continuousflex.protocols.utilities.pdb_parser module

class continuousflex.protocols.utilities.pdb_parser.PDB(recd='ATOM  ', serial=1, type='  ', loc='  ', alt=' ', res='    ', chain=' ', seq=1, icode=' ', x=0.0, y=0.0, z=0.0, occupancy=0.0, beta=0.0, footnote=0, segid='    ', element='  ', charge='  ', weight=0.0)

Bases: object

continuousflex.protocols.utilities.pdb_parser.m_inout_carbon_alphas(pdb_list)

return 0-based indices of carbon alphas in pdb_list

continuousflex.protocols.utilities.pdb_parser.m_inout_import_bfact(filename)

get Bfactor from PDB file

continuousflex.protocols.utilities.pdb_parser.m_inout_import_coords(filename)

get x y z coords from PDB file

continuousflex.protocols.utilities.pdb_parser.m_inout_read_pdb(filename)

Situs 2.x style pdb parser

continuousflex.protocols.utilities.pdb_parser.m_inout_write_pdb(pdb_list, filename, remarks)

pdb writer, Situs 2.x convention, renumbering atoms

continuousflex.protocols.utilities.pdb_parser.m_inout_write_pdb_sampled(pdb_name, filename, step, thr_mass)

pdb writer, Situs 2.x convention, renumbering atoms