def rexHist(iterable, title, write=False, imgFilePath=None):
"""
`iterable` *string # An iterable of the CHARMM .out files
`title` string # The title of the plot.
`write` [`False`,`"svg"`,`"png"`] # The plot's output format,
# False won't write a file.
`imgFilePath` string # The plot's file path, defaults
# to `$cwd/default_title`.
"""
fileList = list(iterable)
fileList = map(expandPath, fileList)
tempArray = []
for fileName in fileList:
print 'Processing %s...' % fileName
filePointer = open(fileName)
rawData = getProp(filePointer, 'averener', 'avertemp')
tempArray.append(np.array(rawData['avertemp']).mean()) # Calc Temp
histData = np.histogram(rawData['averener'], 20, new=True)
pyplot.plot(histData[1][1:],histData[0],label=os.path.basename(fileName))
pyplot.legend( ['%3dK' % tempArray[i] for i in xrange(len(fileList))]
,loc=0, ncol=2)
pyplot.xlabel(r'$Energy\ (kcal\ mol^{-1})$')
pyplot.ylabel(r'$Frequency$')
pyplot.title(r'%s' % title)
if write:
if imgFilePath is None:
imgFilePath = '%s/%s.%s' % (os.path.dirname(fileList[0]), title,
write)
else:
imgFilePath = expandPath(imgFilePath)
pyplot.savefig(imgFilePath, format=write)
else:
pyplot.show()
def fset(self, value):
value = expandPath(value)
if not exists(value):
raise IOError("No such file or directory: '%s'" % value)
self._pdbFilename = value
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
def fset(self, value):
self._filename = expandPath(value)
def __init__(self, filename, **kwargs):
super(BaseCHARMMFile, self).__init__()
self.filename = expandPath(filename)
self.header = []
self.body = []
def write(self, filename, **kwargs):
"""
Writes a file containing the molecular information contained in
:class:`BaseStruct` object.
**kwargs:**
| ``outformat`` ["charmm","pdborg","debug","xdebug","crd","xcrd","mol2"]
| ``old_chainid`` [False,True]
| ``old_segType`` [False,True]
| ``old_resid`` [False,True]
| ``old_atomNum`` [False,True]
| ``ter`` [False,True]
| ``end`` True if `outformat` in ["pdborg","charmm"]
| ``append`` [False,True]
>>> thisSeg.write('~/1yjp.pdb',outformat='charmm',old_resid=True)
"""
# kwargs
kwargs = lowerKeys(kwargs)
outFormat = kwargs.get('outformat', 'charmm')
end = kwargs.get('end', None)
ter = kwargs.get('ter', None)
append = kwargs.get('append', False)
#
filename = expandPath(filename)
writeMe = []
if outFormat in ['pdborg', 'charmm']:
for atom in self:
writeMe.append(atom.Print(**kwargs))
if ter is None:
ter = True
if end is None:
end = True
elif outFormat == 'mol2':
header = kwargs.get('header', None)
bonds = kwargs.get('bonds', None)
writeMe.append('@<TRIPOS>MOLECULE')
if header:
for line in header:
writeMe.append(line)
writeMe.append('')
writeMe.append('@<TRIPOS>ATOM')
for atom in self:
writeMe.append(atom.Print(**kwargs))
writeMe.append('')
writeMe.append('@<TRIPOS>BOND')
if bonds:
for bond in bonds:
writeMe.append(bond.writeOut())
writeMe.append('')
elif outFormat in ['debug', 'xdebug']:
for atom in self:
writeMe.append(atom.Print(**kwargs))
elif outFormat in ['crd', 'cor', 'card', 'short', 'shortcard',
'xcrd', 'xcor', 'xcard', 'long', 'longcard']:
writeMe.append('*')
writeMe.append(' %d' % len(self))
for atom in self:
writeMe.append(atom.Print(**kwargs))
# TER/END
if ter:
writeMe.append('TER')
if end:
writeMe.append('END\n')
# Write file
writeMe = '\n'.join(writeMe)
if append:
writeTo = open(filename,'a')
else:
writeTo = open(filename,'w')
writeTo.write(writeMe)
writeTo.close()