def buildProtein(self, protein):
self.protein = protein
self.handler.startElement("protein",
Attributes(id=protein.id, ac=protein.ac.ac))
self.buildDomains(protein)
self.handler.endElement("protein")
def buildProtein(self, protein, protein_res):
self.handler.startElement(
"protein",
Attributes(id=protein.id, ac=protein.ac.ac, residue=protein_res))
domain, domain_res = self.index.domain(protein, protein_res)
self.buildDomain(domain, domain_res)
self.handler.endElement("protein")
def buildDocument(self, family):
self.handler.startElement("family", Attributes(id=family.id))
# Name, number of columns, etc
self.handler.startElement("name")
self.handler.characters(family.name)
self.handler.endElement("name")
self.handler.startElement("length")
self.handler.characters(
family.alignment.alignment.get_alignment_length())
self.handler.endElement("length")
self.handler.startElement("members")
self.handler.characters(len(family.proteins))
self.handler.endElement("members")
# Proteins and family stuff
self.structureProvider.buildProteins(family)
self.selectionProvider.buildSelection(family)
self.ieaProvider.buildIea(family)
# Columns and Structure
self.columnProvider.buildColumns(self.structureProvider.index)
self.handler.endElement("family")
def buildSCCS(self, sccs, probability):
self.handler.startElement("sccs", Attributes(id=sccs))
#self.handler.startElement("name")
#self.handler.endElement("name")
self.handler.startElement("probability")
self.handler.characters(str(probability))
self.handler.endElement("probability")
self.handler.endElement("sccs")
def buildModel(self, model):
self.handler.startElement("model", Attributes(id=model.model))
if len(model.positive_selection) > 0:
self.handler.startElement("sites")
for ps in model.positive_selection:
self.buildSite(ps)
self.handler.endElement("sites")
self.handler.endElement("model")
def buildDomain(self, domain, domain_num):
self.domain = domain
self.handler.startElement(
"domain",
Attributes(id=domain.id,
num=domain_num,
start=domain.region.start,
stop=domain.region.stop))
self.handler.startElement("domain_type")
self.handler.characters(domain.domain_type)
self.handler.endElement("domain_type")
self.buildStructures(domain)
self.handler.endElement("domain")
def buildDecoy(self, structure, mcmdata):
self.handler.startElement("structure", Attributes(type="decoy"))
self.handler.startElement("id")
self.handler.characters(str(structure.id))
self.handler.endElement("id")
self.handler.startElement("scop")
for mcm in mcmdata:
self.buildSCCS(mcm.sccs, mcm.probability)
self.handler.endElement("scop")
try:
self.buildDecoyIndex(structure)
except Exception, e:
print e
def buildTerm(self, term):
self.handler.startElement("term")
self.handler.startElement("acc")
self.handler.characters(term.acc)
self.handler.endElement("acc")
self.handler.startElement("name")
self.handler.characters(term.name)
self.handler.endElement("name")
self.handler.startElement("term_type")
self.handler.characters(term.term_type)
self.handler.endElement("term_type")
self.handler.startElement("proteins")
for protein in self.index.proteins(term):
self.handler.startElement(
"protein", Attributes(id=protein.id, ac=protein.ac.ac))
self.handler.endElement("protein")
self.handler.endElement("proteins")
self.handler.endElement("term")
def buildStructure(self, structure, structure_res):
self.handler.startElement(
"structure",
Attributes(residue=structure_res,
type=structure.type,
id=structure.index))
self.handler.startElement("id")
self.handler.characters(structure.id)
self.handler.endElement("id")
if structure.chain:
self.handler.startElement("chain")
self.handler.characters(structure.chain)
self.handler.endElement("chain")
att = self.index.attributes(structure, structure_res)
for key, value in att.structure_dict.items():
self.handler.startElement(key)
self.handler.characters(value)
self.handler.endElement(key)
self.handler.endElement("structure")
def buildPDB(self, domain):
if not domain.sccs:
return
self.handler.startElement("structure", Attributes(type="pdb"))
self.handler.startElement("id")
self.handler.characters(str(domain.sccs.pdbid))
self.handler.endElement("id")
self.handler.startElement("chain")
self.handler.characters(str(domain.sccs.chain))
self.handler.endElement("chain")
# This isn't guarenteed to have a superfamily prediction
if domain.sccs and domain.sccs.sccs != None:
self.handler.startElement("scop")
for sccs in domain.sccs.sccs.split(","):
self.buildSCCS(sccs, 1.0)
self.handler.endElement("scop")
try:
self.buildPDBIndex(domain)
except Exception, e:
print e
def buildDomain(self, domain, domain_res):
self.handler.startElement("domain",
Attributes(id=domain.id, residue=domain_res))
self.buildStructures(domain, domain_res)
self.handler.endElement("domain")
def buildProteins(self, column):
self.handler.startElement("proteins", Attributes(id=column))
for protein, protein_res in self.index.proteins(column):
self.buildProtein(protein, protein_res)
self.handler.endElement("proteins")
def buildColumn(self, column):
self.column = column
self.handler.startElement("column", Attributes(id=column))
self.buildProteins(column)
self.handler.endElement("column")