def initialize(self):
self.modelCoordinates = {}
self.patt.update(getRegularExpressions('pdb'))
self.chains = []
def initialize(self):
self.modelCoordinates = {}
self.patt.update(getRegularExpressions('pdb'))
self.chains = []
self.serialToCoord = {}
self.chainIds = 'ABCDEFGHIJKLMNO' #PQRSTUVWXYZ' # Limited to 26!
def __init__(self, name, *args, **keywds):
self.name = name
self.newline = os.linesep
self.version = None
if 'version' in keywds.keys():
self.version = keywds['version']
del (keywds['version'])
self.setGeneric()
self.patt = getRegularExpressions(self.format)
self.initialize(*args, **keywds)
def __init__(self, version = None):
self.patt = getRegularExpressions()
self.readComponents = ['STARTGRP','HEADRES','RESIDUE','TAILRES']
self.refInfo = {}
if version in ['2.1']:
fileName = 'cyana2.1.lib'
else:
fileName = 'cyana.lib'
self.read(getDataPath('ccp', 'cyana', fileName))
self.setAtomPosition()
self.setAngleAtoms()
if funcName == fcInfo[formatName]['export'][component][0]:
exportFormats[formatName].append(component)
break
if not exportFormats[formatName]:
del(exportFormats[formatName])
return exportFormats, ccpnObjects
#
# Get the regular expressions
#
from ccp.format.general.Util import getRegularExpressions
ccpPatt = getRegularExpressions()
def getResName(chainCode,seqCode,atomName,seqInsertCode = '',spinSystemId = None, fixChainCode = True):
if seqCode == None and spinSystemId != None:
seqCode = "SS%d" % spinSystemId
if None in (chainCode,seqCode):
print " Error creating resName: chainCode or seqCode element is None ('%s')" % (str((chainCode,seqCode)))
resName = None
else:
if fixChainCode:
chainCode = '%s' % chainCode
def setFormat(self):
self.format = 'sparky'
self.IOkeywords = IOkeywords
self.patt = getRegularExpressions(format=self.format)