Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z A activate() (pestifer.molecule.bioassemb.BioAssemb method) (pestifer.objs.graft.Graft method) activate_biological_assembly() (pestifer.molecule.molecule.Molecule method) add_atom() (pestifer.molecule.residue.Residue method) (pestifer.psfutil.psfcontents.PSFResidue method) add_collection() (pestifer.charmmff.pdbrepository.PDBRepository method) add_custom_directory() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) add_interval() (pestifer.molecule.stateinterval.StateIntervalList method) add_ligand() (pestifer.psfutil.psfatom.PSFAtom method) add_ligands() (pestifer.psfutil.psfcontents.PSFContents method) add_residue() (pestifer.psfutil.psfcontents.PSFSegment method) add_resource() (pestifer.charmmff.pdbrepository.PDBRepository method) add_segment() (pestifer.molecule.asymmetricunit.AsymmetricUnit method) add_specstring() (pestifer.molecule.bilayer.BilayerSpecString method) add_subparser() (pestifer.cli.subcommand.Subcommand method) (pestifer.subcommands.build.RunSubcommand method) (pestifer.subcommands.build_example.RunExampleSubcommand method) (pestifer.subcommands.config_default.ConfigDefaultSubcommand method) (pestifer.subcommands.config_help.ConfigHelpSubcommand method) (pestifer.subcommands.desolvate.DesolvateSubcommand method) (pestifer.subcommands.fetch_example.FetchExampleSubcommand method) (pestifer.subcommands.follow_namd_log.FollowNAMDLogSubcommand method) (pestifer.subcommands.make_ligand_mol2.MakeLigandMol2Subcommand method) (pestifer.subcommands.make_namd_restart.MakeNAMDRestartSubcommand method) (pestifer.subcommands.make_pdbcollection.MakePDBCollectionSubcommand method) (pestifer.subcommands.mdplot.MDPlotSubcommand method) (pestifer.subcommands.modify_package.ModifyPackageSubcommand method) (pestifer.subcommands.new_system.NewSystemSubcommand method) (pestifer.subcommands.rebuild_charmmff_cache.RebuildCHARMMFFCache method) (pestifer.subcommands.setup_vmd.SetupVMDSubcommand method) (pestifer.subcommands.show_resources.ShowResourcesSubcommand method) (pestifer.subcommands.wheretcl.WhereTCLSubcommand method) addfile() (pestifer.scripters.tcl.TcLScripter method) addline() (pestifer.scripters.generic.GenericScripter method) (pestifer.util.stringthings.ByteCollector method) addpostregenerateline() (pestifer.scripters.psfgen.PsfgenScripter method) adjustSerials() (pestifer.molecule.atom.AtomList method) aliases (pestifer.cli.subcommand.Subcommand attribute) (pestifer.subcommands.build.RunSubcommand attribute) (pestifer.subcommands.build_example.RunExampleSubcommand attribute) Align (class in pestifer.objs.align) align_donor_sel (pestifer.objs.transfer_coords.TransferCoords attribute) align_mobile_sel (pestifer.objs.transfer_coords.TransferCoords attribute) AlignList (class in pestifer.objs.align) all_exist() (pestifer.core.artifacts.FileArtifactList method) altloc (pestifer.molecule.atom.Atom attribute) altloc1 (pestifer.objs.link.Link attribute) altloc2 (pestifer.objs.link.Link attribute) anchor_paths() (in module pestifer.charmmff.graphhelpers) angle (pestifer.objs.crot.Crot attribute) (pestifer.objs.rottrans.RotTrans attribute) angles (pestifer.charmmff.charmmffprm.CharmmParamFile attribute) (pestifer.charmmff.charmmfftop.CharmmIC attribute) (pestifer.psfutil.psfcontents.PSFContents attribute) APP_NAME (pestifer.util.cacheable_object.CacheableObject attribute) APP_VERSION (pestifer.util.cacheable_object.CacheableObject attribute) append() (pestifer.charmmff.charmmfftop.CharmmAtomList method) (pestifer.core.artifacts.ArtifactList method) (pestifer.core.artifacts.CharmmffFileArtifactList method) (pestifer.core.artifacts.CharmmffParFileArtifacts method) (pestifer.core.artifacts.CharmmffStreamFileArtifacts method) (pestifer.core.artifacts.CharmmffTopFileArtifacts method) (pestifer.core.baseobj.BaseObjList method) (pestifer.core.example.ExampleList method) append_example() (pestifer.core.examplemanager.ExampleManager method) (pestifer.core.resourcemanager.ResourceManager method) (pestifer.sphinxext.sphinx_examplemanager.SphinxExampleManager method) applies_chainIDs (pestifer.molecule.transform.Transform attribute) apply_atom_logics() (pestifer.psfutil.psfcontents.PSFContents method) apply_exclusion_logics() (pestifer.molecule.atom.AtomList method) (pestifer.molecule.residue.ResiduePlaceholderList method) (pestifer.psfutil.psfatom.PSFAtomList method) apply_inclusion_logics() (pestifer.molecule.atom.AtomList method) (pestifer.molecule.residue.ResiduePlaceholderList method) (pestifer.psfutil.psfatom.PSFAtomList method) apply_insertions() (pestifer.molecule.residue.ResidueList method) apply_psf_attributes() (pestifer.molecule.atom.AtomList method) apply_segtypes() (pestifer.molecule.residue.ResidueList method) (pestifer.objs.link.LinkList method) (pestifer.psfutil.psfcontents.PSFResidueList method) apply_to (pestifer.objs.align.Align attribute) apply_unified_diff() (in module pestifer.util.patch) Artifact (class in pestifer.core.artifacts) ArtifactDict (class in pestifer.core.artifacts) ArtifactList (class in pestifer.core.artifacts) assign_cell_index() (pestifer.psfutil.psftopoelement.PSFTopoElement method) assign_cell_indexes() (pestifer.psfutil.psftopoelement.PSFTopoElementList method) assign_obj_to_attr() (pestifer.core.baseobj.BaseObj method) assign_objs_to_attr() (pestifer.core.baseobj.BaseObjList method) assign_receiver_residues() (pestifer.objs.graft.Graft method) assign_residue() (pestifer.objs.patch.Patch method) (pestifer.objs.seqadv.Seqadv method) assign_residues() (pestifer.objs.graft.GraftList method) (pestifer.objs.link.LinkList method) (pestifer.objs.patch.PatchList method) (pestifer.objs.seqadv.SeqadvList method) (pestifer.objs.ssbond.SSBondList method) asym_chainID (pestifer.molecule.residue.ResiduePlaceholder attribute) asymmetric_unit (pestifer.molecule.molecule.Molecule attribute) AsymmetricUnit (class in pestifer.molecule.asymmetricunit) Atom (class in pestifer.molecule.atom) atom1 (pestifer.objs.crot.Crot attribute) (pestifer.objs.link.Link attribute) atom2 (pestifer.objs.crot.Crot attribute) (pestifer.objs.link.Link attribute) atom_element (pestifer.charmmff.charmmfftop.CharmmMass attribute) atom_mass (pestifer.charmmff.charmmfftop.CharmmMass attribute) atom_resids() (pestifer.molecule.residue.ResidueList method) atom_resseqnums() (pestifer.molecule.residue.ResidueList method) atom_serials() (pestifer.molecule.residue.ResidueList method) atom_type (pestifer.charmmff.charmmfftop.CharmmMass attribute) atomdict (pestifer.charmmff.charmmfftop.CharmmResi attribute) atomi (pestifer.objs.crot.Crot attribute) atomicwt (pestifer.psfutil.psfatom.PSFAtom attribute) atomj (pestifer.objs.crot.Crot attribute) atomk (pestifer.objs.crot.Crot attribute) AtomList (class in pestifer.molecule.atom) atomname (pestifer.charmmff.charmmfftop.CharmmDelete attribute) (pestifer.psfutil.psfatom.PSFAtom attribute) atoms (pestifer.charmmff.charmmfftop.CharmmIC attribute) (pestifer.charmmff.charmmfftop.CharmmResi attribute) (pestifer.molecule.residue.Residue attribute) (pestifer.psfutil.psfcontents.PSFContents attribute) (pestifer.psfutil.psfcontents.PSFResidue attribute) atoms_in_group (pestifer.charmmff.charmmfftop.CharmmResi attribute) atomserials (pestifer.psfutil.psfcontents.PSFContents attribute) atomtype (pestifer.charmmff.charmmffprm.CharmmNonbondedParam attribute) (pestifer.psfutil.psfatom.PSFAtom attribute) attachments (pestifer.molecule.segment.Segment attribute) attribute (pestifer.tasks.validate.AttributeTest attribute) AttributeTest (class in pestifer.tasks.validate) auth_asym_id (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) auth_atom_id (pestifer.molecule.atom.Atom attribute) auth_comp_id (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) auth_seq_id (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) author_email (pestifer.core.example.Example attribute) author_name (pestifer.core.example.Example attribute) auxiliary_inputs (pestifer.core.example.Example attribute) axis (pestifer.objs.orient.Orient attribute) (pestifer.objs.rottrans.RotTrans attribute) B B (pestifer.psfutil.psftopoelement.PSFTopoElement attribute) b (pestifer.psfutil.psftopoelement.PSFTopoElement attribute) b0 (pestifer.charmmff.charmmffprm.CharmmBondParam attribute) backresolve_lines() (pestifer.util.namdrestart.NAMDConfig method) backup_selection() (pestifer.scripters.vmd.VMDScripter method) bail_out_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) banner() (in module pestifer.util.stringthings) (pestifer.scripters.generic.GenericScripter method) (pestifer.util.stringthings.ByteCollector method) banner_separator (pestifer.logparsers.packmollogparser.PackmolLogParser attribute) BaseObj (class in pestifer.core.baseobj) BaseObjList (class in pestifer.core.baseobj) BaseTask (class in pestifer.tasks.basetask) beta (pestifer.molecule.atom.Atom attribute) Bilayer (class in pestifer.molecule.bilayer) BilayerSpecString (class in pestifer.molecule.bilayer) binnify() (pestifer.core.baseobj.BaseObjList method) BioAssemb (class in pestifer.molecule.bioassemb) BioAssembList (class in pestifer.molecule.bioassemb) biological_assemblies (pestifer.molecule.molecule.Molecule attribute) blockstring (pestifer.charmmff.charmmfftop.CharmmResi attribute) bonds (pestifer.charmmff.charmmffprm.CharmmParamFile attribute) (pestifer.charmmff.charmmfftop.CharmmIC attribute) (pestifer.charmmff.charmmfftop.CharmmResi attribute) (pestifer.psfutil.psfcontents.PSFContents attribute) bounds (pestifer.molecule.stateinterval.StateInterval attribute) build (pestifer.molecule.stateinterval.StateInterval attribute) build_custom() (pestifer.charmmff.pdbrepository.PDBRepository method) build_from_only_pdb_data() (pestifer.molecule.segment.SegmentList method) build_from_psf_and_pdb_data() (pestifer.molecule.segment.SegmentList method) build_from_resources() (pestifer.charmmff.pdbrepository.PDBCollection class method) build_patch() (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) build_tmat() (in module pestifer.util.coord) bury() (pestifer.core.pipeline.PipelineContext method) ByteCollector (class in pestifer.util.stringthings) C CACHE_COMPRESS (pestifer.util.cacheable_object.CacheableObject attribute) CACHE_PREFIX (pestifer.util.cacheable_object.CacheableObject attribute) CacheableObject (class in pestifer.util.cacheable_object) caco_str() (pestifer.molecule.residue.ResidueList method) calculate_stuff() (pestifer.psfutil.psftopoelement.PSFTopoElement method) carbon_component_from_neighbor() (in module pestifer.charmmff.graphhelpers) carbon_neighbors_outside_S() (in module pestifer.charmmff.graphhelpers) card (pestifer.charmmff.charmmfftop.CharmmIC attribute) cell_from_xsc() (in module pestifer.util.util) cell_to_xsc() (in module pestifer.util.util) cellndx_of_ldx() (pestifer.util.linkcell.Linkcell method) cellndx_of_point() (pestifer.util.linkcell.Linkcell method) Cfusion (class in pestifer.objs.cfusion) CfusionList (class in pestifer.objs.cfusion) chainID (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) (pestifer.molecule.segment.Segment attribute) (pestifer.objs.cfusion.Cfusion attribute) (pestifer.objs.cleavagesite.CleavageSite attribute) (pestifer.objs.crot.Crot attribute) (pestifer.objs.deletion.Deletion attribute) (pestifer.objs.graft.Graft attribute) (pestifer.objs.insertion.Insertion attribute) (pestifer.objs.mutation.Mutation attribute) (pestifer.objs.patch.Patch attribute) (pestifer.objs.seqadv.Seqadv attribute) (pestifer.objs.substitution.Substitution attribute) (pestifer.objs.ter.Ter attribute) chainID1 (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) chainID2 (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) ChainIDManager (class in pestifer.molecule.chainidmanager) chainIDmanager (pestifer.molecule.molecule.Molecule attribute) (pestifer.molecule.segment.SegmentList attribute) chainIDmap (pestifer.molecule.transform.Transform attribute) charge (pestifer.charmmff.charmmfftop.CharmmAtom attribute) (pestifer.charmmff.charmmfftop.CharmmResi attribute) (pestifer.molecule.atom.Atom attribute) (pestifer.psfutil.psfatom.PSFAtom attribute) CharmmAngle (class in pestifer.charmmff.charmmfftop) CharmmAngleList (class in pestifer.charmmff.charmmfftop) CharmmAngleParam (class in pestifer.charmmff.charmmffprm) CharmmAtom (class in pestifer.charmmff.charmmfftop) CharmmAtomDict (class in pestifer.charmmff.charmmfftop) CharmmAtomList (class in pestifer.charmmff.charmmfftop) CharmmBond (class in pestifer.charmmff.charmmfftop) CharmmBondList (class in pestifer.charmmff.charmmfftop) CharmmBondParam (class in pestifer.charmmff.charmmffprm) CharmmCMAPParam (class in pestifer.charmmff.charmmffprm) CharmmDelete (class in pestifer.charmmff.charmmfftop) CharmmDeleteList (class in pestifer.charmmff.charmmfftop) CharmmDihedral (class in pestifer.charmmff.charmmfftop) CharmmDihedralList (class in pestifer.charmmff.charmmfftop) CharmmDihedralParam (class in pestifer.charmmff.charmmffprm) charmmff_content (pestifer.core.resourcemanager.ResourceManager property) charmmff_filename (pestifer.charmmff.charmmffcontent.CHARMMFFStreamID attribute) charmmff_filetype() (pestifer.charmmff.charmmffcontent.CHARMMFFContent static method) charmmff_path (pestifer.charmmff.charmmffcontent.CHARMMFFContent attribute) charmmff_version_dirs() (pestifer.core.resourcemanager.ResourceManager method) charmmff_version_key() (in module pestifer.charmmff.charmmffcontent) charmmff_version_path() (pestifer.core.resourcemanager.ResourceManager method) CHARMMFFContent (class in pestifer.charmmff.charmmffcontent) CharmmffFileArtifact (class in pestifer.core.artifacts) CharmmffFileArtifactList (class in pestifer.core.artifacts) CharmmffParFileArtifact (class in pestifer.core.artifacts) CharmmffParFileArtifacts (class in pestifer.core.artifacts) CHARMMFFResiTopCollection (class in pestifer.charmmff.charmmffcontent) CharmmffStreamFileArtifact (class in pestifer.core.artifacts) CharmmffStreamFileArtifacts (class in pestifer.core.artifacts) CHARMMFFStreamID (class in pestifer.charmmff.charmmffcontent) CharmmffTopFileArtifact (class in pestifer.core.artifacts) CharmmffTopFileArtifacts (class in pestifer.core.artifacts) CharmmIC (class in pestifer.charmmff.charmmfftop) CharmmICList (class in pestifer.charmmff.charmmfftop) CharmmImproperParam (class in pestifer.charmmff.charmmffprm) CharmmMass (class in pestifer.charmmff.charmmfftop) CharmmMassDict (class in pestifer.charmmff.charmmfftop) CharmmMassList (class in pestifer.charmmff.charmmfftop) CharmmNBFixParam (class in pestifer.charmmff.charmmffprm) CharmmNonbondedParam (class in pestifer.charmmff.charmmffprm) CharmmParamFile (class in pestifer.charmmff.charmmffprm) CharmmResi (class in pestifer.charmmff.charmmfftop) CharmmResiDict (class in pestifer.charmmff.charmmfftop) CharmmResiList (class in pestifer.charmmff.charmmfftop) check() (pestifer.molecule.chainidmanager.ChainIDManager method) check_packmol_version() (in module pestifer.scripters.packmol) checkin_example() (pestifer.core.examplemanager.ExampleManager method) checkout() (pestifer.charmmff.pdbrepository.PDBCollection method) (pestifer.charmmff.pdbrepository.PDBRepository method) checkout_example() (pestifer.core.examplemanager.ExampleManager method) checkout_pdb() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) cif_residue_map() (pestifer.molecule.residue.ResidueList method) CIFdict (class in pestifer.util.cifutil) CIFFileArtifact (class in pestifer.core.artifacts) CIFload() (in module pestifer.util.cifutil) clean_local_charmmff_files() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) cleanup() (pestifer.scripters.vmd.VMDScripter method) (pestifer.tasks.terminate.TerminateTask method) clear() (pestifer.core.artifacts.ArtifactDict method) CleavageSite (class in pestifer.objs.cleavagesite) CleavageSiteList (class in pestifer.objs.cleavagesite) cleave() (pestifer.molecule.segment.Segment method) cleave_chains() (pestifer.molecule.molecule.Molecule method) CleaveTask (class in pestifer.tasks.cleave) cli() (in module pestifer.cli.pestifer) clone() (pestifer.core.examplemanager.ExampleManager method) cmaps (pestifer.charmmff.charmmffprm.CharmmParamFile attribute) collect_residues() (pestifer.molecule.segment.SegmentList method) collect_validation_results() (pestifer.logparsers.logparser.VMDLogParser method) com (pestifer.charmmff.charmmfftop.CharmmMass attribute) COM (pestifer.psfutil.psftopoelement.PSFTopoElement attribute) Command (class in pestifer.core.command) commands (pestifer.psfutil.psfcontents.PSFSegment attribute) comment (pestifer.charmmff.charmmffprm.CharmmAngleParam attribute) (pestifer.charmmff.charmmffprm.CharmmBondParam attribute) (pestifer.charmmff.charmmffprm.CharmmCMAPParam attribute) (pestifer.charmmff.charmmffprm.CharmmDihedralParam attribute) (pestifer.charmmff.charmmffprm.CharmmImproperParam attribute) (pestifer.charmmff.charmmffprm.CharmmNBFixParam attribute) (pestifer.charmmff.charmmffprm.CharmmNonbondedParam attribute) (pestifer.charmmff.charmmfftop.CharmmDelete attribute) comment() (pestifer.scripters.generic.GenericScripter method) (pestifer.util.stringthings.ByteCollector method) compare() (pestifer.core.artifacts.FileArtifact method) (pestifer.core.artifacts.NAMDConfigFileArtifact method) (pestifer.core.artifacts.PDBFileArtifact method) (pestifer.core.artifacts.PSFFileArtifact method) compression (pestifer.util.cacheable_object.TarBytesFS attribute) Config (class in pestifer.core.config) ConfigDefaultSubcommand (class in pestifer.subcommands.config_default) ConfigHelpSubcommand (class in pestifer.subcommands.config_help) configure() (pestifer.core.config.Config method) (pestifer.core.controller.Controller method) configure_new() (pestifer.core.config.Config method) connect() (pestifer.tasks.ligate.LigateTask method) connect_gaps() (pestifer.tasks.ligate.LigateTask method) connection_count (pestifer.tasks.validate.ConnectionTest attribute) connection_type (pestifer.tasks.validate.ConnectionTest attribute) connection_type_supported (pestifer.tasks.validate.ConnectionTest attribute) ConnectionTest (class in pestifer.tasks.validate) consolidate_params() (pestifer.scripters.namd.NAMDScripter method) construct_on_pdb() (pestifer.scripters.namd_colvar_input.NAMDColvarInputScripter method) contents (pestifer.charmmff.pdbrepository.PDBCollection attribute) context_to_string() (pestifer.core.pipeline.PipelineContext method) ContinuationTask (class in pestifer.tasks.continuation) Controller (class in pestifer.core.controller) controller_index (pestifer.core.pipeline.PipelineContext attribute) coor (pestifer.core.artifacts.StateArtifacts attribute) coor_to_pdb() (pestifer.tasks.basetask.VMDTask method) coorddf_from_pdb() (in module pestifer.util.coord) coormods() (pestifer.tasks.manipulate.ManipulateTask method) (pestifer.tasks.psfgen.PsfgenTask method) copy() (pestifer.core.artifacts.Artifact method) (pestifer.core.baseobj.BaseObj method) (pestifer.psfutil.psftopoelement.PSFTopoElement method) copy_attr() (pestifer.core.baseobj.BaseObj method) copy_charmmfile_local() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) copy_from() (pestifer.core.examplemanager.ExampleManager method) copy_ICs_from() (pestifer.charmmff.charmmfftop.CharmmResi method) copy_state_to_basename() (pestifer.tasks.terminate.TerminateTask method) count_unsats_cc() (in module pestifer.charmmff.graphhelpers) counts_by_header() (pestifer.core.objmanager.ObjManager method) countTime() (in module pestifer.util.util) Crot (class in pestifer.objs.crot) CrotList (class in pestifer.objs.crot) CSVDataFileArtifact (class in pestifer.core.artifacts) CSVDataFileArtifactList (class in pestifer.core.artifacts) cuA_of_nmolec() (in module pestifer.util.units) cycle_atoms_heavy() (in module pestifer.charmmff.graphhelpers) D data (pestifer.charmmff.charmmffprm.CharmmCMAPParam attribute) (pestifer.charmmff.charmmfftop.CharmmAngleList attribute) (pestifer.charmmff.charmmfftop.CharmmBondList attribute) (pestifer.charmmff.charmmfftop.CharmmDihedralList attribute) (pestifer.charmmff.charmmfftop.CharmmMassDict attribute) (pestifer.core.artifacts.Artifact attribute) (pestifer.core.artifacts.FileArtifact attribute) (pestifer.psfutil.psfremark.PSFPatchRemark attribute) (pestifer.psfutil.psfremark.PSFRemark attribute) DataArtifact (class in pestifer.core.artifacts) database (pestifer.objs.seqadv.Seqadv attribute) DataFileArtifact (class in pestifer.core.artifacts) DataFileArtifactList (class in pestifer.core.artifacts) dataframe (pestifer.logparsers.namdlogparser.NAMDxstParser attribute) db_id (pestifer.core.example.Example attribute) dbAccession (pestifer.objs.seqadv.Seqadv attribute) dbRes (pestifer.objs.seqadv.Seqadv attribute) dbSeq (pestifer.objs.seqadv.Seqadv attribute) declare_buildable() (pestifer.molecule.stateinterval.StateInterval method) declare_distance_cv() (pestifer.scripters.namd_colvar_input.NAMDColvarInputScripter method) declare_distance_cv_atoms() (pestifer.scripters.namd_colvar_input.NAMDColvarInputScripter method) declare_harmonic_distance_biases() (pestifer.scripters.namd_colvar_input.NAMDColvarInputScripter method) declare_single_harmonic_distance_bias() (pestifer.scripters.namd_colvar_input.NAMDColvarInputScripter method) declash() (pestifer.tasks.psfgen.PsfgenTask method) declash_glycans() (pestifer.tasks.psfgen.PsfgenTask method) declash_na_loops() (pestifer.tasks.psfgen.PsfgenTask method) declash_protein_loops() (pestifer.tasks.psfgen.PsfgenTask method) declash_segtype() (pestifer.tasks.psfgen.PsfgenTask method) default_etitle_npt (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) default_etitle_nvt (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) degree (pestifer.charmmff.charmmfftop.CharmmBond attribute) degrees (pestifer.charmmff.charmmfftop.CharmmAngle attribute) (pestifer.charmmff.charmmfftop.CharmmDihedral attribute) (pestifer.objs.crot.Crot attribute) Delete (pestifer.charmmff.charmmfftop.CharmmResi attribute) delete_example() (pestifer.core.examplemanager.ExampleManager method) (pestifer.core.resourcemanager.ResourceManager method) (pestifer.sphinxext.sphinx_examplemanager.SphinxExampleManager method) Deletion (class in pestifer.objs.deletion) deletion() (pestifer.molecule.residue.ResidueList method) DeletionList (class in pestifer.objs.deletion) deletions (pestifer.molecule.segment.Segment attribute) delta (pestifer.charmmff.charmmffprm.CharmmDihedralParam attribute) deprovision() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) describe() (pestifer.core.baseobj.BaseObjList method) (pestifer.core.example.ExampleList method) (pestifer.molecule.asymmetricunit.AsymmetricUnit method) (pestifer.molecule.atom.AtomList method) (pestifer.molecule.residue.ResidueList method) (pestifer.molecule.residue.ResiduePlaceholderList method) (pestifer.molecule.segment.SegmentList method) (pestifer.molecule.stateinterval.StateIntervalList method) (pestifer.molecule.transform.TransformList method) (pestifer.objs.align.AlignList method) (pestifer.objs.cfusion.CfusionList method) (pestifer.objs.cleavagesite.CleavageSiteList method) (pestifer.objs.crot.CrotList method) (pestifer.objs.deletion.DeletionList method) (pestifer.objs.graft.GraftList method) (pestifer.objs.insertion.InsertionList method) (pestifer.objs.link.LinkList method) (pestifer.objs.mutation.MutationList method) (pestifer.objs.orient.OrientList method) (pestifer.objs.patch.PatchList method) (pestifer.objs.resid.ResIDList method) (pestifer.objs.rottrans.RotTransList method) (pestifer.objs.seqadv.SeqadvList method) (pestifer.objs.ssbond.SSBondList method) (pestifer.objs.substitution.SubstitutionList method) (pestifer.objs.ter.TerList method) (pestifer.objs.transfer_coords.TransferCoordsList method) (pestifer.psfutil.psfatom.PSFAtomList method) describe_molecule() (pestifer.scripters.psfgen.PsfgenScripter method) description (pestifer.core.artifacts.CharmmffFileArtifact attribute) (pestifer.core.artifacts.CharmmffFileArtifactList attribute) (pestifer.core.artifacts.CharmmffParFileArtifact attribute) (pestifer.core.artifacts.CharmmffParFileArtifacts attribute) (pestifer.core.artifacts.CharmmffStreamFileArtifact attribute) (pestifer.core.artifacts.CharmmffStreamFileArtifacts attribute) (pestifer.core.artifacts.CharmmffTopFileArtifact attribute) (pestifer.core.artifacts.CharmmffTopFileArtifacts attribute) (pestifer.core.artifacts.CIFFileArtifact attribute) (pestifer.core.artifacts.CSVDataFileArtifact attribute) (pestifer.core.artifacts.CSVDataFileArtifactList attribute) (pestifer.core.artifacts.DataArtifact attribute) (pestifer.core.artifacts.DataFileArtifact attribute) (pestifer.core.artifacts.DataFileArtifactList attribute) (pestifer.core.artifacts.FileArtifact attribute) (pestifer.core.artifacts.InputFileArtifact attribute) (pestifer.core.artifacts.JSONFileArtifact attribute) (pestifer.core.artifacts.LogFileArtifact attribute) (pestifer.core.artifacts.LogFileArtifactList attribute) (pestifer.core.artifacts.NAMDColvarsConfigArtifact attribute) (pestifer.core.artifacts.NAMDColvarsStateArtifact attribute) (pestifer.core.artifacts.NAMDColvarsTrajectoryArtifact attribute) (pestifer.core.artifacts.NAMDConfigFileArtifact attribute) (pestifer.core.artifacts.NAMDCoorFileArtifact attribute) (pestifer.core.artifacts.NAMDCoorFileArtifactList attribute) (pestifer.core.artifacts.NAMDDcdFileArtifact attribute) (pestifer.core.artifacts.NAMDExtraBondsFileArtifact attribute) (pestifer.core.artifacts.NAMDLogFileArtifact attribute) (pestifer.core.artifacts.NAMDLogFileArtifactList attribute) (pestifer.core.artifacts.NAMDOutputFileArtifact attribute) (pestifer.core.artifacts.NAMDOutputFileArtifactList attribute) (pestifer.core.artifacts.NAMDVelFileArtifact attribute) (pestifer.core.artifacts.NAMDXscFileArtifact attribute) (pestifer.core.artifacts.NAMDXstFileArtifact attribute) (pestifer.core.artifacts.PackmolInputScriptArtifact attribute) (pestifer.core.artifacts.PackmolLogFileArtifact attribute) (pestifer.core.artifacts.PackMolPDBForcedFileArtifact attribute) (pestifer.core.artifacts.PDBFileArtifact attribute) (pestifer.core.artifacts.PDBFileArtifactList attribute) (pestifer.core.artifacts.PNGImageFileArtifact attribute) (pestifer.core.artifacts.PNGImageFileArtifactList attribute) (pestifer.core.artifacts.PQRFileArtifact attribute) (pestifer.core.artifacts.PSFFileArtifact attribute) (pestifer.core.artifacts.PSFFileArtifactList attribute) (pestifer.core.artifacts.PsfgenInputScriptArtifact attribute) (pestifer.core.artifacts.PsfgenLogFileArtifact attribute) (pestifer.core.artifacts.StateArtifacts attribute) (pestifer.core.artifacts.TclScriptArtifact attribute) (pestifer.core.artifacts.TXTFileArtifact attribute) (pestifer.core.artifacts.VMDLogFileArtifact attribute) (pestifer.core.artifacts.VMDScriptArtifact attribute) (pestifer.core.artifacts.YAMLFileArtifact attribute) DesolvateSubcommand (class in pestifer.subcommands.desolvate) DesolvateTask (class in pestifer.tasks.desolvate) detect_common_prefix() (in module pestifer.sphinxext.toctree_util) detergent_annotate() (pestifer.charmmff.charmmfftop.CharmmResi method) dict_to_condition() (pestifer.core.baseobj.BaseObjList static method) diff() (pestifer.core.artifacts.FileArtifact method) dihedral (pestifer.charmmff.charmmfftop.CharmmIC attribute) dihedral_type (pestifer.charmmff.charmmfftop.CharmmDihedral attribute) (pestifer.charmmff.charmmfftop.CharmmIC attribute) dihedrals (pestifer.charmmff.charmmffprm.CharmmParamFile attribute) (pestifer.psfutil.psfcontents.PSFContents attribute) divider_line_length (pestifer.core.command.Command attribute) do() (pestifer.tasks.basetask.BaseTask method) (pestifer.tasks.cleave.CleaveTask method) (pestifer.tasks.continuation.ContinuationTask method) (pestifer.tasks.desolvate.DesolvateTask method) (pestifer.tasks.domainswap.DomainSwapTask method) (pestifer.tasks.fetch.FetchTask method) (pestifer.tasks.ligate.LigateTask method) (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) (pestifer.tasks.manipulate.ManipulateTask method) (pestifer.tasks.mdplot.MDPlotTask method) (pestifer.tasks.mdtask.MDTask method) (pestifer.tasks.merge.MergeTask method) (pestifer.tasks.pdb2pqr.PDB2PQRTask method) (pestifer.tasks.psfgen.PsfgenTask method) (pestifer.tasks.pytest_buildterminate.Pytest_BuildTerminateTask method) (pestifer.tasks.ringcheck.RingCheckTask method) (pestifer.tasks.solvate.SolvateTask method) (pestifer.tasks.terminate.TerminateTask method) (pestifer.tasks.validate.ValidateTask method) do_cleanup() (in module pestifer.charmmff.make_pdb_collection) do_dcd_prune() (pestifer.tasks.desolvate.DesolvateTask method) do_deletions() (pestifer.molecule.residue.ResidueList method) do_idx_psf_gen() (pestifer.tasks.desolvate.DesolvateTask method) do_psfgen() (in module pestifer.charmmff.make_pdb_collection) (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) do_resi() (in module pestifer.charmmff.make_pdb_collection) do_steered_md() (pestifer.tasks.ligate.LigateTask method) do_tasks() (pestifer.core.controller.Controller method) docs_source_path (pestifer.sphinxext.sphinx_examplemanager.SphinxExampleManager attribute) DomainSwapTask (class in pestifer.tasks.domainswap) donor_external_links (pestifer.objs.graft.Graft attribute) donor_internal_links (pestifer.objs.graft.Graft attribute) donor_pdb (pestifer.objs.transfer_coords.TransferCoords attribute) donor_psf (pestifer.objs.transfer_coords.TransferCoords attribute) donor_residues (pestifer.objs.graft.Graft attribute) donor_sel (pestifer.objs.transfer_coords.TransferCoords attribute) down (pestifer.molecule.residue.Residue attribute) downlink (pestifer.molecule.residue.Residue attribute) dump() (pestifer.core.baseobj.BaseObj method) (pestifer.logparsers.logparser.LogParser method) E effective_ref_pdb (pestifer.objs.align.Align property) elem (pestifer.molecule.atom.Atom attribute) elem() (in module pestifer.charmmff.graphhelpers) element (pestifer.charmmff.charmmfftop.CharmmAtom attribute) embed_protein() (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) Emin (pestifer.charmmff.charmmffprm.CharmmNBFixParam attribute) empty (pestifer.charmmff.charmmfftop.CharmmIC attribute) (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) (pestifer.objs.link.Link attribute) enable_progress_bar() (pestifer.logparsers.logparser.LogParser method) energy_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) epsilon (pestifer.charmmff.charmmffprm.CharmmNonbondedParam attribute) epsilon14 (pestifer.charmmff.charmmffprm.CharmmNonbondedParam attribute) equilibrate_bilayer() (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) error_code (pestifer.charmmff.charmmfftop.CharmmDelete attribute) (pestifer.charmmff.charmmfftop.CharmmResi attribute) etitle_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) Example (class in pestifer.core.example) example_footer() (in module pestifer.util.stringthings) example_id (pestifer.core.example.Example attribute) example_manager (pestifer.core.resourcemanager.ResourceManager property) examplefolderpath() (pestifer.core.examplemanager.ExampleManager method) ExampleList (class in pestifer.core.example) ExampleManager (class in pestifer.core.examplemanager) execute() (pestifer.tasks.basetask.BaseTask method) exists() (pestifer.core.artifacts.FileArtifact method) expel() (pestifer.core.objmanager.ObjManager method) ext (pestifer.core.artifacts.CharmmffParFileArtifact attribute) (pestifer.core.artifacts.CharmmffStreamFileArtifact attribute) (pestifer.core.artifacts.CharmmffTopFileArtifact attribute) (pestifer.core.artifacts.CIFFileArtifact attribute) (pestifer.core.artifacts.CSVDataFileArtifact attribute) (pestifer.core.artifacts.DataFileArtifact attribute) (pestifer.core.artifacts.FileArtifact property) (pestifer.core.artifacts.InputFileArtifact attribute) (pestifer.core.artifacts.JSONFileArtifact attribute) (pestifer.core.artifacts.LogFileArtifact attribute) (pestifer.core.artifacts.NAMDColvarsConfigArtifact attribute) (pestifer.core.artifacts.NAMDColvarsStateArtifact attribute) (pestifer.core.artifacts.NAMDColvarsTrajectoryArtifact attribute) (pestifer.core.artifacts.NAMDConfigFileArtifact attribute) (pestifer.core.artifacts.NAMDCoorFileArtifact attribute) (pestifer.core.artifacts.NAMDDcdFileArtifact attribute) (pestifer.core.artifacts.NAMDExtraBondsFileArtifact attribute) (pestifer.core.artifacts.NAMDVelFileArtifact attribute) (pestifer.core.artifacts.NAMDXscFileArtifact attribute) (pestifer.core.artifacts.NAMDXstFileArtifact attribute) (pestifer.core.artifacts.PackmolInputScriptArtifact attribute) (pestifer.core.artifacts.PackMolPDBForcedFileArtifact attribute) (pestifer.core.artifacts.PDBFileArtifact attribute) (pestifer.core.artifacts.PNGImageFileArtifact attribute) (pestifer.core.artifacts.PQRFileArtifact attribute) (pestifer.core.artifacts.PSFFileArtifact attribute) (pestifer.core.artifacts.TclScriptArtifact attribute) (pestifer.core.artifacts.TXTFileArtifact attribute) (pestifer.core.artifacts.YAMLFileArtifact attribute) extend() (pestifer.core.artifacts.ArtifactList method) (pestifer.core.artifacts.CharmmffFileArtifactList method) (pestifer.core.baseobj.BaseObjList method) extract() (pestifer.util.formatvalidator.FormatValidator method) extract_changelog_from_readme() (in module pestifer.util.readme_to_changelog_with_dates) extract_for_atomtypes() (pestifer.charmmff.charmmffprm.CharmmParamFile method) extract_from_format() (in module pestifer.util.formatvalidator) extract_mass_lines() (in module pestifer.charmmff.charmmffcontent) extract_resi_pres_blocks() (in module pestifer.charmmff.charmmffcontent) F failures (pestifer.charmmff.ligand_paramgen.orchestrator.LigandGenSummary attribute) fetch_ligand_smiles() (in module pestifer.charmmff.ligand_paramgen) (in module pestifer.charmmff.ligand_paramgen.rcsb) fetch_or_load_pdb() (in module pestifer.charmmff.ligand_paramgen.orchestrator) fetch_standard_charmm_parameters() (pestifer.scripters.namd.NAMDScripter method) fetch_standard_charmm_topologies() (pestifer.scripters.psfgen.PsfgenScripter method) FetchExampleSubcommand (class in pestifer.subcommands.fetch_example) FetchTask (class in pestifer.tasks.fetch) FileArtifact (class in pestifer.core.artifacts) FileArtifactDict (class in pestifer.core.artifacts) FileArtifactList (class in pestifer.core.artifacts) FileCollector (class in pestifer.util.stringthings) filenamemap (pestifer.charmmff.charmmffcontent.CHARMMFFContent attribute) filter() (pestifer.core.baseobj.BaseObjList method) filter_by_artifact_type() (pestifer.core.artifacts.ArtifactList method) filter_by_key() (pestifer.core.artifacts.ArtifactList method) filter_by_produced_by() (pestifer.core.artifacts.ArtifactDict method) (pestifer.core.artifacts.ArtifactList method) filter_copy() (pestifer.core.objmanager.ObjManager method) finalize() (pestifer.logparsers.namdlogparser.NAMDLogParser method) (pestifer.logparsers.packmollogparser.PackmolLogParser method) (pestifer.logparsers.pdb2pqrlogparser.PDB2PQRLogParser method) find_resis_and_patches() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) find_toctree_block() (in module pestifer.sphinxext.toctree_util) find_unknown_ligand_residues() (in module pestifer.charmmff.ligand_paramgen.orchestrator) finish() (pestifer.util.progress.PestiferProgress method) flatten() (in module pestifer.util.util) flush() (pestifer.util.stringthings.FileCollector method) folder_name_format (pestifer.core.example.Example attribute) follow() (pestifer.logparsers.logparser.LogParser method) FollowNAMDLogSubcommand (class in pestifer.subcommands.follow_namd_log) FormatValidator (class in pestifer.util.formatvalidator) formula() (pestifer.charmmff.charmmfftop.CharmmResi method) from_blockstring() (pestifer.charmmff.charmmfftop.CharmmResi class method) from_blockstring_list() (pestifer.charmmff.charmmfftop.CharmmResiDict class method) (pestifer.charmmff.charmmfftop.CharmmResiList class method) from_card() (pestifer.charmmff.charmmfftop.CharmmAngleList class method) (pestifer.charmmff.charmmfftop.CharmmAtom class method) (pestifer.charmmff.charmmfftop.CharmmBondList class method) (pestifer.charmmff.charmmfftop.CharmmDelete class method) (pestifer.charmmff.charmmfftop.CharmmDihedralList class method) (pestifer.charmmff.charmmfftop.CharmmIC class method) (pestifer.charmmff.charmmfftop.CharmmMass class method) from_cardlist() (pestifer.charmmff.charmmfftop.CharmmMassList class method) from_cif() (pestifer.molecule.atom.AtomList class method) (pestifer.molecule.residue.ResiduePlaceholderList class method) (pestifer.objs.link.LinkList class method) (pestifer.objs.seqadv.SeqadvList class method) (pestifer.objs.ssbond.SSBondList class method) from_data_container() (pestifer.molecule.bioassemb.BioAssembList static method) from_dict() (pestifer.charmmff.charmmfftop.CharmmAtomList method) (pestifer.charmmff.charmmfftop.CharmmMassList method) (pestifer.charmmff.charmmfftop.CharmmResiDict method) (pestifer.charmmff.charmmfftop.CharmmResiList method) (pestifer.core.artifacts.ArtifactList class method) from_file() (pestifer.charmmff.charmmffprm.CharmmParamFile class method) (pestifer.logparsers.logparser.VMDLogParser class method) (pestifer.logparsers.namdlogparser.NAMDLogParser class method) (pestifer.logparsers.namdlogparser.NAMDxstParser class method) (pestifer.util.cacheable_object.TarBytesFS class method) from_list() (pestifer.charmmff.charmmfftop.CharmmAtomDict method) (pestifer.charmmff.charmmfftop.CharmmMassDict method) (pestifer.core.artifacts.ArtifactDict class method) from_list_of_dicts() (pestifer.core.example.ExampleList class method) from_pdb() (pestifer.molecule.atom.AtomList class method) (pestifer.molecule.residue.ResiduePlaceholderList class method) (pestifer.objs.link.LinkList class method) (pestifer.objs.seqadv.SeqadvList class method) (pestifer.objs.ssbond.SSBondList class method) (pestifer.objs.ter.TerList class method) from_pdb_record_dict() (pestifer.molecule.bioassemb.BioAssembList static method) from_remarkline() (pestifer.psfutil.psfremark.PSFRemark class method) from_residuegrouped_atomlist() (pestifer.molecule.residue.ResidueList class method) from_ResiduePlaceholderlist() (pestifer.molecule.residue.ResidueList class method) from_text() (pestifer.charmmff.charmmffprm.CharmmParamFile class method) from_yaml() (pestifer.core.example.ExampleList method) (pestifer.tasks.taskcollections.TaskList class method) fs() (pestifer.util.cacheable_object.TarBytesFS method) fullmatch() (pestifer.util.formatvalidator.FormatValidator method) func() (pestifer.cli.subcommand.Subcommand static method) (pestifer.subcommands.build.RunSubcommand static method) (pestifer.subcommands.build_example.RunExampleSubcommand static method) (pestifer.subcommands.config_default.ConfigDefaultSubcommand static method) (pestifer.subcommands.config_help.ConfigHelpSubcommand static method) (pestifer.subcommands.desolvate.DesolvateSubcommand static method) (pestifer.subcommands.fetch_example.FetchExampleSubcommand static method) (pestifer.subcommands.follow_namd_log.FollowNAMDLogSubcommand static method) (pestifer.subcommands.make_ligand_mol2.MakeLigandMol2Subcommand static method) (pestifer.subcommands.make_namd_restart.MakeNAMDRestartSubcommand static method) (pestifer.subcommands.make_pdbcollection.MakePDBCollectionSubcommand static method) (pestifer.subcommands.mdplot.MDPlotSubcommand static method) (pestifer.subcommands.modify_package.ModifyPackageSubcommand static method) (pestifer.subcommands.new_system.NewSystemSubcommand static method) (pestifer.subcommands.rebuild_charmmff_cache.RebuildCHARMMFFCache static method) (pestifer.subcommands.setup_vmd.SetupVMDSubcommand static method) (pestifer.subcommands.show_resources.ShowResourcesSubcommand static method) (pestifer.subcommands.wheretcl.WhereTCLSubcommand static method) func_returns_type (pestifer.cli.subcommand.Subcommand attribute) (pestifer.subcommands.build.RunSubcommand attribute) (pestifer.subcommands.build_example.RunExampleSubcommand attribute) (pestifer.subcommands.desolvate.DesolvateSubcommand attribute) (pestifer.subcommands.fetch_example.FetchExampleSubcommand attribute) (pestifer.subcommands.make_ligand_mol2.MakeLigandMol2Subcommand attribute) (pestifer.subcommands.mdplot.MDPlotSubcommand attribute) G generate_chainIDmap() (pestifer.molecule.transform.Transform method) generate_from_residues() (pestifer.molecule.segment.SegmentList method) generate_ligand_mol2s() (in module pestifer.charmmff.ligand_paramgen.orchestrator) generate_minimal_params() (pestifer.tasks.terminate.TerminateTask method) generate_next_map() (pestifer.molecule.chainidmanager.ChainIDManager method) generic_lipid_annotate() (pestifer.charmmff.charmmfftop.CharmmResi method) GenericListMeta (class in pestifer.core.baseobj) GenericScripter (class in pestifer.scripters.generic) get() (pestifer.core.artifacts.ArtifactDict method) (pestifer.core.baseobj.BaseObjList method) (pestifer.molecule.bioassemb.BioAssembList method) (pestifer.psfutil.psftopoelement.PSFTopoElementList method) get_all_file_artifacts() (pestifer.core.pipeline.PipelineContext method) get_artifact_series_by_key() (pestifer.core.pipeline.PipelineContext method) get_atom() (pestifer.charmmff.charmmfftop.CharmmAtomList method) get_chainmaps() (pestifer.molecule.molecule.Molecule method) get_charge() (pestifer.charmmff.pdbrepository.PDBInput method) (pestifer.psfutil.psfcontents.PSFContents method) get_charmmff_customdir() (pestifer.core.resourcemanager.ResourceManager method) get_conformer_data() (pestifer.charmmff.pdbrepository.PDBInput method) get_current_artifact() (pestifer.core.pipeline.PipelineContext method) (pestifer.tasks.basetask.BaseTask method) get_current_artifact_data() (pestifer.core.pipeline.PipelineContext method) (pestifer.tasks.basetask.BaseTask method) get_current_artifact_path() (pestifer.tasks.basetask.BaseTask method) get_down_group() (pestifer.molecule.residue.Residue method) get_element() (pestifer.charmmff.charmmfftop.CharmmAtomList method) get_example_by_example_id() (pestifer.core.example.ExampleList method) get_example_by_shortname() (pestifer.core.example.ExampleList method) get_filename() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) get_git_origin_url() (in module pestifer.util.gitutil) get_git_tag_dates() (in module pestifer.util.readme_to_changelog_with_dates) get_head_tail_length() (pestifer.charmmff.pdbrepository.PDBInput method) get_mass() (pestifer.charmmff.charmmfftop.CharmmAtomList method) get_mass_of_member() (pestifer.charmmff.charmmfftop.CharmmAtomList method) get_max_internal_length() (pestifer.charmmff.pdbrepository.PDBInput method) get_my_artifactfile_collection() (pestifer.tasks.basetask.BaseTask method) get_name_from_toctree() (in module pestifer.sphinxext.toctree_util) get_num_entries_in_toctree() (in module pestifer.sphinxext.toctree_util) get_packmol_version() (in module pestifer.scripters.packmol) get_parameters() (pestifer.charmmff.pdbrepository.PDBInput method) get_patchremarks() (pestifer.psfutil.psfremark.PSFRemarkList method) get_pdb() (pestifer.charmmff.pdbrepository.PDBInput method) get_pres() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) get_pypi_release_dates() (in module pestifer.util.readme_to_changelog_with_dates) get_ref_atoms() (pestifer.charmmff.pdbrepository.PDBInput method) get_resi() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) get_residue() (pestifer.charmmff.charmmfftop.CharmmResiDict method) get_residue_to_segname_map() (pestifer.molecule.segment.SegmentList method) get_resnames_of_streamID() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) get_resource_path() (pestifer.core.resourcemanager.ResourceManager method) get_scripter() (pestifer.core.config.Config method) (pestifer.tasks.basetask.BaseTask method) get_segment_of_residue() (pestifer.molecule.segment.SegmentList method) get_segmentremarks() (pestifer.psfutil.psfremark.PSFRemarkList method) get_serial() (pestifer.charmmff.charmmfftop.CharmmAtomList method) get_single() (in module pestifer.logparsers.logparser) get_state_artifact() (pestifer.core.pipeline.PipelineContext method) get_tcl_pkgdir() (pestifer.core.resourcemanager.ResourceManager method) get_tcl_scriptsdir() (pestifer.core.resourcemanager.ResourceManager method) get_tcldir() (pestifer.core.resourcemanager.ResourceManager method) get_toeol() (in module pestifer.logparsers.logparser) get_toflag() (in module pestifer.logparsers.logparser) get_tokens() (in module pestifer.logparsers.logparser) get_topfile_of_resname() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) get_toporemarks() (pestifer.psfutil.psfremark.PSFRemarkList method) get_toppar_from_psf() (in module pestifer.psfutil.psfcontents) get_values() (in module pestifer.logparsers.logparser) give_item() (pestifer.core.baseobj.BaseObjList method) glycan_segment_parents (pestifer.molecule.segment.SegmentList attribute) go() (pestifer.util.progress.PestiferProgress method) Graft (class in pestifer.objs.graft) graft_residues (pestifer.objs.graft.Graft attribute) graft_segname (pestifer.objs.graft.Graft attribute) GraftList (class in pestifer.objs.graft) grafts (pestifer.molecule.segment.Segment attribute) graph() (pestifer.psfutil.psfatom.PSFAtomList method) grid_size (pestifer.charmmff.charmmffprm.CharmmCMAPParam attribute) H has_content (pestifer.sphinxext.task_table.TaskTableDirective attribute) (pestifer.sphinxext.tclscript.TclScriptDirective attribute) has_serials() (pestifer.objs.ter.TerList method) has_stamp() (pestifer.core.artifacts.Artifact method) has_statement() (pestifer.scripters.generic.GenericScripter method) (pestifer.util.stringthings.ByteCollector method) head (pestifer.core.pipeline.PipelineContext attribute) head_tail_pairs() (in module pestifer.charmmff.graphhelpers) heavy_degree() (in module pestifer.charmmff.graphhelpers) heavy_neighbors() (in module pestifer.charmmff.graphhelpers) heavy_only_nodes() (in module pestifer.charmmff.graphhelpers) Hetatm (class in pestifer.molecule.atom) history (pestifer.core.pipeline.PipelineContext attribute) history_to_string() (pestifer.core.pipeline.PipelineContext method) hms() (in module pestifer.util.util) hmsf() (in module pestifer.util.util) hue() (pestifer.util.colors.PestiferColorMap method) I ic_reference_closest() (in module pestifer.objs.link) ICs (pestifer.charmmff.charmmfftop.CharmmResi attribute) idCode (pestifer.objs.seqadv.Seqadv attribute) identity() (pestifer.molecule.transform.Transform class method) (pestifer.molecule.transform.TransformList class method) ifilter() (pestifer.core.baseobj.BaseObjList method) iget() (pestifer.core.baseobj.BaseObjList method) ignored (pestifer.charmmff.charmmffprm.CharmmNonbondedParam attribute) ignored14 (pestifer.charmmff.charmmffprm.CharmmNonbondedParam attribute) import_artifacts() (pestifer.core.pipeline.PipelineContext method) (pestifer.tasks.basetask.BaseTask method) impropers (pestifer.charmmff.charmmffprm.CharmmParamFile attribute) increment() (pestifer.objs.resid.ResID method) increment_rightbound() (pestifer.molecule.stateinterval.StateInterval method) index (pestifer.molecule.bioassemb.BioAssemb attribute) (pestifer.molecule.transform.Transform attribute) index_internal_links (pestifer.objs.graft.Graft attribute) index_residues (pestifer.objs.graft.Graft attribute) info (pestifer.charmmff.pdbrepository.PDBCollection attribute) (pestifer.charmmff.pdbrepository.PDBInput attribute) info_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) info_keys (pestifer.logparsers.psfgenlogparser.PsfgenLogParser attribute) ingest() (pestifer.core.objmanager.ObjManager method) ingest_coordinates() (pestifer.psfutil.psftopoelement.PSFTopoElement method) (pestifer.psfutil.psftopoelement.PSFTopoElementList method) ingest_file() (pestifer.scripters.generic.GenericScripter method) (pestifer.util.stringthings.ByteCollector method) ingest_grafts() (pestifer.molecule.asymmetricunit.AsymmetricUnit method) ingest_molecules() (pestifer.tasks.psfgen.PsfgenTask method) inherit_objs() (pestifer.molecule.segment.SegmentList method) initialize() (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) inlist() (pestifer.core.baseobj.BaseObj method) inpatch (pestifer.charmmff.charmmfftop.CharmmAtom attribute) input (pestifer.core.example.Example attribute) InputFileArtifact (class in pestifer.core.artifacts) inputs_subdir (pestifer.core.example.Example attribute) inputspath (pestifer.core.example.Example property) inputspath() (pestifer.core.examplemanager.ExampleManager method) insert() (pestifer.core.baseobj.BaseObjList method) Insertion (class in pestifer.objs.insertion) insertion (pestifer.objs.resid.ResID attribute) InsertionList (class in pestifer.objs.insertion) integer_increment (pestifer.objs.insertion.Insertion attribute) is_C() (in module pestifer.charmmff.graphhelpers) is_deleted() (pestifer.objs.ssbonddelete.SSBondDeleteList method) is_H() (in module pestifer.charmmff.graphhelpers) is_identity() (pestifer.molecule.transform.Transform method) is_N() (in module pestifer.charmmff.graphhelpers) is_O() (in module pestifer.charmmff.graphhelpers) is_P() (in module pestifer.charmmff.graphhelpers) is_pep() (pestifer.psfutil.psfatom.PSFAtom method) is_periodic() (in module pestifer.util.util) is_provisioned (pestifer.tasks.basetask.BaseTask property) is_root (pestifer.psfutil.psfatom.PSFAtom attribute) is_S() (in module pestifer.charmmff.graphhelpers) isH() (pestifer.psfutil.psfatom.PSFAtom method) ispatch (pestifer.charmmff.charmmfftop.CharmmResi attribute) items() (pestifer.core.artifacts.ArtifactDict method) J join_ri() (pestifer.objs.resid.ResID static method) JSONFileArtifact (class in pestifer.core.artifacts) K Kb (pestifer.charmmff.charmmffprm.CharmmBondParam attribute) Kchi (pestifer.charmmff.charmmffprm.CharmmDihedralParam attribute) keep (pestifer.core.artifacts.FileArtifact attribute) key (pestifer.charmmff.charmmfftop.CharmmResi attribute) (pestifer.core.artifacts.Artifact attribute) (pestifer.core.artifacts.CharmmffFileArtifactList attribute) (pestifer.core.artifacts.CharmmffTopFileArtifacts attribute) (pestifer.core.artifacts.StateArtifacts attribute) keys() (pestifer.core.artifacts.ArtifactDict method) Kpsi (pestifer.charmmff.charmmffprm.CharmmImproperParam attribute) Ktheta (pestifer.charmmff.charmmffprm.CharmmAngleParam attribute) Kub (pestifer.charmmff.charmmffprm.CharmmAngleParam attribute) L label_lipid_chains_heavy_aware() (in module pestifer.charmmff.graphhelpers) LabelMappers (class in pestifer.core.labels) Labels (in module pestifer.core.labels) lastline() (pestifer.util.stringthings.ByteCollector method) lawofcos() (in module pestifer.util.coord) ldx_of_cellndx() (pestifer.util.linkcell.Linkcell method) ldx_searchlist_of_ldx() (pestifer.util.linkcell.Linkcell method) leafs_in() (in module pestifer.charmmff.graphhelpers) length (pestifer.charmmff.charmmfftop.CharmmBond attribute) (pestifer.objs.ssbond.SSBond attribute) LigandGenSummary (class in pestifer.charmmff.ligand_paramgen.orchestrator) LigandProtonationError, [1] LigandResult (class in pestifer.charmmff.ligand_paramgen.orchestrator) ligands (pestifer.psfutil.psfatom.PSFAtom attribute) LigateTask (class in pestifer.tasks.ligate) LineList (class in pestifer.psfutil.psftopoelement) linesplit() (in module pestifer.util.stringthings) Link (class in pestifer.objs.link) link (pestifer.molecule.atom.Atom attribute) link_distance (pestifer.objs.link.Link attribute) link_to() (pestifer.molecule.residue.Residue method) Linkcell (class in pestifer.util.linkcell) LinkList (class in pestifer.objs.link) links (pestifer.psfutil.psfcontents.PSFContents attribute) lipid_annotate() (pestifer.charmmff.charmmfftop.CharmmResi method) load_project() (pestifer.scripters.psfgen.PsfgenScripter method) load_psf_pdb() (pestifer.scripters.vmd.VMDScripter method) log() (pestifer.util.stringthings.ByteCollector method) log_error_patterns (pestifer.scripters.packmol.PackmolScripter attribute) log_file (pestifer.cli.subcommand.Subcommand attribute) (pestifer.subcommands.mdplot.MDPlotSubcommand attribute) log_message() (pestifer.tasks.basetask.BaseTask method) LogFileArtifact (class in pestifer.core.artifacts) LogFileArtifactList (class in pestifer.core.artifacts) LogParser (class in pestifer.logparsers.logparser) long_help (pestifer.cli.subcommand.Subcommand attribute) (pestifer.subcommands.build.RunSubcommand attribute) (pestifer.subcommands.build_example.RunExampleSubcommand attribute) (pestifer.subcommands.config_default.ConfigDefaultSubcommand attribute) (pestifer.subcommands.config_help.ConfigHelpSubcommand attribute) (pestifer.subcommands.desolvate.DesolvateSubcommand attribute) (pestifer.subcommands.fetch_example.FetchExampleSubcommand attribute) (pestifer.subcommands.follow_namd_log.FollowNAMDLogSubcommand attribute) (pestifer.subcommands.make_ligand_mol2.MakeLigandMol2Subcommand attribute) (pestifer.subcommands.make_namd_restart.MakeNAMDRestartSubcommand attribute) (pestifer.subcommands.make_pdbcollection.MakePDBCollectionSubcommand attribute) (pestifer.subcommands.mdplot.MDPlotSubcommand attribute) (pestifer.subcommands.modify_package.ModifyPackageSubcommand attribute) (pestifer.subcommands.new_system.NewSystemSubcommand attribute) (pestifer.subcommands.rebuild_charmmff_cache.RebuildCHARMMFFCache attribute) (pestifer.subcommands.setup_vmd.SetupVMDSubcommand attribute) (pestifer.subcommands.show_resources.ShowResourcesSubcommand attribute) (pestifer.subcommands.wheretcl.WhereTCLSubcommand attribute) longname() (pestifer.charmmff.pdbrepository.PDBInput method) loop_counts() (pestifer.molecule.molecule.Molecule method) ls() (pestifer.util.cacheable_object.TarBytesFS method) M make_constraint_pdb() (pestifer.tasks.basetask.VMDTask method) make_inputs() (pestifer.tasks.domainswap.DomainSwapTask method) make_namd_restart_subcommand() (in module pestifer.util.namdrestart) make_package() (pestifer.tasks.terminate.TerminateTask method) make_pdb_collection() (in module pestifer.charmmff.make_pdb_collection) make_quilt_from_patch() (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) make_ssrestraints_file() (pestifer.tasks.basetask.VMDTask method) make_tarball() (pestifer.core.artifacts.FileArtifactList method) MakeLigandMol2Subcommand (class in pestifer.subcommands.make_ligand_mol2) MakeMembraneSystemTask (class in pestifer.tasks.make_membrane_system) MakeNAMDRestartSubcommand (class in pestifer.subcommands.make_namd_restart) MakePDBCollectionSubcommand (class in pestifer.subcommands.make_pdbcollection) ManipulateTask (class in pestifer.tasks.manipulate) map_attr() (pestifer.core.baseobj.BaseObj method) (pestifer.core.baseobj.BaseObjList method) map_chainIDs_label_to_auth() (pestifer.molecule.residue.ResidueList method) mark_cc_doubles_by_degree() (in module pestifer.charmmff.graphhelpers) mass (pestifer.charmmff.charmmfftop.CharmmAtom attribute) (pestifer.charmmff.charmmfftop.CharmmResi attribute) match() (pestifer.psfutil.psftopoelement.PSFTopoElement method) MDPlotSubcommand (class in pestifer.subcommands.mdplot) MDPlotTask (class in pestifer.tasks.mdplot) MDTask (class in pestifer.tasks.mdtask) measure_dihedral() (in module pestifer.util.coord) measure_distances() (pestifer.tasks.ligate.LigateTask method) measure_progress() (pestifer.logparsers.logparser.LogParser method) (pestifer.logparsers.namdlogparser.NAMDLogParser method) (pestifer.logparsers.packmollogparser.PackmolLogParser method) merge() (pestifer.charmmff.charmmffprm.CharmmParamFile method) MergeTask (class in pestifer.tasks.merge) message (pestifer.charmmff.ligand_paramgen.orchestrator.LigandResult attribute) metadata (pestifer.charmmff.charmmfftop.CharmmResi attribute) mic_shift() (in module pestifer.util.coord) (pestifer.psfutil.psftopoelement.PSFTopoElement method) mime_type (pestifer.core.artifacts.FileArtifact attribute) (pestifer.core.artifacts.JSONFileArtifact attribute) (pestifer.core.artifacts.NAMDOutputFileArtifact attribute) (pestifer.core.artifacts.PNGImageFileArtifact attribute) (pestifer.core.artifacts.TclScriptArtifact attribute) (pestifer.core.artifacts.TXTFileArtifact attribute) (pestifer.core.artifacts.YAMLFileArtifact attribute) minimal_prm (pestifer.core.artifacts.StateArtifacts attribute) mobile_sel (pestifer.objs.align.Align attribute) (pestifer.objs.transfer_coords.TransferCoords attribute) model (pestifer.molecule.residue.ResiduePlaceholder attribute) model_annotate() (pestifer.charmmff.charmmfftop.CharmmResi method) model_config (pestifer.core.baseobj.BaseObj attribute) (pestifer.core.example.Example attribute) (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.atom.Hetatm attribute) (pestifer.molecule.residue.Residue attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) (pestifer.molecule.segment.Segment attribute) (pestifer.molecule.stateinterval.StateInterval attribute) (pestifer.molecule.transform.Transform attribute) (pestifer.objs.align.Align attribute) (pestifer.objs.cfusion.Cfusion attribute) (pestifer.objs.cleavagesite.CleavageSite attribute) (pestifer.objs.crot.Crot attribute) (pestifer.objs.deletion.Deletion attribute) (pestifer.objs.graft.Graft attribute) (pestifer.objs.insertion.Insertion attribute) (pestifer.objs.link.Link attribute) (pestifer.objs.mutation.Mutation attribute) (pestifer.objs.orient.Orient attribute) (pestifer.objs.patch.Patch attribute) (pestifer.objs.resid.ResID attribute) (pestifer.objs.rottrans.RotTrans attribute) (pestifer.objs.seqadv.Seqadv attribute) (pestifer.objs.ssbond.SSBond attribute) (pestifer.objs.ssbonddelete.SSBondDelete attribute) (pestifer.objs.substitution.Substitution attribute) (pestifer.objs.ter.Ter attribute) (pestifer.objs.transfer_coords.TransferCoords attribute) (pestifer.psfutil.psfatom.PSFAtom attribute) model_post_init() (pestifer.core.example.Example method) (pestifer.molecule.atom.Atom method) (pestifer.molecule.residue.Residue method) (pestifer.molecule.residue.ResiduePlaceholder method) (pestifer.molecule.segment.Segment method) (pestifer.molecule.stateinterval.StateInterval method) (pestifer.molecule.transform.Transform method) (pestifer.objs.align.Align method) (pestifer.objs.cfusion.Cfusion method) (pestifer.objs.cleavagesite.CleavageSite method) (pestifer.objs.crot.Crot method) (pestifer.objs.deletion.Deletion method) (pestifer.objs.graft.Graft method) (pestifer.objs.insertion.Insertion method) (pestifer.objs.link.Link method) (pestifer.objs.mutation.Mutation method) (pestifer.objs.orient.Orient method) (pestifer.objs.patch.Patch method) (pestifer.objs.resid.ResID method) (pestifer.objs.rottrans.RotTrans method) (pestifer.objs.seqadv.Seqadv method) (pestifer.objs.ssbond.SSBond method) (pestifer.objs.substitution.Substitution method) (pestifer.objs.ter.Ter method) (pestifer.objs.transfer_coords.TransferCoords method) (pestifer.psfutil.psfatom.PSFAtom method) modify_entries() (in module pestifer.sphinxext.toctree_util) modify_toctree() (in module pestifer.sphinxext.toctree_util) ModifyPackageSubcommand (class in pestifer.subcommands.modify_package) module pestifer pestifer.charmmff pestifer.charmmff.charmmffcontent pestifer.charmmff.charmmffprm pestifer.charmmff.charmmfftop pestifer.charmmff.graphhelpers pestifer.charmmff.ligand_paramgen pestifer.charmmff.ligand_paramgen.mol2_writer pestifer.charmmff.ligand_paramgen.orchestrator pestifer.charmmff.ligand_paramgen.protonation pestifer.charmmff.ligand_paramgen.rcsb pestifer.charmmff.make_pdb_collection pestifer.charmmff.pdbrepository pestifer.cli pestifer.cli.pestifer pestifer.cli.subcommand pestifer.core pestifer.core.artifacts pestifer.core.baseobj pestifer.core.command pestifer.core.config pestifer.core.controller pestifer.core.errors pestifer.core.example pestifer.core.examplemanager pestifer.core.labels pestifer.core.objmanager pestifer.core.pipeline pestifer.core.resourcemanager pestifer.logparsers pestifer.logparsers.logparser pestifer.logparsers.namdlogparser pestifer.logparsers.packmollogparser pestifer.logparsers.pdb2pqrlogparser pestifer.logparsers.psfgenlogparser pestifer.molecule pestifer.molecule.asymmetricunit pestifer.molecule.atom pestifer.molecule.bilayer pestifer.molecule.bioassemb pestifer.molecule.chainidmanager pestifer.molecule.molecule pestifer.molecule.residue pestifer.molecule.segment pestifer.molecule.stateinterval pestifer.molecule.transform pestifer.objs pestifer.objs.align pestifer.objs.cfusion pestifer.objs.cleavagesite pestifer.objs.crot pestifer.objs.deletion pestifer.objs.graft pestifer.objs.insertion pestifer.objs.link pestifer.objs.mutation pestifer.objs.orient pestifer.objs.patch pestifer.objs.resid pestifer.objs.rottrans pestifer.objs.seqadv pestifer.objs.ssbond pestifer.objs.ssbonddelete pestifer.objs.substitution pestifer.objs.ter pestifer.objs.transfer_coords pestifer.psfutil pestifer.psfutil.psfangle pestifer.psfutil.psfatom pestifer.psfutil.psfbond pestifer.psfutil.psfcontents pestifer.psfutil.psfdihedral pestifer.psfutil.psfpairex pestifer.psfutil.psfpatch pestifer.psfutil.psfremark pestifer.psfutil.psfring pestifer.psfutil.psftopoelement pestifer.resources pestifer.schema pestifer.scripters pestifer.scripters.generic pestifer.scripters.namd pestifer.scripters.namd_colvar_input pestifer.scripters.packmol pestifer.scripters.psfgen pestifer.scripters.tcl pestifer.scripters.vmd pestifer.sphinxext pestifer.sphinxext.sphinx_examplemanager pestifer.sphinxext.task_table pestifer.sphinxext.tclscript pestifer.sphinxext.toctree_util pestifer.subcommands pestifer.subcommands.build pestifer.subcommands.build_example pestifer.subcommands.config_default pestifer.subcommands.config_help pestifer.subcommands.desolvate pestifer.subcommands.fetch_example pestifer.subcommands.follow_namd_log pestifer.subcommands.make_ligand_mol2 pestifer.subcommands.make_namd_restart pestifer.subcommands.make_pdbcollection pestifer.subcommands.mdplot pestifer.subcommands.modify_package pestifer.subcommands.new_system pestifer.subcommands.rebuild_charmmff_cache pestifer.subcommands.setup_vmd pestifer.subcommands.show_resources pestifer.subcommands.wheretcl pestifer.tasks pestifer.tasks.basetask pestifer.tasks.cleave pestifer.tasks.continuation pestifer.tasks.desolvate pestifer.tasks.domainswap pestifer.tasks.fetch pestifer.tasks.ligate pestifer.tasks.make_membrane_system pestifer.tasks.manipulate pestifer.tasks.mdplot pestifer.tasks.mdtask pestifer.tasks.merge pestifer.tasks.pdb2pqr pestifer.tasks.psfgen pestifer.tasks.pytest_buildterminate pestifer.tasks.ringcheck pestifer.tasks.solvate pestifer.tasks.taskcollections pestifer.tasks.terminate pestifer.tasks.validate pestifer.util pestifer.util.cacheable_object pestifer.util.cifutil pestifer.util.colors pestifer.util.coord pestifer.util.formatvalidator pestifer.util.gitutil pestifer.util.linkcell pestifer.util.namdrestart pestifer.util.patch pestifer.util.progress pestifer.util.pytest_plugin pestifer.util.readme_to_changelog_with_dates pestifer.util.spinner_wrapper pestifer.util.stringthings pestifer.util.units pestifer.util.util Mol2WriteError Molecule (class in pestifer.molecule.molecule) molid (pestifer.molecule.molecule.Molecule attribute) movetype (pestifer.objs.rottrans.RotTrans attribute) Mutation (class in pestifer.objs.mutation) MutationList (class in pestifer.objs.mutation) mutations (pestifer.molecule.segment.Segment attribute) my_logger() (in module pestifer.util.stringthings) N n (pestifer.charmmff.charmmffprm.CharmmDihedralParam attribute) (pestifer.charmmff.charmmffprm.CharmmImproperParam attribute) NAMDColvarInputScripter (class in pestifer.scripters.namd_colvar_input) NAMDColvarsConfigArtifact (class in pestifer.core.artifacts) NAMDColvarsStateArtifact (class in pestifer.core.artifacts) NAMDColvarsTrajectoryArtifact (class in pestifer.core.artifacts) NAMDConfig (class in pestifer.util.namdrestart) NAMDConfigFileArtifact (class in pestifer.core.artifacts) NAMDCoorFileArtifact (class in pestifer.core.artifacts) NAMDCoorFileArtifactList (class in pestifer.core.artifacts) NAMDDcdFileArtifact (class in pestifer.core.artifacts) NAMDExtraBondsFileArtifact (class in pestifer.core.artifacts) NAMDLogFileArtifact (class in pestifer.core.artifacts) NAMDLogFileArtifactList (class in pestifer.core.artifacts) NAMDLogParser (class in pestifer.logparsers.namdlogparser) NAMDOutputFileArtifact (class in pestifer.core.artifacts) NAMDOutputFileArtifactList (class in pestifer.core.artifacts) NAMDProgress (class in pestifer.util.progress) namdrun() (pestifer.tasks.mdtask.MDTask method) NAMDScripter (class in pestifer.scripters.namd) NAMDVelFileArtifact (class in pestifer.core.artifacts) NAMDXscFileArtifact (class in pestifer.core.artifacts) NAMDXstFileArtifact (class in pestifer.core.artifacts) NAMDxstParser (class in pestifer.logparsers.namdlogparser) name (pestifer.charmmff.charmmfftop.CharmmAtom attribute) (pestifer.charmmff.pdbrepository.PDBInput attribute) (pestifer.cli.subcommand.Subcommand attribute) (pestifer.core.artifacts.FileArtifact property) (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.bioassemb.BioAssemb attribute) (pestifer.subcommands.build.RunSubcommand attribute) (pestifer.subcommands.build_example.RunExampleSubcommand attribute) (pestifer.subcommands.config_default.ConfigDefaultSubcommand attribute) (pestifer.subcommands.config_help.ConfigHelpSubcommand attribute) (pestifer.subcommands.desolvate.DesolvateSubcommand attribute) (pestifer.subcommands.fetch_example.FetchExampleSubcommand attribute) (pestifer.subcommands.follow_namd_log.FollowNAMDLogSubcommand attribute) (pestifer.subcommands.make_ligand_mol2.MakeLigandMol2Subcommand attribute) (pestifer.subcommands.make_namd_restart.MakeNAMDRestartSubcommand attribute) (pestifer.subcommands.make_pdbcollection.MakePDBCollectionSubcommand attribute) (pestifer.subcommands.mdplot.MDPlotSubcommand attribute) (pestifer.subcommands.modify_package.ModifyPackageSubcommand attribute) (pestifer.subcommands.new_system.NewSystemSubcommand attribute) (pestifer.subcommands.rebuild_charmmff_cache.RebuildCHARMMFFCache attribute) (pestifer.subcommands.setup_vmd.SetupVMDSubcommand attribute) (pestifer.subcommands.show_resources.ShowResourcesSubcommand attribute) (pestifer.subcommands.wheretcl.WhereTCLSubcommand attribute) (pestifer.tasks.validate.AttributeTest attribute) (pestifer.tasks.validate.ConnectionTest attribute) name1 (pestifer.charmmff.charmmfftop.CharmmAngle attribute) (pestifer.charmmff.charmmfftop.CharmmBond attribute) (pestifer.charmmff.charmmfftop.CharmmDihedral attribute) (pestifer.objs.link.Link attribute) name2 (pestifer.charmmff.charmmfftop.CharmmAngle attribute) (pestifer.charmmff.charmmfftop.CharmmBond attribute) (pestifer.charmmff.charmmfftop.CharmmDihedral attribute) (pestifer.objs.link.Link attribute) name3 (pestifer.charmmff.charmmfftop.CharmmAngle attribute) (pestifer.charmmff.charmmfftop.CharmmDihedral attribute) name4 (pestifer.charmmff.charmmfftop.CharmmDihedral attribute) name_from_blockstring() (pestifer.charmmff.charmmfftop.CharmmResi static method) nbfix (pestifer.charmmff.charmmffprm.CharmmParamFile attribute) new_example_yaml() (pestifer.core.examplemanager.ExampleManager method) new_rst() (pestifer.sphinxext.sphinx_examplemanager.SphinxExampleManager method) newfile() (pestifer.scripters.generic.GenericScripter method) newresname (pestifer.objs.mutation.Mutation attribute) newscript() (pestifer.scripters.namd.NAMDScripter method) (pestifer.scripters.packmol.PackmolScripter method) (pestifer.scripters.psfgen.PsfgenScripter method) (pestifer.scripters.tcl.TcLScripter method) (pestifer.scripters.vmd.VMDScripter method) NewSystemSubcommand (class in pestifer.subcommands.new_system) next_basename() (pestifer.tasks.basetask.BaseTask method) next_reserved_chainID() (pestifer.molecule.chainidmanager.ChainIDManager method) next_unused_chainID() (pestifer.molecule.chainidmanager.ChainIDManager method) nglycans() (pestifer.molecule.molecule.Molecule method) NiceHelpFormatter (class in pestifer.cli.pestifer) nmolec_in_cuA() (in module pestifer.util.units) nonbonded (pestifer.charmmff.charmmffprm.CharmmParamFile attribute) nonbonded_header (pestifer.charmmff.charmmffprm.CharmmParamFile attribute) nonstate_results (pestifer.core.artifacts.FileArtifact attribute) (pestifer.core.artifacts.PNGImageFileArtifact attribute) num_atoms() (pestifer.charmmff.charmmfftop.CharmmResi method) (pestifer.molecule.molecule.Molecule method) (pestifer.psfutil.psfcontents.PSFSegmentList method) num_images() (pestifer.molecule.molecule.Molecule method) num_items() (pestifer.molecule.stateinterval.StateInterval method) (pestifer.molecule.stateinterval.StateIntervalList method) num_residues() (pestifer.molecule.molecule.Molecule method) (pestifer.psfutil.psfcontents.PSFSegmentList method) num_segments() (pestifer.molecule.molecule.Molecule method) O obj_id (pestifer.molecule.residue.ResiduePlaceholder attribute) (pestifer.objs.cfusion.Cfusion attribute) (pestifer.objs.graft.Graft attribute) objcat (pestifer.core.baseobj.BaseObj property) ObjManager (class in pestifer.core.objmanager) objmanager (pestifer.molecule.molecule.Molecule attribute) (pestifer.molecule.segment.Segment attribute) occ (pestifer.molecule.atom.Atom attribute) open() (pestifer.util.cacheable_object.TarBytesFS method) opt_tags (pestifer.charmmff.pdbrepository.PDBInput attribute) optional_arguments (pestifer.sphinxext.task_table.TaskTableDirective attribute) Orient (class in pestifer.objs.orient) orient_protein() (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) OrientList (class in pestifer.objs.orient) ORIGINAL_ATTRIBUTES (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) origresname (pestifer.objs.mutation.Mutation attribute) orthohexagonal_cell() (in module pestifer.molecule.bilayer) orthohexagonal_patch() (in module pestifer.molecule.bilayer) outputs (pestifer.core.example.Example attribute) outputs_subdir (pestifer.core.example.Example attribute) outputspath (pestifer.core.example.Example property) outputspath() (pestifer.core.examplemanager.ExampleManager method) override_taskname() (pestifer.tasks.basetask.BaseTask method) overwrite_position() (pestifer.molecule.atom.Atom method) overwrite_positions() (pestifer.molecule.atom.AtomList method) oxford() (in module pestifer.util.stringthings) P P (pestifer.psfutil.psftopoelement.PSFTopoElement attribute) pack_patch() (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) PackmolInputScriptArtifact (class in pestifer.core.artifacts) PackmolLogFileArtifact (class in pestifer.core.artifacts) PackmolLogParser (class in pestifer.logparsers.packmollogparser) PackMolPDBForcedFileArtifact (class in pestifer.core.artifacts) PackmolProgress (class in pestifer.util.progress) PackmolScripter (class in pestifer.scripters.packmol) pairex (pestifer.psfutil.psfcontents.PSFContents attribute) parent_chain (pestifer.molecule.segment.Segment attribute) parent_molecule (pestifer.molecule.segment.Segment attribute) parse_conditional_script() (in module pestifer.charmmff.charmmffcontent) parse_filter_expression() (in module pestifer.util.stringthings) parse_toctree_entries() (in module pestifer.sphinxext.toctree_util) parsed_struct (pestifer.molecule.molecule.Molecule attribute) parser (pestifer.cli.subcommand.Subcommand attribute) Patch (class in pestifer.objs.patch) patch_topologies() (pestifer.tasks.psfgen.PsfgenTask method) PatchApplyError patches (pestifer.molecule.segment.Segment attribute) (pestifer.psfutil.psfcontents.PSFContents attribute) patchhead (pestifer.objs.link.Link attribute) PatchList (class in pestifer.objs.patch) patchname (pestifer.objs.link.Link attribute) (pestifer.objs.patch.Patch attribute) (pestifer.psfutil.psfremark.PSFPatchRemark attribute) patchspecs (pestifer.psfutil.psfremark.PSFPatchRemark attribute) path (pestifer.charmmff.ligand_paramgen.orchestrator.LigandResult attribute) (pestifer.core.artifacts.FileArtifact property) path_or_tarball (pestifer.charmmff.pdbrepository.PDBCollection attribute) paths_to_list() (pestifer.core.artifacts.FileArtifactList method) pattern (pestifer.util.formatvalidator.FormatValidator property) pdb (pestifer.core.artifacts.StateArtifacts attribute) (pestifer.molecule.stateinterval.StateInterval attribute) PDB2PQRLogParser (class in pestifer.logparsers.pdb2pqrlogparser) PDB2PQRProgress (class in pestifer.util.progress) PDB2PQRTask (class in pestifer.tasks.pdb2pqr) pdb_ins_code (pestifer.molecule.residue.ResiduePlaceholder attribute) pdb_line() (pestifer.molecule.atom.Atom method) (pestifer.molecule.residue.ResiduePlaceholder method) (pestifer.objs.seqadv.Seqadv method) (pestifer.objs.ssbond.SSBond method) pdb_to_coor() (pestifer.tasks.basetask.VMDTask method) PDBCollection (class in pestifer.charmmff.pdbrepository) PDBCollectionDict (class in pestifer.charmmff.pdbrepository) pdbcontents (pestifer.charmmff.pdbrepository.PDBInput attribute) PDBFileArtifact (class in pestifer.core.artifacts) PDBFileArtifactList (class in pestifer.core.artifacts) PDBInput (class in pestifer.charmmff.pdbrepository) PDBInputDict (class in pestifer.charmmff.pdbrepository) PDBRepository (class in pestifer.charmmff.pdbrepository) pdbresid (pestifer.objs.resid.ResID property) pdbx_auth_seq_num (pestifer.objs.mutation.Mutation attribute) (pestifer.objs.seqadv.Seqadv attribute) pdbx_ordinal (pestifer.objs.seqadv.Seqadv attribute) pdbx_pdb_ins_code (pestifer.molecule.atom.Atom attribute) pdbx_stash (pestifer.objs.seqadv.Seqadv attribute) performance_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) pestifer module pestifer.charmmff module pestifer.charmmff.charmmffcontent module pestifer.charmmff.charmmffprm module pestifer.charmmff.charmmfftop module pestifer.charmmff.graphhelpers module pestifer.charmmff.ligand_paramgen module pestifer.charmmff.ligand_paramgen.mol2_writer module pestifer.charmmff.ligand_paramgen.orchestrator module pestifer.charmmff.ligand_paramgen.protonation module pestifer.charmmff.ligand_paramgen.rcsb module pestifer.charmmff.make_pdb_collection module pestifer.charmmff.pdbrepository module pestifer.cli module pestifer.cli.pestifer module pestifer.cli.subcommand module pestifer.core module pestifer.core.artifacts module pestifer.core.baseobj module pestifer.core.command module pestifer.core.config module pestifer.core.controller module pestifer.core.errors module pestifer.core.example module pestifer.core.examplemanager module pestifer.core.labels module pestifer.core.objmanager module pestifer.core.pipeline module pestifer.core.resourcemanager module pestifer.logparsers module pestifer.logparsers.logparser module pestifer.logparsers.namdlogparser module pestifer.logparsers.packmollogparser module pestifer.logparsers.pdb2pqrlogparser module pestifer.logparsers.psfgenlogparser module pestifer.molecule module pestifer.molecule.asymmetricunit module pestifer.molecule.atom module pestifer.molecule.bilayer module pestifer.molecule.bioassemb module pestifer.molecule.chainidmanager module pestifer.molecule.molecule module pestifer.molecule.residue module pestifer.molecule.segment module pestifer.molecule.stateinterval module pestifer.molecule.transform module pestifer.objs module pestifer.objs.align module pestifer.objs.cfusion module pestifer.objs.cleavagesite module pestifer.objs.crot module pestifer.objs.deletion module pestifer.objs.graft module pestifer.objs.insertion module pestifer.objs.link module pestifer.objs.mutation module pestifer.objs.orient module pestifer.objs.patch module pestifer.objs.resid module pestifer.objs.rottrans module pestifer.objs.seqadv module pestifer.objs.ssbond module pestifer.objs.ssbonddelete module pestifer.objs.substitution module pestifer.objs.ter module pestifer.objs.transfer_coords module pestifer.psfutil module pestifer.psfutil.psfangle module pestifer.psfutil.psfatom module pestifer.psfutil.psfbond module pestifer.psfutil.psfcontents module pestifer.psfutil.psfdihedral module pestifer.psfutil.psfpairex module pestifer.psfutil.psfpatch module pestifer.psfutil.psfremark module pestifer.psfutil.psfring module pestifer.psfutil.psftopoelement module pestifer.resources module pestifer.schema module pestifer.scripters module pestifer.scripters.generic module pestifer.scripters.namd module pestifer.scripters.namd_colvar_input module pestifer.scripters.packmol module pestifer.scripters.psfgen module pestifer.scripters.tcl module pestifer.scripters.vmd module pestifer.sphinxext module pestifer.sphinxext.sphinx_examplemanager module pestifer.sphinxext.task_table module pestifer.sphinxext.tclscript module pestifer.sphinxext.toctree_util module pestifer.subcommands module pestifer.subcommands.build module pestifer.subcommands.build_example module pestifer.subcommands.config_default module pestifer.subcommands.config_help module pestifer.subcommands.desolvate module pestifer.subcommands.fetch_example module pestifer.subcommands.follow_namd_log module pestifer.subcommands.make_ligand_mol2 module pestifer.subcommands.make_namd_restart module pestifer.subcommands.make_pdbcollection module pestifer.subcommands.mdplot module pestifer.subcommands.modify_package module pestifer.subcommands.new_system module pestifer.subcommands.rebuild_charmmff_cache module pestifer.subcommands.setup_vmd module pestifer.subcommands.show_resources module pestifer.subcommands.wheretcl module pestifer.tasks module pestifer.tasks.basetask module pestifer.tasks.cleave module pestifer.tasks.continuation module pestifer.tasks.desolvate module pestifer.tasks.domainswap module pestifer.tasks.fetch module pestifer.tasks.ligate module pestifer.tasks.make_membrane_system module pestifer.tasks.manipulate module pestifer.tasks.mdplot module pestifer.tasks.mdtask module pestifer.tasks.merge module pestifer.tasks.pdb2pqr module pestifer.tasks.psfgen module pestifer.tasks.pytest_buildterminate module pestifer.tasks.ringcheck module pestifer.tasks.solvate module pestifer.tasks.taskcollections module pestifer.tasks.terminate module pestifer.tasks.validate module pestifer.util module pestifer.util.cacheable_object module pestifer.util.cifutil module pestifer.util.colors module pestifer.util.coord module pestifer.util.formatvalidator module pestifer.util.gitutil module pestifer.util.linkcell module pestifer.util.namdrestart module pestifer.util.patch module pestifer.util.progress module pestifer.util.pytest_plugin module pestifer.util.readme_to_changelog_with_dates module pestifer.util.spinner_wrapper module pestifer.util.stringthings module pestifer.util.units module pestifer.util.util module PestiferBuildError PestiferColorMap (class in pestifer.util.colors) PestiferError PestiferProgress (class in pestifer.util.progress) pierced_by() (pestifer.psfutil.psfring.PSFRing method) PipelineContext (class in pestifer.core.pipeline) plu() (in module pestifer.util.stringthings) PNGImageFileArtifact (class in pestifer.core.artifacts) PNGImageFileArtifactList (class in pestifer.core.artifacts) pop() (pestifer.core.artifacts.ArtifactDict method) positionN() (in module pestifer.util.coord) PQRFileArtifact (class in pestifer.core.artifacts) pre_align (pestifer.objs.transfer_coords.TransferCoords property) prep_input() (pestifer.tasks.pdb2pqr.PDB2PQRTask method) prep_mods() (pestifer.tasks.pdb2pqr.PDB2PQRTask method) pressureprofile_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) print_system_report() (pestifer.tasks.terminate.TerminateTask method) process_banner() (pestifer.logparsers.packmollogparser.PackmolLogParser method) process_energy_line() (pestifer.logparsers.namdlogparser.NAMDLogParser method) process_energy_title() (pestifer.logparsers.namdlogparser.NAMDLogParser method) process_gencan_report() (pestifer.logparsers.packmollogparser.PackmolLogParser method) process_gencan_success() (pestifer.logparsers.packmollogparser.PackmolLogParser method) process_header() (pestifer.logparsers.packmollogparser.PackmolLogParser method) process_info_line() (pestifer.logparsers.namdlogparser.NAMDLogParser method) (pestifer.logparsers.psfgenlogparser.PsfgenLogParser method) process_itemlist() (pestifer.molecule.stateinterval.StateIntervalList class method) process_line() (pestifer.logparsers.namdlogparser.NAMDLogParser method) (pestifer.logparsers.psfgenlogparser.PsfgenLogParser method) process_molecule_report() (pestifer.logparsers.packmollogparser.PackmolLogParser method) process_moving_worst_molecules() (pestifer.logparsers.packmollogparser.PackmolLogParser method) process_performance_line() (pestifer.logparsers.namdlogparser.NAMDLogParser method) process_pressureprofile_line() (pestifer.logparsers.namdlogparser.NAMDLogParser method) process_psfgen_line() (pestifer.logparsers.psfgenlogparser.PsfgenLogParser method) process_restart_line() (pestifer.logparsers.namdlogparser.NAMDLogParser method) process_section() (pestifer.logparsers.packmollogparser.PackmolLogParser method) (pestifer.logparsers.pdb2pqrlogparser.PDB2PQRLogParser method) process_struct_summ_datum() (pestifer.logparsers.namdlogparser.NAMDLogParser method) process_summary() (pestifer.logparsers.pdb2pqrlogparser.PDB2PQRLogParser method) process_tcl_line() (pestifer.logparsers.namdlogparser.NAMDLogParser method) process_timing_line() (pestifer.logparsers.namdlogparser.NAMDLogParser method) process_wallclock_line() (pestifer.logparsers.namdlogparser.NAMDLogParser method) produced_by (pestifer.core.artifacts.Artifact attribute) protect_str_arg() (in module pestifer.util.util) protonate_ligand() (in module pestifer.charmmff.ligand_paramgen) (in module pestifer.charmmff.ligand_paramgen.protonation) provenance (pestifer.core.artifacts.Artifact attribute) provision() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) (pestifer.tasks.basetask.BaseTask method) (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) (pestifer.tasks.manipulate.ManipulateTask method) (pestifer.tasks.mdtask.MDTask method) (pestifer.tasks.psfgen.PsfgenTask method) (pestifer.tasks.validate.ValidateTask method) provision_pdbrepository() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) provision_residueobjects() (pestifer.charmmff.charmmffcontent.CHARMMFFContent method) provision_tasks() (pestifer.core.controller.Controller method) prune_exclusions() (pestifer.core.baseobj.BaseObjList method) prune_topology() (pestifer.molecule.segment.SegmentList method) psf (pestifer.core.artifacts.StateArtifacts attribute) PSFAngle (class in pestifer.psfutil.psfangle) PSFAngleList (class in pestifer.psfutil.psfangle) PSFAtom (class in pestifer.psfutil.psfatom) PSFAtomList (class in pestifer.psfutil.psfatom) PSFBond (class in pestifer.psfutil.psfbond) PSFBondList (class in pestifer.psfutil.psfbond) psfcompanion (pestifer.molecule.segment.SegmentList attribute) PSFContents (class in pestifer.psfutil.psfcontents) PSFDihedral (class in pestifer.psfutil.psfdihedral) PSFDihedralList (class in pestifer.psfutil.psfdihedral) PSFDISUPatch (class in pestifer.psfutil.psfpatch) PSFFileArtifact (class in pestifer.core.artifacts) PSFFileArtifactList (class in pestifer.core.artifacts) psfgen() (pestifer.tasks.psfgen.PsfgenTask method) psfgen_key (pestifer.logparsers.psfgenlogparser.PsfgenLogParser attribute) psfgen_segname (pestifer.molecule.segment.Segment attribute) PsfgenInputScriptArtifact (class in pestifer.core.artifacts) PsfgenLogFileArtifact (class in pestifer.core.artifacts) PsfgenLogParser (class in pestifer.logparsers.psfgenlogparser) PsfgenProgress (class in pestifer.util.progress) PsfgenScripter (class in pestifer.scripters.psfgen) PsfgenTask (class in pestifer.tasks.psfgen) PSFLinkPatch (class in pestifer.psfutil.psfpatch) PSFPairEx (class in pestifer.psfutil.psfpairex) PSFPairExList (class in pestifer.psfutil.psfpairex) PSFPatchRemark (class in pestifer.psfutil.psfremark) PSFPatchRemarkList (class in pestifer.psfutil.psfremark) PSFRemark (class in pestifer.psfutil.psfremark) PSFRemarkList (class in pestifer.psfutil.psfremark) PSFResidue (class in pestifer.psfutil.psfcontents) PSFResidueList (class in pestifer.psfutil.psfcontents) PSFRing (class in pestifer.psfutil.psfring) PSFSegment (class in pestifer.psfutil.psfcontents) PSFSegmentList (class in pestifer.psfutil.psfcontents) PSFSegmentRemark (class in pestifer.psfutil.psfremark) PSFSegmentRemarkList (class in pestifer.psfutil.psfremark) PSFTopoElement (class in pestifer.psfutil.psftopoelement) PSFTopoElementList (class in pestifer.psfutil.psftopoelement) PSFTopoRemark (class in pestifer.psfutil.psfremark) PSFTopoRemarkList (class in pestifer.psfutil.psfremark) psi0 (pestifer.charmmff.charmmffprm.CharmmImproperParam attribute) ptnr1_auth_asym_id (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) ptnr1_auth_comp_id (pestifer.objs.link.Link attribute) ptnr1_auth_seq_id (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) ptnr1_label_asym_id (pestifer.objs.link.Link attribute) ptnr1_label_comp_id (pestifer.objs.link.Link attribute) ptnr1_label_seq_id (pestifer.objs.link.Link attribute) ptnr2_auth_asym_id (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) ptnr2_auth_comp_id (pestifer.objs.link.Link attribute) ptnr2_auth_seq_id (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) ptnr2_label_asym_id (pestifer.objs.link.Link attribute) ptnr2_label_comp_id (pestifer.objs.link.Link attribute) ptnr2_label_seq_id (pestifer.objs.link.Link attribute) puniq() (pestifer.core.baseobj.BaseObjList method) puniquify() (pestifer.core.baseobj.BaseObjList method) (pestifer.molecule.residue.ResidueList method) pytest_addoption() (in module pestifer.util.pytest_plugin) Pytest_BuildTerminateTask (class in pestifer.tasks.pytest_buildterminate) pytest_configure() (in module pestifer.util.pytest_plugin) pytestable (pestifer.core.artifacts.FileArtifact attribute) R Radii (pestifer.psfutil.psftopoelement.PSFTopoElement attribute) radii (pestifer.psfutil.psftopoelement.PSFTopoElement attribute) raise_clean() (in module pestifer.util.stringthings) raw_string (pestifer.charmmff.charmmfftop.CharmmDelete attribute) rcsb_file_format (pestifer.molecule.molecule.Molecule attribute) RCSBLookupError, [1] read_rst_file() (in module pestifer.sphinxext.toctree_util) read_yaml() (pestifer.core.example.ExampleList class method) reassign() (pestifer.util.stringthings.ByteCollector method) RebuildCHARMMFFCache (class in pestifer.subcommands.rebuild_charmmff_cache) reconfigure_tasks() (pestifer.core.controller.Controller method) reconstruct_toctree_block() (in module pestifer.sphinxext.toctree_util) recordname (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) reduce_intlist() (in module pestifer.util.util) ref_pdb (pestifer.objs.align.Align attribute) ref_psf (pestifer.objs.align.Align attribute) ref_sel (pestifer.objs.align.Align attribute) ref_sourceID (pestifer.objs.align.Align attribute) refatom (pestifer.objs.orient.Orient attribute) register() (pestifer.core.pipeline.PipelineContext method) (pestifer.tasks.basetask.BaseTask method) register_if_exists() (pestifer.core.pipeline.PipelineContext method) (pestifer.tasks.basetask.BaseTask method) register_mapping() (pestifer.molecule.transform.Transform method) register_tmpfiles_from_tcl() (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) register_tops_streams_from_psfgen() (pestifer.tasks.make_membrane_system.MakeMembraneSystemTask method) register_update_function() (pestifer.util.progress.PestiferProgress method) registration_place (pestifer.charmmff.pdbrepository.PDBCollection attribute) rekey() (pestifer.core.pipeline.PipelineContext method) remap_chainIDs() (pestifer.molecule.residue.ResidueList method) remarkify() (pestifer.psfutil.psfcontents.PSFSegment method) (pestifer.psfutil.psfcontents.PSFSegmentList method) remarkline (pestifer.psfutil.psfremark.PSFRemark attribute) remove() (pestifer.core.artifacts.ArtifactList method) (pestifer.core.artifacts.FileArtifact method) (pestifer.molecule.segment.SegmentList method) remove_and_return() (pestifer.core.baseobj.BaseObjList method) remove_argument() (in module pestifer.util.util) remove_duplicates() (pestifer.core.baseobj.BaseObjList method) remove_ignored_residues() (pestifer.psfutil.psfcontents.PSFContents method) remove_instance() (pestifer.core.baseobj.BaseObjList method) remove_links_to() (pestifer.objs.link.LinkList method) rename_example() (pestifer.core.examplemanager.ExampleManager method) (pestifer.core.resourcemanager.ResourceManager method) renumber() (pestifer.molecule.residue.ResidueList method) replace() (in module pestifer.util.util) replace_command() (pestifer.util.namdrestart.NAMDConfig method) report() (pestifer.objs.link.LinkList method) report_examples() (pestifer.core.examplemanager.ExampleManager method) report_line() (pestifer.core.example.Example method) required_arguments (pestifer.sphinxext.task_table.TaskTableDirective attribute) (pestifer.sphinxext.tclscript.TclScriptDirective attribute) reserialize() (pestifer.molecule.atom.AtomList method) reset() (pestifer.util.stringthings.ByteCollector method) resi_topologies() (pestifer.tasks.psfgen.PsfgenTask method) ResID (class in pestifer.objs.resid) resid (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) (pestifer.objs.insertion.Insertion attribute) (pestifer.objs.mutation.Mutation attribute) (pestifer.objs.patch.Patch attribute) (pestifer.objs.resid.ResID property) (pestifer.objs.seqadv.Seqadv attribute) (pestifer.objs.ter.Ter attribute) (pestifer.psfutil.psfatom.PSFAtom attribute) (pestifer.psfutil.psfcontents.PSFResidue attribute) resid1 (pestifer.objs.cfusion.Cfusion attribute) (pestifer.objs.cleavagesite.CleavageSite attribute) (pestifer.objs.crot.Crot attribute) (pestifer.objs.deletion.Deletion attribute) (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) (pestifer.objs.substitution.Substitution attribute) resid2 (pestifer.objs.cfusion.Cfusion attribute) (pestifer.objs.cleavagesite.CleavageSite attribute) (pestifer.objs.crot.Crot attribute) (pestifer.objs.deletion.Deletion attribute) (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) (pestifer.objs.substitution.Substitution attribute) resid3 (pestifer.objs.crot.Crot attribute) residi (pestifer.objs.crot.Crot attribute) residj (pestifer.objs.crot.Crot attribute) residk (pestifer.objs.crot.Crot attribute) ResIDList (class in pestifer.objs.resid) Residue (class in pestifer.molecule.residue) residue (pestifer.objs.patch.Patch attribute) (pestifer.objs.seqadv.Seqadv attribute) residue1 (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) residue2 (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) ResidueList (class in pestifer.molecule.residue) ResiduePlaceholder (class in pestifer.molecule.residue) ResiduePlaceholderList (class in pestifer.molecule.residue) residues (pestifer.molecule.segment.Segment attribute) (pestifer.molecule.segment.SegmentList attribute) (pestifer.objs.graft.Graft attribute) (pestifer.psfutil.psfcontents.PSFSegment attribute) ResidueTest (class in pestifer.tasks.validate) resname (pestifer.charmmff.charmmfftop.CharmmResi attribute) (pestifer.charmmff.ligand_paramgen.orchestrator.LigandResult attribute) (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) (pestifer.objs.seqadv.Seqadv attribute) (pestifer.objs.ter.Ter attribute) (pestifer.psfutil.psfatom.PSFAtom attribute) (pestifer.psfutil.psfcontents.PSFResidue attribute) resname1 (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) resname2 (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) resolved (pestifer.molecule.residue.ResiduePlaceholder attribute) ResourceManager (class in pestifer.core.resourcemanager) resrange() (pestifer.molecule.residue.ResidueList method) resseqnum (pestifer.objs.resid.ResID attribute) restart_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) restore_selection() (pestifer.scripters.vmd.VMDScripter method) retire() (pestifer.core.objmanager.ObjManager method) return_TcL() (pestifer.objs.patch.Patch method) ri() (pestifer.molecule.residue.Residue method) ri_range() (pestifer.objs.resid.ResIDList static method) ring_check() (in module pestifer.psfutil.psfring) RingCheckTask (class in pestifer.tasks.ringcheck) RingList (class in pestifer.psfutil.psfring) Rmin (pestifer.charmmff.charmmffprm.CharmmNBFixParam attribute) Rmin_half (pestifer.charmmff.charmmffprm.CharmmNonbondedParam attribute) Rmin_half14 (pestifer.charmmff.charmmffprm.CharmmNonbondedParam attribute) rootfolderpath (pestifer.core.example.Example property) RotTrans (class in pestifer.objs.rottrans) RotTransList (class in pestifer.objs.rottrans) run() (pestifer.core.command.Command method) (pestifer.sphinxext.task_table.TaskTableDirective method) (pestifer.sphinxext.tclscript.TclScriptDirective method) run_pdb2pqr() (pestifer.tasks.pdb2pqr.PDB2PQRTask method) RunExampleSubcommand (class in pestifer.subcommands.build_example) running_under_pytest() (in module pestifer.util.util) runscript() (pestifer.scripters.namd.NAMDScripter method) (pestifer.scripters.packmol.PackmolScripter method) (pestifer.scripters.psfgen.PsfgenScripter method) (pestifer.scripters.vmd.VMDScripter method) RunSubcommand (class in pestifer.subcommands.build) S S0 (pestifer.charmmff.charmmffprm.CharmmAngleParam attribute) sacres (pestifer.molecule.stateinterval.StateInterval attribute) same_image (pestifer.psfutil.psftopoelement.PSFTopoElement attribute) same_resid() (pestifer.molecule.residue.Residue method) sandbag() (pestifer.molecule.chainidmanager.ChainIDManager method) scriptname (pestifer.core.example.Example property) scriptpath (pestifer.core.example.Example property) scriptpath() (pestifer.core.examplemanager.ExampleManager method) section_separator (pestifer.logparsers.packmollogparser.PackmolLogParser attribute) (pestifer.logparsers.pdb2pqrlogparser.PDB2PQRLogParser attribute) seed_set() (in module pestifer.charmmff.graphhelpers) segdata (pestifer.psfutil.psfremark.PSFSegmentRemark attribute) segfile (pestifer.objs.graft.Graft attribute) Segment (class in pestifer.molecule.segment) SegmentList (class in pestifer.molecule.segment) segname (pestifer.molecule.atom.Atom attribute) (pestifer.molecule.residue.ResiduePlaceholder attribute) (pestifer.molecule.segment.Segment attribute) (pestifer.objs.crot.Crot attribute) (pestifer.psfutil.psfatom.PSFAtom attribute) (pestifer.psfutil.psfcontents.PSFResidue attribute) (pestifer.psfutil.psfcontents.PSFSegment attribute) (pestifer.psfutil.psfremark.PSFSegmentRemark attribute) segname1 (pestifer.objs.crot.Crot attribute) (pestifer.objs.link.Link attribute) segname2 (pestifer.objs.crot.Crot attribute) (pestifer.objs.link.Link attribute) segname_by_type_map (pestifer.molecule.transform.Transform attribute) segnamei (pestifer.objs.crot.Crot attribute) segnamejk (pestifer.objs.crot.Crot attribute) segtype (pestifer.molecule.residue.ResiduePlaceholder attribute) (pestifer.molecule.segment.Segment attribute) (pestifer.psfutil.psfatom.PSFAtom attribute) (pestifer.psfutil.psfcontents.PSFResidue attribute) (pestifer.psfutil.psfcontents.PSFSegment attribute) segtype1 (pestifer.objs.link.Link attribute) segtype2 (pestifer.objs.link.Link attribute) selection (pestifer.tasks.validate.AttributeTest attribute) (pestifer.tasks.validate.ConnectionTest attribute) selname (pestifer.molecule.stateinterval.StateInterval attribute) Seqadv (class in pestifer.objs.seqadv) seqadv_details_keyword() (pestifer.objs.seqadv.Seqadv method) SeqadvList (class in pestifer.objs.seqadv) sequence (pestifer.objs.insertion.Insertion attribute) serial (pestifer.molecule.atom.Atom attribute) (pestifer.objs.ter.Ter attribute) (pestifer.psfutil.psfatom.PSFAtom attribute) serial_number (pestifer.objs.ssbond.SSBond attribute) serialize() (pestifer.core.baseobj.BaseObj method) set() (pestifer.core.baseobj.BaseObj method) (pestifer.core.baseobj.BaseObjList method) set_chainID() (pestifer.molecule.residue.Residue method) set_chainIDmap() (pestifer.molecule.transform.Transform method) set_chainIDs() (pestifer.molecule.residue.ResidueList method) set_coords() (pestifer.molecule.asymmetricunit.AsymmetricUnit method) (pestifer.molecule.molecule.Molecule method) set_example_author() (pestifer.core.examplemanager.ExampleManager method) (pestifer.core.resourcemanager.ResourceManager method) set_internal_resids() (pestifer.objs.graft.Graft method) set_mass() (pestifer.charmmff.charmmfftop.CharmmAtom method) (pestifer.charmmff.charmmfftop.CharmmResi method) set_masses() (pestifer.charmmff.charmmfftop.CharmmAtomList method) set_molecule() (pestifer.scripters.vmd.VMDScripter method) set_nested() (pestifer.core.baseobj.BaseObj method) set_parent_molecule() (pestifer.molecule.asymmetricunit.AsymmetricUnit method) (pestifer.molecule.bioassemb.BioAssemb method) (pestifer.molecule.bioassemb.BioAssembList method) (pestifer.molecule.segment.Segment method) set_patchname() (pestifer.objs.link.Link method) set_segname() (pestifer.molecule.residue.Residue method) (pestifer.molecule.residue.ResidueList method) SetupVMDSubcommand (class in pestifer.subcommands.setup_vmd) short_help (pestifer.cli.subcommand.Subcommand attribute) (pestifer.subcommands.build.RunSubcommand attribute) (pestifer.subcommands.build_example.RunExampleSubcommand attribute) (pestifer.subcommands.config_default.ConfigDefaultSubcommand attribute) (pestifer.subcommands.config_help.ConfigHelpSubcommand attribute) (pestifer.subcommands.desolvate.DesolvateSubcommand attribute) (pestifer.subcommands.fetch_example.FetchExampleSubcommand attribute) (pestifer.subcommands.follow_namd_log.FollowNAMDLogSubcommand attribute) (pestifer.subcommands.make_ligand_mol2.MakeLigandMol2Subcommand attribute) (pestifer.subcommands.make_namd_restart.MakeNAMDRestartSubcommand attribute) (pestifer.subcommands.make_pdbcollection.MakePDBCollectionSubcommand attribute) (pestifer.subcommands.mdplot.MDPlotSubcommand attribute) (pestifer.subcommands.modify_package.ModifyPackageSubcommand attribute) (pestifer.subcommands.new_system.NewSystemSubcommand attribute) (pestifer.subcommands.rebuild_charmmff_cache.RebuildCHARMMFFCache attribute) (pestifer.subcommands.setup_vmd.SetupVMDSubcommand attribute) (pestifer.subcommands.show_resources.ShowResourcesSubcommand attribute) (pestifer.subcommands.wheretcl.WhereTCLSubcommand attribute) shortcode() (pestifer.molecule.atom.Atom method) (pestifer.molecule.residue.ResiduePlaceholder method) (pestifer.objs.cfusion.Cfusion method) (pestifer.objs.cleavagesite.CleavageSite method) (pestifer.objs.crot.Crot method) (pestifer.objs.deletion.Deletion method) (pestifer.objs.graft.Graft method) (pestifer.objs.insertion.Insertion method) (pestifer.objs.link.Link method) (pestifer.objs.mutation.Mutation method) (pestifer.objs.patch.Patch method) (pestifer.objs.rottrans.RotTrans method) (pestifer.objs.ssbond.SSBond method) (pestifer.objs.substitution.Substitution method) shortname (pestifer.core.example.Example attribute) show() (pestifer.charmmff.pdbrepository.PDBCollection method) (pestifer.charmmff.pdbrepository.PDBRepository method) (pestifer.core.resourcemanager.ResourceManager method) show_artifact() (pestifer.core.pipeline.PipelineContext method) show_artifacts() (pestifer.core.pipeline.PipelineContext method) show_error() (pestifer.charmmff.charmmfftop.CharmmResi method) ShowResourcesSubcommand (class in pestifer.subcommands.show_resources) skipped_known (pestifer.charmmff.ligand_paramgen.orchestrator.LigandGenSummary attribute) smiles (pestifer.charmmff.ligand_paramgen.orchestrator.LigandResult attribute) SolvateTask (class in pestifer.tasks.solvate) sort() (pestifer.core.artifacts.ArtifactList method) (pestifer.core.baseobj.BaseObjList method) source_chainID (pestifer.objs.graft.Graft attribute) source_end (pestifer.objs.graft.Graft attribute) source_file (pestifer.charmmff.charmmfftop.CharmmResi attribute) source_molecule (pestifer.objs.graft.Graft attribute) source_partners (pestifer.objs.graft.Graft attribute) source_pdbid (pestifer.objs.graft.Graft attribute) source_root (pestifer.objs.graft.Graft attribute) source_seg (pestifer.objs.graft.Graft attribute) sourcefile (pestifer.objs.cfusion.Cfusion attribute) sourceseg (pestifer.objs.cfusion.Cfusion attribute) sourcespecs (pestifer.molecule.molecule.Molecule attribute) spawn_subcontroller() (pestifer.core.controller.Controller class method) spec_out() (pestifer.molecule.bilayer.Bilayer method) specs (pestifer.molecule.segment.Segment attribute) specstrings_builddict() (in module pestifer.molecule.bilayer) SphinxExampleManager (class in pestifer.sphinxext.sphinx_examplemanager) split_ri() (pestifer.objs.resid.ResID static method) squareish_lattice() (in module pestifer.molecule.bilayer) SSBond (class in pestifer.objs.ssbond) SSBondDelete (class in pestifer.objs.ssbonddelete) SSBondDeleteList (class in pestifer.objs.ssbonddelete) SSBondList (class in pestifer.objs.ssbond) ssbonds (pestifer.psfutil.psfcontents.PSFContents attribute) stamp() (pestifer.core.artifacts.Artifact method) (pestifer.core.artifacts.ArtifactDict method) (pestifer.core.artifacts.ArtifactList method) (pestifer.core.artifacts.StateArtifacts method) stash() (pestifer.core.pipeline.PipelineContext method) stash_current_artifact() (pestifer.tasks.basetask.BaseTask method) state (pestifer.molecule.stateinterval.StateInterval attribute) state_bounds() (pestifer.molecule.residue.ResidueList method) StateArtifacts (class in pestifer.core.artifacts) StateInterval (class in pestifer.molecule.stateinterval) StateIntervalList (class in pestifer.molecule.stateinterval) static() (pestifer.logparsers.logparser.LogParser method) (pestifer.logparsers.namdlogparser.NAMDLogParser method) status (pestifer.charmmff.ligand_paramgen.orchestrator.LigandResult attribute) sterol_annotate() (pestifer.charmmff.charmmfftop.CharmmResi method) streamID (pestifer.charmmff.charmmffcontent.CHARMMFFStreamID attribute) (pestifer.charmmff.pdbrepository.PDBCollection attribute) strhash() (pestifer.core.baseobj.BaseObj method) strip_remarks() (pestifer.tasks.psfgen.PsfgenTask method) striplist() (in module pestifer.util.stringthings) struct_sep (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) structure_url() (pestifer.sphinxext.sphinx_examplemanager.SphinxExampleManager method) Subcommand (class in pestifer.cli.subcommand) subcommand_follow_namd_log() (in module pestifer.logparsers.namdlogparser) subsegments (pestifer.molecule.segment.Segment attribute) subseq (pestifer.objs.substitution.Substitution attribute) Substitution (class in pestifer.objs.substitution) SubstitutionList (class in pestifer.objs.substitution) substitutions() (pestifer.molecule.residue.ResidueList method) substreamID (pestifer.charmmff.charmmffcontent.CHARMMFFStreamID attribute) success() (pestifer.logparsers.logparser.LogParser method) (pestifer.logparsers.namdlogparser.NAMDLogParser method) (pestifer.logparsers.psfgenlogparser.PsfgenLogParser method) successes (pestifer.charmmff.ligand_paramgen.orchestrator.LigandGenSummary attribute) summary() (pestifer.charmmff.charmmffprm.CharmmParamFile method) swap_attr() (pestifer.core.baseobj.BaseObj method) sym1 (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) sym2 (pestifer.objs.link.Link attribute) (pestifer.objs.ssbond.SSBond attribute) synonym (pestifer.charmmff.charmmfftop.CharmmResi attribute) T take_item() (pestifer.core.baseobj.BaseObjList method) tally_masses() (pestifer.charmmff.charmmfftop.CharmmResiDict method) (pestifer.charmmff.charmmfftop.CharmmResiList method) tar_bytes (pestifer.util.cacheable_object.TarBytesFS attribute) tarball() (pestifer.util.stringthings.FileCollector method) tarball_walk() (in module pestifer.util.util) TarBytesFS (class in pestifer.util.cacheable_object) tarfilename (pestifer.charmmff.charmmffcontent.CHARMMFFContent attribute) target_partners (pestifer.objs.graft.Graft attribute) target_root (pestifer.objs.graft.Graft attribute) TaskDict (class in pestifer.tasks.taskcollections) taskless_subconfig() (pestifer.core.config.Config method) TaskList (class in pestifer.tasks.taskcollections) TaskTableDirective (class in pestifer.sphinxext.task_table) tcl_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) TclScriptArtifact (class in pestifer.core.artifacts) TclScriptDirective (class in pestifer.sphinxext.tclscript) TcLScripter (class in pestifer.scripters.tcl) Ter (class in pestifer.objs.ter) TerList (class in pestifer.objs.ter) TerminateTask (class in pestifer.tasks.terminate) test_standard() (pestifer.tasks.terminate.TerminateTask method) Theta0 (pestifer.charmmff.charmmffprm.CharmmAngleParam attribute) thru_map() (pestifer.molecule.chainidmanager.ChainIDManager method) timing_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) title (pestifer.core.example.Example attribute) tmat (pestifer.molecule.transform.Transform attribute) to_dict() (pestifer.charmmff.charmmfftop.CharmmAtomList method) (pestifer.charmmff.charmmfftop.CharmmMassList method) (pestifer.charmmff.charmmfftop.CharmmResiDict method) (pestifer.charmmff.charmmfftop.CharmmResiList method) (pestifer.core.artifacts.ArtifactList method) (pestifer.core.example.Example method) to_file() (pestifer.charmmff.charmmfftop.CharmmResi method) to_graph() (pestifer.charmmff.charmmfftop.CharmmResi method) (pestifer.psfutil.psfbond.PSFBondList method) to_latex_math() (in module pestifer.util.stringthings) to_list() (pestifer.charmmff.charmmfftop.CharmmAtomDict method) (pestifer.charmmff.charmmfftop.CharmmMassDict method) (pestifer.core.artifacts.ArtifactDict method) (pestifer.core.artifacts.StateArtifacts method) to_list_of_dicts() (pestifer.core.example.ExampleList method) to_psfgen() (pestifer.charmmff.charmmfftop.CharmmResi method) to_resi_pres() (pestifer.charmmff.charmmfftop.CharmmResiDict method) (pestifer.charmmff.charmmfftop.CharmmResiList method) to_yaml() (pestifer.core.example.Example method) (pestifer.core.example.ExampleList method) topofilename (pestifer.psfutil.psfremark.PSFTopoRemark attribute) touch() (pestifer.molecule.chainidmanager.ChainIDManager method) TransferCoords (class in pestifer.objs.transfer_coords) TransferCoordsList (class in pestifer.objs.transfer_coords) Transform (class in pestifer.molecule.transform) TransformList (class in pestifer.molecule.transform) transforms (pestifer.molecule.bioassemb.BioAssemb attribute) treadmill() (pestifer.psfutil.psfring.PSFRing method) TXTFileArtifact (class in pestifer.core.artifacts) type (pestifer.charmmff.charmmfftop.CharmmAtom attribute) type1 (pestifer.charmmff.charmmffprm.CharmmAngleParam attribute) (pestifer.charmmff.charmmffprm.CharmmBondParam attribute) (pestifer.charmmff.charmmffprm.CharmmDihedralParam attribute) (pestifer.charmmff.charmmffprm.CharmmImproperParam attribute) (pestifer.charmmff.charmmffprm.CharmmNBFixParam attribute) type2 (pestifer.charmmff.charmmffprm.CharmmAngleParam attribute) (pestifer.charmmff.charmmffprm.CharmmBondParam attribute) (pestifer.charmmff.charmmffprm.CharmmDihedralParam attribute) (pestifer.charmmff.charmmffprm.CharmmImproperParam attribute) (pestifer.charmmff.charmmffprm.CharmmNBFixParam attribute) type3 (pestifer.charmmff.charmmffprm.CharmmAngleParam attribute) (pestifer.charmmff.charmmffprm.CharmmDihedralParam attribute) (pestifer.charmmff.charmmffprm.CharmmImproperParam attribute) type4 (pestifer.charmmff.charmmffprm.CharmmDihedralParam attribute) (pestifer.charmmff.charmmffprm.CharmmImproperParam attribute) typekey (pestifer.objs.mutation.Mutation attribute) (pestifer.objs.seqadv.Seqadv attribute) types (pestifer.charmmff.charmmffprm.CharmmCMAPParam attribute) U uniqattrs() (pestifer.core.baseobj.BaseObjList method) unique_paths() (pestifer.core.artifacts.FileArtifactList method) unlink() (pestifer.molecule.residue.Residue method) unregister_chain() (pestifer.molecule.chainidmanager.ChainIDManager method) up (pestifer.molecule.residue.Residue attribute) update() (pestifer.logparsers.logparser.LogParser method) (pestifer.logparsers.namdlogparser.NAMDLogParser method) (pestifer.logparsers.packmollogparser.PackmolLogParser method) (pestifer.logparsers.pdb2pqrlogparser.PDB2PQRLogParser method) (pestifer.logparsers.psfgenlogparser.PsfgenLogParser method) update_alias_mappings() (pestifer.core.labels.LabelMappers method) update_aliases() (pestifer.core.labels.LabelMappers method) update_atomselect_macros() (pestifer.core.labels.LabelMappers method) (pestifer.core.resourcemanager.ResourceManager method) update_attr_from_obj_attr() (pestifer.core.baseobj.BaseObj method) (pestifer.core.baseobj.BaseObjList method) update_attr_from_objlist_elem_attr() (pestifer.core.baseobj.BaseObj method) (pestifer.core.baseobj.BaseObjList method) update_example() (pestifer.core.examplemanager.ExampleManager method) (pestifer.core.resourcemanager.ResourceManager method) (pestifer.sphinxext.sphinx_examplemanager.SphinxExampleManager method) update_from_residue() (pestifer.objs.seqadv.Seqadv method) update_from_residues() (pestifer.objs.seqadv.SeqadvList method) update_item() (pestifer.core.artifacts.ArtifactDict method) update_molecule() (pestifer.tasks.psfgen.PsfgenTask method) update_options() (pestifer.core.example.Example method) update_progress_bar() (pestifer.logparsers.logparser.LogParser method) update_residue() (pestifer.objs.link.Link method) update_segtypes() (pestifer.core.labels.LabelMappers method) uplink (pestifer.molecule.residue.Residue attribute) use_after_regenerate (pestifer.objs.patch.Patch attribute) use_in_segment (pestifer.objs.patch.Patch attribute) used (pestifer.core.objmanager.ObjManager attribute) USER_TOPPAR_DIR (in module pestifer.core.resourcemanager) usescript() (pestifer.scripters.vmd.VMDScripter method) V validate() (pestifer.core.artifacts.FileArtifact method) (pestifer.core.baseobj.BaseObjList class method) (pestifer.psfutil.psfcontents.PSFSegment method) (pestifer.psfutil.psfcontents.PSFSegmentList method) validate_format() (in module pestifer.util.formatvalidator) validate_image() (pestifer.psfutil.psftopoelement.PSFTopoElement method) validate_images() (pestifer.psfutil.psftopoelement.PSFTopoElementList method) ValidateTask (class in pestifer.tasks.validate) value (pestifer.tasks.validate.AttributeTest attribute) value_count (pestifer.tasks.validate.AttributeTest attribute) values() (pestifer.core.artifacts.ArtifactDict method) var_backresolve() (pestifer.util.namdrestart.NAMDConfig method) vel (pestifer.core.artifacts.StateArtifacts attribute) VERSION_SCOPE (pestifer.util.cacheable_object.CacheableObject attribute) VMDLogFileArtifact (class in pestifer.core.artifacts) VMDLogParser (class in pestifer.logparsers.logparser) VMDScriptArtifact (class in pestifer.core.artifacts) VMDScripter (class in pestifer.scripters.vmd) VMDTask (class in pestifer.tasks.basetask) W wallclock_key (pestifer.logparsers.namdlogparser.NAMDLogParser attribute) weak_lt() (pestifer.core.baseobj.BaseObj method) WhereTCLSubcommand (class in pestifer.subcommands.wheretcl) wildmatch() (pestifer.core.baseobj.BaseObj method) with_spinner() (in module pestifer.util.spinner_wrapper) wrap_point() (pestifer.util.linkcell.Linkcell method) write() (pestifer.charmmff.charmmffprm.CharmmParamFile method) (pestifer.psfutil.psfcontents.PSFContents method) (pestifer.tasks.validate.AttributeTest method) (pestifer.tasks.validate.ConnectionTest method) (pestifer.tasks.validate.ResidueTest method) (pestifer.util.namdrestart.NAMDConfig method) (pestifer.util.stringthings.ByteCollector method) write_align() (pestifer.scripters.vmd.VMDScripter method) write_cfusion_insegment() (pestifer.scripters.psfgen.PsfgenScripter method) write_cfusion_postsegment() (pestifer.scripters.psfgen.PsfgenScripter method) write_cfusion_presegment() (pestifer.scripters.psfgen.PsfgenScripter method) write_chainmaps() (pestifer.tasks.terminate.TerminateTask method) write_complete_config() (pestifer.core.controller.Controller method) write_connect_patches() (pestifer.molecule.molecule.Molecule method) (pestifer.tasks.ligate.LigateTask method) write_crot() (pestifer.scripters.vmd.VMDScripter method) write_crots() (pestifer.scripters.vmd.VMDScripter method) write_csv() (pestifer.logparsers.namdlogparser.NAMDLogParser method) write_file() (pestifer.util.stringthings.ByteCollector method) write_gaps() (pestifer.molecule.molecule.Molecule method) (pestifer.tasks.ligate.LigateTask method) write_generic_stanza() (pestifer.scripters.psfgen.PsfgenScripter method) write_glycan_stanza() (pestifer.scripters.psfgen.PsfgenScripter method) write_graft_presegment() (pestifer.scripters.psfgen.PsfgenScripter method) write_link() (pestifer.scripters.psfgen.PsfgenScripter method) write_links() (pestifer.scripters.psfgen.PsfgenScripter method) write_mol2() (in module pestifer.charmmff.ligand_paramgen.mol2_writer) write_mol_tcl() (pestifer.scripters.psfgen.PsfgenScripter method) write_mutation() (pestifer.scripters.psfgen.PsfgenScripter method) write_mutations() (pestifer.scripters.psfgen.PsfgenScripter method) write_nucleicacid_stanza() (pestifer.scripters.psfgen.PsfgenScripter method) write_orient() (pestifer.scripters.vmd.VMDScripter method) write_orients() (pestifer.scripters.vmd.VMDScripter method) write_packmol() (pestifer.molecule.bilayer.Bilayer method) write_pdb() (pestifer.scripters.vmd.VMDScripter method) write_polymer_stanza() (pestifer.scripters.psfgen.PsfgenScripter method) write_protein_loop_lines() (pestifer.scripters.vmd.VMDScripter method) write_residue_map() (in module pestifer.util.util) write_rottrans() (pestifer.scripters.vmd.VMDScripter method) write_rottranslist() (pestifer.scripters.vmd.VMDScripter method) write_rst_file() (in module pestifer.sphinxext.toctree_util) write_segment() (pestifer.scripters.psfgen.PsfgenScripter method) write_segments() (pestifer.scripters.psfgen.PsfgenScripter method) write_ssbond() (pestifer.scripters.psfgen.PsfgenScripter method) write_ssbonds() (pestifer.scripters.psfgen.PsfgenScripter method) write_TcL() (pestifer.molecule.transform.Transform method) (pestifer.objs.mutation.Mutation method) write_transfer_coords() (pestifer.scripters.vmd.VMDScripter method) writefile() (pestifer.scripters.generic.GenericScripter method) writescript() (pestifer.scripters.namd.NAMDScripter method) (pestifer.scripters.packmol.PackmolScripter method) (pestifer.scripters.psfgen.PsfgenScripter method) (pestifer.scripters.tcl.TcLScripter method) (pestifer.scripters.vmd.VMDScripter method) X x (pestifer.molecule.atom.Atom attribute) (pestifer.objs.rottrans.RotTrans attribute) xsc (pestifer.core.artifacts.StateArtifacts attribute) Y y (pestifer.molecule.atom.Atom attribute) (pestifer.objs.rottrans.RotTrans attribute) YAMLFileArtifact (class in pestifer.core.artifacts) Z z (pestifer.molecule.atom.Atom attribute) (pestifer.objs.rottrans.RotTrans attribute)