pestifer package¶
Subpackages¶
- pestifer.charmmff package
- Subpackages
- Submodules
- pestifer.charmmff.charmmffcontent module
- pestifer.charmmff.charmmffprm module
- pestifer.charmmff.charmmfftop module
- pestifer.charmmff.graphhelpers module
anchor_paths()carbon_component_from_neighbor()carbon_neighbors_outside_S()count_unsats_cc()cycle_atoms_heavy()elem()head_tail_pairs()heavy_degree()heavy_neighbors()heavy_only_nodes()is_C()is_H()is_N()is_O()is_P()is_S()label_lipid_chains_heavy_aware()leafs_in()mark_cc_doubles_by_degree()seed_set()
- pestifer.charmmff.make_pdb_collection module
- pestifer.charmmff.pdbrepository module
- pestifer.cli package
- pestifer.core package
- Submodules
- pestifer.core.artifacts module
ArtifactArtifactDictArtifactListCIFFileArtifactCSVDataFileArtifactCSVDataFileArtifactListCharmmffFileArtifactCharmmffFileArtifactListCharmmffParFileArtifactCharmmffParFileArtifactsCharmmffStreamFileArtifactCharmmffStreamFileArtifactsCharmmffTopFileArtifactCharmmffTopFileArtifactsDataArtifactDataFileArtifactDataFileArtifactListFileArtifactFileArtifactDictFileArtifactListInputFileArtifactJSONFileArtifactLogFileArtifactLogFileArtifactListNAMDColvarsConfigArtifactNAMDColvarsStateArtifactNAMDColvarsTrajectoryArtifactNAMDConfigFileArtifactNAMDCoorFileArtifactNAMDCoorFileArtifactListNAMDDcdFileArtifactNAMDExtraBondsFileArtifactNAMDLogFileArtifactNAMDLogFileArtifactListNAMDOutputFileArtifactNAMDOutputFileArtifactListNAMDVelFileArtifactNAMDXscFileArtifactNAMDXstFileArtifactPDBFileArtifactPDBFileArtifactListPNGImageFileArtifactPNGImageFileArtifactListPQRFileArtifactPSFFileArtifactPSFFileArtifactListPackMolPDBForcedFileArtifactPackmolInputScriptArtifactPackmolLogFileArtifactPsfgenInputScriptArtifactPsfgenLogFileArtifactStateArtifactsTXTFileArtifactTclScriptArtifactVMDLogFileArtifactVMDScriptArtifactYAMLFileArtifact
- 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.core.artifacts module
- Submodules
- pestifer.logparsers package
- pestifer.molecule package
- Submodules
- 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
- Submodules
- pestifer.objs package
- Submodules
- 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
- Submodules
- pestifer.psfutil package
- Submodules
- 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
- Submodules
- pestifer.resources package
- pestifer.schema package
- pestifer.scripters package
- pestifer.sphinxext package
- pestifer.subcommands package
- Submodules
- 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
- Submodules
- pestifer.tasks package
- Submodules
- 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
- Submodules
- pestifer.util package
- Submodules
- 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
- Submodules