#!/user/bin/env python
'''polymerComposition.py
This filter returns entries that contain chains made of the specified
monomer types.
'''
__author__ = "Mars (Shih-Cheng) Huang"
__maintainer__ = "Mars (Shih-Cheng) Huang"
__email__ = "marshuang80@gmail.com"
__version__ = "0.2.0"
__status__ = "done"
[docs]class PolymerComposition(object):
'''The default constructor returns entries that contain at least
one chain that matches the conditions. If the "exclusive" flag is set to true
in the constructor, all chains must match the conditions. For a multi-model
structure, this filter only checks the first model.
Optional constructor that can be used to filter entries that exclusively
match all chains.
Attributes
----------
exclusive : bool
if true, all chains must be made of the specified monomers
'''
# define sets of residue types eg:
# 20 nat. amino acids, 22 nat. amino acids, nat. DnNA, nat. RNA
# custom sets
AMINO_ACIDS_20 = ["ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", "HIS",
"ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL"]
AMINO_ACIDS_22 = ["ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", "HIS", "ILE",
"LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL", "SEC", "PYL"]
DNA_STD_NUCLEOTIDES = ["DA", "DC", "DG", "DT"]
RNA_STD_NUCLEOTIDES = ["A", "C", "G", "U"]
def __init__(self, monomer_type, exclusive=False):
if type(monomer_type) == str:
monomer_type = monomer_type.split(",")
self.exclusive = exclusive
self.residues = monomer_type
def __call__(self, t):
structure = t[1]
contains_polymer = False
global_match = False
# get number of chains in first model, nessary?
num_chains = structure.chains_per_model[0]
# chain types in entity as key, enetity from entity_list
group_counter = 0
for i in range(num_chains):
match = True
chain_type = [chain['type'] for chain in structure.entity_list
if i in chain['chainIndexList']][0]
polymer = chain_type == "polymer"
if polymer:
contains_polymer = True
else:
match = False
# group_type_list
for j in range(structure.groups_per_chain[i]):
if match and polymer:
group_idx = structure.group_type_list[group_counter]
group_type = structure.group_list[group_idx]['groupName']
match = (group_type in self.residues)
group_counter += 1
if (polymer and match and not self.exclusive):
return True
if (polymer and not match and self.exclusive):
return False
if match:
global_match = True
return global_match and contains_polymer
