├── .gitattributes ├── .github └── workflows │ ├── multiversion_docs.py │ └── test_and_deploy.yml ├── .gitignore ├── LICENSE.rst ├── README.rst ├── benchmarks ├── __init__.py ├── conftest.py ├── sequence │ ├── __init__.py │ ├── align │ │ ├── __init__.py │ │ └── benchmark_kmers.py │ └── benchmark_fasta.py └── structure │ ├── __init__.py │ ├── benchmark_alphabet.py │ ├── benchmark_celllist.py │ ├── benchmark_compare.py │ ├── benchmark_pdbx.py │ └── benchmark_superimpose.py ├── doc ├── 404.rst ├── apidoc.json ├── apidoc.py ├── bibliography.py ├── conf.py ├── contribution │ ├── deployment.rst │ ├── development.rst │ ├── documentation.rst │ ├── index.rst │ └── testing.rst ├── examples │ ├── download │ │ ├── Array_Seq.txt │ │ ├── FCR3_10ug.csv │ │ ├── NF54_10ug.csv │ │ ├── dppc_n128.pdb │ │ ├── glycosylase_anm_vectors.csv │ │ ├── lysozyme_md.pdb │ │ ├── lysozyme_md.xtc │ │ ├── waterbox_md.pdb │ │ └── waterbox_md.xtc │ ├── index.rst │ └── scripts │ │ ├── sequence │ │ ├── README.rst │ │ ├── annotation │ │ │ ├── README.rst │ │ │ ├── operon_map.py │ │ │ ├── plasmid_map.py │ │ │ ├── plasmid_map_custom.py │ │ │ ├── region_visualization.py │ │ │ └── sigma_domains.py │ │ ├── homology │ │ │ ├── README.rst │ │ │ ├── avidin_alignment.py │ │ │ ├── bionigma_alignment.py │ │ │ ├── genome_comparison.py │ │ │ ├── genome_search.py │ │ │ ├── gpcr_evolution.py │ │ │ ├── hcn_hydropathy.py │ │ │ ├── hcn_similarity.py │ │ │ ├── homolog_msa.py │ │ │ ├── lexa_conservation.py │ │ │ ├── luxa_comparison.py │ │ │ ├── pi3k_alignment.py │ │ │ ├── plotepiscan.py │ │ │ ├── residue_coevolution.py │ │ │ └── thca_synthase_polymorphism.py │ │ ├── misc │ │ │ ├── README.rst │ │ │ ├── blosum_dendrogram.py │ │ │ ├── codon_usage.py │ │ │ ├── color_schemes.py │ │ │ ├── color_schemes_protein.py │ │ │ ├── local_alignment_statistics.py │ │ │ └── orf_identification.py │ │ ├── profile │ │ │ ├── README.rst │ │ │ ├── anderson_logo.py │ │ │ └── rbs_identification.py │ │ └── sequencing │ │ │ ├── README.rst │ │ │ ├── gene_counts.py │ │ │ ├── genome_assembly.py │ │ │ ├── quality_control.py │ │ │ └── read_quality.py │ │ └── structure │ │ ├── README.rst │ │ ├── alphabet │ │ ├── README.rst │ │ ├── msa.py │ │ └── structure_search.py │ │ ├── contacts │ │ ├── README.rst │ │ ├── adjacency_matrix.py │ │ ├── contact_sites.py │ │ ├── disulfide_bonds.py │ │ ├── domain_hbonds.py │ │ └── leaflet.py │ │ ├── misc │ │ ├── README.rst │ │ ├── biological_assembly.py │ │ ├── diameter.py │ │ ├── gap_bars.py │ │ ├── glycan_visualization.license │ │ ├── glycan_visualization.py │ │ ├── homolog_superimposition.py │ │ └── pdb_statistics.py │ │ ├── modeling │ │ ├── README.rst │ │ ├── docking.py │ │ ├── md_analysis.py │ │ ├── mmtf_trajectory.py │ │ ├── model_lddt.py │ │ ├── normal_modes.py │ │ ├── rotamer_library.py │ │ ├── solvation_shells.py │ │ ├── trajectory_sse.py │ │ ├── water_exchange.png │ │ └── water_exchange_noexec.py │ │ ├── molecule │ │ ├── README.rst │ │ ├── alkane_isomers.py │ │ ├── molecular_visualization.py │ │ └── peoe_visualization.py │ │ ├── nucleotide │ │ ├── README.rst │ │ ├── base_pairs.py │ │ ├── leontis_westhof.py │ │ ├── transfer_rnas.py │ │ └── watson_crick.py │ │ └── protein │ │ ├── README.rst │ │ ├── peptide_assembly.py │ │ ├── ramachandran.py │ │ ├── residue_chirality.py │ │ ├── sheet_arrangement.py │ │ └── transketolase_sse.py ├── extensions.rst ├── index.rst ├── install.rst ├── logo.rst ├── preamble.py ├── references.bib ├── scraper.py ├── static │ ├── assets │ │ ├── figures │ │ │ ├── app_lifecycle.png │ │ │ ├── dihedral.svg │ │ │ ├── rmsf.svg │ │ │ ├── sasa.svg │ │ │ └── symbol_encoding.png │ │ ├── general │ │ │ ├── biotite_icon.svg │ │ │ ├── biotite_icon_32p.png │ │ │ ├── biotite_icon_404.svg │ │ │ ├── biotite_icon_64p.png │ │ │ ├── biotite_icon_thumb.png │ │ │ ├── biotite_logo.svg │ │ │ ├── biotite_logo_l.png │ │ │ ├── biotite_logo_m.png │ │ │ ├── biotite_logo_s.png │ │ │ └── button_pypi.svg │ │ └── sponsors │ │ │ ├── LICENSE.rst │ │ │ └── vantai_logo.jpg │ ├── biotite.css │ ├── fonts.css │ └── fonts │ │ ├── LICENSE │ │ ├── crete-round-v13-latin-italic.woff │ │ ├── crete-round-v13-latin-italic.woff2 │ │ ├── crete-round-v13-latin-regular.woff │ │ ├── crete-round-v13-latin-regular.woff2 │ │ ├── fira-sans-v15-latin-italic.woff │ │ ├── fira-sans-v15-latin-italic.woff2 │ │ ├── fira-sans-v15-latin-regular.woff │ │ └── fira-sans-v15-latin-regular.woff2 ├── switcher.py ├── tutorial │ ├── application │ │ ├── blast.rst │ │ ├── dssp.rst │ │ ├── index.rst │ │ └── msa.rst │ ├── database │ │ ├── entrez.rst │ │ ├── index.rst │ │ └── rcsb.rst │ ├── index.rst │ ├── interface │ │ ├── index.rst │ │ ├── openmm.rst │ │ ├── pymol.rst │ │ └── rdkit.rst │ ├── preamble.rst │ ├── sequence │ │ ├── align_heuristic.rst │ │ ├── align_multiple.rst │ │ ├── align_optimal.rst │ │ ├── annotations.rst │ │ ├── encoding.rst │ │ ├── index.rst │ │ ├── io.rst │ │ ├── profiles.rst │ │ └── types.rst │ └── structure │ │ ├── alphabet.rst │ │ ├── atoms.rst │ │ ├── bonds.rst │ │ ├── editing.rst │ │ ├── filter.rst │ │ ├── index.rst │ │ ├── io.rst │ │ ├── measurement.rst │ │ └── trajectories.rst └── viewcode.py ├── environment.yml ├── pyproject.toml ├── src └── biotite │ ├── __init__.py │ ├── application │ ├── __init__.py │ ├── application.py │ ├── autodock │ │ ├── __init__.py │ │ └── app.py │ ├── blast │ │ ├── __init__.py │ │ ├── alignment.py │ │ └── webapp.py │ ├── clustalo │ │ ├── __init__.py │ │ └── app.py │ ├── dssp │ │ ├── __init__.py │ │ └── app.py │ ├── localapp.py │ ├── mafft │ │ ├── __init__.py │ │ └── app.py │ ├── msaapp.py │ ├── muscle │ │ ├── __init__.py │ │ ├── app3.py │ │ └── app5.py │ ├── sra │ │ ├── __init__.py │ │ └── app.py │ ├── tantan │ │ ├── __init__.py │ │ └── app.py │ ├── util.py │ ├── viennarna │ │ ├── __init__.py │ │ ├── rnaalifold.py │ │ ├── rnafold.py │ │ ├── rnaplot.py │ │ └── util.py │ └── webapp.py │ ├── copyable.py │ ├── database │ ├── __init__.py │ ├── afdb │ │ ├── __init__.py │ │ └── download.py │ ├── entrez │ │ ├── __init__.py │ │ ├── check.py │ │ ├── dbnames.py │ │ ├── download.py │ │ ├── key.py │ │ └── query.py │ ├── error.py │ ├── pubchem │ │ ├── __init__.py │ │ ├── download.py │ │ ├── error.py │ │ ├── query.py │ │ └── throttle.py │ ├── rcsb │ │ ├── __init__.py │ │ ├── download.py │ │ └── query.py │ └── uniprot │ │ ├── __init__.py │ │ ├── check.py │ │ ├── download.py │ │ └── query.py │ ├── file.py │ ├── interface │ ├── __init__.py │ ├── openmm │ │ ├── __init__.py │ │ ├── state.py │ │ └── system.py │ ├── pymol │ │ ├── __init__.py │ │ ├── cgo.py │ │ ├── convert.py │ │ ├── display.py │ │ ├── object.py │ │ ├── shapes.py │ │ └── startup.py │ ├── rdkit │ │ ├── __init__.py │ │ └── mol.py │ ├── version.py │ └── warning.py │ ├── sequence │ ├── __init__.py │ ├── align │ │ ├── __init__.py │ │ ├── alignment.py │ │ ├── banded.pyx │ │ ├── buckets.py │ │ ├── cigar.py │ │ ├── kmeralphabet.pyx │ │ ├── kmersimilarity.pyx │ │ ├── kmertable.pyx │ │ ├── localgapped.pyx │ │ ├── localungapped.pyx │ │ ├── matrix.py │ │ ├── matrix_data │ │ │ ├── 3Di.mat │ │ │ ├── BLOSUM100.mat │ │ │ ├── BLOSUM30.mat │ │ │ ├── BLOSUM35.mat │ │ │ ├── BLOSUM40.mat │ │ │ ├── BLOSUM45.mat │ │ │ ├── BLOSUM50.mat │ │ │ ├── BLOSUM50_13p.mat │ │ │ ├── BLOSUM50_14.3.mat │ │ │ ├── BLOSUM50_5.0.mat │ │ │ ├── BLOSUM55.mat │ │ │ ├── BLOSUM60.mat │ │ │ ├── BLOSUM62.mat │ │ │ ├── BLOSUM62_13p.mat │ │ │ ├── BLOSUM62_14.3.mat │ │ │ ├── BLOSUM62_5.0.mat │ │ │ ├── BLOSUM65.mat │ │ │ ├── BLOSUM70.mat │ │ │ ├── BLOSUM75.mat │ │ │ ├── BLOSUM80.mat │ │ │ ├── BLOSUM85.mat │ │ │ ├── BLOSUM90.mat │ │ │ ├── BLOSUMN.mat │ │ │ ├── CorBLOSUM49_5.0.mat │ │ │ ├── CorBLOSUM57_13p.mat │ │ │ ├── CorBLOSUM57_14.3.mat │ │ │ ├── CorBLOSUM61_5.0.mat │ │ │ ├── CorBLOSUM66_13p.mat │ │ │ ├── CorBLOSUM67_14.3.mat │ │ │ ├── DAYHOFF.mat │ │ │ ├── GONNET.mat │ │ │ ├── IDENTITY.mat │ │ │ ├── MATCH.mat │ │ │ ├── NUC.mat │ │ │ ├── PAM10.mat │ │ │ ├── PAM100.mat │ │ │ ├── PAM110.mat │ │ │ ├── PAM120.mat │ │ │ ├── PAM130.mat │ │ │ ├── PAM140.mat │ │ │ ├── PAM150.mat │ │ │ ├── PAM160.mat │ │ │ ├── PAM170.mat │ │ │ ├── PAM180.mat │ │ │ ├── PAM190.mat │ │ │ ├── PAM20.mat │ │ │ ├── PAM200.mat │ │ │ ├── PAM210.mat │ │ │ ├── PAM220.mat │ │ │ ├── PAM230.mat │ │ │ ├── PAM240.mat │ │ │ ├── PAM250.mat │ │ │ ├── PAM260.mat │ │ │ ├── PAM270.mat │ │ │ ├── PAM280.mat │ │ │ ├── PAM290.mat │ │ │ ├── PAM30.mat │ │ │ ├── PAM300.mat │ │ │ ├── PAM310.mat │ │ │ ├── PAM320.mat │ │ │ ├── PAM330.mat │ │ │ ├── PAM340.mat │ │ │ ├── PAM350.mat │ │ │ ├── PAM360.mat │ │ │ ├── PAM370.mat │ │ │ ├── PAM380.mat │ │ │ ├── PAM390.mat │ │ │ ├── PAM40.mat │ │ │ ├── PAM400.mat │ │ │ ├── PAM410.mat │ │ │ ├── PAM420.mat │ │ │ ├── PAM430.mat │ │ │ ├── PAM440.mat │ │ │ ├── PAM450.mat │ │ │ ├── PAM460.mat │ │ │ ├── PAM470.mat │ │ │ ├── PAM480.mat │ │ │ ├── PAM490.mat │ │ │ ├── PAM50.mat │ │ │ ├── PAM500.mat │ │ │ ├── PAM60.mat │ │ │ ├── PAM70.mat │ │ │ ├── PAM80.mat │ │ │ ├── PAM90.mat │ │ │ ├── PB.license │ │ │ ├── PB.mat │ │ │ ├── RBLOSUM52_5.0.mat │ │ │ ├── RBLOSUM59_13p.mat │ │ │ ├── RBLOSUM59_14.3.mat │ │ │ ├── RBLOSUM64_5.0.mat │ │ │ ├── RBLOSUM69_13p.mat │ │ │ └── RBLOSUM69_14.3.mat │ │ ├── multiple.pyx │ │ ├── pairwise.pyx │ │ ├── permutation.pyx │ │ ├── primes.txt │ │ ├── selector.pyx │ │ ├── statistics.py │ │ ├── tracetable.pxd │ │ └── tracetable.pyx │ ├── alphabet.py │ ├── annotation.py │ ├── codec.pyx │ ├── codon.py │ ├── codon_tables.txt │ ├── graphics │ │ ├── __init__.py │ │ ├── alignment.py │ │ ├── color_schemes │ │ │ ├── 3di_flower.json │ │ │ ├── autumn.json │ │ │ ├── blossom.json │ │ │ ├── clustalx_dna.json │ │ │ ├── clustalx_protein.json │ │ │ ├── flower.json │ │ │ ├── jalview_buried.json │ │ │ ├── jalview_hydrophobicity.json │ │ │ ├── jalview_prop_helix.json │ │ │ ├── jalview_prop_strand.json │ │ │ ├── jalview_prop_turn.json │ │ │ ├── jalview_taylor.json │ │ │ ├── jalview_zappo.json │ │ │ ├── ocean.json │ │ │ ├── pb_flower.json │ │ │ ├── rainbow_dna.json │ │ │ ├── rainbow_protein.json │ │ │ ├── spring.json │ │ │ ├── sunset.json │ │ │ └── wither.json │ │ ├── colorschemes.py │ │ ├── dendrogram.py │ │ ├── features.py │ │ ├── logo.py │ │ └── plasmid.py │ ├── io │ │ ├── __init__.py │ │ ├── fasta │ │ │ ├── __init__.py │ │ │ ├── convert.py │ │ │ └── file.py │ │ ├── fastq │ │ │ ├── __init__.py │ │ │ ├── convert.py │ │ │ └── file.py │ │ ├── genbank │ │ │ ├── __init__.py │ │ │ ├── annotation.py │ │ │ ├── file.py │ │ │ ├── metadata.py │ │ │ └── sequence.py │ │ ├── general.py │ │ └── gff │ │ │ ├── __init__.py │ │ │ ├── convert.py │ │ │ └── file.py │ ├── phylo │ │ ├── __init__.py │ │ ├── nj.pyx │ │ ├── tree.pyx │ │ └── upgma.pyx │ ├── profile.py │ ├── search.py │ ├── seqtypes.py │ └── sequence.py │ ├── setup_ccd.py │ ├── structure │ ├── __init__.py │ ├── alphabet │ │ ├── __init__.py │ │ ├── encoder.py │ │ ├── encoder_weights_3di.kerasify │ │ ├── i3d.py │ │ ├── layers.py │ │ ├── pb.license │ │ ├── pb.py │ │ └── unkerasify.py │ ├── atoms.py │ ├── basepairs.py │ ├── bonds.pyx │ ├── box.py │ ├── celllist.pyx │ ├── chains.py │ ├── charges.pyx │ ├── compare.py │ ├── density.py │ ├── dotbracket.py │ ├── error.py │ ├── filter.py │ ├── geometry.py │ ├── graphics │ │ ├── __init__.py │ │ ├── atoms.py │ │ └── rna.py │ ├── hbond.py │ ├── info │ │ ├── __init__.py │ │ ├── atom_masses.json │ │ ├── atoms.py │ │ ├── bonds.py │ │ ├── ccd.py │ │ ├── groups.py │ │ ├── masses.py │ │ ├── misc.py │ │ ├── radii.py │ │ └── standardize.py │ ├── integrity.py │ ├── io │ │ ├── __init__.py │ │ ├── dcd │ │ │ ├── __init__.py │ │ │ └── file.py │ │ ├── general.py │ │ ├── gro │ │ │ ├── __init__.py │ │ │ └── file.py │ │ ├── mol │ │ │ ├── __init__.py │ │ │ ├── convert.py │ │ │ ├── ctab.py │ │ │ ├── header.py │ │ │ ├── mol.py │ │ │ └── sdf.py │ │ ├── netcdf │ │ │ ├── __init__.py │ │ │ └── file.py │ │ ├── pdb │ │ │ ├── __init__.py │ │ │ ├── convert.py │ │ │ ├── file.py │ │ │ └── hybrid36.pyx │ │ ├── pdbqt │ │ │ ├── __init__.py │ │ │ ├── convert.py │ │ │ └── file.py │ │ ├── pdbx │ │ │ ├── __init__.py │ │ │ ├── bcif.py │ │ │ ├── cif.py │ │ │ ├── component.py │ │ │ ├── compress.py │ │ │ ├── convert.py │ │ │ └── encoding.pyx │ │ ├── trajfile.py │ │ ├── trr │ │ │ ├── __init__.py │ │ │ └── file.py │ │ ├── util.py │ │ └── xtc │ │ │ ├── __init__.py │ │ │ └── file.py │ ├── mechanics.py │ ├── molecules.py │ ├── pseudoknots.py │ ├── rdf.py │ ├── repair.py │ ├── residues.py │ ├── rings.py │ ├── sasa.pyx │ ├── segments.py │ ├── sequence.py │ ├── spacegroups.json │ ├── spacegroups.license │ ├── sse.py │ ├── superimpose.py │ ├── tm.py │ ├── transform.py │ └── util.py │ └── visualize.py └── tests ├── __init__.py ├── application ├── __init__.py ├── data │ └── 2rtg.bcif ├── test_autodock.py ├── test_blast.py ├── test_dssp.py ├── test_msa.py ├── test_rnaalifold.py ├── test_rnafold.py ├── test_rnaplot.py ├── test_sra.py └── test_tantan.py ├── conftest.py ├── database ├── __init__.py ├── test_afdb.py ├── test_entrez.py ├── test_pubchem.py ├── test_rcsb.py └── test_uniprot.py ├── interface ├── __init__.py ├── data │ ├── README.rst │ └── smiles.txt ├── pymol │ ├── __init__.py │ ├── conftest.py │ ├── test_cgo.py │ ├── test_command.py │ ├── test_conversion.py │ ├── test_display.py │ ├── test_selection.py │ ├── test_shapes.py │ └── test_startup.py ├── test_openmm.py ├── test_rdkit.py └── test_version.py ├── sequence ├── __init__.py ├── align │ ├── __init__.py │ ├── conftest.py │ ├── test_alignment.py │ ├── test_banded.py │ ├── test_cigar.py │ ├── test_kmeralphabet.py │ ├── test_kmersimilarity.py │ ├── test_kmertable.py │ ├── test_localgapped.py │ ├── test_localungapped.py │ ├── test_matrix.py │ ├── test_multiple.py │ ├── test_pairwise.py │ ├── test_permutation.py │ ├── test_selector.py │ └── test_statistics.py ├── data │ ├── 1a00_A_uniref90.a3m │ ├── alignment.fasta │ ├── bt_lysozyme.gff3 │ ├── bt_lysozyme.gp │ ├── cas9.fasta │ ├── distances.txt │ ├── ec_bl21.fasta │ ├── ec_bl21.gb │ ├── ec_bl21.gff3 │ ├── gg_avidin.gb │ ├── gg_avidin.gff3 │ ├── indexing_test.gff3 │ ├── influenca.gb │ ├── invalid.fasta │ ├── multifile.gp │ ├── newick_upgma.txt │ ├── nuc.fasta │ ├── percent_test.gff3 │ ├── prot.fasta │ ├── random.fasta │ ├── random.fastq │ ├── sc_chrom1.gb │ ├── sc_chrom1.gff3 │ └── selenocysteine.fasta ├── test_alphabet.py ├── test_annotation.py ├── test_codon.py ├── test_fasta.py ├── test_fastq.py ├── test_genbank.py ├── test_generalio.py ├── test_gff.py ├── test_graphics.py ├── test_phylo.py ├── test_profile.py ├── test_search.py ├── test_seqtypes.py └── test_sequence.py ├── structure ├── __init__.py ├── alphabet │ ├── __init__.py │ ├── test_i3d.py │ └── test_pb.py ├── data │ ├── 1aki.bcif │ ├── 1aki.cif │ ├── 1aki.gro │ ├── 1aki.pdb │ ├── 1crr.bcif │ ├── 1crr.cif │ ├── 1crr.gro │ ├── 1crr.pdb │ ├── 1dix.bcif │ ├── 1dix.cif │ ├── 1dix.gro │ ├── 1dix.pdb │ ├── 1f2n.bcif │ ├── 1f2n.cif │ ├── 1f2n.gro │ ├── 1f2n.pdb │ ├── 1gya.bcif │ ├── 1gya.cif │ ├── 1gya.gro │ ├── 1gya.pdb │ ├── 1igy.bcif │ ├── 1igy.cif │ ├── 1igy.gro │ ├── 1igy.pdb │ ├── 1l2y.bcif │ ├── 1l2y.cif │ ├── 1l2y.dcd │ ├── 1l2y.gro │ ├── 1l2y.netcdf │ ├── 1l2y.pdb │ ├── 1l2y.trr │ ├── 1l2y.xtc │ ├── 1ncb.bcif │ ├── 1ncb.cif │ ├── 1o1z.bcif │ ├── 1o1z.cif │ ├── 1o1z.gro │ ├── 1o1z.pdb │ ├── 2axd.bcif │ ├── 2axd.cif │ ├── 2axd.pdb │ ├── 2d0f.bcif │ ├── 2d0f.cif │ ├── 2d0f.pdb │ ├── 3o5r.bcif │ ├── 3o5r.cif │ ├── 3o5r.gro │ ├── 3o5r.pdb │ ├── 3wip.bcif │ ├── 3wip.cif │ ├── 3wip.pdb │ ├── 4gxy.bcif │ ├── 4gxy.cif │ ├── 4gxy.gro │ ├── 4gxy.pdb │ ├── 4i39.bcif │ ├── 4i39.cif │ ├── 4p5j.bcif │ ├── 4p5j.cif │ ├── 4p5j.gro │ ├── 4p5j.pdb │ ├── 4zxb.bcif │ ├── 4zxb.cif │ ├── 5eil.bcif │ ├── 5eil.cif │ ├── 5eil.pdb │ ├── 5h73.bcif │ ├── 5h73.cif │ ├── 5h73.gro │ ├── 5h73.pdb │ ├── 5ugo.bcif │ ├── 5ugo.cif │ ├── 5ugo.gro │ ├── 5ugo.pdb │ ├── 5zng.bcif │ ├── 5zng.cif │ ├── 5zng.pdb │ ├── 7gsa.bcif │ ├── 7gsa.cif │ ├── README.rst │ ├── alphabet │ │ ├── 1ay7.bcif │ │ ├── README.rst │ │ ├── i3d.fasta │ │ └── pb.fasta │ ├── base_pairs │ │ ├── 1bna.cif │ │ ├── 1bna.pdb │ │ ├── 1gid.cif │ │ ├── 1gid_edges.json │ │ ├── 1gid_sugar.json │ │ ├── 1nkw.cif │ │ ├── 1nkw_edges.json │ │ ├── 1nkw_sugar.json │ │ ├── 1qxb.cif │ │ ├── 1xnr.cif │ │ ├── 1xnr_edges.json │ │ ├── 1xnr_sugar.json │ │ ├── create_bond_orientation_test_data.py │ │ └── create_interacting_edge_test_data.py │ ├── create_test_structures.py │ ├── edge_cases │ │ ├── README.rst │ │ ├── altloc.cif │ │ ├── hetatm.pdb │ │ └── res_ids.cif │ ├── homologs │ │ ├── 1gl4.bcif │ │ ├── 1hml.bcif │ │ ├── 1p4k.bcif │ │ ├── 1qgi.bcif │ │ ├── 2nwd.bcif │ │ ├── 3kcs.bcif │ │ ├── 3lsj.bcif │ │ ├── 3lzm.bcif │ │ ├── 3rd3.bcif │ │ ├── 4osx.bcif │ │ ├── 6oa8.bcif │ │ └── README.rst │ ├── ids.txt │ ├── misc │ │ ├── README.rst │ │ ├── dihedrals.json │ │ ├── dihedrals.py │ │ ├── hbond.json │ │ ├── hbond.py │ │ ├── rdf.json │ │ ├── rdf.py │ │ ├── sasa.json │ │ └── sasa.py │ ├── molecules │ │ ├── 03F.cif │ │ ├── 03F.sdf │ │ ├── 03F.v3000.sdf │ │ ├── 13136.sdf │ │ ├── 13136.v3000.sdf │ │ ├── CYN.cif │ │ ├── CYN.sdf │ │ ├── CYN.v3000.sdf │ │ ├── HWB.cif │ │ ├── HWB.sdf │ │ ├── HWB.v3000.sdf │ │ ├── README.rst │ │ ├── TYR.cif │ │ ├── TYR.sdf │ │ ├── TYR.v3000.sdf │ │ └── create_v3000_sdf.py │ ├── psea.fasta │ ├── pseudoknots │ │ ├── test0_knotted.json │ │ ├── test0_unknotted.json │ │ ├── test10_knotted.json │ │ ├── test10_unknotted.json │ │ ├── test11_knotted.json │ │ ├── test11_unknotted.json │ │ ├── test12_knotted.json │ │ ├── test12_unknotted.json │ │ ├── test13_knotted.json │ │ ├── test13_unknotted.json │ │ ├── test14_knotted.json │ │ ├── test14_unknotted.json │ │ ├── test15_knotted.json │ │ ├── test15_unknotted.json │ │ ├── test16_knotted.json │ │ ├── test16_unknotted.json │ │ ├── test17_knotted.json │ │ ├── test17_unknotted.json │ │ ├── test18_knotted.json │ │ ├── test18_unknotted.json │ │ ├── test19_knotted.json │ │ ├── test19_unknotted.json │ │ ├── test1_knotted.json │ │ ├── test1_unknotted.json │ │ ├── test20_knotted.json │ │ ├── test20_unknotted.json │ │ ├── test2_knotted.json │ │ ├── test2_unknotted.json │ │ ├── test3_knotted.json │ │ ├── test3_unknotted.json │ │ ├── test4_knotted.json │ │ ├── test4_unknotted.json │ │ ├── test5_knotted.json │ │ ├── test5_unknotted.json │ │ ├── test6_knotted.json │ │ ├── test6_unknotted.json │ │ ├── test7_knotted.json │ │ ├── test7_unknotted.json │ │ ├── test8_knotted.json │ │ ├── test8_unknotted.json │ │ ├── test9_knotted.json │ │ └── test9_unknotted.json │ ├── tm │ │ ├── README.rst │ │ ├── tm.py │ │ └── tm_scores.json │ └── waterbox.gro ├── io │ ├── __init__.py │ ├── test_gro.py │ ├── test_mol.py │ ├── test_pdb.py │ ├── test_pdbqt.py │ ├── test_pdbx.py │ └── test_trajectory.py ├── test_atoms.py ├── test_basepairs.py ├── test_bonds.py ├── test_box.py ├── test_celllist.py ├── test_chains.py ├── test_charges.py ├── test_compare.py ├── test_density.py ├── test_dotbracket.py ├── test_filter.py ├── test_generalio.py ├── test_geometry.py ├── test_hbond.py ├── test_info.py ├── test_integrity.py ├── test_mechanics.py ├── test_molecules.py ├── test_pseudoknots.py ├── test_rdf.py ├── test_repair.py ├── test_residues.py ├── test_rings.py ├── 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