def main():
"""
To be called if module run from command line.
"""
from helper import cmdline
# Parse command line
cmdline.initializeParser(__description__, __date__)
cmdline.addOption(short_flag="c",
long_flag="chains",
action="store",
default=None,
help="File containing chains to take",
nargs=1)
cmdline.addOption(short_flag="o",
long_flag="out_suffix",
action="store",
default="clean",
help="suffix to append to output pdb",
nargs=1)
cmdline.addOption(short_flag="r",
long_flag="renumber_residues",
action="store_true",
default=False,
help="Renumber residues from 1")
cmdline.addOption(short_flag="k",
long_flag="keep_temp",
action="store_true",
default=False,
help="Keep temporary files")
cmdline.addOption(short_flag="s",
long_flag="skip",
action="store_true",
default=True,
help="skip messed up pdb files")
cmdline.addOption(short_flag="f",
long_flag="fix_atoms",
action="store_false",
default=True,
help="fix atoms in original file")
cmdline.addOption(short_flag="n",
long_flag="num_steps",
action="store",
default=500,
help="number of minimization steps",
nargs=1)
file_list, options = cmdline.parseCommandLine()
# Parse command line options
if options.chains == None:
chains = "all"
else:
chains = cmdline.readFile(options.chains)
suffix = options.out_suffix
renumber_residues = options.renumber_residues
keep_temp = options.keep_temp
fix_atoms = options.fix_atoms
num_steps = options.num_steps
for pdb_file in file_list:
f = open(pdb_file, 'r')
pdb = f.readlines()
f.close()
print "Loading %s" % pdb_file
pdb_id = pdb_file[:-4]
try:
pdb = pdbClean(pdb, pdb_id, chains, renumber_residues, keep_temp,
fix_atoms, num_steps)
except PdbCleanError, (strerror):
err = "Error cleaning \"%s\"\n%s\n" % (pdb_file, strerror)
print err,
if options.skip:
g = open("error.log", "a")
g.write(err)
g.close()
continue
else:
sys.exit()
out_file = "%s_%s.pdb" % (pdb_id, suffix)
g = open(out_file, "w")
g.writelines(pdb)
g.close()
print "Cleaned pdb written to %s" % out_file
def main():
"""
To be called if module run from command line.
"""
from helper import cmdline
# Parse command line
cmdline.initializeParser(__description__,__date__)
cmdline.addOption(short_flag="c",
long_flag="chains",
action="store",
default=None,
help="File containing chains to take",
nargs=1)
cmdline.addOption(short_flag="o",
long_flag="out_suffix",
action="store",
default="clean",
help="suffix to append to output pdb",
nargs=1)
cmdline.addOption(short_flag="r",
long_flag="renumber_residues",
action="store_true",
default=False,
help="Renumber residues from 1")
cmdline.addOption(short_flag="k",
long_flag="keep_temp",
action="store_true",
default=False,
help="Keep temporary files")
cmdline.addOption(short_flag="s",
long_flag="skip",
action="store_true",
default=True,
help="skip messed up pdb files")
cmdline.addOption(short_flag="f",
long_flag="fix_atoms",
action="store_false",
default=True,
help="fix atoms in original file")
cmdline.addOption(short_flag="n",
long_flag="num_steps",
action="store",
default=500,
help="number of minimization steps",
nargs=1)
file_list, options = cmdline.parseCommandLine()
# Parse command line options
if options.chains == None:
chains = "all"
else:
chains = cmdline.readFile(options.chains)
suffix = options.out_suffix
renumber_residues = options.renumber_residues
keep_temp = options.keep_temp
fix_atoms = options.fix_atoms
num_steps = options.num_steps
for pdb_file in file_list:
f = open(pdb_file,'r')
pdb = f.readlines()
f.close()
print "Loading %s" % pdb_file
pdb_id = pdb_file[:-4]
try:
pdb = pdbClean(pdb,pdb_id,chains,renumber_residues,keep_temp,
fix_atoms,num_steps)
except PdbCleanError, (strerror):
err = "Error cleaning \"%s\"\n%s\n" % (pdb_file,strerror)
print err,
if options.skip:
g = open("error.log","a")
g.write(err)
g.close()
continue
else:
sys.exit()
out_file = "%s_%s.pdb" % (pdb_id,suffix)
g = open(out_file,"w")
g.writelines(pdb)
g.close()
print "Cleaned pdb written to %s" % out_file
def main():
"""
Call if program called from command line.
"""
# Parse command line
cmdline.initializeParser(__description__,__date__)
cmdline.addOption(short_flag="t",
long_flag="his_tautomers",
action="store",
default=None,
help="File containing his tautomers to use",
nargs=1)
cmdline.addOption(short_flag="k",
long_flag="keep_temp",
action="store_true",
default=False,
help="Keep temporary files")
cmdline.addOption(short_flag="f",
long_flag="full",
action="store_true",
default=False,
help="Add hydrogens for UHBD full calculation")
cmdline.addOption(short_flag="b",
long_flag="hbond",
action="store",
default=None,
help="Write out hbonds to file",
nargs=1,
type=str)
cmdline.addOption(short_flag="u",
long_flag="uhbd_style",
action="store_true",
default=False,
help="Write out in non-standard uhbd format")
cmdline.addOption(short_flag="s",
long_flag="skip",
action="store_true",
default=True,
help="skip messed up pdb files")
file_list, options = cmdline.parseCommandLine()
# Deal with his_tautomers file
if options.his_tautomers != None:
# Read in as a standard ascii file.
his_types = cmdline.readFile(options.his_tautomers)
try:
his_types = [int(h) for h in his_types]
# Make sure that entries are valid
check = [h == 1 or h == 2 for h in his_types]
if False in check:
raise ValueError
except ValueError:
err = "His tautomer file can contain only 1's (HISB) and 2's (HISA)"
cmdline.parser.error(err)
else:
his_types = None
# Decide whether to keep temp files and how to format output
keep_temp = options.keep_temp
uhbd_style = options.uhbd_style
hbond = options.hbond
# Decide whether to add "full" hydrogens.
if options.full:
calc_type = "full"
else:
calc_type = "single"
# Add hydrogens for every file in file_list
file_list.sort()
for file in file_list:
pdb_id = os.path.split(file)[-1][:-4]
out_file = "%sH.pdb" % pdb_id
print "%s --> %s" % (file,out_file)
# Load in file
f = open(file,'r')
pdb = f.readlines()
f.close()
# Add hydrogens
try:
pdb_out = pdbAddH(pdb,pdb_id,uhbd_style=uhbd_style,
his_types=his_types,
keep_temp=keep_temp,
calc_type=calc_type,
hbond=hbond)
except PdbAddHError, (strerror):
err = "Addition of hydrogens failed for %s\n" % file
err += "Problem was with CHARMM\n.%s" % strerror
print err
if options.skip:
print "CHARMM output written to error.log"
g = open("error.log","a")
g.write(err)
g.write("charmm.out copied below\n%s\n" % (79*"-"))
h = open("charmm.out",'r')
charmm_out = h.readlines()
h.close()
g.writelines(charmm_out)
g.write("\n\n")
g.close()
continue
else:
sys.exit()
# Dump to output file
g = open(out_file,'w')
g.writelines(pdb_out)
g.close()
