pestifer.psfutil package

A package for handling PSF utilities in the Pestifer project. This package provides classes and methods for managing various PSF-related objects.

Submodules

• pestifer.psfutil.psfangle module
  • PSFAngle
  • PSFAngleList
• pestifer.psfutil.psfatom module
  • PSFAtom
    • PSFAtom.add_ligand()
    • PSFAtom.atomicwt
    • PSFAtom.atomname
    • PSFAtom.atomtype
    • PSFAtom.charge
    • PSFAtom.isH()
    • PSFAtom.is_pep()
    • PSFAtom.is_root
    • PSFAtom.ligands
    • PSFAtom.model_config
    • PSFAtom.model_post_init()
    • PSFAtom.resid
    • PSFAtom.resname
    • PSFAtom.segname
    • PSFAtom.segtype
    • PSFAtom.serial
  • PSFAtomList
    • PSFAtomList.apply_exclusion_logics()
    • PSFAtomList.apply_inclusion_logics()
    • PSFAtomList.describe()
    • PSFAtomList.graph()
• pestifer.psfutil.psfbond module
  • PSFBond
  • PSFBondList
    • PSFBondList.to_graph()
• pestifer.psfutil.psfcontents module
  • PSFContents
    • PSFContents.atoms
    • PSFContents.atomserials
    • PSFContents.ssbonds
    • PSFContents.links
    • PSFContents.patches
    • PSFContents.bonds
    • PSFContents.angles
    • PSFContents.dihedrals
    • PSFContents.pairex
    • PSFContents.add_ligands()
    • PSFContents.apply_atom_logics()
    • PSFContents.get_charge()
    • PSFContents.remove_ignored_residues()
    • PSFContents.write()
  • PSFResidue
    • PSFResidue.add_atom()
    • PSFResidue.atoms
    • PSFResidue.resid
    • PSFResidue.resname
    • PSFResidue.segname
    • PSFResidue.segtype
  • PSFResidueList
    • PSFResidueList.apply_segtypes()
  • PSFSegment
    • PSFSegment.add_residue()
    • PSFSegment.commands
    • PSFSegment.remarkify()
    • PSFSegment.residues
    • PSFSegment.segname
    • PSFSegment.segtype
    • PSFSegment.validate()
  • PSFSegmentList
    • PSFSegmentList.num_atoms()
    • PSFSegmentList.num_residues()
    • PSFSegmentList.remarkify()
    • PSFSegmentList.validate()
  • get_toppar_from_psf()
• pestifer.psfutil.psfdihedral module
  • PSFDihedral
  • PSFDihedralList
• pestifer.psfutil.psfpairex module
  • PSFPairEx
  • PSFPairExList
• pestifer.psfutil.psfpatch module
  • PSFDISUPatch
  • PSFLinkPatch
• pestifer.psfutil.psfremark module
  • PSFPatchRemark
    • PSFPatchRemark.data
    • PSFPatchRemark.patchname
    • PSFPatchRemark.patchspecs
  • PSFPatchRemarkList
  • PSFRemark
    • PSFRemark.data
    • PSFRemark.from_remarkline()
    • PSFRemark.remarkline
  • PSFRemarkList
    • PSFRemarkList.get_patchremarks()
    • PSFRemarkList.get_segmentremarks()
    • PSFRemarkList.get_toporemarks()
  • PSFSegmentRemark
    • PSFSegmentRemark.segdata
    • PSFSegmentRemark.segname
  • PSFSegmentRemarkList
  • PSFTopoRemark
    • PSFTopoRemark.topofilename
  • PSFTopoRemarkList
• pestifer.psfutil.psfring module
  • PSFRing
    • PSFRing.pierced_by()
    • PSFRing.treadmill()
  • RingList
  • ring_check()
• pestifer.psfutil.psftopoelement module
  • LineList
  • PSFTopoElement
    • PSFTopoElement.assign_cell_index()
    • PSFTopoElement.calculate_stuff()
      • PSFTopoElement.COM
      • PSFTopoElement.Radii
      • PSFTopoElement.radii
      • PSFTopoElement.B
      • PSFTopoElement.b
    • PSFTopoElement.copy()
    • PSFTopoElement.ingest_coordinates()
      • PSFTopoElement.P
      • PSFTopoElement.same_image
    • PSFTopoElement.match()
    • PSFTopoElement.mic_shift()
    • PSFTopoElement.validate_image()
  • PSFTopoElementList
    • PSFTopoElementList.assign_cell_indexes()
    • PSFTopoElementList.get()
    • PSFTopoElementList.ingest_coordinates()
    • PSFTopoElementList.validate_images()