os.mkdir(dir)
#
# Does the PDB file exist?
#
if not os.path.isfile(pdb):
failed.append(pdbid)
continue
os.system('cp %s %s' %(pdb,newpdb))
#
# Correct with WI
#
import WI_tools
renumb=1
setcha=None
readallmodels=None
logifile,files=WI_tools.delwat_dellig_corall(newpdb,renumb,readallmodels,setcha)
filenms=files.keys()
if len(filenms)!=1:
print 'More than one filename',filenms
failed.append(pdbid)
continue
import string
#
# Do we have a chain identifier?
#
chainid=-1
changes=0
for line in files[filenms[0]]:
split=string.split(line)
#print split
if split[0]=='ATOM':
def main():
#
# Run pKa calculations in all subdirs given as argument
#
import sys
print
print 'Run pKa calculations in all subdirs. '
print
print 'Looking for pdb files with the name: %s' %sys.argv[1]
print 'Running pKa calculations for: '
import os, sys, string
initial_pdbfile='pdbfile.pdb'
dirs=sys.argv[1:]
#
# if the last argument is '-name', then the name of the dir is part of the pdbfile name
#
top=os.getcwd()
for dir in dirs:
if os.path.isdir(dir):
print dir
print
print '----------------------'
for dir in dirs:
if os.path.isdir(dir):
initial_pdbfile=dir+'.pdb'
pkafile=os.path.join(dir,'clean.pka.pdb')
if not os.path.isfile(pkafile):
import WI_tools
logfile,files=WI_tools.delwat_dellig_corall(os.path.join(os.getcwd(),dir,initial_pdbfile),None,1)
print os.path.join(os.getcwd(),dir,initial_pdbfile)
for line in logfile:
print line,
fs=files.keys()
print fs
if len(fs)!=1:
done=None
print dir
import string
pdbfile=string.lower(dir[-4:])+'.pdb.gz'
pdbdir='/net/scratch67/jnielsen/pdb'
pdbfile=os.path.join(pdbdir,pdbfile)
if os.path.isfile(pdbfile):
print 'Could not find file'
#a=raw_input('Get file from pdb dir? ')
#a='y'
a='n'
if a=='y':
destination=os.path.join(os.getcwd(),dir,os.path.split(pdbfile)[1])
print destination
os.system('cp '+pdbfile+' '+destination)
os.system(gunzip+' '+destination)
destination=destination[:-3]
print destination
os.link(destination,os.path.join(os.getcwd(),dir,initial_pdbfile))
done=1
if not done:
print initial_pdbfile
raise 'Huh? - could not clean PDB file'
else:
fd=open(pkafile,'w')
fd2=open(pkafile+'.backup','w')
for line in files[fs[0]]:
fd2.write(line)
fd.write(line)
fd.close()
fd2.close()
print 'Cleaned PDB file written'
#
# Prepare the pKa calculation (write the Invocation file)
#
import splitpdb
splitpdb.prep_pKa(dir,os.path.split(pkafile)[1])
os.chdir(dir)
import pKa
#
# Read the parameters
#
infile='Invocation'
fd=open(infile)
line=fd.readline()
fd.close()
argv=string.split(line)
#
# Do we need to run the pKa calculations for this dir?
#
pdbfile=argv[1]
if not os.path.isfile(pdbfile+'.PKA.DAT'):
print 'Running pKa calculations for: %s ' %dir
print
print 'Using command:',string.join(argv)
#
# Parse parameters
#
x=pKa.pKamisc()
params=x.parse_parameterlist(argv)
X=pKa.pKarun(os.getcwd(),pdbfile,params)
X.runseq()
print '============================='
print
os.chdir(top)
return
def main():
#
# Run pKa calculations in all subdirs given as argument
#
import sys
print
print 'Run pKa calculations in all subdirs. '
print
print 'Looking for pdb files with the name: %s' % sys.argv[1]
print 'Running pKa calculations for: '
import os, sys, string
initial_pdbfile = 'pdbfile.pdb'
dirs = sys.argv[1:]
#
# if the last argument is '-name', then the name of the dir is part of the pdbfile name
#
top = os.getcwd()
for dir in dirs:
if os.path.isdir(dir):
print dir
print
print '----------------------'
for dir in dirs:
if os.path.isdir(dir):
initial_pdbfile = dir + '.pdb'
pkafile = os.path.join(dir, 'clean.pka.pdb')
if not os.path.isfile(pkafile):
import WI_tools
logfile, files = WI_tools.delwat_dellig_corall(
os.path.join(os.getcwd(), dir, initial_pdbfile), None, 1)
print os.path.join(os.getcwd(), dir, initial_pdbfile)
for line in logfile:
print line,
fs = files.keys()
print fs
if len(fs) != 1:
done = None
print dir
import string
pdbfile = string.lower(dir[-4:]) + '.pdb.gz'
pdbdir = '/net/scratch67/jnielsen/pdb'
pdbfile = os.path.join(pdbdir, pdbfile)
if os.path.isfile(pdbfile):
print 'Could not find file'
#a=raw_input('Get file from pdb dir? ')
#a='y'
a = 'n'
if a == 'y':
destination = os.path.join(
os.getcwd(), dir,
os.path.split(pdbfile)[1])
print destination
os.system('cp ' + pdbfile + ' ' + destination)
os.system(gunzip + ' ' + destination)
destination = destination[:-3]
print destination
os.link(
destination,
os.path.join(os.getcwd(), dir,
initial_pdbfile))
done = 1
if not done:
print initial_pdbfile
raise 'Huh? - could not clean PDB file'
else:
fd = open(pkafile, 'w')
fd2 = open(pkafile + '.backup', 'w')
for line in files[fs[0]]:
fd2.write(line)
fd.write(line)
fd.close()
fd2.close()
print 'Cleaned PDB file written'
#
# Prepare the pKa calculation (write the Invocation file)
#
import splitpdb
splitpdb.prep_pKa(dir, os.path.split(pkafile)[1])
os.chdir(dir)
import pKa
#
# Read the parameters
#
infile = 'Invocation'
fd = open(infile)
line = fd.readline()
fd.close()
argv = string.split(line)
#
# Do we need to run the pKa calculations for this dir?
#
pdbfile = argv[1]
if not os.path.isfile(pdbfile + '.PKA.DAT'):
print 'Running pKa calculations for: %s ' % dir
print
print 'Using command:', string.join(argv)
#
# Parse parameters
#
x = pKa.pKamisc()
params = x.parse_parameterlist(argv)
X = pKa.pKarun(os.getcwd(), pdbfile, params)
X.runseq()
print '============================='
print
os.chdir(top)
return
os.mkdir(dir)
#
# Does the PDB file exist?
#
if not os.path.isfile(pdb):
failed.append(pdbid)
continue
os.system('cp %s %s' % (pdb, newpdb))
#
# Correct with WI
#
import WI_tools
renumb = 1
setcha = None
readallmodels = None
logifile, files = WI_tools.delwat_dellig_corall(newpdb, renumb,
readallmodels, setcha)
filenms = files.keys()
if len(filenms) != 1:
print 'More than one filename', filenms
failed.append(pdbid)
continue
import string
#
# Do we have a chain identifier?
#
chainid = -1
changes = 0
for line in files[filenms[0]]:
split = string.split(line)
#print split
if split[0] == 'ATOM':
