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)