├── .github ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── SUPPORT.md ├── pull_request_template.md └── workflows │ └── main.yml ├── .gitignore ├── CMakeLists.txt ├── CODE_OF_CONDUCT.md ├── COPYING ├── ChangeLog ├── INSTALL.md ├── Packages ├── CMakeLists.txt ├── Clustering │ ├── AverageLinkage.cpp │ ├── AverageLinkage.hpp │ ├── CMakeLists.txt │ ├── Clustering.hpp │ ├── ClusteringOptions.cpp │ ├── ClusteringOptions.hpp │ ├── ClusteringTypedefs.hpp │ ├── ClusteringUtils.cpp │ ├── ClusteringUtils.hpp │ ├── HAC.cpp │ ├── HAC.hpp │ ├── KGS.cpp │ ├── KGS.hpp │ ├── cluster-kgs.cpp │ ├── cluster_pops.py │ ├── frame-picker.py │ └── rmsds-align.py ├── Convergence │ ├── CMakeLists.txt │ ├── ConvergenceOptions.hpp │ ├── assign_frames.cpp │ ├── avgconv.cpp │ ├── bcom.cpp │ ├── bcomlib.hpp │ ├── block_average.cpp │ ├── block_avgconv.cpp │ ├── boot_bcom.cpp │ ├── bootstrap_overlap.pl │ ├── chist.cpp │ ├── coscon.cpp │ ├── decorr_time.cpp │ ├── effsize.pl │ ├── expfit.cpp │ ├── fid-lib.cpp │ ├── fid-lib.hpp │ ├── fidpick.cpp │ ├── hierarchy.cpp │ ├── neff.cpp │ ├── qcoscon.cpp │ ├── rsv-coscon.cpp │ ├── sortfids.cpp │ └── ufidpick.cpp ├── DensityTools │ ├── CMakeLists.txt │ ├── DensityGrid.hpp │ ├── DensityOptions.hpp │ ├── DensityTools.hpp │ ├── GridUtils.cpp │ ├── GridUtils.hpp │ ├── SimpleMeta.hpp │ ├── blob_contact.cpp │ ├── blob_stats.cpp │ ├── blobid.cpp │ ├── contained.cpp │ ├── grid2ascii.cpp │ ├── grid2xplor.cpp │ ├── grid_slicer.pl │ ├── gridautoscale.cpp │ ├── gridavg.cpp │ ├── griddiff.cpp │ ├── gridgauss.cpp │ ├── gridinfo.cpp │ ├── gridmask.cpp │ ├── gridscale.cpp │ ├── gridslice.cpp │ ├── gridstat.cpp │ ├── internal-water-filter.cpp │ ├── internal-water-filter.hpp │ ├── near_blobs.cpp │ ├── peakify.cpp │ ├── pick_blob.cpp │ ├── water-autocorrel.cpp │ ├── water-count.cpp │ ├── water-extract.cpp │ ├── water-hist-lib.cpp │ ├── water-hist-lib.hpp │ ├── water-hist.cpp │ ├── water-inside.cpp │ ├── water-lib.cpp │ ├── water-lib.hpp │ ├── water-sides.cpp │ ├── water-survival.cpp │ └── xplor-edm-writer.hpp ├── ElasticNetworks │ ├── CMakeLists.txt │ ├── anm-lib.hpp │ ├── anm.cpp │ ├── eigenflucc.cpp │ ├── enm-lib.cpp │ ├── enm-lib.hpp │ ├── enmovie.cpp │ ├── gnm.cpp │ ├── heavy-ca.cpp │ ├── hessian.hpp │ ├── mc_fit.hpp │ ├── psf-masses.cpp │ ├── side-nodes.cpp │ ├── spring_functions.cpp │ ├── spring_functions.hpp │ ├── vsa-lib.cpp │ ├── vsa-lib.hpp │ └── vsa.cpp ├── HydrogenBonds │ ├── CMakeLists.txt │ ├── hbonds.cpp │ ├── hcontacts.cpp │ ├── hcore.cpp │ ├── hcore.hpp │ ├── hcorrelation.cpp │ ├── hmatrix.cpp │ └── hoccupancies.pl ├── PyLOOS │ ├── CMakeLists.txt │ ├── add_bonds.py │ ├── all_contacts.py │ ├── all_stacking.py │ ├── axis_with_membrane.py │ ├── center_molecule.py │ ├── cluster-structures.py │ ├── contact_distance.py │ ├── cylindrical-density.py │ ├── cylindrical-thickness.py │ ├── domain.py │ ├── flip_chirality.py │ ├── helix_axes.py │ ├── hierarchical-cluster.py │ ├── inside_helices.py │ ├── native-hbs.py │ ├── packing_score_per_res.py │ ├── protein_tilt.py │ ├── rare-event-detection.py │ ├── renum-by-mol.py │ ├── rmsd_to_average.py │ ├── scattering.py │ ├── set_segids.py │ ├── simple_model_calc.py │ ├── simple_model_transform.py │ ├── simple_traj_calc.py │ ├── simple_traj_transform.py │ ├── sysinfo.py │ └── total_charge.py └── User │ ├── CMakeLists.txt │ ├── README.md │ ├── model_calc.cpp │ ├── simple_model_calc.cpp │ ├── simple_model_transform.cpp │ ├── test_mmcif.cpp │ ├── test_mmcif_2.cpp │ ├── traj_calc.cpp │ └── traj_transform.cpp ├── README.md ├── Tools ├── .ycm_extra_conf.py ├── CMakeLists.txt ├── aligner.cpp ├── area_per_lipid.cpp ├── atomic-rdf.cpp ├── averager.cpp ├── big-svd.cpp ├── blurrogram.pl ├── bounding.cpp ├── center-molecule.cpp ├── clipper.cpp ├── concat-selection.cpp ├── contact-time.cpp ├── contacts.cpp ├── convert2pdb.cpp ├── coverlap.cpp ├── cross-dist.cpp ├── crossing-waters.cpp ├── dcdinfo.cpp ├── density-dist-windowed.cpp ├── density-dist.cpp ├── dibmops.cpp ├── dihedrals.cpp ├── distance_prob.cpp ├── drifter.cpp ├── dumpmol.cpp ├── esp_mesh.cpp ├── exposure.cpp ├── fcontacts.cpp ├── fixdcd.cpp ├── frame2pdb.cpp ├── gmxdump2pdb.pl ├── helix_kink.cpp ├── interdist.cpp ├── kurskew.cpp ├── lipid_survival.cpp ├── long-bond-finder.cpp ├── loos_version.cpp ├── mat2loos.pl ├── membrane_map.cpp ├── membrane_map.hpp ├── merge-traj.cpp ├── model-meta-stats.cpp ├── model-select.cpp ├── model2matlab.cpp ├── molshape.cpp ├── mops.cpp ├── multi-rmsds.cpp ├── native_contacts.cpp ├── ocf.cpp ├── order_params.cpp ├── packing_score.cpp ├── paxes.cpp ├── periodic_box.cpp ├── perturb-structure.cpp ├── phase-pdb.cpp ├── porcupine.cpp ├── potential_profile.py ├── rad-gyr.cpp ├── ramachandran.cpp ├── rdf.cpp ├── rebond.cpp ├── recenter-trj.cpp ├── reimage-by-molecule.cpp ├── renum-pdb.cpp ├── residue-contact-map.cpp ├── rgyr.cpp ├── rms-overlap.cpp ├── rmsd2ref.cpp ├── rmsds.cpp ├── rmsf.cpp ├── rmsfit.cpp ├── rna_suites.cpp ├── rotamer.cpp ├── serialize-selection.cpp ├── smooth-traj.cpp ├── subsetter.cpp ├── svd.cpp ├── svdcolmap.cpp ├── torsion.cpp ├── traj2dcd.cpp ├── traj2matlab.cpp ├── traj2pdb.cpp ├── trajinfo.cpp ├── transition_contacts.cpp ├── verap.cpp ├── xtcinfo.cpp ├── xy_rdf.cpp └── xy_rdf_timeseries.cpp ├── archive └── README.md ├── conda_build.sh ├── fullhelper.py ├── images ├── gplv3.png ├── grossfield_logo.jpg ├── loos_logo.pdf ├── loos_logo.png ├── loos_logo.svg ├── loos_logo2.pdf ├── loos_logo2.png └── loos_logo2.svg ├── loos.dox ├── loos ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── pyproject.toml ├── setup.cfg └── src │ └── loos │ ├── OptimalMembraneGenerator │ ├── LipidLibrary.py │ ├── NAMD.py │ ├── OptimalMembraneGenerator.py │ ├── PSFGen.py │ ├── ParseOptions.py │ ├── WaterBox.py │ ├── __init__.py │ ├── add_molecules.py │ ├── doc │ │ ├── doc.pdf │ │ └── doc.tex │ ├── example │ │ ├── README │ │ ├── par_build.inp │ │ ├── popc │ │ │ └── popc.cfg │ │ ├── pope-popg │ │ │ └── pope-popg.cfg │ │ ├── rhod-water │ │ │ └── rhodopsin.cfg │ │ ├── rhodopsin │ │ │ ├── all-rhod.pdb │ │ │ ├── all-rhod.psf │ │ │ ├── rhodopsin.cfg │ │ │ └── toppar_retp.inp │ │ ├── run_examples │ │ └── top_build.inp │ ├── make_library.py │ ├── omg_copy.py │ ├── solvate.py │ └── water_small.pdb │ ├── Voronoi │ ├── Voronoi.py │ ├── __init__.py │ ├── area_per_molecule.py │ ├── area_profile.py │ ├── lipid_lifetime.py │ └── run_areas.py │ ├── __init__.py │ └── pyloos │ ├── ConvexHull.py │ ├── NAMDBin.py │ ├── SymmMatrix.py │ ├── __init__.py │ ├── alignment.py │ ├── ensembles.py │ ├── options.py │ ├── subspace.py │ └── trajectories.py ├── loos_setup.csh.in ├── loos_setup.sh.in ├── modules ├── Copyright_for_FindNetCDF.txt └── FindNetCDF.cmake ├── share ├── CMakeLists.txt ├── stack_vals.json └── suitename_definitions.dat ├── src ├── .ycm_extra_conf.py ├── AG_linalg.cpp ├── AG_numerical.cpp ├── Atom.cpp ├── Atom.hpp ├── Atom.i ├── AtomicGroup.cpp ├── AtomicGroup.hpp ├── AtomicGroup.i ├── AtomicNumberDeducer.cpp ├── AtomicNumberDeducer.hpp ├── CMakeLists.txt ├── Coord.hpp ├── Coord.i ├── FlexLexer.h ├── Fmt.cpp ├── Fmt.hpp ├── FormFactor.cpp ├── FormFactor.hpp ├── FormFactor.i ├── FormFactorSet.cpp ├── FormFactorSet.hpp ├── FormFactorSet.i ├── Geometry.cpp ├── Geometry.hpp ├── Geometry.i ├── HBondDetector.cpp ├── HBondDetector.hpp ├── HBondDetector.i ├── Kernel.cpp ├── Kernel.hpp ├── KernelActions.cpp ├── KernelActions.hpp ├── KernelStack.cpp ├── KernelStack.hpp ├── KernelValue.cpp ├── KernelValue.hpp ├── LineReader.cpp ├── LineReader.hpp ├── LoosLexer.hpp ├── Matrix.hpp ├── Matrix44.hpp ├── Matrix44.i ├── MatrixIO.hpp ├── MatrixImpl.hpp ├── MatrixOps.cpp ├── MatrixOps.hpp ├── MatrixOrder.hpp ├── MatrixRead.hpp ├── MatrixStorage.hpp ├── MatrixUtils.hpp ├── MatrixWrite.hpp ├── MultiTraj.cpp ├── MultiTraj.hpp ├── OptionsFramework.cpp ├── OptionsFramework.hpp ├── Parser.hpp ├── ParserDriver.hpp ├── PeriodicBox.hpp ├── ProgressCounters.cpp ├── ProgressCounters.hpp ├── ProgressTriggers.cpp ├── ProgressTriggers.hpp ├── RnaSuite.cpp ├── RnaSuite.hpp ├── RnaSuite.i ├── Selectors.cpp ├── Selectors.hpp ├── Simplex.hpp ├── StreamWrapper.hpp ├── TimeSeries.hpp ├── TimeSeries.i ├── Trajectory.hpp ├── Trajectory.i ├── UniformWeight.cpp ├── UniformWeight.hpp ├── UniqueStrings.hpp ├── Weights.cpp ├── Weights.hpp ├── Weights.i ├── WeightsFromFile.cpp ├── WeightsFromFile.hpp ├── XForm.cpp ├── XForm.hpp ├── XForm.i ├── alignment.cpp ├── alignment.hpp ├── alignment.i ├── amber.cpp ├── amber.hpp ├── amber_netcdf.cpp ├── amber_netcdf.hpp ├── amber_rst.cpp ├── amber_rst.hpp ├── amber_traj.cpp ├── amber_traj.hpp ├── catch_it.i ├── ccpdb.cpp ├── ccpdb.hpp ├── charmm.cpp ├── charmm.hpp ├── cryst.hpp ├── cryst.i ├── dcd.cpp ├── dcd.hpp ├── dcd_utils.hpp ├── dcdwriter.cpp ├── dcdwriter.hpp ├── dcdwriter.i ├── ensembles.cpp ├── ensembles.hpp ├── ensembles.i ├── exceptions.hpp ├── exceptions.i ├── grammar.cc ├── grammar.hh ├── grammar.yy ├── gro.cpp ├── gro.hpp ├── gro.i ├── index_range_parser.cpp ├── index_range_parser.hpp ├── location.hh ├── loos.hpp ├── loos.i ├── loos_defs.hpp ├── loos_timer.hpp ├── mdtraj.cpp ├── mdtraj.hpp ├── mdtraj.i ├── mdtrajtraj.cpp ├── mdtrajtraj.hpp ├── mmcif.cpp ├── mmcif.hpp ├── numpy.i ├── pdb.cpp ├── pdb.hpp ├── pdb.i ├── pdb_remarks.cpp ├── pdb_remarks.hpp ├── pdb_remarks.i ├── pdbtraj.cpp ├── pdbtraj.hpp ├── position.hh ├── psf.cpp ├── psf.hpp ├── scanner.cc ├── scanner.ll ├── setup.py.in ├── sfactories.cpp ├── sfactories.hpp ├── sfactories.i ├── sorting.hpp ├── stack.hh ├── tinker_arc.cpp ├── tinker_arc.hpp ├── tinkerxyz.cpp ├── tinkerxyz.hpp ├── trajwriter.hpp ├── trajwriter.i ├── trr.cpp ├── trr.hpp ├── utils.cpp ├── utils.hpp ├── utils.i ├── utils_random.cpp ├── utils_random.hpp ├── utils_random.i ├── utils_structural.cpp ├── utils_structural.hpp ├── utils_structural.i ├── version.cpp.in ├── version.hpp.in ├── xdr.hpp ├── xtc.cpp ├── xtc.hpp ├── xtcwriter.cpp ├── xtcwriter.hpp └── xtcwriter.i └── utils ├── check_loos_install.pl ├── 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