pestifer.objs package¶
Object subpackage for pestifer.
Each module in this subpackage defines a class that represents a specific type of object used in the Pestifer runtime.
Each class is a subclass of the abstract pestifer.core.baseobj.BaseObj. pestifer.core.baseobj.BaseObj is a subclass of pydantic.BaseModel and provides additional functionality for Pestifer objects, such as YAML serialization and deserialization, and a unique object ID.
Subclasses can define their own required and optional fields, as well as overriding the _adapt class method to handle initialization from a specific input data format, such as a shortcode.
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
GraftGraft.activate()Graft.assign_receiver_residues()Graft.chainIDGraft.donor_external_linksGraft.donor_internal_linksGraft.donor_residuesGraft.graft_residuesGraft.graft_segnameGraft.index_internal_linksGraft.index_residuesGraft.model_configGraft.model_post_init()Graft.obj_idGraft.residuesGraft.segfileGraft.set_internal_resids()Graft.shortcode()Graft.source_chainIDGraft.source_endGraft.source_moleculeGraft.source_partnersGraft.source_pdbidGraft.source_rootGraft.source_segGraft.target_partnersGraft.target_root
GraftList
- pestifer.objs.insertion module
- pestifer.objs.link module
LinkLink.altloc1Link.altloc2Link.atom1Link.atom2Link.chainID1Link.chainID2Link.emptyLink.link_distanceLink.model_configLink.model_post_init()Link.name1Link.name2Link.patchheadLink.patchnameLink.ptnr1_auth_asym_idLink.ptnr1_auth_comp_idLink.ptnr1_auth_seq_idLink.ptnr1_label_asym_idLink.ptnr1_label_comp_idLink.ptnr1_label_seq_idLink.ptnr2_auth_asym_idLink.ptnr2_auth_comp_idLink.ptnr2_auth_seq_idLink.ptnr2_label_asym_idLink.ptnr2_label_comp_idLink.ptnr2_label_seq_idLink.resid1Link.resid2Link.residue1Link.residue2Link.resname1Link.resname2Link.segname1Link.segname2Link.segtype1Link.segtype2Link.set_patchname()Link.shortcode()Link.sym1Link.sym2Link.update_residue()
LinkListic_reference_closest()
- pestifer.objs.mutation module
- pestifer.objs.orient module
- pestifer.objs.patch module
- pestifer.objs.resid module
- pestifer.objs.rottrans module
- pestifer.objs.seqadv module
SeqadvSeqadv.assign_residue()Seqadv.chainIDSeqadv.databaseSeqadv.dbAccessionSeqadv.dbResSeqadv.dbSeqSeqadv.idCodeSeqadv.model_configSeqadv.model_post_init()Seqadv.pdb_line()Seqadv.pdbx_auth_seq_numSeqadv.pdbx_ordinalSeqadv.pdbx_stashSeqadv.residSeqadv.residueSeqadv.resnameSeqadv.seqadv_details_keyword()Seqadv.typekeySeqadv.update_from_residue()
SeqadvList
- pestifer.objs.ssbond module
SSBondSSBond.chainID1SSBond.chainID2SSBond.lengthSSBond.model_configSSBond.model_post_init()SSBond.pdb_line()SSBond.ptnr1_auth_asym_idSSBond.ptnr1_auth_seq_idSSBond.ptnr2_auth_asym_idSSBond.ptnr2_auth_seq_idSSBond.resid1SSBond.resid2SSBond.residue1SSBond.residue2SSBond.resname1SSBond.resname2SSBond.serial_numberSSBond.shortcode()SSBond.sym1SSBond.sym2
SSBondList
- pestifer.objs.ssbonddelete module
- pestifer.objs.substitution module
- pestifer.objs.ter module
- pestifer.objs.transfer_coords module