class Pair:
def __init__(self, receptordb, liganddb):
self.ligand = Ligand(liganddb)
self.receptor = Receptor(receptordb)
def foreachPair(self, pid, sink):
self.ligand.foreachId(lambda cid: sink(pid, cid))
def foreach(self, sink, criteria=''):
self.receptor.foreachId(lambda pid: self.foreachPair(pid, sink))
def size(self, rcriteria='1=1', lcriteria='1=1'):
ligands = self.ligand.size(lcriteria)
receptors = self.receptor.size(rcriteria)
return ligands * receptors
def close(self):
self.ligand.close()
self.receptor.close()
import os
from parameter import Parameter
from ligand import Ligand
from receptor import Receptor
from path import Path
def print_pairs(pid, ligand):
ligand.foreachId(lambda cid: print(pid, cid, sep='\t'))
p = Parameter()
pt = Path(p)
ligand = Ligand(pt.data + p._('project.wizard.ligand.db'))
receptor = Receptor(pt.data + p._('project.wizard.receptor.db'))
receptor.foreachId(lambda id: print_pairs(id, ligand))
ligand.close()
receptor.close()
from parameter import Parameter
from ligand import Ligand
from receptor import Receptor
def line(id, ligand):
ids = [str(id)]
ligand.foreachId(lambda id: ids.append(str(id)))
return '\t'.join(ids)
p = Parameter()
ligand = Ligand(p._('project.ligand.db'))
receptor = Receptor(p._('project.receptor.db'))
receptor.foreachId(lambda id: print(line(id, ligand)))
ligand.close()
receptor.close()
def ok(line):
field = re.split('\s+', line)
if field[0] == 'ANISOU':
return False
if field[0] in ['ATOM', 'HETATM']:
return field[2].upper() not in ['NA']
return True
def remove_noise(id, path, incl):
if id in incl:
content = open(path).read().strip('\n').split('\n')
newcontent = [s for s in content if ok(s)]
if len(content) != len(newcontent):
open(path, 'w').write('\n'.join(newcontent))
print(id)
p = Parameter()
pt = Path(p)
molecule = Receptor(pt.receptordb)
incl = p._('project.wizard.receptor_remove_noise.include').split(',')
molecule.foreachId(lambda id: remove_noise(id, pt.receptor(id), incl))