def write_correlInput(self, **kwargs):
kwargs = lowerKeys(kwargs)
header = kwargs.get('header', [])
#
print self.anlPathname
if self.anlPathname is None:
raise IOError("No directory specified.")
mkdir(self.anlPathname)
#
for i, group in enumerate(grouper(self.nativeContacts, 100)):
String = self.get_correlInputHeader(header)
String.append('! anl :: write')
for j, contact in enumerate(group):
String.append('open unit %03d write card name %s/natq%02d%02d.anl' % (j+100, self.anlPathname, i, j))
String.append('')
String.append('correl maxtimesteps %d maxatom %d maxseries %d' % (self.correlArrayLength, 1000, len(group)))
for j, contact in enumerate(group):
String.append('enter n%03d bond bynum %d bynum %d geometry' % (j, contact.i.atomNum, contact.j.atomNum))
String.append('traj firstu 10 nunit 1 begin %d stop %d skip %d select all end' % (self.correlStart, self.correlStop, self.correlSkip))
String.append('')
for j, contact in enumerate(group):
String.append('write n%03d card unit %03d' % (j, j+100))
String.append('* Contact %02d%02d: between cgAtoms %s and %s' % (i, j, contact.i.addr, contact.j.addr))
String.append('* Native Contact - Interaction between %s and %s' % (contact.i.prmString, contact.j.prmString))
String.append('*')
String.append('')
String.append('end')
String.append('')
String.append('rewind unit 10')
String.append('')
String.append('stop')
String = '\n'.join(String)
# Write file
self.inpFilename = '%s/natq%02d.inp' % (self.inpPathname, i)
print '%s' % self.inpFilename
write_to = open(self.inpFilename, 'w')
write_to.write(String)
write_to.close()
def fset(self, value):
self._outPathname = self.expandPath(value)
mkdir(self._outPathname)
def parse(pdbFilename, **kwargs):
"""
Parse a *.pdb* plain text file into its constituent chains and segments, and
print one CHARMM formatted *.pdb* file per chain/segment combination.
*kwarg defaults are listed first*
**kwargs:**
| ``informat`` ['auto', 'pdborg', 'charmm'] # 'auto' -> detects input formatting
| ``outformat`` ['charmm', 'pdborg', 'auto'] # 'auto' -> same as input formatting
| ``outpath`` ['auto', user_specified_path] # 'auto' -> same as pdbFilename path
| ``fix_chainid`` [True, False]
| ``autofix`` [True, False]
| ``modelnum`` ['auto', 0, 1, 2, ...] # 'auto' -> uses the first model found
| ``pickleme`` [False, True] # pickles the PDBFile object for later use
| ``verbose`` [False, True]
| ``old_resid`` [False, True]
>>> parse('~/pychm/1yjp/1yjp.pdb',outpath='~',pickleme=True)
"""
# kwargs
kwargs = lowerKeys(kwargs)
inFormat = kwargs.get('informat', 'auto')
outFormat = kwargs.get('outformat', 'charmm')
outPath = kwargs.get('outpath', 'auto')
fix_chainid = kwargs.get('fix_chainid', True)
autoFix = kwargs.get('autofix', True)
modelNum = kwargs.get('modelnum', 'auto')
pickleMe = kwargs.get('pickleme', False)
verbose = kwargs.get('verbose', False)
old_resid = kwargs.get('old_resid', False)
# Repackage the PDBFile kwargs, make pdbFile object
pdbFileArgs = {'informat':inFormat, 'fix_chainid':fix_chainid,
'autofix':autoFix, 'verbose':verbose}
pdb = PDBFile(pdbFilename, **pdbFileArgs)
if verbose:
print '%s: Output formatting set to `%s`' % (pdb.code, outFormat)
# Get model number...
if modelNum == 'auto':
thisMol = pdb.iter_models().next()
else:
thisMol = pdb[modelNum]
if verbose:
print '%s: Loading `%s`' % (pdb.code, thisMol.name)
# Determine explicit output Path
if outPath == 'auto':
outPath = pdb.path
else:
outPath = expandPath(outPath)
mkdir(outPath)
if verbose:
print '%s: Output path set to `%s`' % (pdb.code, outPath)
# Do Work
thisMol.parse()
if verbose:
print '%s: Parsing `%s`' % (pdb.code, thisMol.name)
# Write CHARMMing style output.
segDict = {'nuc':'nuc', 'pro':'pro', 'good':'goodhet', 'bad':'het',
'dna':'dna', 'rna':'rna'}
stdoutList = []
# Write pdb files
writeArgs = {'outformat':outFormat, 'ter':True, 'end':False,
'old_resid':old_resid}
for seg in thisMol.iter_seg():
stdoutList.append('%s-%s' % (seg.chainid, segDict[seg.segType]))
name = '%s/new_%s-%s-%s.pdb' % (outPath, thisMol.code, seg.chainid,
segDict[seg.segType])
if verbose:
print '%s: Writing output to file `%s`' % (pdb.code, name)
seg.write(filename=name, **writeArgs)
# Write pickle (chk) file
if pickleMe:
pickleFilename = '%s/%s.chk' % (outPath, pdb.code)
pickleFile = open(pickleFilename,'w')
dump(pdb,pickleFile)
pickleFile.close()
if verbose:
print '%s: Writing pickle to file `%s`' % (pdb.code, pickleFilename)
if verbose:
print '\n\nEnd of verbosity\n\n'
# To STDOUT
print 'natom=%d' % len(thisMol)
print 'nwarn=%d' % len(thisMol.warnings)
if thisMol.warnings:
print 'warnings=%r' % thisMol.warnings
print 'seg=%r' % stdoutList