ │ ├── more │ │ │ │ │ │ │ │ ├── AFLOWReader.js │ │ │ │ │ │ │ │ ├── BinaryDcdReader.js │ │ │ │ │ │ │ │ ├── ForceFieldReader.js │ │ │ │ │ │ │ │ ├── GromacsReader.js │ │ │ │ │ │ │ │ ├── JcampdxReader.js │ │ │ │ │ │ │ │ ├── MdCrdReader.js │ │ │ │ │ │ │ │ ├── MdTopReader.js │ │ │ │ │ │ │ │ ├── Mol2Reader.js │ │ │ │ │ │ │ │ └── TlsDataOnlyReader.js │ │ │ │ │ │ │ ├── pdb │ │ │ │ │ │ │ │ ├── JmolDataReader.js │ │ │ │ │ │ │ │ ├── P2nReader.js │ │ │ │ │ │ │ │ ├── PdbReader.js │ │ │ │ │ │ │ │ └── PqrReader.js │ │ │ │ │ │ │ ├── pymol │ │ │ │ │ │ │ │ ├── JmolObject.js │ │ │ │ │ │ │ │ ├── PickleReader.js │ │ │ │ │ │ │ │ ├── PyMOL.js │ │ │ │ │ │ │ │ ├── PyMOLGroup.js │ │ │ │ │ │ │ │ ├── PyMOLReader.js │ │ │ │ │ │ │ │ └── PyMOLScene.js │ │ │ │ │ │ │ ├── quantum │ │ │ │ │ │ │ │ ├── AdfReader.js │ │ │ │ │ │ │ │ ├── BasisFunctionReader.js │ │ │ │ │ │ │ │ ├── CsfReader.js │ │ │ │ │ │ │ │ ├── DgridReader.js │ │ │ │ │ │ │ │ ├── GamessReader.js │ │ │ │ │ │ │ │ ├── GamessUKReader.js │ │ │ │ │ │ │ │ ├── GamessUSReader.js │ │ │ │ │ │ │ │ ├── GaussianFchkReader.js │ │ │ │ │ │ │ │ ├── GaussianReader.js │ │ │ │ │ │ │ │ ├── GaussianWfnReader.js │ │ │ │ │ │ │ │ ├── GenNBOReader.js │ │ │ │ │ │ │ │ ├── JaguarReader.js │ │ │ │ │ │ │ │ ├── MOReader.js │ │ │ │ │ │ │ │ ├── MoldenReader.js │ │ │ │ │ │ │ │ ├── MopacGraphfReader.js │ │ │ │ │ │ │ │ ├── MopacSlaterReader.js │ │ │ │ │ │ │ │ ├── NBOParser.js │ │ │ │ │ │ │ │ ├── NWChemReader.js │ │ │ │ │ │ │ │ ├── PsiReader.js │ │ │ │ │ │ │ │ ├── QCJSONReader.js │ │ │ │ │ │ │ │ ├── QchemReader.js │ │ │ │ │ │ │ │ ├── SlaterReader.js │ │ │ │ │ │ │ │ └── WebMOReader.js │ │ │ │ │ │ │ ├── simple │ │ │ │ │ │ │ │ ├── AlchemyReader.js │ │ │ │ │ │ │ │ ├── AmpacReader.js │ │ │ │ │ │ │ │ ├── CubeReader.js │ │ │ │ │ │ │ │ ├── FAHReader.js │ │ │ │ │ │ │ │ ├── FoldingXyzReader.js │ │ │ │ │ │ │ │ ├── GhemicalMMReader.js │ │ │ │ │ │ │ │ ├── HyperChemReader.js │ │ │ │ │ │ │ │ ├── InputReader.js │ │ │ │ │ │ │ │ ├── JSONReader.js │ │ │ │ │ │ │ │ ├── JmeReader.js │ │ │ │ │ │ │ │ ├── MopacArchiveReader.js │ │ │ │ │ │ │ │ ├── MopacReader.js │ │ │ │ │ │ │ │ └── TinkerReader.js │ │ │ │ │ │ │ ├── spartan │ │ │ │ │ │ │ │ ├── OdysseyReader.js │ │ │ │ │ │ │ │ ├── SpartanArchive.js │ │ │ │ │ │ │ │ ├── SpartanInputReader.js │ │ │ │ │ │ │ │ ├── SpartanReader.js │ │ │ │ │ │ │ │ ├── SpartanSmolReader.js │ │ │ │ │ │ │ │ └── SpartanUtil.js │ │ │ │ │ │ │ ├── xml │ │ │ │ │ │ │ │ ├── XmlArgusReader.js │ │ │ │ │ │ │ │ ├── XmlChem3dReader.js │ │ │ │ │ │ │ │ ├── XmlCmlReader.js │ │ │ │ │ │ │ │ ├── XmlHandler.js │ │ │ │ │ │ │ │ ├── XmlMOReader.js │ │ │ │ │ │ │ │ ├── XmlMagResReader.js │ │ │ │ │ │ │ │ ├── XmlMolproReader.js │ │ │ │ │ │ │ │ ├── XmlOdysseyReader.js │ │ │ │ │ │ │ │ ├── XmlQEReader.js │ │ │ │ │ │ │ │ ├── XmlReader.js │ │ │ │ │ │ │ │ ├── XmlVaspReader.js │ │ │ │ │ │ │ │ └── XmlXsdReader.js │ │ │ │ │ │ │ └── xtal │ │ │ │ │ │ │ │ ├── AbinitReader.js │ │ │ │ │ │ │ │ ├── AimsReader.js │ │ │ │ │ │ │ │ ├── BilbaoReader.js │ │ │ │ │ │ │ │ ├── CastepReader.js │ │ │ │ │ │ │ │ ├── CgdReader.js │ │ │ │ │ │ │ │ ├── CrystalReader.js │ │ │ │ │ │ │ │ ├── DmolReader.js │ │ │ │ │ │ │ │ ├── EspressoReader.js │ │ │ │ │ │ │ │ ├── GulpReader.js │ │ │ │ │ │ │ │ ├── JanaReader.js │ │ │ │ │ │ │ │ ├── MagresReader.js │ │ │ │ │ │ │ │ ├── ShelxReader.js │ │ │ │ │ │ │ │ ├── SiestaReader.js │ │ │ │ │ │ │ │ ├── VaspChgcarReader.js │ │ │ │ │ │ │ │ ├── VaspOutcarReader.js │ │ │ │ │ │ │ │ ├── VaspPoscarReader.js │ │ │ │ │ │ │ │ ├── Wien2kReader.js │ │ │ │ │ │ │ │ └── XcrysdenReader.js │ │ │ │ │ │ ├── smarter │ │ │ │ │ │ │ ├── Atom.js │ │ │ │ │ │ │ ├── AtomIterator.js │ │ │ │ │ │ │ ├── AtomSetCollection.js │ │ │ │ │ │ │ ├── AtomSetCollectionReader.js │ │ │ │ │ │ │ ├── AtomSetObject.js │ │ │ │ │ │ │ ├── Bond.js │ │ │ │ │ │ │ ├── BondIterator.js │ │ │ │ │ │ │ ├── MSInterface.js │ │ │ │ │ │ │ ├── Resolver.js │ │ │ │ │ │ │ ├── SmarterJmolAdapter.js │ │ │ │ │ │ │ ├── Structure.js │ │ │ │ │ │ │ ├── StructureIterator.js │ │ │ │ │ │ │ └── XtalSymmetry.js │ │ │ │ │ │ └── writers │ │ │ │ │ │ │ └── QCJSONWriter.js │ │ │ │ │ ├── api │ │ │ │ │ │ ├── AtomIndexIterator.js │ │ │ │ │ │ ├── EventManager.js │ │ │ │ │ │ ├── FontManager.js │ │ │ │ │ │ ├── GenericFileInterface.js │ │ │ │ │ │ ├── GenericGraphics.js │ │ │ │ │ │ ├── GenericImageDialog.js │ │ │ │ │ │ ├── GenericMenuInterface.js │ │ │ │ │ │ ├── GenericMouseInterface.js │ │ │ │ │ │ ├── GenericPlatform.js │ │ │ │ │ │ ├── Interface.js │ │ │ │ │ │ ├── JSVInterface.js │ │ │ │ │ │ ├── JmolAbstractButton.js │ │ │ │ │ │ ├── JmolAdapter.js │ │ │ │ │ │ ├── JmolAdapterAtomIterator.js │ │ │ │ │ │ ├── JmolAdapterBondIterator.js │ │ │ │ │ │ ├── JmolAdapterStructureIterator.js │ │ │ │ │ │ ├── JmolAnnotationParser.js │ │ │ │ │ │ ├── JmolAppAPI.js │ │ │ │ │ │ ├── JmolAppConsoleInterface.js │ │ │ │ │ │ ├── JmolAppletInterface.js │ │ │ │ │ │ ├── JmolAudioPlayer.js │ │ │ │ │ │ ├── JmolCallbackListener.js │ │ │ │ │ │ ├── JmolDataManager.js │ │ │ │ │ │ ├── JmolDialogInterface.js │ │ │ │ │ │ ├── JmolDomReaderInterface.js │ │ │ │ │ │ ├── JmolDropEditor.js │ │ │ │ │ │ ├── JmolEnvCalc.js │ │ │ │ │ │ ├── JmolFilesReaderInterface.js │ │ │ │ │ │ ├── JmolGestureServerInterface.js │ │ │ │ │ │ ├── JmolGraphicsInterface.js │ │ │ │ │ │ ├── JmolJDXMOLParser.js │ │ │ │ │ │ ├── JmolJDXMOLReader.js │ │ │ │ │ │ ├── JmolJSpecView.js │ │ │ │ │ │ ├── JmolMeasurementClient.js │ │ │ │ │ │ ├── JmolModulationSet.js │ │ │ │ │ │ ├── JmolMovieCreatorInterface.js │ │ │ │ │ │ ├── JmolNMRInterface.js │ │ │ │ │ │ ├── JmolNavigatorInterface.js │ │ │ │ │ │ ├── JmolParallelProcessor.js │ │ │ │ │ │ ├── JmolPatternMatcher.js │ │ │ │ │ │ ├── JmolPdfCreatorInterface.js │ │ │ │ │ │ ├── JmolPropertyManager.js │ │ │ │ │ │ ├── JmolRendererInterface.js │ │ │ │ │ │ ├── JmolRepaintManager.js │ │ │ │ │ │ ├── JmolSceneGenerator.js │ │ │ │ │ │ ├── JmolScriptEditorInterface.js │ │ │ │ │ │ ├── JmolScriptEvaluator.js │ │ │ │ │ │ ├── JmolScriptFunction.js │ │ │ │ │ │ ├── JmolScriptManager.js │ │ │ │ │ │ ├── JmolSelectionListener.js │ │ │ │ │ │ ├── JmolStatusListener.js │ │ │ │ │ │ ├── JmolSyncInterface.js │ │ │ │ │ │ ├── JmolTouchSimulatorInterface.js │ │ │ │ │ │ ├── JmolViewer.js │ │ │ │ │ │ ├── JmolZipUtilities.js │ │ │ │ │ │ ├── PlatformViewer.js │ │ │ │ │ │ ├── PymolAtomReader.js │ │ │ │ │ │ ├── SC.js │ │ │ │ │ │ ├── SmilesMatcherInterface.js │ │ │ │ │ │ ├── SymmetryInterface.js │ │ │ │ │ │ ├── Translator.js │ │ │ │ │ │ └── js │ │ │ │ │ │ │ ├── GenericConsoleTextArea.js │ │ │ │ │ │ │ ├── JSConsole.js │ │ │ │ │ │ │ ├── JSmolAppletObject.js │ │ │ │ │ │ │ └── JmolToJSmolInterface.js │ │ │ │ │ ├── appletjs │ │ │ │ │ │ └── Jmol.js │ │ │ │ │ ├── atomdata │ │ │ │ │ │ ├── AtomData.js │ │ │ │ │ │ ├── AtomDataServer.js │ │ │ │ │ │ └── RadiusData.js │ │ │ │ │ ├── awtjs │ │ │ │ │ │ ├── Event.js │ │ │ │ │ │ ├── Platform.js │ │ │ │ │ │ └── swing │ │ │ │ │ │ │ ├── AbstractButton.js │ │ │ │ │ │ │ ├── AbstractTableModel.js │ │ │ │ │ │ │ ├── BorderLayout.js │ │ │ │ │ │ │ ├── ButtonGroup.js │ │ │ │ │ │ │ ├── Cell.js │ │ │ │ │ │ │ ├── Color.js │ │ │ │ │ │ │ ├── ColumnSelectionModel.js │ │ │ │ │ │ │ ├── Component.js │ │ │ │ │ │ │ ├── Container.js │ │ │ │ │ │ │ ├── Dimension.js │ │ │ │ │ │ │ ├── Document.js │ │ │ │ │ │ │ ├── FlowLayout.js │ │ │ │ │ │ │ ├── Grid.js │ │ │ │ │ │ │ ├── GridBagConstraints.js │ │ │ │ │ │ │ ├── GridBagLayout.js │ │ │ │ │ │ │ ├── HTMLElement.js │ │ │ │ │ │ │ ├── HTMLWindowEvent.js │ │ │ │ │ │ │ ├── Insets.js │ │ │ │ │ │ │ ├── JButton.js │ │ │ │ │ │ │ ├── JCheckBox.js │ │ │ │ │ │ │ ├── JCheckBoxMenuItem.js │ │ │ │ │ │ │ ├── JComboBox.js │ │ │ │ │ │ │ ├── JComponent.js │ │ │ │ │ │ │ ├── JComponentImp.js │ │ │ │ │ │ │ ├── JContentPane.js │ │ │ │ │ │ │ ├── JDialog.js │ │ │ │ │ │ │ ├── JEditorPane.js │ │ │ │ │ │ │ ├── JLabel.js │ │ │ │ │ │ │ ├── JMenu.js │ │ │ │ │ │ │ ├── JMenuItem.js │ │ │ │ │ │ │ ├── JPanel.js │ │ │ │ │ │ │ ├── JPopupMenu.js │ │ │ │ │ │ │ ├── JRadioButtonMenuItem.js │ │ │ │ │ │ │ ├── JScrollPane.js │ │ │ │ │ │ │ ├── JSplitPane.js │ │ │ │ │ │ │ ├── JTable.js │ │ │ │ │ │ │ ├── JTextField.js │ │ │ │ │ │ │ ├── JTextPane.js │ │ │ │ │ │ │ ├── LayoutManager.js │ │ │ │ │ │ │ ├── ListSelectionModel.js │ │ │ │ │ │ │ ├── SwingConstants.js │ │ │ │ │ │ │ ├── SwingController.js │ │ │ │ │ │ │ ├── TableCellRenderer.js │ │ │ │ │ │ │ └── TableColumn.js │ │ │ │ │ ├── awtjs2d │ │ │ │ │ │ ├── Display.js │ │ │ │ │ │ ├── Image.js │ │ │ │ │ │ ├── JSFile.js │ │ │ │ │ │ ├── JSFont.js │ │ │ │ │ │ ├── JSJmolPopup.js │ │ │ │ │ │ ├── JSModelKitPopup.js │ │ │ │ │ │ ├── JSPopupHelper.js │ │ │ │ │ │ ├── JsG2D.js │ │ │ │ │ │ ├── Mouse.js │ │ │ │ │ │ └── Platform.js │ │ │ │ │ ├── bspt │ │ │ │ │ │ ├── Bspf.js │ │ │ │ │ │ ├── Bspt.js │ │ │ │ │ │ ├── CubeIterator.js │ │ │ │ │ │ ├── Element.js │ │ │ │ │ │ ├── Leaf.js │ │ │ │ │ │ ├── Node.js │ │ │ │ │ │ └── PointIterator.js │ │ │ │ │ ├── c │ │ │ │ │ │ ├── CBK.js │ │ │ │ │ │ ├── FIL.js │ │ │ │ │ │ ├── HB.js │ │ │ │ │ │ ├── PAL.js │ │ │ │ │ │ ├── STER.js │ │ │ │ │ │ ├── STR.js │ │ │ │ │ │ └── VDW.js │ │ │ │ │ ├── console │ │ │ │ │ │ ├── GenericConsole.js │ │ │ │ │ │ └── GenericTextArea.js │ │ │ │ │ ├── consolejs │ │ │ │ │ │ ├── AppletConsole.js │ │ │ │ │ │ └── JSConsole.js │ │ │ │ │ ├── dssx │ │ │ │ │ │ ├── AnnotationParser.js │ │ │ │ │ │ ├── Bridge.js │ │ │ │ │ │ ├── DSSP.js │ │ │ │ │ │ ├── DSSR0.js │ │ │ │ │ │ └── DSSR1.js │ │ │ │ │ ├── export │ │ │ │ │ │ ├── Export3D.js │ │ │ │ │ │ ├── JSExporter.js │ │ │ │ │ │ ├── MeshData.js │ │ │ │ │ │ ├── UseTable.js │ │ │ │ │ │ ├── _IdtfExporter.js │ │ │ │ │ │ ├── _MayaExporter.js │ │ │ │ │ │ ├── _ObjExporter.js │ │ │ │ │ │ ├── _PovrayExporter.js │ │ │ │ │ │ ├── _StlExporter.js │ │ │ │ │ │ ├── _TachyonExporter.js │ │ │ │ │ │ ├── _VrmlExporter.js │ │ │ │ │ │ ├── _X3dExporter.js │ │ │ │ │ │ ├── __CartesianExporter.js │ │ │ │ │ │ ├── __RayTracerExporter.js │ │ │ │ │ │ └── ___Exporter.js │ │ │ │ │ ├── g3d │ │ │ │ │ │ ├── CircleRenderer.js │ │ │ │ │ │ ├── CylinderRenderer.js │ │ │ │ │ │ ├── G3DRenderer.js │ │ │ │ │ │ ├── Graphics3D.js │ │ │ │ │ │ ├── HermiteRenderer.js │ │ │ │ │ │ ├── LineRenderer.js │ │ │ │ │ │ ├── Pixelator.js │ │ │ │ │ │ ├── PixelatorScreened.js │ │ │ │ │ │ ├── PixelatorShaded.js │ │ │ │ │ │ ├── PixelatorT.js │ │ │ │ │ │ ├── Platform3D.js │ │ │ │ │ │ ├── PrecisionRenderer.js │ │ │ │ │ │ ├── SphereRenderer.js │ │ │ │ │ │ ├── TextRenderer.js │ │ │ │ │ │ ├── TextString.js │ │ │ │ │ │ └── TriangleRenderer.js │ │ │ │ │ ├── geodesic │ │ │ │ │ │ └── EnvelopeCalculation.js │ │ │ │ │ ├── i18n │ │ │ │ │ │ ├── GT.js │ │ │ │ │ │ ├── Language.js │ │ │ │ │ │ └── Resource.js │ │ │ │ │ ├── image │ │ │ │ │ │ └── AviCreator.js │ │ │ │ │ ├── io │ │ │ │ │ │ ├── DOMReader.js │ │ │ │ │ │ ├── FileReader.js │ │ │ │ │ │ ├── FilesReader.js │ │ │ │ │ │ └── JmolUtil.js │ │ │ │ │ ├── jsv │ │ │ │ │ │ ├── JDXMOLParser.js │ │ │ │ │ │ └── JSpecView.js │ │ │ │ │ ├── jvxl │ │ │ │ │ │ ├── api │ │ │ │ │ │ │ ├── MeshDataServer.js │ │ │ │ │ │ │ └── VertexDataServer.js │ │ │ │ │ │ ├── calc │ │ │ │ │ │ │ ├── MarchingCubes.js │ │ │ │ │ │ │ └── MarchingSquares.js │ │ │ │ │ │ ├── data │ │ │ │ │ │ │ ├── JvxlCoder.js │ │ │ │ │ │ │ ├── JvxlData.js │ │ │ │ │ │ │ ├── MeshData.js │ │ │ │ │ │ │ └── VolumeData.js │ │ │ │ │ │ └── readers │ │ │ │ │ │ │ ├── ApbsReader.js │ │ │ │ │ │ │ ├── AtomDataReader.js │ │ │ │ │ │ │ ├── AtomPropertyMapper.js │ │ │ │ │ │ │ ├── BCifDensityReader.js │ │ │ │ │ │ │ ├── CastepDensityReader.js │ │ │ │ │ │ │ ├── CifDensityReader.js │ │ │ │ │ │ │ ├── CubeReader.js │ │ │ │ │ │ │ ├── DelPhiBinaryReader.js │ │ │ │ │ │ │ ├── Dsn6BinaryReader.js │ │ │ │ │ │ │ ├── EfvetReader.js │ │ │ │ │ │ │ ├── IsoFxyReader.js │ │ │ │ │ │ │ ├── IsoFxyzReader.js │ │ │ │ │ │ │ ├── IsoIntersectAtomReader.js │ │ │ │ │ │ │ ├── IsoIntersectGridReader.js │ │ │ │ │ │ │ ├── IsoIntersectReader.js │ │ │ │ │ │ │ ├── IsoMOReader.js │ │ │ │ │ │ │ ├── IsoMepReader.js │ │ │ │ │ │ │ ├── IsoMlpReader.js │ │ │ │ │ │ │ ├── IsoPlaneReader.js │ │ │ │ │ │ │ ├── IsoShapeReader.js │ │ │ │ │ │ │ ├── IsoSolventReader.js │ │ │ │ │ │ │ ├── JaguarReader.js │ │ │ │ │ │ │ ├── JvxlReader.js │ │ │ │ │ │ │ ├── JvxlXmlReader.js │ │ │ │ │ │ │ ├── KinemageReader.js │ │ │ │ │ │ │ ├── MapFileReader.js │ │ │ │ │ │ │ ├── MrcBinaryReader.js │ │ │ │ │ │ │ ├── MsmsReader.js │ │ │ │ │ │ │ ├── NffReader.js │ │ │ │ │ │ │ ├── ObjReader.js │ │ │ │ │ │ │ ├── Parameters.js │ │ │ │ │ │ │ ├── PeriodicVolumeFileReader.js │ │ │ │ │ │ │ ├── PltFormattedReader.js │ │ │ │ │ │ │ ├── Pmesh4Reader.js │ │ │ │ │ │ │ ├── PmeshReader.js │ │ │ │ │ │ │ ├── PolygonFileReader.js │ │ │ │ │ │ │ ├── PyMOLMeshReader.js │ │ │ │ │ │ │ ├── Ras3DReader.js │ │ │ │ │ │ │ ├── SurfaceFileReader.js │ │ │ │ │ │ │ ├── SurfaceGenerator.js │ │ │ │ │ │ │ ├── SurfaceReader.js │ │ │ │ │ │ │ ├── UhbdReader.js │ │ │ │ │ │ │ ├── VaspChgcarReader.js │ │ │ │ │ │ │ ├── VolumeDataReader.js │ │ │ │ │ │ │ ├── VolumeFileReader.js │ │ │ │ │ │ │ ├── XmlReader.js │ │ │ │ │ │ │ ├── XplorReader.js │ │ │ │ │ │ │ └── XsfReader.js │ │ │ │ │ ├── modelkit │ │ │ │ │ │ ├── Constraint.js │ │ │ │ │ │ ├── ModelKitPopup.js │ │ │ │ │ │ ├── ModelKitPopupResourceBundle.js │ │ │ │ │ │ └── images │ │ │ │ │ │ │ ├── atoms.png │ │ │ │ │ │ │ ├── bonds.png │ │ │ │ │ │ │ ├── dotdotdot.png │ │ │ │ │ │ │ ├── undoButton.gif │ │ │ │ │ │ │ ├── xtal.png │ │ │ │ │ │ │ └── xtal_pngj.png │ │ │ │ │ ├── navigate │ │ │ │ │ │ └── Navigator.js │ │ │ │ │ ├── popup │ │ │ │ │ │ ├── GenericPopup.js │ │ │ │ │ │ ├── JmolGenericPopup.js │ │ │ │ │ │ ├── JmolPopup.js │ │ │ │ │ │ ├── MainPopupResourceBundle.js │ │ │ │ │ │ ├── PopupHelper.js │ │ │ │ │ │ └── PopupResource.js │ │ │ │ │ ├── quantum │ │ │ │ │ │ ├── MOCalculation.js │ │ │ │ │ │ ├── MepCalculation.js │ │ │ │ │ │ ├── MlpCalculation.js │ │ │ │ │ │ ├── NMRCalculation.js │ │ │ │ │ │ ├── NMRNoeMatrix.js │ │ │ │ │ │ ├── NciCalculation.js │ │ │ │ │ │ ├── QMAtom.js │ │ │ │ │ │ ├── QS.js │ │ │ │ │ │ ├── QuantumCalculation.js │ │ │ │ │ │ ├── QuantumPlaneCalculation.js │ │ │ │ │ │ ├── SlaterData.js │ │ │ │ │ │ ├── atomicLipophilicity.txt │ │ │ │ │ │ ├── mo │ │ │ │ │ │ │ ├── DataAdder.js │ │ │ │ │ │ │ ├── DataAdder11H.js │ │ │ │ │ │ │ ├── DataAdder13I.js │ │ │ │ │ │ │ ├── DataAdder7F.js │ │ │ │ │ │ │ ├── DataAdder9G.js │ │ │ │ │ │ │ ├── DataAdderF.js │ │ │ │ │ │ │ ├── DataAdderG.js │ │ │ │ │ │ │ ├── DataAdderH.js │ │ │ │ │ │ │ └── DataAdderI.js │ │ │ │ │ │ └── nmr_data.txt │ │ │ │ │ ├── render │ │ │ │ │ │ ├── AxesRenderer.js │ │ │ │ │ │ ├── BallsRenderer.js │ │ │ │ │ │ ├── BbcageRenderer.js │ │ │ │ │ │ ├── CageRenderer.js │ │ │ │ │ │ ├── EchoRenderer.js │ │ │ │ │ │ ├── FontLineShapeRenderer.js │ │ │ │ │ │ ├── FrankRenderer.js │ │ │ │ │ │ ├── HalosRenderer.js │ │ │ │ │ │ ├── HoverRenderer.js │ │ │ │ │ │ ├── LabelsRenderer.js │ │ │ │ │ │ ├── MeasuresRenderer.js │ │ │ │ │ │ ├── MeshRenderer.js │ │ │ │ │ │ ├── RepaintManager.js │ │ │ │ │ │ ├── ShapeRenderer.js │ │ │ │ │ │ ├── StarsRenderer.js │ │ │ │ │ │ ├── SticksRenderer.js │ │ │ │ │ │ ├── TextRenderer.js │ │ │ │ │ │ └── UccageRenderer.js │ │ │ │ │ ├── renderbio │ │ │ │ │ │ ├── BackboneRenderer.js │ │ │ │ │ │ ├── BioMeshRenderer.js │ │ │ │ │ │ ├── BioShapeRenderer.js │ │ │ │ │ │ ├── CartoonRenderer.js │ │ │ │ │ │ ├── MeshRibbonRenderer.js │ │ │ │ │ │ ├── NucleicRenderer.js │ │ │ │ │ │ ├── RibbonsRenderer.js │ │ │ │ │ │ ├── RocketRenderer.js │ │ │ │ │ │ ├── RocketsRenderer.js │ │ │ │ │ │ ├── StrandsRenderer.js │ │ │ │ │ │ └── TraceRenderer.js │ │ │ │ │ ├── rendercgo │ │ │ │ │ │ └── CGORenderer.js │ │ │ │ │ ├── renderspecial │ │ │ │ │ │ ├── DipolesRenderer.js │ │ │ │ │ │ ├── DotsRenderer.js │ │ │ │ │ │ ├── DrawRenderer.js │ │ │ │ │ │ ├── EllipsoidsRenderer.js │ │ │ │ │ │ ├── GeoSurfaceRenderer.js │ │ │ │ │ │ ├── PolyhedraRenderer.js │ │ │ │ │ │ └── VectorsRenderer.js │ │ │ │ │ ├── rendersurface │ │ │ │ │ │ ├── ContactRenderer.js │ │ │ │ │ │ ├── IsosurfaceRenderer.js │ │ │ │ │ │ ├── LcaoCartoonRenderer.js │ │ │ │ │ │ ├── MolecularOrbitalRenderer.js │ │ │ │ │ │ ├── NBORenderer.js │ │ │ │ │ │ ├── Plot3DRenderer.js │ │ │ │ │ │ └── PmeshRenderer.js │ │ │ │ │ ├── shape │ │ │ │ │ │ ├── AtomShape.js │ │ │ │ │ │ ├── Axes.js │ │ │ │ │ │ ├── Balls.js │ │ │ │ │ │ ├── Bbcage.js │ │ │ │ │ │ ├── Echo.js │ │ │ │ │ │ ├── FontLineShape.js │ │ │ │ │ │ ├── Frank.js │ │ │ │ │ │ ├── Halos.js │ │ │ │ │ │ ├── Hover.js │ │ │ │ │ │ ├── Labels.js │ │ │ │ │ │ ├── Measures.js │ │ │ │ │ │ ├── Mesh.js │ │ │ │ │ │ ├── MeshCollection.js │ │ │ │ │ │ ├── Shape.js │ │ │ │ │ │ ├── Stars.js │ │ │ │ │ │ ├── Sticks.js │ │ │ │ │ │ ├── TextShape.js │ │ │ │ │ │ └── Uccage.js │ │ │ │ │ ├── shapebio │ │ │ │ │ │ ├── Backbone.js │ │ │ │ │ │ ├── BioShape.js │ │ │ │ │ │ ├── BioShapeCollection.js │ │ │ │ │ │ ├── Cartoon.js │ │ │ │ │ │ ├── MeshRibbon.js │ │ │ │ │ │ ├── Ribbons.js │ │ │ │ │ │ ├── Rockets.js │ │ │ │ │ │ ├── Strands.js │ │ │ │ │ │ └── Trace.js │ │ │ │ │ ├── shapecgo │ │ │ │ │ │ ├── CGO.js │ │ │ │ │ │ └── CGOMesh.js │ │ │ │ │ ├── shapespecial │ │ │ │ │ │ ├── Dipole.js │ │ │ │ │ │ ├── Dipoles.js │ │ │ │ │ │ ├── Dots.js │ │ │ │ │ │ ├── Draw.js │ │ │ │ │ │ ├── DrawMesh.js │ │ │ │ │ │ ├── Ellipsoid.js │ │ │ │ │ │ ├── Ellipsoids.js │ │ │ │ │ │ ├── GeoSurface.js │ │ │ │ │ │ ├── Polyhedra.js │ │ │ │ │ │ ├── Polyhedron.js │ │ │ │ │ │ └── Vectors.js │ │ │ │ │ ├── shapesurface │ │ │ │ │ │ ├── Contact.js │ │ │ │ │ │ ├── Isosurface.js │ │ │ │ │ │ ├── IsosurfaceMesh.js │ │ │ │ │ │ ├── LcaoCartoon.js │ │ │ │ │ │ ├── MolecularOrbital.js │ │ │ │ │ │ ├── NBO.js │ │ │ │ │ │ ├── PMeshWriter.js │ │ │ │ │ │ ├── Plot3D.js │ │ │ │ │ │ └── Pmesh.js │ │ │ │ │ ├── thread │ │ │ │ │ │ ├── AnimationThread.js │ │ │ │ │ │ ├── HoverWatcherThread.js │ │ │ │ │ │ ├── JmolThread.js │ │ │ │ │ │ ├── MoveToThread.js │ │ │ │ │ │ ├── SpinThread.js │ │ │ │ │ │ ├── TimeoutThread.js │ │ │ │ │ │ └── VibrationThread.js │ │ │ │ │ └── translation │ │ │ │ │ │ └── PO.js │ │ │ │ ├── JM │ │ │ │ │ ├── AlphaMonomer.js │ │ │ │ │ ├── AlphaPolymer.js │ │ │ │ │ ├── AminoMonomer.js │ │ │ │ │ ├── AminoPolymer.js │ │ │ │ │ ├── Annotation.js │ │ │ │ │ ├── Atom.js │ │ │ │ │ ├── AtomCollection.js │ │ │ │ │ ├── AtomIteratorWithinModel.js │ │ │ │ │ ├── AtomIteratorWithinModelSet.js │ │ │ │ │ ├── BasePair.js │ │ │ │ │ ├── BioExt.js │ │ │ │ │ ├── BioModel.js │ │ │ │ │ ├── BioModelSet.js │ │ │ │ │ ├── BioPolymer.js │ │ │ │ │ ├── BioResolver.js │ │ │ │ │ ├── Bond.js │ │ │ │ │ ├── BondCollection.js │ │ │ │ │ ├── BondIterator.js │ │ │ │ │ ├── BondIteratorSelected.js │ │ │ │ │ ├── BondSet.js │ │ │ │ │ ├── CarbohydrateMonomer.js │ │ │ │ │ ├── CarbohydratePolymer.js │ │ │ │ │ ├── Chain.js │ │ │ │ │ ├── FF │ │ │ │ │ │ ├── AtomType.js │ │ │ │ │ │ ├── Calculation.js │ │ │ │ │ │ ├── Calculations.js │ │ │ │ │ │ ├── CalculationsMMFF.js │ │ │ │ │ │ ├── CalculationsUFF.js │ │ │ │ │ │ ├── FFParam.js │ │ │ │ │ │ ├── ForceField.js │ │ │ │ │ │ ├── ForceFieldMMFF.js │ │ │ │ │ │ ├── ForceFieldUFF.js │ │ │ │ │ │ ├── MMFFAngleCalc.js │ │ │ │ │ │ ├── MMFFDistanceCalc.js │ │ │ │ │ │ ├── MMFFESCalc.js │ │ │ │ │ │ ├── MMFFOOPCalc.js │ │ │ │ │ │ ├── MMFFSBCalc.js │ │ │ │ │ │ ├── MMFFTorsionCalc.js │ │ │ │ │ │ ├── MMFFVDWCalc.js │ │ │ │ │ │ ├── UFFAngleCalc.js │ │ │ │ │ │ ├── UFFDistanceCalc.js │ │ │ │ │ │ ├── UFFOOPCalc.js │ │ │ │ │ │ ├── UFFTorsionCalc.js │ │ │ │ │ │ ├── UFFVDWCalc.js │ │ │ │ │ │ └── data │ │ │ │ │ │ │ ├── MMFF94-smarts.txt │ │ │ │ │ │ │ ├── UFF.txt │ │ │ │ │ │ │ └── mmff94.par.txt │ │ │ │ │ ├── Group.js │ │ │ │ │ ├── HBond.js │ │ │ │ │ ├── Helix.js │ │ │ │ │ ├── LabelToken.js │ │ │ │ │ ├── MMConstraint.js │ │ │ │ │ ├── Measurement.js │ │ │ │ │ ├── MeasurementData.js │ │ │ │ │ ├── MeasurementPending.js │ │ │ │ │ ├── MinAngle.js │ │ │ │ │ ├── MinAtom.js │ │ │ │ │ ├── MinBond.js │ │ │ │ │ ├── MinObject.js │ │ │ │ │ ├── MinPosition.js │ │ │ │ │ ├── MinTorsion.js │ │ │ │ │ ├── MinimizationThread.js │ │ │ │ │ ├── Minimizer.js │ │ │ │ │ ├── Model.js │ │ │ │ │ ├── ModelLoader.js │ │ │ │ │ ├── ModelSet.js │ │ │ │ │ ├── Monomer.js │ │ │ │ │ ├── NucleicMonomer.js │ │ │ │ │ ├── NucleicPolymer.js │ │ │ │ │ ├── Orientation.js │ │ │ │ │ ├── PhosphorusMonomer.js │ │ │ │ │ ├── PhosphorusPolymer.js │ │ │ │ │ ├── ProteinStructure.js │ │ │ │ │ ├── Sheet.js │ │ │ │ │ ├── StateScript.js │ │ │ │ │ ├── Structure.js │ │ │ │ │ ├── Text.js │ │ │ │ │ ├── TickInfo.js │ │ │ │ │ ├── Trajectory.js │ │ │ │ │ ├── Turn.js │ │ │ │ │ └── Util.js │ │ │ │ ├── JS │ │ │ │ │ ├── AbstractButton.js │ │ │ │ │ ├── AbstractTableModel.js │ │ │ │ │ ├── BorderLayout.js │ │ │ │ │ ├── ButtonGroup.js │ │ │ │ │ ├── CIPChirality.js │ │ │ │ │ ├── CIPData.js │ │ │ │ │ ├── CIPDataSmiles.js │ │ │ │ │ ├── CIPDataTracker.js │ │ │ │ │ ├── Cell.js │ │ │ │ │ ├── CmdExt.js │ │ │ │ │ ├── Color.js │ │ │ │ │ ├── ColumnSelectionModel.js │ │ │ │ │ ├── CommandWatcherThread.js │ │ │ │ │ ├── Component.js │ │ │ │ │ ├── Container.js │ │ │ │ │ ├── ContextToken.js │ │ │ │ │ ├── Dimension.js │ │ │ │ │ ├── Document.js │ │ │ │ │ ├── FileLoadThread.js │ │ │ │ │ ├── FlowLayout.js │ │ │ │ │ ├── Grid.js │ │ │ │ │ ├── GridBagConstraints.js │ │ │ │ │ ├── GridBagLayout.js │ │ │ │ │ ├── HTMLElement.js │ │ │ │ │ ├── HTMLWindowEvent.js │ │ │ │ │ ├── HallInfo.js │ │ │ │ │ ├── HallRotation.js │ │ │ │ │ ├── HallRotationTerm.js │ │ │ │ │ ├── HallTranslation.js │ │ │ │ │ ├── Insets.js │ │ │ │ │ ├── InvalidSmilesException.js │ │ │ │ │ ├── IsoExt.js │ │ │ │ │ ├── JButton.js │ │ │ │ │ ├── JCheckBox.js │ │ │ │ │ ├── JCheckBoxMenuItem.js │ │ │ │ │ ├── JComboBox.js │ │ │ │ │ ├── JComponent.js │ │ │ │ │ ├── JComponentImp.js │ │ │ │ │ ├── JContentPane.js │ │ │ │ │ ├── JDialog.js │ │ │ │ │ ├── JEditorPane.js │ │ │ │ │ ├── JLabel.js │ │ │ │ │ ├── JMenu.js │ │ │ │ │ ├── JMenuItem.js │ │ │ │ │ ├── JPanel.js │ │ │ │ │ ├── JPopupMenu.js │ │ │ │ │ ├── JRadioButtonMenuItem.js │ │ │ │ │ ├── JScrollPane.js │ │ │ │ │ ├── JSplitPane.js │ │ │ │ │ ├── JTable.js │ │ │ │ │ ├── JTextField.js │ │ │ │ │ ├── JTextPane.js │ │ │ │ │ ├── LayoutManager.js │ │ │ │ │ ├── ListSelectionModel.js │ │ │ │ │ ├── MathExt.js │ │ │ │ │ ├── PointGroup.js │ │ │ │ │ ├── PolyhedronStereoSorter.js │ │ │ │ │ ├── SV.js │ │ │ │ │ ├── ScriptCompiler.js │ │ │ │ │ ├── ScriptContext.js │ │ │ │ │ ├── ScriptDelayThread.js │ │ │ │ │ ├── ScriptError.js │ │ │ │ │ ├── ScriptEval.js │ │ │ │ │ ├── ScriptException.js │ │ │ │ │ ├── ScriptExpr.js │ │ │ │ │ ├── ScriptExt.js │ │ │ │ │ ├── ScriptFlowContext.js │ │ │ │ │ ├── ScriptFunction.js │ │ │ │ │ ├── ScriptInterruption.js │ │ │ │ │ ├── ScriptManager.js │ │ │ │ │ ├── ScriptMathProcessor.js │ │ │ │ │ ├── ScriptParallelProcessor.js │ │ │ │ │ ├── ScriptParam.js │ │ │ │ │ ├── ScriptProcess.js │ │ │ │ │ ├── ScriptProcessRunnable.js │ │ │ │ │ ├── ScriptQueueThread.js │ │ │ │ │ ├── ScriptTokenParser.js │ │ │ │ │ ├── SmilesAromatic.js │ │ │ │ │ ├── SmilesAtom.js │ │ │ │ │ ├── SmilesBond.js │ │ │ │ │ ├── SmilesExt.js │ │ │ │ │ ├── SmilesGenerator.js │ │ │ │ │ ├── SmilesMatcher.js │ │ │ │ │ ├── SmilesMeasure.js │ │ │ │ │ ├── SmilesParser.js │ │ │ │ │ ├── SmilesRing.js │ │ │ │ │ ├── SmilesRingSet.js │ │ │ │ │ ├── SmilesSearch.js │ │ │ │ │ ├── SmilesStereo.js │ │ │ │ │ ├── SpaceGroup.js │ │ │ │ │ ├── SwingConstants.js │ │ │ │ │ ├── SwingController.js │ │ │ │ │ ├── Symmetry.js │ │ │ │ │ ├── SymmetryDesc.js │ │ │ │ │ ├── SymmetryInfo.js │ │ │ │ │ ├── SymmetryOperation.js │ │ │ │ │ ├── T.js │ │ │ │ │ ├── TableCellRenderer.js │ │ │ │ │ ├── TableColumn.js │ │ │ │ │ ├── UnitCell.js │ │ │ │ │ ├── UnitCellIterator.js │ │ │ │ │ └── VTemp.js │ │ │ │ ├── JSV │ │ │ │ │ ├── api │ │ │ │ │ │ ├── AnnotationData.js │ │ │ │ │ │ ├── AppletFrame.js │ │ │ │ │ │ ├── ExportInterface.js │ │ │ │ │ │ ├── JSVAppInterface.js │ │ │ │ │ │ ├── JSVAppletInterface.js │ │ │ │ │ │ ├── JSVExporter.js │ │ │ │ │ │ ├── JSVFileDropper.js │ │ │ │ │ │ ├── JSVFileHelper.js │ │ │ │ │ │ ├── JSVMainPanel.js │ │ │ │ │ │ ├── JSVPanel.js │ │ │ │ │ │ ├── JSVPdfWriter.js │ │ │ │ │ │ ├── JSVPrintDialog.js │ │ │ │ │ │ ├── JSVTree.js │ │ │ │ │ │ ├── JSVTreeNode.js │ │ │ │ │ │ ├── JSVTreePath.js │ │ │ │ │ │ ├── JSVViewPanel.js │ │ │ │ │ │ ├── JSVZipInterface.js │ │ │ │ │ │ ├── JSVZipReader.js │ │ │ │ │ │ ├── PanelListener.js │ │ │ │ │ │ ├── PlatformDialog.js │ │ │ │ │ │ ├── ScriptInterface.js │ │ │ │ │ │ ├── SourceReader.js │ │ │ │ │ │ ├── VisibleInterface.js │ │ │ │ │ │ └── js │ │ │ │ │ │ │ ├── JSVAppletObject.js │ │ │ │ │ │ │ └── JSVToJSmolInterface.js │ │ │ │ │ ├── app │ │ │ │ │ │ ├── GenericMouse.js │ │ │ │ │ │ ├── JSVApp.js │ │ │ │ │ │ └── JSVAppPro.js │ │ │ │ │ ├── appletjs │ │ │ │ │ │ ├── JSVApplet.js │ │ │ │ │ │ └── JSVAppletPro.js │ │ │ │ │ ├── common │ │ │ │ │ │ ├── Annotation.js │ │ │ │ │ │ ├── ColorParameters.js │ │ │ │ │ │ ├── ColoredAnnotation.js │ │ │ │ │ │ ├── CoordComparator.js │ │ │ │ │ │ ├── Coordinate.js │ │ │ │ │ │ ├── ExportType.js │ │ │ │ │ │ ├── GraphSet.js │ │ │ │ │ │ ├── ImageView.js │ │ │ │ │ │ ├── Integral.js │ │ │ │ │ │ ├── IntegralComparator.js │ │ │ │ │ │ ├── IntegralData.js │ │ │ │ │ │ ├── JSVFileManager.js │ │ │ │ │ │ ├── JSVZipFileSequentialReader.js │ │ │ │ │ │ ├── JSVZipUtil.js │ │ │ │ │ │ ├── JSVersion.js │ │ │ │ │ │ ├── JSViewer.js │ │ │ │ │ │ ├── Measurement.js │ │ │ │ │ │ ├── MeasurementData.js │ │ │ │ │ │ ├── PDFWriter.js │ │ │ │ │ │ ├── PanelData.js │ │ │ │ │ │ ├── PanelNode.js │ │ │ │ │ │ ├── Parameters.js │ │ │ │ │ │ ├── PeakData.js │ │ │ │ │ │ ├── PeakInfo.js │ │ │ │ │ │ ├── PeakPick.js │ │ │ │ │ │ ├── PeakPickEvent.js │ │ │ │ │ │ ├── PlotWidget.js │ │ │ │ │ │ ├── PrintLayout.js │ │ │ │ │ │ ├── RepaintManager.js │ │ │ │ │ │ ├── ScaleData.js │ │ │ │ │ │ ├── ScriptToken.js │ │ │ │ │ │ ├── ScriptTokenizer.js │ │ │ │ │ │ ├── Spectrum.js │ │ │ │ │ │ ├── SubSpecChangeEvent.js │ │ │ │ │ │ ├── TODO.txt │ │ │ │ │ │ ├── ViewData.js │ │ │ │ │ │ ├── Visible.js │ │ │ │ │ │ ├── XYScaleConverter.js │ │ │ │ │ │ └── ZoomEvent.js │ │ │ │ │ ├── dialog │ │ │ │ │ │ ├── DialogManager.js │ │ │ │ │ │ ├── DialogParams.js │ │ │ │ │ │ ├── IntegrationDialog.js │ │ │ │ │ │ ├── JSVDialog.js │ │ │ │ │ │ ├── MeasurementsDialog.js │ │ │ │ │ │ ├── OverlayLegendDialog.js │ │ │ │ │ │ ├── PeakListDialog.js │ │ │ │ │ │ └── ViewsDialog.js │ │ │ │ │ ├── exception │ │ │ │ │ │ └── JSVException.js │ │ │ │ │ ├── export │ │ │ │ │ │ ├── AMLExporter.js │ │ │ │ │ │ ├── CMLExporter.js │ │ │ │ │ │ ├── ExportInterface.js │ │ │ │ │ │ ├── Exporter.js │ │ │ │ │ │ ├── FormContext.js │ │ │ │ │ │ ├── FormExporter.js │ │ │ │ │ │ ├── JDXCompressor.js │ │ │ │ │ │ ├── JDXExporter.js │ │ │ │ │ │ ├── SVGExporter.js │ │ │ │ │ │ ├── XMLExporter.js │ │ │ │ │ │ └── resources │ │ │ │ │ │ │ ├── animl_nmr.vm │ │ │ │ │ │ │ ├── animl_tmp.vm │ │ │ │ │ │ │ ├── cml_nmr.vm │ │ │ │ │ │ │ ├── cml_tmp.vm │ │ │ │ │ │ │ ├── plot.vm │ │ │ │ │ │ │ └── plot_ink.vm │ │ │ │ │ ├── js2d │ │ │ │ │ │ ├── DialogTableModel.js │ │ │ │ │ │ ├── Display.js │ │ │ │ │ │ ├── Image.js │ │ │ │ │ │ ├── JsDialog.js │ │ │ │ │ │ ├── JsDialogManager.js │ │ │ │ │ │ ├── JsFile.js │ │ │ │ │ │ ├── JsFileHelper.js │ │ │ │ │ │ ├── JsFont.js │ │ │ │ │ │ ├── JsG2D.js │ │ │ │ │ │ ├── JsMainPanel.js │ │ │ │ │ │ ├── JsPanel.js │ │ │ │ │ │ ├── JsParameters.js │ │ │ │ │ │ ├── JsPlatform.js │ │ │ │ │ │ └── JsPopup.js │ │ │ │ │ ├── popup │ │ │ │ │ │ ├── JSVGenericPopup.js │ │ │ │ │ │ └── JSVPopupResourceBundle.js │ │ │ │ │ ├── source │ │ │ │ │ │ ├── AnIMLReader.js │ │ │ │ │ │ ├── CMLReader.js │ │ │ │ │ │ ├── JDXDataObject.js │ │ │ │ │ │ ├── JDXDecompressor.js │ │ │ │ │ │ ├── JDXHeader.js │ │ │ │ │ │ ├── JDXReader.js │ │ │ │ │ │ ├── JDXSource.js │ │ │ │ │ │ ├── JDXSourceStreamTokenizer.js │ │ │ │ │ │ ├── XMLParser.js │ │ │ │ │ │ └── XMLReader.js │ │ │ │ │ └── tree │ │ │ │ │ │ ├── SimpleTree.js │ │ │ │ │ │ ├── SimpleTreeEnumeration.js │ │ │ │ │ │ ├── SimpleTreeModel.js │ │ │ │ │ │ ├── SimpleTreeNode.js │ │ │ │ │ │ └── SimpleTreePath.js │ │ │ │ ├── JU │ │ │ │ │ ├── A4.js │ │ │ │ │ ├── AU.js │ │ │ │ │ ├── Adler32.js │ │ │ │ │ ├── AjaxURLConnection.js │ │ │ │ │ ├── AjaxURLStreamHandler.js │ │ │ │ │ ├── AjaxURLStreamHandlerFactory.js │ │ │ │ │ ├── ArrayDataReader.js │ │ │ │ │ ├── BArray.js │ │ │ │ │ ├── BC.js │ │ │ │ │ ├── BS.js │ │ │ │ │ ├── BSUtil.js │ │ │ │ │ ├── BZone.js │ │ │ │ │ ├── Base64.js │ │ │ │ │ ├── BinaryDocument.js │ │ │ │ │ ├── BoxInfo.js │ │ │ │ │ ├── C.js │ │ │ │ │ ├── CRC32.js │ │ │ │ │ ├── CU.js │ │ │ │ │ ├── Checksum.js │ │ │ │ │ ├── CifDataParser.js │ │ │ │ │ ├── ColorEncoder.js │ │ │ │ │ ├── CommandHistory.js │ │ │ │ │ ├── CompoundDocDirEntry.js │ │ │ │ │ ├── CompoundDocHeader.js │ │ │ │ │ ├── CompoundDocument.js │ │ │ │ │ ├── ContactPair.js │ │ │ │ │ ├── DF.js │ │ │ │ │ ├── DataReader.js │ │ │ │ │ ├── DebugJS.js │ │ │ │ │ ├── DefaultLogger.js │ │ │ │ │ ├── Deflate.js │ │ │ │ │ ├── Deflater.js │ │ │ │ │ ├── DeflaterOutputStream.js │ │ │ │ │ ├── Edge.js │ │ │ │ │ ├── Eigen.js │ │ │ │ │ ├── EigenSort.js │ │ │ │ │ ├── Elements.js │ │ │ │ │ ├── Encoding.js │ │ │ │ │ ├── Escape.js │ │ │ │ │ ├── Font.js │ │ │ │ │ ├── GData.js │ │ │ │ │ ├── GZIPException.js │ │ │ │ │ ├── GZIPHeader.js │ │ │ │ │ ├── GZIPInputStream.js │ │ │ │ │ ├── GZIPOutputStream.js │ │ │ │ │ ├── GenericApplet.js │ │ │ │ │ ├── Geodesic.js │ │ │ │ │ ├── InfBlocks.js │ │ │ │ │ ├── InfCodes.js │ │ │ │ │ ├── InfTree.js │ │ │ │ │ ├── Inflate.js │ │ │ │ │ ├── Inflater.js │ │ │ │ │ ├── InflaterInputStream.js │ │ │ │ │ ├── Int2IntHash.js │ │ │ │ │ ├── JSJSONParser.js │ │ │ │ │ ├── JSONException.js │ │ │ │ │ ├── JSONWriter.js │ │ │ │ │ ├── JZlib.js │ │ │ │ │ ├── JmolAudio.js │ │ │ │ │ ├── JmolMolecule.js │ │ │ │ │ ├── LimitedLineReader.js │ │ │ │ │ ├── ListDataReader.js │ │ │ │ │ ├── Logger.js │ │ │ │ │ ├── LoggerInterface.js │ │ │ │ │ ├── Lst.js │ │ │ │ │ ├── M3.js │ │ │ │ │ ├── M34.js │ │ │ │ │ ├── M4.js │ │ │ │ │ ├── Matrix.js │ │ │ │ │ ├── Measure.js │ │ │ │ │ ├── MeshCapper.js │ │ │ │ │ ├── MeshSlicer.js │ │ │ │ │ ├── MeshSurface.js │ │ │ │ │ ├── MessagePackReader.js │ │ │ │ │ ├── Modulation.js │ │ │ │ │ ├── ModulationSet.js │ │ │ │ │ ├── MolWriter.js │ │ │ │ │ ├── Node.js │ │ │ │ │ ├── Normix.js │ │ │ │ │ ├── OC.js │ │ │ │ │ ├── P3.js │ │ │ │ │ ├── P3i.js │ │ │ │ │ ├── P4.js │ │ │ │ │ ├── PT.js │ │ │ │ │ ├── Parser.js │ │ │ │ │ ├── PatternMatcher.js │ │ │ │ │ ├── Point3fi.js │ │ │ │ │ ├── Quat.js │ │ │ │ │ ├── Rdr.js │ │ │ │ │ ├── Rectangle.js │ │ │ │ │ ├── Rgb16.js │ │ │ │ │ ├── SB.js │ │ │ │ │ ├── Shader.js │ │ │ │ │ ├── SimpleEdge.js │ │ │ │ │ ├── SimpleNode.js │ │ │ │ │ ├── SimpleUnitCell.js │ │ │ │ │ ├── StaticTree.js │ │ │ │ │ ├── StringDataReader.js │ │ │ │ │ ├── T3.js │ │ │ │ │ ├── T3d.js │ │ │ │ │ ├── T3i.js │ │ │ │ │ ├── T4.js │ │ │ │ │ ├── TempArray.js │ │ │ │ │ ├── Tensor.js │ │ │ │ │ ├── Tree.js │ │ │ │ │ ├── TriangleData.js │ │ │ │ │ ├── Triangulator.js │ │ │ │ │ ├── Txt.js │ │ │ │ │ ├── V3.js │ │ │ │ │ ├── V3d.js │ │ │ │ │ ├── Vibration.js │ │ │ │ │ ├── XmlUtil.js │ │ │ │ │ ├── ZStream.js │ │ │ │ │ ├── ZStreamException.js │ │ │ │ │ ├── ZipData.js │ │ │ │ │ ├── ZipTools.js │ │ │ │ │ └── package.js │ │ │ │ ├── JV │ │ │ │ │ ├── ActionManager.js │ │ │ │ │ ├── AnimationManager.js │ │ │ │ │ ├── ChimeMessenger.js │ │ │ │ │ ├── ColorManager.js │ │ │ │ │ ├── DataManager.js │ │ │ │ │ ├── FileManager.js │ │ │ │ │ ├── GlobalSettings.js │ │ │ │ │ ├── JC.js │ │ │ │ │ ├── JmolAsyncException.js │ │ │ │ │ ├── JmolChimeMessenger.js │ │ │ │ │ ├── JmolStateCreator.js │ │ │ │ │ ├── ModelManager.js │ │ │ │ │ ├── MouseState.js │ │ │ │ │ ├── OutputManager.js │ │ │ │ │ ├── OutputManagerJS.js │ │ │ │ │ ├── PropertyManager.js │ │ │ │ │ ├── SelectionManager.js │ │ │ │ │ ├── ShapeManager.js │ │ │ │ │ ├── StateCreator.js │ │ │ │ │ ├── StateManager.js │ │ │ │ │ ├── StatusManager.js │ │ │ │ │ ├── TransformManager.js │ │ │ │ │ ├── TransformManager4D.js │ │ │ │ │ ├── Viewer.js │ │ │ │ │ ├── binding │ │ │ │ │ │ ├── Binding.js │ │ │ │ │ │ ├── DragBinding.js │ │ │ │ │ │ ├── JmolBinding.js │ │ │ │ │ │ ├── PfaatBinding.js │ │ │ │ │ │ └── RasmolBinding.js │ │ │ │ │ └── package.js │ │ │ │ ├── Jmol.properties │ │ │ │ ├── core │ │ │ │ │ ├── corebinary.js │ │ │ │ │ ├── corebinary.z.js │ │ │ │ │ ├── corebio.js │ │ │ │ │ ├── corebio.z.js │ │ │ │ │ ├── coreconsole.js │ │ │ │ │ ├── coreconsole.z.js │ │ │ │ │ ├── corejmol.js │ │ │ │ │ ├── corejmol.z.js │ │ │ │ │ ├── corejmoljsv.js │ │ │ │ │ ├── corejmoljsv.z.js │ │ │ │ │ ├── corejsv.js │ │ │ │ │ ├── corejsv.z.js │ │ │ │ │ ├── corejsvdialog.js │ │ │ │ │ ├── corejsvdialog.z.js │ │ │ │ │ ├── corejsvexport.js │ │ │ │ │ ├── corejsvexport.z.js │ │ │ │ │ ├── corejsvmenu.js │ │ │ │ │ ├── corejsvmenu.z.js │ │ │ │ │ ├── coremenu.js │ │ │ │ │ ├── coremenu.z.js │ │ │ │ │ ├── coremin.js │ │ │ │ │ ├── coremin.z.js │ │ │ │ │ ├── coreprop.js │ │ │ │ │ ├── coreprop.z.js │ │ │ │ │ ├── corepymol.js │ │ │ │ │ ├── corepymol.z.js │ │ │ │ │ ├── corescript.js │ │ │ │ │ ├── corescript.z.js │ │ │ │ │ ├── corescriptcmd.js │ │ │ │ │ ├── corescriptcmd.z.js │ │ │ │ │ ├── corescriptmath.js │ │ │ │ │ ├── corescriptmath.z.js │ │ │ │ │ ├── coresmiles.js │ │ │ │ │ ├── coresmiles.z.js │ │ │ │ │ ├── corestate.js │ │ │ │ │ ├── corestate.z.js │ │ │ │ │ ├── coresurface.js │ │ │ │ │ ├── coresurface.z.js │ │ │ │ │ ├── coreswing.js │ │ │ │ │ ├── coreswing.z.js │ │ │ │ │ ├── coresym.js │ │ │ │ │ ├── coresym.z.js │ │ │ │ │ ├── coretext.js │ │ │ │ │ ├── coretext.z.js │ │ │ │ │ ├── corezip.js │ │ │ │ │ ├── corezip.z.js │ │ │ │ │ └── package.js │ │ │ │ ├── img │ │ │ │ │ ├── JSmol_spinner.gif │ │ │ │ │ ├── cursor_wait.gif │ │ │ │ │ └── play_make_live.jpg │ │ │ │ ├── java │ │ │ │ │ ├── awt │ │ │ │ │ │ ├── Event.js │ │ │ │ │ │ └── event │ │ │ │ │ │ │ ├── InputEvent.js │ │ │ │ │ │ │ ├── KeyEvent.js │ │ │ │ │ │ │ ├── MouseEvent.js │ │ │ │ │ │ │ └── MouseWheelEvent.js │ │ │ │ │ ├── error.z.js │ │ │ │ │ ├── io │ │ │ │ │ │ ├── BufferedInputStream.js │ │ │ │ │ │ ├── BufferedOutputStream.js │ │ │ │ │ │ ├── BufferedReader.js │ │ │ │ │ │ ├── BufferedWriter.js │ │ │ │ │ │ ├── ByteArrayInputStream.js │ │ │ │ │ │ ├── ByteArrayOutputStream.js │ │ │ │ │ │ ├── CharArrayReader.js │ │ │ │ │ │ ├── CharArrayWriter.js │ │ │ │ │ │ ├── CharConversionException.js │ │ │ │ │ │ ├── Closeable.js │ │ │ │ │ │ ├── DataInput.js │ │ │ │ │ │ ├── DataInputStream.js │ │ │ │ │ │ ├── DataOutput.js │ │ │ │ │ │ ├── EOFException.js │ │ │ │ │ │ ├── Externalizable.js │ │ │ │ │ │ ├── FileInputStream.js │ │ │ │ │ │ ├── FileNotFoundException.js │ │ │ │ │ │ ├── FileOutputStream.js │ │ │ │ │ │ ├── FilterInputStream.js │ │ │ │ │ │ ├── FilterOutputStream.js │ │ │ │ │ │ ├── Flushable.js │ │ │ │ │ │ ├── IOException.js │ │ │ │ │ │ ├── InputStream.js │ │ │ │ │ │ ├── InputStreamReader.js │ │ │ │ │ │ ├── InterruptedIOException.js │ │ │ │ │ │ ├── InvalidClassException.js │ │ │ │ │ │ ├── InvalidObjectException.js │ │ │ │ │ │ ├── NotActiveException.js │ │ │ │ │ │ ├── NotSerializableException.js │ │ │ │ │ │ ├── ObjectStreamException.js │ │ │ │ │ │ ├── ObjectStreamField.js │ │ │ │ │ │ ├── OptionalDataException.js │ │ │ │ │ │ ├── OutputStream.js │ │ │ │ │ │ ├── PushbackInputStream.js │ │ │ │ │ │ ├── Reader.js │ │ │ │ │ │ ├── SequenceInputStream.js │ │ │ │ │ │ ├── Serializable.js │ │ │ │ │ │ ├── StreamCorruptedException.js │ │ │ │ │ │ ├── StringBufferInputStream.js │ │ │ │ │ │ ├── StringReader.js │ │ │ │ │ │ ├── StringWriter.js │ │ │ │ │ │ ├── SyncFailedException.js │ │ │ │ │ │ ├── UTFDataFormatException.js │ │ │ │ │ │ ├── UnsupportedEncodingException.js │ │ │ │ │ │ ├── WriteAbortedException.js │ │ │ │ │ │ └── Writer.js │ │ │ │ │ ├── lang │ │ │ │ │ │ ├── AbstractMethodError.js │ │ │ │ │ │ ├── AbstractStringBuilder.js │ │ │ │ │ │ ├── Appendable.js │ │ │ │ │ │ ├── ArithmeticException.js │ │ │ │ │ │ ├── ArrayIndexOutOfBoundsException.js │ │ │ │ │ │ ├── ArrayStoreException.js │ │ │ │ │ │ ├── AssertionError.js │ │ │ │ │ │ ├── Boolean.js │ │ │ │ │ │ ├── Byte.js │ │ │ │ │ │ ├── CharSequence.js │ │ │ │ │ │ ├── Character.js │ │ │ │ │ │ ├── Class.js │ │ │ │ │ │ ├── ClassCastException.js │ │ │ │ │ │ ├── ClassCircularityError.js │ │ │ │ │ │ ├── ClassExt.js │ │ │ │ │ │ ├── ClassFormatError.js │ │ │ │ │ │ ├── ClassLoader.js │ │ │ │ │ │ ├── ClassLoaderProgressMonitor.js │ │ │ │ │ │ ├── ClassNotFoundException.js │ │ │ │ │ │ ├── CloneNotSupportedException.js │ │ │ │ │ │ ├── Cloneable.js │ │ │ │ │ │ ├── Comparable.js │ │ │ │ │ │ ├── Console.js │ │ │ │ │ │ ├── Double.js │ │ │ │ │ │ ├── Encoding.js │ │ │ │ │ │ ├── Enum.js │ │ │ │ │ │ ├── Error.js │ │ │ │ │ │ ├── Exception.js │ │ │ │ │ │ ├── ExceptionInInitializerError.js │ │ │ │ │ │ ├── Float.js │ │ │ │ │ │ ├── IllegalAccessError.js │ │ │ │ │ │ ├── IllegalAccessException.js │ │ │ │ │ │ ├── IllegalArgumentException.js │ │ │ │ │ │ ├── IllegalMonitorStateException.js │ │ │ │ │ │ ├── IllegalStateException.js │ │ │ │ │ │ ├── IllegalThreadStateException.js │ │ │ │ │ │ ├── IncompatibleClassChangeError.js │ │ │ │ │ │ ├── IndexOutOfBoundsException.js │ │ │ │ │ │ ├── InstantiationError.js │ │ │ │ │ │ ├── InstantiationException.js │ │ │ │ │ │ ├── Integer.js │ │ │ │ │ │ ├── InternalError.js │ │ │ │ │ │ ├── InterruptedException.js │ │ │ │ │ │ ├── Iterable.js │ │ │ │ │ │ ├── LinkageError.js │ │ │ │ │ │ ├── Long.js │ │ │ │ │ │ ├── NegativeArraySizeException.js │ │ │ │ │ │ ├── NoClassDefFoundError.js │ │ │ │ │ │ ├── NoSuchFieldError.js │ │ │ │ │ │ ├── NoSuchFieldException.js │ │ │ │ │ │ ├── NoSuchMethodError.js │ │ │ │ │ │ ├── NoSuchMethodException.js │ │ │ │ │ │ ├── NullPointerException.js │ │ │ │ │ │ ├── Number.js │ │ │ │ │ │ ├── NumberFormatException.js │ │ │ │ │ │ ├── OutOfMemoryError.js │ │ │ │ │ │ ├── Readable.js │ │ │ │ │ │ ├── Runnable.js │ │ │ │ │ │ ├── RuntimeException.js │ │ │ │ │ │ ├── SecurityException.js │ │ │ │ │ │ ├── Short.js │ │ │ │ │ │ ├── StackOverflowError.js │ │ │ │ │ │ ├── StackTraceElement.js │ │ │ │ │ │ ├── StrictMath.js │ │ │ │ │ │ ├── String.js │ │ │ │ │ │ ├── StringBuffer.js │ │ │ │ │ │ ├── StringBuilder.js │ │ │ │ │ │ ├── StringBuilder.z.js │ │ │ │ │ │ ├── StringIndexOutOfBoundsException.js │ │ │ │ │ │ ├── Thread.js │ │ │ │ │ │ ├── ThreadDeath.js │ │ │ │ │ │ ├── ThreadGroup.js │ │ │ │ │ │ ├── Throwable.js │ │ │ │ │ │ ├── TypeNotPresentException.js │ │ │ │ │ │ ├── UnknownError.js │ │ │ │ │ │ ├── UnsatisfiedLinkError.js │ │ │ │ │ │ ├── UnsupportedClassVersionError.js │ │ │ │ │ │ ├── UnsupportedOperationException.js │ │ │ │ │ │ ├── VerifyError.js │ │ │ │ │ │ ├── VirtualMachineError.js │ │ │ │ │ │ ├── Void.js │ │ │ │ │ │ ├── reflect.z.js │ │ │ │ │ │ └── reflect │ │ │ │ │ │ │ ├── AccessibleObject.js │ │ │ │ │ │ │ ├── AnnotatedElement.js │ │ │ │ │ │ │ ├── Array.js │ │ │ │ │ │ │ ├── Constructor.js │ │ │ │ │ │ │ ├── Field.js │ │ │ │ │ │ │ ├── GenericDeclaration.js │ │ │ │ │ │ │ ├── GenericSignatureFormatError.js │ │ │ │ │ │ │ ├── InvocationHandler.js │ │ │ │ │ │ │ ├── InvocationTargetException.js │ │ │ │ │ │ │ ├── MalformedParameterizedTypeException.js │ │ │ │ │ │ │ ├── Member.js │ │ │ │ │ │ │ ├── Method.js │ │ │ │ │ │ │ ├── Modifier.js │ │ │ │ │ │ │ ├── Proxy.js │ │ │ │ │ │ │ ├── ReflectPermission.js │ │ │ │ │ │ │ ├── TypeVariable.js │ │ │ │ │ │ │ └── UndeclaredThrowableException.js │ │ │ │ │ ├── net │ │ │ │ │ │ ├── MalformedURLException.js │ │ │ │ │ │ ├── Parts.js │ │ │ │ │ │ ├── URL.js │ │ │ │ │ │ ├── URLConnection.js │ │ │ │ │ │ ├── URLDecoder.js │ │ │ │ │ │ ├── URLEncoder.js │ │ │ │ │ │ ├── URLStreamHandler.js │ │ │ │ │ │ ├── URLStreamHandlerFactory.js │ │ │ │ │ │ └── UnknownServiceException.js │ │ │ │ │ ├── text │ │ │ │ │ │ ├── Annotation.js │ │ │ │ │ │ └── MessageFormat.js │ │ │ │ │ └── util │ │ │ │ │ │ ├── AbstractCollection.js │ │ │ │ │ │ ├── AbstractList.js │ │ │ │ │ │ ├── AbstractMap.js │ │ │ │ │ │ ├── AbstractQueue.js │ │ │ │ │ │ ├── AbstractSequentialList.js │ │ │ │ │ │ ├── AbstractSet.js │ │ │ │ │ │ ├── ArrayList.js │ │ │ │ │ │ ├── Arrays.js │ │ │ │ │ │ ├── BitSet.js │ │ │ │ │ │ ├── Collection.js │ │ │ │ │ │ ├── Collections.js │ │ │ │ │ │ ├── Comparator.js │ │ │ │ │ │ ├── ConcurrentModificationException.js │ │ │ │ │ │ ├── Date.js │ │ │ │ │ │ ├── Dictionary.js │ │ │ │ │ │ ├── DuplicateFormatFlagsException.js │ │ │ │ │ │ ├── EmptyStackException.js │ │ │ │ │ │ ├── Enumeration.js │ │ │ │ │ │ ├── EventListener.js │ │ │ │ │ │ ├── EventListenerProxy.js │ │ │ │ │ │ ├── EventObject.js │ │ │ │ │ │ ├── FormatFlagsConversionMismatchException.js │ │ │ │ │ │ ├── FormatterClosedException.js │ │ │ │ │ │ ├── HashMap.js │ │ │ │ │ │ ├── HashSet.js │ │ │ │ │ │ ├── Hashtable.js │ │ │ │ │ │ ├── IdentityHashMap.js │ │ │ │ │ │ ├── IllegalFormatCodePointException.js │ │ │ │ │ │ ├── IllegalFormatConversionException.js │ │ │ │ │ │ ├── IllegalFormatException.js │ │ │ │ │ │ ├── IllegalFormatFlagsException.js │ │ │ │ │ │ ├── IllegalFormatPrecisionException.js │ │ │ │ │ │ ├── IllegalFormatWidthException.js │ │ │ │ │ │ ├── InputMismatchException.js │ │ │ │ │ │ ├── InvalidPropertiesFormatException.js │ │ │ │ │ │ ├── Iterator.js │ │ │ │ │ │ ├── LinkedHashMap.js │ │ │ │ │ │ ├── LinkedHashSet.js │ │ │ │ │ │ ├── LinkedList.js │ │ │ │ │ │ ├── List.js │ │ │ │ │ │ ├── ListIterator.js │ │ │ │ │ │ ├── ListResourceBundle.js │ │ │ │ │ │ ├── Locale.js │ │ │ │ │ │ ├── Map.js │ │ │ │ │ │ ├── MapEntry.js │ │ │ │ │ │ ├── MissingFormatArgumentException.js │ │ │ │ │ │ ├── MissingFormatWidthException.js │ │ │ │ │ │ ├── MissingResourceException.js │ │ │ │ │ │ ├── NoSuchElementException.js │ │ │ │ │ │ ├── Observable.js │ │ │ │ │ │ ├── Observer.js │ │ │ │ │ │ ├── Properties.js │ │ │ │ │ │ ├── Queue.js │ │ │ │ │ │ ├── Random.js │ │ │ │ │ │ ├── RandomAccess.js │ │ │ │ │ │ ├── ResourceBundle.js │ │ │ │ │ │ ├── Set.js │ │ │ │ │ │ ├── SortedMap.js │ │ │ │ │ │ ├── SortedSet.js │ │ │ │ │ │ ├── Stack.js │ │ │ │ │ │ ├── StringTokenizer.js │ │ │ │ │ │ ├── TooManyListenersException.js │ │ │ │ │ │ ├── TreeMap.js │ │ │ │ │ │ ├── TreeSet.js │ │ │ │ │ │ ├── UnknownFormatConversionException.js │ │ │ │ │ │ ├── UnknownFormatFlagsException.js │ │ │ │ │ │ ├── Vector.js │ │ │ │ │ │ ├── WeakHashMap.js │ │ │ │ │ │ ├── regex │ │ │ │ │ │ ├── MatchResult.js │ │ │ │ │ │ ├── Matcher.js │ │ │ │ │ │ ├── Pattern.js │ │ │ │ │ │ └── PatternSyntaxException.js │ │ │ │ │ │ └── zip │ │ │ │ │ │ ├── CRC32.js │ │ │ │ │ │ ├── CheckedInputStream.js │ │ │ │ │ │ ├── Checksum.js │ │ │ │ │ │ ├── Deflater.js │ │ │ │ │ │ ├── DeflaterOutputStream.js │ │ │ │ │ │ ├── GZIPInputStream.js │ │ │ │ │ │ ├── Inflater.js │ │ │ │ │ │ ├── InflaterInputStream.js │ │ │ │ │ │ ├── ZStreamRef.js │ │ │ │ │ │ ├── ZipConstants.js │ │ │ │ │ │ ├── ZipConstants64.js │ │ │ │ │ │ ├── ZipEntry.js │ │ │ │ │ │ ├── ZipException.js │ │ │ │ │ │ ├── ZipInputStream.js │ │ │ │ │ │ └── ZipOutputStream.js │ │ │ │ ├── javajs │ │ │ │ │ ├── J2SIgnoreImport.js │ │ │ │ │ ├── J2SRequireImport.js │ │ │ │ │ ├── api │ │ │ │ │ │ ├── BytePoster.js │ │ │ │ │ │ ├── EigenInterface.js │ │ │ │ │ │ ├── GenericBinaryDocument.js │ │ │ │ │ │ ├── GenericBinaryDocumentReader.js │ │ │ │ │ │ ├── GenericCifDataParser.js │ │ │ │ │ │ ├── GenericColor.js │ │ │ │ │ │ ├── GenericImageEncoder.js │ │ │ │ │ │ ├── GenericLineReader.js │ │ │ │ │ │ ├── GenericOutputChannel.js │ │ │ │ │ │ ├── GenericZipInputStream.js │ │ │ │ │ │ ├── GenericZipTools.js │ │ │ │ │ │ ├── Interface.js │ │ │ │ │ │ ├── JSFunction.js │ │ │ │ │ │ ├── JSInterface.js │ │ │ │ │ │ ├── JSONEncodable.js │ │ │ │ │ │ ├── ZInputStream.js │ │ │ │ │ │ └── js │ │ │ │ │ │ │ ├── J2SObjectInterface.js │ │ │ │ │ │ │ └── JSAppletObject.js │ │ │ │ │ ├── export │ │ │ │ │ │ ├── PDFCreator.js │ │ │ │ │ │ └── PDFObject.js │ │ │ │ │ └── img │ │ │ │ │ │ ├── BMPDecoder.js │ │ │ │ │ │ ├── CRCEncoder.js │ │ │ │ │ │ ├── GifEncoder.js │ │ │ │ │ │ ├── ImageEncoder.js │ │ │ │ │ │ ├── Jpg64Encoder.js │ │ │ │ │ │ ├── JpgEncoder.js │ │ │ │ │ │ ├── PdfEncoder.js │ │ │ │ │ │ ├── PngEncoder.js │ │ │ │ │ │ ├── PpmEncoder.js │ │ │ │ │ │ └── package.js │ │ │ │ └── org │ │ │ │ │ ├── apache │ │ │ │ │ └── tools │ │ │ │ │ │ └── bzip2 │ │ │ │ │ │ ├── BZip2Constants.js │ │ │ │ │ │ ├── CBZip2InputStream.js │ │ │ │ │ │ ├── CBZip2InputStreamFactory.js │ │ │ │ │ │ └── CRC.js │ │ │ │ │ └── qcschema │ │ │ │ │ └── QCSchemaUnits.js │ │ │ ├── php │ │ │ │ └── jsmol.php │ │ │ └── version.info │ │ ├── phasediagram_home.js │ │ ├── phasediagram_home.min.js │ │ └── plotly-v1.49.4.min.js │ └── robots.txt │ ├── templates │ ├── 404.html │ ├── 500.html │ ├── analysis │ │ ├── calculation.html │ │ ├── chem_pots.html │ │ ├── gclp.html │ │ ├── index.html │ │ ├── phase_diagram.html │ │ ├── symmetry │ │ │ ├── index.html │ │ │ ├── operation.html │ │ │ └── spacegroup.html │ │ └── view_data.html │ ├── api │ │ ├── api_gen.html │ │ ├── index.html │ │ ├── optimade.html │ │ ├── plain_text.html │ │ └── search_data.html │ ├── base.html │ ├── base_site.html │ ├── computing │ │ ├── allocation.html │ │ ├── base.html │ │ ├── host.html │ │ ├── hosts.html │ │ ├── index.html │ │ ├── job.html │ │ ├── new_host.html │ │ ├── online_submit.html │ │ ├── project.html │ │ ├── project_state.html │ │ ├── projects.html │ │ ├── queue.html │ │ ├── task.html │ │ └── user.html │ ├── construction.html │ ├── data │ │ └── reference │ │ │ ├── author.html │ │ │ ├── journal.html │ │ │ └── paper.html │ ├── documentation │ │ ├── doc_base.html │ │ ├── index.html │ │ ├── overview.html │ │ ├── pots.html │ │ ├── pubs.html │ │ ├── qmpy.html │ │ ├── structures.html │ │ └── vasp.html │ ├── download.html │ ├── faq.html │ ├── index.html │ ├── materials │ │ ├── chem_pots.html │ │ ├── composition.html │ │ ├── deposit.html │ │ ├── discovery.html │ │ ├── duplicates.html │ │ ├── element_groups.html │ │ ├── entry.html │ │ ├── generic_composition.html │ │ ├── index.html │ │ ├── keyword.html │ │ ├── phasespace.html │ │ ├── prototype.html │ │ ├── prototypes.html │ │ ├── structure.html │ │ └── substitution.html │ └── play.html │ ├── urls.py │ └── views │ ├── __init__.py │ ├── analysis │ ├── __init__.py │ ├── calculation.py │ ├── symmetry.py │ ├── thermodynamics.py │ └── visualize.py │ ├── api │ ├── __init__.py │ ├── calculation_list_view.py │ ├── entry_list_view.py │ ├── formationenergy_list_view.py │ ├── optimade_api.py │ ├── search_data.py │ └── search_data_forms.py │ ├── computing │ ├── __init__.py │ ├── new.py │ ├── queue.py │ └── resources.py │ ├── data │ ├── __init__.py │ └── references.py │ ├── documentation.py │ ├── download.py │ ├── home.py │ ├── materials │ ├── __init__.py │ ├── chem_pots.py │ ├── composition.py │ ├── deposit.py │ ├── discovery.py │ ├── element_groups.py │ ├── entry.py │ └── structure.py │ └── tools.py ├── requirements.txt └── setup.py /.gitattributes: -------------------------------------------------------------------------------- 1 | qmpy/web/static/js/* linguist-vendored 2 | 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