Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
PDB_complex_to_unbound_partners_matcher Class Reference

Public Member Functions

def __init__ (self, exe_path, bpfp, upfp, bc, uc, od=".", occ=1, mn1=1, mn2=1, cm={}, verb=False #)
def write_matchings_files (self)
def bound_pdb_file_path (self)
def unbound_pdb_file_path (self)
def bound_chains (self)
def unbound_chains (self)
def output_directory (self)
def atom_matchings_file_suffix (self)
def residue_matchings_file_suffix (self)
def occupancy_policy_index (self)
def pdb_sequence_alignment_executable_path (self)
def __str__ (self)

Detailed Description

Given two PDB files and their respective selected chains, infers the matchings at the chain, residue and atom level.

The chain matching is straightforward if there is one chain specified per PDB. If there are several, we assume that several chains in the complex can be matched to the same chain in the unbound version. This is motivated mostly by the cases when the receptor is an homodimer and one of the two chains has more missing atoms that the other.

NB: the default occupancy policy is set to <all> because multiple conformations do not matter for sequence alignment. see the Molecular_geometry_loader doc (1 = All, 2 = forbidden, 3 = None, 4 = Max, 5 = min).

Constructor & Destructor Documentation

◆ __init__()

def __init__ (   self,
  od = ".",
  occ = 1,
  mn1 = 1,
  mn2 = 1,
  cm = {},
  verb = False # 

Member Function Documentation

◆ __str__()

def __str__ (   self)

◆ atom_matchings_file_suffix()

def atom_matchings_file_suffix (   self)

◆ bound_chains()

def bound_chains (   self)

◆ bound_pdb_file_path()

def bound_pdb_file_path (   self)

◆ occupancy_policy_index()

def occupancy_policy_index (   self)

◆ output_directory()

def output_directory (   self)

◆ pdb_sequence_alignment_executable_path()

def pdb_sequence_alignment_executable_path (   self)

◆ residue_matchings_file_suffix()

def residue_matchings_file_suffix (   self)

◆ unbound_chains()

def unbound_chains (   self)

◆ unbound_pdb_file_path()

def unbound_pdb_file_path (   self)

◆ write_matchings_files()

def write_matchings_files (   self)