def run_pdb2pqr(pdblines):
"""
Runs PDB2PQR on the input
"""
oldsyspath = sys.path
pqrhandle, pqrfile = tempfile.mkstemp()
tmphandle, tmpfile = tempfile.mkstemp()
tmpf = open(tmpfile, "w")
err = "/tmp/pdb2pqr.err"
for l in pdblines:
if l.find("XXX") == -1:
print(l, file=tmpf)
tmpf.close()
try:
import pdb2pqr
args = [pdb2pqr.__file__, "--ff=AMBER", tmpfile, pqrfile]
#if pdb2pqr.PACKAGE_PATH != "":
# sys.path.extend(pdb2pqr.PACKAGE_PATH.split(":"))
oldstdout = sys.stdout
sys.stdout = sys.stderr
oldargv = list(sys.argv)
sys.argv[:] = args
try:
pdb2pqr.mainCommand(args)
except ValueError as exc:
msg = exc.args[0]
if msg.startswith("This PDB file is missing too many"):
raise FixError(msg)
else:
raise
finally:
sys.argv[:] = oldargv
sys.stdout = oldstdout
pqr = os.fdopen(pqrhandle)
pqrlines = pqr.readlines()
pqr.close()
except:
os.system("pdb2pqr --ff=AMBER %s %s 2> %s" % (tmpfile, pqrfile, err))
os.system("cat %s" % err)
pqrlines = list(open(pqrfile))
finally:
os.remove(tmpfile)
os.remove(pqrfile)
result = []
repl = (
(" H ", " HN "),
(" H ", " HT1"),
(" H2 ", " HT2"),
(" H3 ", " HT3"),
)
for l in pqrlines:
result.append(l)
atom2 = l[12:16]
for pin, pout in repl:
if atom2 == pin:
p = l[:12] + pout + l[16:]
result.append(p)
return result
def _get_pqr(self):
"""Run PDB2PQR to get charge for each atom
TODO: figure out why unknown residues fro hetatms are absent
"""
if self.pqr is None:
pdbfd, tmp_pdb_path = tempfile.mkstemp()
with os.fdopen(pdbfd, 'w') as tmp:
# writer.set_structure(self.structure)
# writer.save(tmp)
# tmp.seek(0)
self.save_pdb(tmp, True)
_, tmp_pqr_path = tempfile.mkstemp()
with silence_stdout(), silence_stderr():
mainCommand(["pdb2pqr.py", "--ff=amber", "--whitespace", tmp_pdb_path, tmp_pqr_path])
os.remove(tmp_pdb_path)
self.pqr = {}
with open(tmp_pqr_path) as pqr:
for line in pqr:
for line in pqr:
if line.startswith("REMARK"): continue
fields = line.rstrip().split()
if len(fields) == 11:
recordName, serial, atomName, residueName, chainID, residueNumber, X, Y, Z, charge, radius = fields
elif len(fields) == 10:
recordName, serial, atomName, residueName, residueNumber, X, Y, Z, charge, radius = fields
else:
print len(fields)
raise RuntimeError("Invalid PQR File")
resseq = int("".join([i for i in residueNumber if i.isdigit()]))
icode = "".join([i for i in residueNumber if not i.isdigit()])
if icode == "":
icode = " "
if recordName == "HETATM": # hetero atom flag
if residueName in ["HOH", "WAT"]:
hetero_flag = "W"
else:
hetero_flag = "H_{}".format(residueName)
else:
hetero_flag = " "
residue_id = (hetero_flag, resseq, icode)
key = resseq #(residue_id, (atomName.strip(), ' '))
self.pqr[key] = float(charge)
os.remove(tmp_pqr_path)
return self.pqr
def get_pqr(pdb, sdie="78.5400", save_path="./"):
sys.path.insert(0, VISUALDEP_CONFIG["pdb2pqr_path"])
import pdb2pqr
pqr = os.path.join(save_path, pdb.split(os.sep)[-1][:-4] + ".pqr")
l = "./ --ff AMBER -v --whitespace --chain %s %s" % (pdb, pqr)
sys.argv = l.split()
pdb2pqr.mainCommand(sys.argv)
return pqr
def run_pdb2pqr(pdblines):
"""
Runs PDB2PQR on the input
"""
import pdb2pqr
oldsyspath = sys.path
pqrhandle, pqrfile = tempfile.mkstemp()
tmphandle, tmpfile = tempfile.mkstemp()
tmpf = open(tmpfile, "w")
for l in pdblines:
if l.find("XXX") == -1:
print >> tmpf, l
tmpf.close()
try:
args = [pdb2pqr.__file__, "--ff=charmm", tmpfile, pqrfile]
#if pdb2pqr.PACKAGE_PATH != "":
# sys.path.extend(pdb2pqr.PACKAGE_PATH.split(":"))
oldstdout = sys.stdout
sys.stdout = sys.stderr
oldargv = list(sys.argv)
sys.argv[:] = args
pdb2pqr.mainCommand(args)
sys.argv[:] = oldargv
sys.stdout = oldstdout
pqr = os.fdopen(pqrhandle)
pqrlines = pqr.readlines()
pqr.close()
finally:
os.remove(tmpfile)
os.remove(pqrfile)
result = []
repl = (
(" H ", " HN "),
(" H ", " HT1"),
(" H2 ", " HT2"),
(" H3 ", " HT3"),
)
for l in pqrlines:
result.append(l)
atom2 = l[12:16]
for pin, pout in repl:
if atom2 == pin:
p = l[:12] + pout + l[16:]
result.append(p)
return result
# -*- coding: utf-8 -*-
import re
import sys
from pdb2pqr import mainCommand
if __name__ == '__main__':
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
sys.exit(mainCommand())