def addReactionRulesBlock(self,
rrBlock,
dimerGenBlock,
omniGenBlock,
uniMolGenBlock,
overwrite=False):
if self.reactionRulesBlock and not overwrite:
raise MzrExceptions.MoleculizerException(
"Error: Cannot add a reaction rules block twice.")
if not self.BlockPassesSanityCheck(rrBlock):
raise InsaneBlockOnTheLooseException(rrBlock, "reaction rules")
if not self.BlockPassesSanityCheck(dimerGenBlock):
raise InsaneBlockOnTheLooseException(dimerGenBlock,
"dimerization gen block")
if not self.BlockPassesSanityCheck(omniGenBlock):
raise InsaneBlockOnTheLooseException(omniGenBlock,
"omni-gen block")
if not self.BlockPassesSanityCheck(uniMolGenBlock):
raise InsaneBlockOnTheLooseException(uniMolGenBlock,
"uni-mol-gen block")
self.reactionRulesBlock.extend(rrBlock)
self.dimerizationGenBlock.extend(dimerGenBlock)
self.omniGenBlock.extend(omniGenBlock)
self.uniMolGenBlock.extend(uniMolGenBlock)
self.reactionGensSection = ReactionRulesSection(
self.reactionRulesBlock, self.dimerizationGenBlock,
self.omniGenBlock, self.uniMolGenBlock)
def addUniMolGenStatement(self, uniMolGenLine):
uniMolGenLine = self.PreProcessStatement(uniMolGenLine)
self.uniMolGenBlock.append(uniMolGenLine)
self.reactionGensSection = ReactionRulesSection(
self.reactionRulesBlock, self.dimerizationGenBlock,
self.omniGenBlock, self.uniMolGenBlock)
return
def addReactionRulesBlock( self, rrBlock, dimerGenBlock, omniGenBlock, uniMolGenBlock, overwrite = False):
if self.reactionRulesBlock and not overwrite:
raise MzrExceptions.MoleculizerException("Error: Cannot add a reaction rules block twice.")
if not self.BlockPassesSanityCheck( rrBlock ):
raise InsaneBlockOnTheLooseException(rrBlock, "reaction rules")
if not self.BlockPassesSanityCheck( dimerGenBlock ):
raise InsaneBlockOnTheLooseException(dimerGenBlock, "dimerization gen block")
if not self.BlockPassesSanityCheck( omniGenBlock ):
raise InsaneBlockOnTheLooseException(omniGenBlock, "omni-gen block")
if not self.BlockPassesSanityCheck( uniMolGenBlock ):
raise InsaneBlockOnTheLooseException(uniMolGenBlock, "uni-mol-gen block")
self.reactionRulesBlock.extend( rrBlock )
self.dimerizationGenBlock.extend( dimerGenBlock )
self.omniGenBlock.extend( omniGenBlock )
self.uniMolGenBlock.extend( uniMolGenBlock )
self.reactionGensSection = ReactionRulesSection( self.reactionRulesBlock,
self.dimerizationGenBlock,
self.omniGenBlock,
self.uniMolGenBlock)
def addUniMolGenStatement(self, uniMolGenLine):
uniMolGenLine = self.PreProcessStatement( uniMolGenLine )
self.uniMolGenBlock.append( uniMolGenLine )
self.reactionGensSection = ReactionRulesSection( self.reactionRulesBlock,
self.dimerizationGenBlock,
self.omniGenBlock,
self.uniMolGenBlock)
return
class MoleculizerRulesFile:
"""
This object acts as an parsing thing that outputs moleculizer files xml,
suitable for processing internally by a mzr::moleculizer instance."""
def BlockPassesSanityCheck( linearray ):
linearray = [x for x in linearray if x.strip() != ""]
if len(linearray) == 0: return True
everyLineEndsWithSemiColon = [ x[-1] == ";" and x.count(";") == 1for x in linearray]
noWhiteSpace = [ (x.count("\n") + x.count(" ") + x.count("\t") == 0) for x in linearray]
return reduce(util.And, everyLineEndsWithSemiColon) and reduce(util.And, noWhiteSpace)
BlockPassesSanityCheck = staticmethod( BlockPassesSanityCheck )
def addWholeRulesString( self, rulesString):
print "Reading file '%s' " % rulesString
lines = rulesString.split("\n")
parameterBlock, modificationsBlock, molsBlock, allostericPlexes, allostericOmnis,\
reactionRulesBlock, dimerizationGenBlock, omniGenBlock, \
explicitSpeciesBlock, speciesStreamBlock = parseBlockTypesFromRulesFile( lines )
self.addParameterBlock( parameterBlock )
self.addModicationsBlock( modificationsBlock )
self.addMolsBlock( molsBlock )
self.addAllostericPlexesBlock( allostericPlexes )
self.addAllostericOmnisBlock( allostericOmnis )
self.addReactionRulesBlock( reactionRulesBlock, dimerizationGenBlock, \
omniGenBlock, [] )
self.addExplicitSpeciesBlock( explicitSpeciesBlock )
self.addSpeciesStreamsBlock( speciesStreamBlock )
return
def addWholeRulesFile(self, rulesFile):
parameterBlock, modificationsBlock, molsBlock, allostericPlexes, allostericOmnis, \
reactionRulesBlock, dimerizationGenBlock, omniGenBlock, \
explicitSpeciesBlock, speciesStreamBlock = parseBlockTypesFromRulesFile( open(rulesFile).readlines() )
self.addParameterBlock( parameterBlock )
self.addModicationsBlock( modificationsBlock )
self.addMolsBlock( molsBlock )
self.addAllostericPlexesBlock( allostericPlexes )
self.addAllostericOmnisBlock( allostericOmnis )
self.addReactionRulesBlock( reactionRulesBlock, dimerizationGenBlock, \
omniGenBlock, [] )
self.addExplicitSpeciesBlock( explicitSpeciesBlock )
self.addSpeciesStreamsBlock( speciesStreamBlock )
return
def addParameterStatement(self, paramStatement):
paramStatement = self.PreProcessStatement( paramStatement )
print "Adding param line: '%s'" % paramStatement
self.parameterBlock.append( paramStatement)
self.parameterEE = SymbolicExpressionEvaluator( self.parameterBlock )
return
def addModificationStatement(self, modLine):
modLine = self.PreProcessStatement( modLine )
print "Adding mod line: '%s'" % modLine
self.modificationsBlock.append( modLine)
self.modificationsSection = ModificationsSection( self.modificationsBlock )
return
def addMolsStatement(self, molsLine):
molsLine = self.PreProcessStatement( molsLine )
self.molsBlock.append( molsLine )
self.molsSection = MolsSection( molsBlock )
return
def addAllostericPlexStatement(self, alloPlexLine):
alloPlexLine = self.PreProcessStatement( alloPlexLine )
self.allostericPlexes.append( alloPlexLine )
self.allostericPlexesSection = AllostericPlexesSection( self.allostericPlexes )
return
def addAllostericOmniStatement(self, alloOmniLine):
alloOmniLine = self.PreProcessStatement( alloOmniLine )
self.allostericOmnis.append( alloOmniLine )
self.allostericOmnisSection = AllostericOmnisSection( self.allostericOmnis )
return
def addDimerizationGenStatement(self, dimerGenLine):
dimerGenLine = self.PreProcessStatement( dimerGenLine )
self.dimerizationGenBlock.append(dimerGenLine)
self.reactionGensSection = ReactionRulesSection( self.reactionRulesBlock,
self.dimerizationGenBlock,
self.omniGenBlock,
self.uniMolGenBlock)
return
def addOmniGenStatement(self, omniGenLine):
omniGenLine = self.PreProcessStatement( omniGenLine )
self.omniGenLine.append( omniGenLine )
self.reactionGensSection = ReactionRulesSection( self.reactionRulesBlock,
self.dimerizationGenBlock,
self.omniGenBlock,
self.uniMolGenBlock)
return
def addUniMolGenStatement(self, uniMolGenLine):
uniMolGenLine = self.PreProcessStatement( uniMolGenLine )
self.uniMolGenBlock.append( uniMolGenLine )
self.reactionGensSection = ReactionRulesSection( self.reactionRulesBlock,
self.dimerizationGenBlock,
self.omniGenBlock,
self.uniMolGenBlock)
return
def addExplicitSpeciesStatement(self, explicitSpeciesStatement):
explicitSpeciesStatement = self.PreProcessStatement( explicitSpeciesStatement )
self.explicitSpeciesBlock.append( explicitSpeciesStatement )
self.explicitSpeciesSection = ExplicitSpeciesSection( self.explicitSpeciesBlock )
return
def addSpeciesStreamStatement(self, speciesStreamLine):
speciesStreamLine = self.PreProcessStatement( speciesStreamLine )
self.speciesStreamBlock.append( speciesStreamLine )
self.speciesStreamSection = SpeciesStreamsSection( self.speciesStreamBlock )
return
def __init__(self):
# These are the lines of input, in one statement per line form, with no whitespace
self.parameterBlock = []
self.modificationsBlock = []
self.molsBlock = []
self.allostericPlexes = []
self.allostericOmnis = []
self.reactionRulesBlock = []
self.dimerizationGenBlock = []
self.omniGenBlock = []
self.uniMolGenBlock = []
self.explicitSpeciesBlock = []
self.speciesStreamBlock = []
# These are the objects that will be used to process the parsed
# data.
# A section is an intermediate between a rules file (they have lines, for example,
# and can answer questions about what has been parsed ) and an xml section (it can
# write out an xml section -
# Parameters doesn't write anything out currently, but easily could
self.parameterSection = 0
self.modificationsSection = 0
self.molsSection = 0
self.allostericPlexesSection = 0
self.allostericOmnisSection = 0
self.reactionGensSection = 0
self.explicitSpeciesSection = 0
self.speciesStreamSection = 0
def getOutputFileName(self):
return self.outputFileName
def write(self):
self.openXmlFile = open(self.outputFileName, 'w')
self.__writeOutput(self.openXmlFile)
return
def writeToString(self):
myString = StringIO.StringIO()
self.__writeOutput( myString )
return myString.getvalue()
def close(self):
self.openXmlFile.close()
def addParameterBlock(self, parameterBlock, overwrite = False):
if self.parameterBlock and not overwrite:
raise MzrExceptions.MoleculizerException("Error: Cannot add a parameter block twice.")
if not self.BlockPassesSanityCheck( parameterBlock ):
raise InsaneBlockOnTheLooseException(parameterBlock, "parameter block")
self.parameterBlock = parameterBlock[:]
self.parameterEE = SymbolicExpressionEvaluator( self.parameterBlock )
def addModicationsBlock(self, modificationsBlock, overwrite = False):
if self.modificationsBlock and not overwrite:
raise MzrExceptions.MoleculizerException("Error: Cannot add a modifications block twice.")
if not self.BlockPassesSanityCheck( modificationsBlock ):
raise InsaneBlockOnTheLooseException(modificationsBlock, "modifications block")
self.modificationsBlock = modificationsBlock[:]
self.modificationsSection = ModificationsSection( self.modificationsBlock )
return
def addMolsBlock(self, molsBlock):
if self.molsBlock and not overwrite:
raise MzrExceptions.MoleculizerException("Error: Cannot add a mols block twice.")
if not self.BlockPassesSanityCheck( molsBlock ):
raise InsaneBlockOnTheLooseException(molsBlock, "mols block")
self.molsBlock = molsBlock[:]
self.molsSection = MolsSection( molsBlock )
def addAllostericPlexesBlock(self, apBlock, overwrite = False):
if self.allostericPlexes and not overwrite:
raise MzrExceptions.MoleculizerException("Error: Cannot add an allosteric plexes block twice.")
if not self.BlockPassesSanityCheck( apBlock ):
raise InsaneBlockOnTheLooseException(apBlock, "allosteric plexes block")
self.allostericPlexes = apBlock[:]
self.allostericPlexesSection = AllostericPlexesSection( self.allostericPlexes )
def addAllostericOmnisBlock(self, aoBlock, overwrite = False):
if self.allostericOmnis and not overwrite: raise MzrExceptions.MoleculizerException("Error: Cannot add an allosteric omnis block twice.")
if not self.BlockPassesSanityCheck( aoBlock ):
raise InsaneBlockOnTheLooseException( aoBlock, "allosteric omnis block")
self.allostericOmnis = aoBlock[:]
self.allostericOmnisSection = AllostericOmnisSection( self.allostericOmnis )
def addReactionRulesBlock( self, rrBlock, dimerGenBlock, omniGenBlock, uniMolGenBlock, overwrite = False):
if self.reactionRulesBlock and not overwrite:
raise MzrExceptions.MoleculizerException("Error: Cannot add a reaction rules block twice.")
if not self.BlockPassesSanityCheck( rrBlock ):
raise InsaneBlockOnTheLooseException(rrBlock, "reaction rules")
if not self.BlockPassesSanityCheck( dimerGenBlock ):
raise InsaneBlockOnTheLooseException(dimerGenBlock, "dimerization gen block")
if not self.BlockPassesSanityCheck( omniGenBlock ):
raise InsaneBlockOnTheLooseException(omniGenBlock, "omni-gen block")
if not self.BlockPassesSanityCheck( uniMolGenBlock ):
raise InsaneBlockOnTheLooseException(uniMolGenBlock, "uni-mol-gen block")
self.reactionRulesBlock.extend( rrBlock )
self.dimerizationGenBlock.extend( dimerGenBlock )
self.omniGenBlock.extend( omniGenBlock )
self.uniMolGenBlock.extend( uniMolGenBlock )
self.reactionGensSection = ReactionRulesSection( self.reactionRulesBlock,
self.dimerizationGenBlock,
self.omniGenBlock,
self.uniMolGenBlock)
def addExplicitSpeciesBlock( self, esBlock, overwrite = False):
if self.explicitSpeciesBlock and not overwrite:
raise MzrExceptions.MoleculizerException("Error: Cannot add an explicit species block twice.")
if not self.BlockPassesSanityCheck( esBlock ):
raise InsaneBlockOnTheLooseException(esBlock, "explicit-species")
self.explicitSpeciesBlock = esBlock[:]
self.explicitSpeciesSection = ExplicitSpeciesSection( esBlock )
def addSpeciesStreamsBlock(self, ssBlock, overwrite = False):
if self.speciesStreamBlock and not overwrite:
raise MzrExceptions.MoleculizerException("Error: Cannot add a species stream block twice.")
if not self.BlockPassesSanityCheck( ssBlock ):
raise InsaneBlockOnTheLooseException(ssBlock, "")
self.speciesStreamBlock = ssBlock[:]
self.speciesStreamSection = SpeciesStreamsSection( self.speciesStreamBlock )
def __processAllostericRulesBlocks( self, allostericPlexBlock, allostericOmniBlock):
return 0
def __processReactionRulesBlocks( self, rxnRulesBlock, dimerBlock, omniGenBlock, uniGenBlock):
return 0
def __processExplicitSpeciesBlock( self, explicitSpeciesBlock):
return 0
def __processSpeciesStreamBlock( self, ssBlock):
return 0
def __writeOutput(self, openXMLFile):
xmlobject = self.__constructXMLRepresentation()
xmlobject.writeall(openXMLFile)
def __constructXMLRepresentation(self):
rootNode = XmlObject("moleculizer-input")
modelElmt = XmlObject("model")
modelElmt.attachToParent(rootNode)
streamsElmt = XmlObject("streams", rootNode)
self.__addModifications( modelElmt )
self.__addMols( modelElmt )
self.__addAllostericPlexes( modelElmt )
self.__addAllostericOmnis( modelElmt )
self.__addReactionGens( modelElmt )
self.__addExplicitSpecies( modelElmt )
self.__addExplicitReactions( modelElmt )
self.__addSpeciesStreams( streamsElmt )
return rootNode
def __addModifications(self, parentObject):
# Write me!!!
modificationsSection = XmlObject("modifications", parentObject)
if self.modificationsSection:
self.modificationsSection.writeModificationsSections( modificationsSection )
return
def __addMols(self, parentObject):
molsSection = XmlObject("mols", parentObject)
if self.molsSection:
self.molsSection.writeMolsSection( molsSection)
return
def __addAllostericPlexes(self, parentObject):
allostericPlexes = XmlObject("allosteric-plexes", parentObject)
if self.allostericPlexesSection:
self.allostericPlexesSection.writeAllostericPlexesSection(allostericPlexes)
return
def __addAllostericOmnis(self, parentObject):
allostericOmnis = XmlObject("allosteric-omnis", parentObject)
if self.allostericOmnisSection:
self.allostericOmnisSection.writeAllostericOmnisSection( allostericOmnis )
return
def __addReactionGens(self, parentObject):
reactionGenElmt = XmlObject("reaction-gens", parentObject)
if self.reactionGensSection:
self.reactionGensSection.writeReactionGensSection( reactionGenElmt )
return
def __addSpeciesStreams( self, parentObject):
speciesStreamsElement = XmlObject("species-streams", parentObject)
if self.speciesStreamSection:
self.speciesStreamSection.writeSpeciesStreamSection( speciesStreamsElement )
def __addExplicitSpecies(self, parentObject):
explicitSpeciesElmt = XmlObject("explicit-species", parentObject)
if self.explicitSpeciesSection:
self.explicitSpeciesSection.writeExplicitSpeciesSection( explicitSpeciesElmt )
return
def __addExplicitReactions( self, modelElmt ):
explicitReactionsElmt = XmlObject("explicit-reactions", modelElmt)
return
class MoleculizerRulesFile:
"""
This object acts as an parsing thing that outputs moleculizer files xml,
suitable for processing internally by a mzr::moleculizer instance."""
def BlockPassesSanityCheck(linearray):
linearray = [x for x in linearray if x.strip() != ""]
if len(linearray) == 0: return True
everyLineEndsWithSemiColon = [
x[-1] == ";" and x.count(";") == 1 for x in linearray
]
noWhiteSpace = [(x.count("\n") + x.count(" ") + x.count("\t") == 0)
for x in linearray]
return reduce(util.And, everyLineEndsWithSemiColon) and reduce(
util.And, noWhiteSpace)
BlockPassesSanityCheck = staticmethod(BlockPassesSanityCheck)
def addWholeRulesString(self, rulesString):
print "Reading file '%s' " % rulesString
lines = rulesString.split("\n")
parameterBlock, modificationsBlock, molsBlock, allostericPlexes, allostericOmnis,\
reactionRulesBlock, dimerizationGenBlock, omniGenBlock, \
explicitSpeciesBlock, speciesStreamBlock = parseBlockTypesFromRulesFile( lines )
self.addParameterBlock(parameterBlock)
self.addModicationsBlock(modificationsBlock)
self.addMolsBlock(molsBlock)
self.addAllostericPlexesBlock(allostericPlexes)
self.addAllostericOmnisBlock(allostericOmnis)
self.addReactionRulesBlock( reactionRulesBlock, dimerizationGenBlock, \
omniGenBlock, [] )
self.addExplicitSpeciesBlock(explicitSpeciesBlock)
self.addSpeciesStreamsBlock(speciesStreamBlock)
return
def addWholeRulesFile(self, rulesFile):
parameterBlock, modificationsBlock, molsBlock, allostericPlexes, allostericOmnis, \
reactionRulesBlock, dimerizationGenBlock, omniGenBlock, \
explicitSpeciesBlock, speciesStreamBlock = parseBlockTypesFromRulesFile( open(rulesFile).readlines() )
self.addParameterBlock(parameterBlock)
self.addModicationsBlock(modificationsBlock)
self.addMolsBlock(molsBlock)
self.addAllostericPlexesBlock(allostericPlexes)
self.addAllostericOmnisBlock(allostericOmnis)
self.addReactionRulesBlock( reactionRulesBlock, dimerizationGenBlock, \
omniGenBlock, [] )
self.addExplicitSpeciesBlock(explicitSpeciesBlock)
self.addSpeciesStreamsBlock(speciesStreamBlock)
return
def addParameterStatement(self, paramStatement):
paramStatement = self.PreProcessStatement(paramStatement)
print "Adding param line: '%s'" % paramStatement
self.parameterBlock.append(paramStatement)
self.parameterEE = SymbolicExpressionEvaluator(self.parameterBlock)
return
def addModificationStatement(self, modLine):
modLine = self.PreProcessStatement(modLine)
print "Adding mod line: '%s'" % modLine
self.modificationsBlock.append(modLine)
self.modificationsSection = ModificationsSection(
self.modificationsBlock)
return
def addMolsStatement(self, molsLine):
molsLine = self.PreProcessStatement(molsLine)
self.molsBlock.append(molsLine)
self.molsSection = MolsSection(molsBlock)
return
def addAllostericPlexStatement(self, alloPlexLine):
alloPlexLine = self.PreProcessStatement(alloPlexLine)
self.allostericPlexes.append(alloPlexLine)
self.allostericPlexesSection = AllostericPlexesSection(
self.allostericPlexes)
return
def addAllostericOmniStatement(self, alloOmniLine):
alloOmniLine = self.PreProcessStatement(alloOmniLine)
self.allostericOmnis.append(alloOmniLine)
self.allostericOmnisSection = AllostericOmnisSection(
self.allostericOmnis)
return
def addDimerizationGenStatement(self, dimerGenLine):
dimerGenLine = self.PreProcessStatement(dimerGenLine)
self.dimerizationGenBlock.append(dimerGenLine)
self.reactionGensSection = ReactionRulesSection(
self.reactionRulesBlock, self.dimerizationGenBlock,
self.omniGenBlock, self.uniMolGenBlock)
return
def addOmniGenStatement(self, omniGenLine):
omniGenLine = self.PreProcessStatement(omniGenLine)
self.omniGenLine.append(omniGenLine)
self.reactionGensSection = ReactionRulesSection(
self.reactionRulesBlock, self.dimerizationGenBlock,
self.omniGenBlock, self.uniMolGenBlock)
return
def addUniMolGenStatement(self, uniMolGenLine):
uniMolGenLine = self.PreProcessStatement(uniMolGenLine)
self.uniMolGenBlock.append(uniMolGenLine)
self.reactionGensSection = ReactionRulesSection(
self.reactionRulesBlock, self.dimerizationGenBlock,
self.omniGenBlock, self.uniMolGenBlock)
return
def addExplicitSpeciesStatement(self, explicitSpeciesStatement):
explicitSpeciesStatement = self.PreProcessStatement(
explicitSpeciesStatement)
self.explicitSpeciesBlock.append(explicitSpeciesStatement)
self.explicitSpeciesSection = ExplicitSpeciesSection(
self.explicitSpeciesBlock)
return
def addSpeciesStreamStatement(self, speciesStreamLine):
speciesStreamLine = self.PreProcessStatement(speciesStreamLine)
self.speciesStreamBlock.append(speciesStreamLine)
self.speciesStreamSection = SpeciesStreamsSection(
self.speciesStreamBlock)
return
def __init__(self):
# These are the lines of input, in one statement per line form, with no whitespace
self.parameterBlock = []
self.modificationsBlock = []
self.molsBlock = []
self.allostericPlexes = []
self.allostericOmnis = []
self.reactionRulesBlock = []
self.dimerizationGenBlock = []
self.omniGenBlock = []
self.uniMolGenBlock = []
self.explicitSpeciesBlock = []
self.speciesStreamBlock = []
# These are the objects that will be used to process the parsed
# data.
# A section is an intermediate between a rules file (they have lines, for example,
# and can answer questions about what has been parsed ) and an xml section (it can
# write out an xml section -
# Parameters doesn't write anything out currently, but easily could
self.parameterSection = 0
self.modificationsSection = 0
self.molsSection = 0
self.allostericPlexesSection = 0
self.allostericOmnisSection = 0
self.reactionGensSection = 0
self.explicitSpeciesSection = 0
self.speciesStreamSection = 0
def getOutputFileName(self):
return self.outputFileName
def write(self):
self.openXmlFile = open(self.outputFileName, 'w')
self.__writeOutput(self.openXmlFile)
return
def writeToString(self):
myString = StringIO.StringIO()
self.__writeOutput(myString)
return myString.getvalue()
def close(self):
self.openXmlFile.close()
def addParameterBlock(self, parameterBlock, overwrite=False):
if self.parameterBlock and not overwrite:
raise MzrExceptions.MoleculizerException(
"Error: Cannot add a parameter block twice.")
if not self.BlockPassesSanityCheck(parameterBlock):
raise InsaneBlockOnTheLooseException(parameterBlock,
"parameter block")
self.parameterBlock = parameterBlock[:]
self.parameterEE = SymbolicExpressionEvaluator(self.parameterBlock)
def addModicationsBlock(self, modificationsBlock, overwrite=False):
if self.modificationsBlock and not overwrite:
raise MzrExceptions.MoleculizerException(
"Error: Cannot add a modifications block twice.")
if not self.BlockPassesSanityCheck(modificationsBlock):
raise InsaneBlockOnTheLooseException(modificationsBlock,
"modifications block")
self.modificationsBlock = modificationsBlock[:]
self.modificationsSection = ModificationsSection(
self.modificationsBlock)
return
def addMolsBlock(self, molsBlock):
if self.molsBlock and not overwrite:
raise MzrExceptions.MoleculizerException(
"Error: Cannot add a mols block twice.")
if not self.BlockPassesSanityCheck(molsBlock):
raise InsaneBlockOnTheLooseException(molsBlock, "mols block")
self.molsBlock = molsBlock[:]
self.molsSection = MolsSection(molsBlock)
def addAllostericPlexesBlock(self, apBlock, overwrite=False):
if self.allostericPlexes and not overwrite:
raise MzrExceptions.MoleculizerException(
"Error: Cannot add an allosteric plexes block twice.")
if not self.BlockPassesSanityCheck(apBlock):
raise InsaneBlockOnTheLooseException(apBlock,
"allosteric plexes block")
self.allostericPlexes = apBlock[:]
self.allostericPlexesSection = AllostericPlexesSection(
self.allostericPlexes)
def addAllostericOmnisBlock(self, aoBlock, overwrite=False):
if self.allostericOmnis and not overwrite:
raise MzrExceptions.MoleculizerException(
"Error: Cannot add an allosteric omnis block twice.")
if not self.BlockPassesSanityCheck(aoBlock):
raise InsaneBlockOnTheLooseException(aoBlock,
"allosteric omnis block")
self.allostericOmnis = aoBlock[:]
self.allostericOmnisSection = AllostericOmnisSection(
self.allostericOmnis)
def addReactionRulesBlock(self,
rrBlock,
dimerGenBlock,
omniGenBlock,
uniMolGenBlock,
overwrite=False):
if self.reactionRulesBlock and not overwrite:
raise MzrExceptions.MoleculizerException(
"Error: Cannot add a reaction rules block twice.")
if not self.BlockPassesSanityCheck(rrBlock):
raise InsaneBlockOnTheLooseException(rrBlock, "reaction rules")
if not self.BlockPassesSanityCheck(dimerGenBlock):
raise InsaneBlockOnTheLooseException(dimerGenBlock,
"dimerization gen block")
if not self.BlockPassesSanityCheck(omniGenBlock):
raise InsaneBlockOnTheLooseException(omniGenBlock,
"omni-gen block")
if not self.BlockPassesSanityCheck(uniMolGenBlock):
raise InsaneBlockOnTheLooseException(uniMolGenBlock,
"uni-mol-gen block")
self.reactionRulesBlock.extend(rrBlock)
self.dimerizationGenBlock.extend(dimerGenBlock)
self.omniGenBlock.extend(omniGenBlock)
self.uniMolGenBlock.extend(uniMolGenBlock)
self.reactionGensSection = ReactionRulesSection(
self.reactionRulesBlock, self.dimerizationGenBlock,
self.omniGenBlock, self.uniMolGenBlock)
def addExplicitSpeciesBlock(self, esBlock, overwrite=False):
if self.explicitSpeciesBlock and not overwrite:
raise MzrExceptions.MoleculizerException(
"Error: Cannot add an explicit species block twice.")
if not self.BlockPassesSanityCheck(esBlock):
raise InsaneBlockOnTheLooseException(esBlock, "explicit-species")
self.explicitSpeciesBlock = esBlock[:]
self.explicitSpeciesSection = ExplicitSpeciesSection(esBlock)
def addSpeciesStreamsBlock(self, ssBlock, overwrite=False):
if self.speciesStreamBlock and not overwrite:
raise MzrExceptions.MoleculizerException(
"Error: Cannot add a species stream block twice.")
if not self.BlockPassesSanityCheck(ssBlock):
raise InsaneBlockOnTheLooseException(ssBlock, "")
self.speciesStreamBlock = ssBlock[:]
self.speciesStreamSection = SpeciesStreamsSection(
self.speciesStreamBlock)
def __processAllostericRulesBlocks(self, allostericPlexBlock,
allostericOmniBlock):
return 0
def __processReactionRulesBlocks(self, rxnRulesBlock, dimerBlock,
omniGenBlock, uniGenBlock):
return 0
def __processExplicitSpeciesBlock(self, explicitSpeciesBlock):
return 0
def __processSpeciesStreamBlock(self, ssBlock):
return 0
def __writeOutput(self, openXMLFile):
xmlobject = self.__constructXMLRepresentation()
xmlobject.writeall(openXMLFile)
def __constructXMLRepresentation(self):
rootNode = XmlObject("moleculizer-input")
modelElmt = XmlObject("model")
modelElmt.attachToParent(rootNode)
streamsElmt = XmlObject("streams", rootNode)
self.__addModifications(modelElmt)
self.__addMols(modelElmt)
self.__addAllostericPlexes(modelElmt)
self.__addAllostericOmnis(modelElmt)
self.__addReactionGens(modelElmt)
self.__addExplicitSpecies(modelElmt)
self.__addExplicitReactions(modelElmt)
self.__addSpeciesStreams(streamsElmt)
return rootNode
def __addModifications(self, parentObject):
# Write me!!!
modificationsSection = XmlObject("modifications", parentObject)
if self.modificationsSection:
self.modificationsSection.writeModificationsSections(
modificationsSection)
return
def __addMols(self, parentObject):
molsSection = XmlObject("mols", parentObject)
if self.molsSection:
self.molsSection.writeMolsSection(molsSection)
return
def __addAllostericPlexes(self, parentObject):
allostericPlexes = XmlObject("allosteric-plexes", parentObject)
if self.allostericPlexesSection:
self.allostericPlexesSection.writeAllostericPlexesSection(
allostericPlexes)
return
def __addAllostericOmnis(self, parentObject):
allostericOmnis = XmlObject("allosteric-omnis", parentObject)
if self.allostericOmnisSection:
self.allostericOmnisSection.writeAllostericOmnisSection(
allostericOmnis)
return
def __addReactionGens(self, parentObject):
reactionGenElmt = XmlObject("reaction-gens", parentObject)
if self.reactionGensSection:
self.reactionGensSection.writeReactionGensSection(reactionGenElmt)
return
def __addSpeciesStreams(self, parentObject):
speciesStreamsElement = XmlObject("species-streams", parentObject)
if self.speciesStreamSection:
self.speciesStreamSection.writeSpeciesStreamSection(
speciesStreamsElement)
def __addExplicitSpecies(self, parentObject):
explicitSpeciesElmt = XmlObject("explicit-species", parentObject)
if self.explicitSpeciesSection:
self.explicitSpeciesSection.writeExplicitSpeciesSection(
explicitSpeciesElmt)
return
def __addExplicitReactions(self, modelElmt):
explicitReactionsElmt = XmlObject("explicit-reactions", modelElmt)
return