def printScore( name, rogScore ):
clist = rogScore.colorCommentList.zap(1)
if len(clist) == 0:
clist.append('---')
printf('%-20s%-10s %s\n', name, rogScore, clist[0])
for c in clist[1:]:
printf('%-20s%-10s %s\n', '', '', c)
def printResidueScores( projects ):
n = len(projects)
print constants.dots20*(n+1)
print ' Residues'
print constants.dots20*(n+1)
p0 = projects[0]
for res in p0.molecule.allResidues():
printf('%s %s %s\n', '-'*5, res, '-'*5 )
# printf('%-20s%-10s %s\n', p0.name, res.rogScore, res.rogScore.colorCommentList.zap(1).format())
printScore( p0.name, res.rogScore )
# find the corresponding residues
for p in projects[1:]:
nameTuple = (p.molecule.name, res.chain.name, res.resNum, None, None, None, constants.INTERNAL)
res2 = p.decodeNameTuple( nameTuple )
if res2:
#printf('%-20s%-10s %s\n', p.name, res2.rogScore, res2.rogScore.colorCommentList.zap(1).format())
printScore( p.name, res2.rogScore )
else:
printf('%-20s%-10s\n', p.name, 'Not found')
#end if
#end for
print
def exportDef(self, stream=sys.stdout, convention=constants.INTERNAL):
"""export definitions to stream"""
io.printf(stream, "\n#=======================================================================\n")
io.printf(stream, "#\t%-8s %-8s\n", "internal", "short")
io.printf(stream, "RESIDUE\t%-8s %-8s\n", self.translate(convention), self.shortName)
io.printf(stream, "#=======================================================================\n")
# saving different residue attributes
for attr in ["nameDict", "comment"]:
io.printf(stream, "\t%s = %s\n", attr, repr(self[attr]))
# end for
# clean the properties list
props = []
for prop in self.properties:
# Do not store name and residueDef.name as property. Add those dynamically upon reading
if not prop in [self.name, self.shortName] and not prop in props:
props.append(prop)
# end if
# end for
io.printf(stream, "\t%s = %s\n", "properties", repr(props))
for dh in self.dihedrals:
dh.exportDef(stream=stream, convention=convention)
# end for
for atm in self.atoms:
atm.exportDef(stream=stream, convention=convention)
# end for
io.printf(stream, "END_RESIDUE\n")
io.printf(stream, "#=======================================================================\n")
def exportDef(self, stream=sys.stdout, convention=constants.INTERNAL):
"""export definitions to stream"""
io.printf(stream, "\t#---------------------------------------------------------------\n")
io.printf(stream, "\tDIHEDRAL %-8s\n", self.name)
io.printf(stream, "\t#---------------------------------------------------------------\n")
if convention == constants.INTERNAL:
atms = self.atoms
else:
# convert atoms
atms = []
for resId, atmName in self.atoms:
if resId != 0:
nTwarning("DihedralDef.exportDef: %s topology (%d,%s) skipped translation", self, resId, atmName)
atms.append((resId, atmName))
elif not atmName in self.residueDef:
nTerror("DihedralDef.exportDef: %s topology (%d,%s) not decoded", self, resId, atmName)
atms.append((resId, atmName))
else:
atm = self.residueDef[atmName]
atms.append((resId, atm.translate(convention)))
# end if
# end for
# print 'atms', atms
# end if
io.printf(stream, "\t\t%s = %s\n", "atoms", repr(atms))
for attr in ["karplus"]:
io.printf(stream, "\t\t%s = %s\n", attr, repr(self[attr]))
# end for
io.printf(stream, "\tEND_DIHEDRAL\n")
def exportDef(self, stream=sys.stdout, convention=constants.INTERNAL):
"""export definitions to stream"""
io.printf(stream, "\t#---------------------------------------------------------------\n")
io.printf(stream, "\tATOM %-8s\n", self.translate(convention))
io.printf(stream, "\t#---------------------------------------------------------------\n")
# Topology; optionally convert
if convention == constants.INTERNAL:
top2 = self.topology
else:
# convert topology
top2 = []
for resId, atmName in self.topology:
if resId != 0:
nTwarning("AtomDef.exportDef: %s topology (%d,%s) skipped translation", self, resId, atmName)
top2.append((resId, atmName))
elif not atmName in self.residueDef:
nTerror("AtomDef.exportDef: %s topology (%d,%s) not decoded", self, resId, atmName)
top2.append((resId, atmName))
else:
atm = self.residueDef[atmName]
top2.append((resId, atm.translate(convention)))
# end if
# end for
# print 'top2', top2
# end if
io.printf(stream, "\t\t%s = %s\n", "topology", repr(top2))
# clean the properties list
props = []
for prop in self.properties:
# Do not store name and residueDef.name as property. Add those dynamically upon reading
if (
not prop in [self.name, self.residueDef.name, self.residueDef.shortName, self.spinType]
and not prop in props
):
props.append(prop)
# end if
# end for
io.printf(stream, "\t\t%s = %s\n", "properties", repr(props))
# Others
for attr in ["nameDict", "aliases", "pseudo", "real", "type", "spinType", "shift", "hetatm"]:
if self.has_key(attr):
io.printf(stream, "\t\t%s = %s\n", attr, repr(self[attr]))
# end for
io.printf(stream, "\tEND_ATOM\n")
