def mkJmolMacros(project):
"""
Generate the Jmol macros in the moleculeDirectories.Jmol dir.
"""
if not project.molecule:
nTerror("mkJmolMacros: no molecule defined")
return
# end if
# save first model
molName = project.molecule.name + "_0"
path = project.moleculePath("jmol", molName + ".pdb")
project.molecule.toPDBfile(path, model=0)
# mkYasaraByResidueMacro(project, ['procheck','gf'],
# minValue=-3.0,maxValue=1.0,
# reverseColorScheme=True,
# path=project.moleculePath('yasara','gf.mcr')
# )
#
# mkYasaraByResidueMacro(project, ['Qshift','backbone'],
# minValue=0.0,maxValue=0.05,
# reverseColorScheme=False,
# path=project.moleculePath('yasara','Qshift.mcr')
# )
mkJmolByResidueROGMacro(project, object=1, path=project.moleculePath("jmol", "rog.spt"))
def mkJmolByResidueROGMacro(project, object=None, path=None, stream=None):
if path:
stream = open(path, "w")
elif stream:
pass
else:
stream = sys.stdout
# end if
if not stream:
nTerror("mkJmolByResidueROGMacro: undefined output stream")
return
# endif
if object == None:
fprintf(stream, "select *; color grey\n")
else:
fprintf(stream, "select */%d; color grey\n", object)
for res in project.molecule.allResidues():
if object == None:
fprintf(stream, "select %d:%s.*; ", res.resNum, res.chain.name)
else:
fprintf(stream, "select %d:%s.*/%d; ", res.resNum, res.chain.name, object)
fprintf(stream, "color %s\n", res.rogScore.colorLabel)
# end for
if path:
stream.close()
def select(self, rangesString, filter=True):
"""
select residues on the basis of rangesString
Only convert a residue ranges string, e.g. 'A.-10--2,B.3'
return True on error
Adapted from code in Molecule class
"""
#GWV 20130524: convert unicode to string as procheckStatus.ranges field sometimes?? is stored in unicode
if type(rangesString) == unicode:
rangesString = str(rangesString)
if type(rangesString) != str:
nTerror('ResidueRange.select: ranges type [%s] should have been a string' % type(ranges) )
return True
rangesString = rangesString.strip()
# clear self
self.clear()
# everything
if rangesString == '*' or rangesString == 'all':
[self.append(res) for res in self.molecule.allResidues()]
self.method = ResidueRange.FROM_STRING
return False
#selections
for substr in rangesString.split(','):
self._parseSubstring(substr.strip())
if filter:
self.filter()
self.method = ResidueRange.FROM_STRING
return False
def mkJmolByResidueROGMacro(project, object=None, path=None, stream=None):
if path:
stream = open(path, 'w')
elif stream:
pass
else:
stream = sys.stdout
#end if
if not stream:
nTerror('mkJmolByResidueROGMacro: undefined output stream')
return
#endif
if object == None:
fprintf(stream, 'select *; color grey\n')
else:
fprintf(stream, 'select */%d; color grey\n', object)
for res in project.molecule.allResidues():
if object == None:
fprintf(stream, 'select %d:%s.*; ', res.resNum, res.chain.name)
else:
fprintf(stream, 'select %d:%s.*/%d; ', res.resNum, res.chain.name,
object)
fprintf(stream, 'color %s\n', res.rogScore.colorLabel)
#end for
if path:
stream.close()
def mkJmolMacros(project):
"""
Generate the Jmol macros in the moleculeDirectories.Jmol dir.
"""
if not project.molecule:
nTerror('mkJmolMacros: no molecule defined')
return
#end if
# save first model
molName = project.molecule.name + '_0'
path = project.moleculePath('jmol', molName + '.pdb')
project.molecule.toPDBfile(path, model=0)
# mkYasaraByResidueMacro(project, ['procheck','gf'],
# minValue=-3.0,maxValue=1.0,
# reverseColorScheme=True,
# path=project.moleculePath('yasara','gf.mcr')
# )
#
# mkYasaraByResidueMacro(project, ['Qshift','backbone'],
# minValue=0.0,maxValue=0.05,
# reverseColorScheme=False,
# path=project.moleculePath('yasara','Qshift.mcr')
# )
mkJmolByResidueROGMacro(project,
object=1,
path=project.moleculePath('jmol', 'rog.spt'))
def calculate(self, residue):
"""Calculate the PseudoRotation angles and pucker amplitudes
for all models of residue.
return a (Ntlist,NTlist,ETclassification) tuple with the PseudoRotation angles
and pucker amplitudes, or (None,None,None) on error.
"""
from cing import printf, nTerror, NTlist
from math import atan2
if not residue.hasProperties('nucleic'):
nTerror('PseudoRotation.calculate: residue %s is not nucleic acid',
residue)
return (None, None, None)
#end if
diheds = []
for J, dihed in self.angleMap:
if dihed not in residue:
nTerror(
'PseudoRotation.calculate: dihedral "%s" not defined for residue %s',
dihed, residue)
return (None, None, None)
#end if
diheds.append(residue[dihed])
#end for
#print diheds
nmodels = len(diheds[0])
Plist = NTlist()
tauMlist = NTlist()
for i in range(nmodels):
taus = []
for d in diheds:
taus.append(d[i])
#end for
# Do fit and calculate P and pucker
c = self.fit(taus)
P = atan2(-c[1], c[0])
tauM = c[0] / cos(P)
P = P / pi * 180.0 # convert to degrees
Plist.append(P)
tauMlist.append(tauM)
#printf( '%1d %8.2f %8.2f\n',i, P, tauM )
#end for
Plist.cAverage()
Plist.limit(Plist.cav - 180.0,
Plist.cav + 180.0) # Center around circular average,
Plist.average() # to calculate sd in this step
Plist.limit(0.0, 360.0) # and rescale to 0,360 range
tauMlist.average()
ETname = self.getETnomenclature(Plist.cav, Plist.sd)
return Plist, tauMlist, ETname
def calculate(self, residue):
"""Calculate the PseudoRotation angles and pucker amplitudes
for all models of residue.
return a (Ntlist,NTlist,ETclassification) tuple with the PseudoRotation angles
and pucker amplitudes, or (None,None,None) on error.
"""
from cing import printf, nTerror, NTlist
from math import atan2
if not residue.hasProperties("nucleic"):
nTerror("PseudoRotation.calculate: residue %s is not nucleic acid", residue)
return (None, None, None)
# end if
diheds = []
for J, dihed in self.angleMap:
if dihed not in residue:
nTerror('PseudoRotation.calculate: dihedral "%s" not defined for residue %s', dihed, residue)
return (None, None, None)
# end if
diheds.append(residue[dihed])
# end for
# print diheds
nmodels = len(diheds[0])
Plist = NTlist()
tauMlist = NTlist()
for i in range(nmodels):
taus = []
for d in diheds:
taus.append(d[i])
# end for
# Do fit and calculate P and pucker
c = self.fit(taus)
P = atan2(-c[1], c[0])
tauM = c[0] / cos(P)
P = P / pi * 180.0 # convert to degrees
Plist.append(P)
tauMlist.append(tauM)
# printf( '%1d %8.2f %8.2f\n',i, P, tauM )
# end for
Plist.cAverage()
Plist.limit(Plist.cav - 180.0, Plist.cav + 180.0) # Center around circular average,
Plist.average() # to calculate sd in this step
Plist.limit(0.0, 360.0) # and rescale to 0,360 range
tauMlist.average()
ETname = self.getETnomenclature(Plist.cav, Plist.sd)
return Plist, tauMlist, ETname
def procheck_old( project, ranges=None ):
"""
Adds <Procheck> instance to molecule. Run procheck and parse result
"""
if not project.molecule:
nTerror('ERROR procheck: no molecule defined\n')
return None
#end if
if project.molecule.has_key('procheck'):
del(project.molecule.procheck)
#end if
pcheck = gvProcheck( project )
if not pcheck: return None
pcheck.run( ranges=ranges )
project.molecule.procheck = pcheck
return project.molecule.procheck
def procheck_old(project, ranges=None):
"""
Adds <Procheck> instance to molecule. Run procheck and parse result
"""
if not project.molecule:
nTerror('ERROR procheck: no molecule defined\n')
return None
#end if
if project.molecule.has_key('procheck'):
del (project.molecule.procheck)
#end if
pcheck = gvProcheck(project)
if not pcheck: return None
pcheck.run(ranges=ranges)
project.molecule.procheck = pcheck
return project.molecule.procheck
def parseResult(self):
"""
Get summary
Parse procheck .rin files and store result in procheck NTdict
of each residue of mol
"""
path = os.path.join(self.rootPath, sprintf('%s.sum',
self.molecule.name))
fp = open(path, 'r')
if not fp:
nTerror('gvProcheck.parseResult: %s not found', path)
else:
self.summary = ''.join(fp.readlines())
fp.close()
#end if
for i in range(1, self.molecule.modelCount + 1):
path = os.path.join(self.rootPath,
sprintf('%s_%03d.rin', self.molecule.name, i))
#print '> parsing >', path
for line in AwkLike(path, minLength=64, commentString="#"):
result = self._parseProcheckLine(line.dollar[0])
chain = result['chain']
resNum = result['resNum']
residue = self.molecule.decodeNameTuple(
(cing.PDB, chain, resNum, None))
if not residue:
nTerror('Procheck.parseResult: residue not found (%s,%d)',
chain, resNum)
else:
residue.setdefault('procheck', NTstruct())
for field, value in result.iteritems():
residue.procheck.setdefault(field, NTlist())
residue.procheck[field].append(value)
#end for
#end if
del (result)
def parseResult(self):
"""
Get summary
Parse procheck .rin files and store result in procheck NTdict
of each residue of mol
"""
path = os.path.join(self.rootPath, sprintf("%s.sum", self.molecule.name))
fp = open(path, "r")
if not fp:
nTerror("gvProcheck.parseResult: %s not found", path)
else:
self.summary = "".join(fp.readlines())
fp.close()
# end if
for i in range(1, self.molecule.modelCount + 1):
path = os.path.join(self.rootPath, sprintf("%s_%03d.rin", self.molecule.name, i))
# print '> parsing >', path
for line in AwkLike(path, minLength=64, commentString="#"):
result = self._parseProcheckLine(line.dollar[0])
chain = result["chain"]
resNum = result["resNum"]
residue = self.molecule.decodeNameTuple((cing.PDB, chain, resNum, None))
if not residue:
nTerror("Procheck.parseResult: residue not found (%s,%d)", chain, resNum)
else:
residue.setdefault("procheck", NTstruct())
for field, value in result.iteritems():
residue.procheck.setdefault(field, NTlist())
residue.procheck[field].append(value)
# end for
# end if
del (result)