def talosPlus2restraints( project, name=constants.TALOSPLUS_LIST_STR, status='noRefine', errorFactor=2.0 ):
"""
Convert talos+ results to a CING dihedral restraint list
"""
if project == None:
nTmessage("talosPlus2restraints: No project defined")
return True
if project.molecule == None:
nTmessage("talosPlus2restraints: No project defined")
return True
if not project.status.has_key('talosPlus') or not project.status.talosPlus.completed:
nTmessage("talosPlus2restraints: No talos+ data")
return True
if name in project.dihedrals.names():
project.dihedrals.delete(name)
dhl = project.dihedrals.new(name=name, status=status)
for res in project.molecule.allResidues():
if res.talosPlus and res.talosPlus.classification=='Good':
lower = res.talosPlus.phi.value-errorFactor*res.talosPlus.phi.error
upper = res.talosPlus.phi.value+errorFactor*res.talosPlus.phi.error
atoms = getDeepByKeysOrAttributes( res, constants.PHI_STR, constants.ATOMS_STR )
if atoms:
d = DihedralRestraint(atoms, lower, upper)
dhl.append(d)
lower = res.talosPlus.psi.value-errorFactor*res.talosPlus.psi.error
upper = res.talosPlus.psi.value+errorFactor*res.talosPlus.psi.error
atoms = getDeepByKeysOrAttributes( res, constants.PSI_STR, constants.ATOMS_STR )
if atoms:
d = DihedralRestraint(atoms, lower, upper)
dhl.append(d)
#end if
#end for
nTmessage('==> Created %s', dhl)
def test( projects, stream=sys.stdout ):
# A hack to get residue specific results
selectedResidues = projects[0].molecule.setResiduesFromRanges('all')
for res in selectedResidues:
rmsds3 = calcPhiPsiRmsds( projects, ranges=[res.resNum] )
printRmsds('Relative Phi-Psi '+res.name, rmsds3, stream )
res.phipsiRmsds = rmsds3
for p in projects.entries[1:]:
val = getDeepByKeysOrAttributes(projects, 'moleculeMap', res, p.name)
if val == None:
nTerror('Setting phipsiRmsds residue %s project %s (mapping not found)', res.name, p)
continue
val.phipsiRmsds = rmsds3
def filterListByObjectClassName( myList, className ):
'Return new list with only those objects that have given class name.'
result = []
if myList == None:
return result
if not isinstance(myList, list):
nTerror('Input is not a list but a %s' % str(myList))
return result
# if len(myList) == 0:
# return result
for obj in myList:
oClassName = getDeepByKeysOrAttributes(obj, '__class__', '__name__' )
# nTdebug("oClassName: %s" % oClassName)
if oClassName == className:
result.append(obj)
return result
def filterListByObjectClassName(myList, className):
'Return new list with only those objects that have given class name.'
result = []
if myList == None:
return result
if not isinstance(myList, list):
nTerror('Input is not a list but a %s' % str(myList))
return result
# if len(myList) == 0:
# return result
for obj in myList:
oClassName = getDeepByKeysOrAttributes(obj, '__class__', '__name__')
# nTdebug("oClassName: %s" % oClassName)
if oClassName == className:
result.append(obj)
return result
def mkYasaraByResidueMacro(projects, keys,
minValue = 0.0, maxValue = 1.0, reverseColorScheme = False,
path = None
):
# nTdebug('mkYasaraByResidueMacro: keys: %s, minValue: %s maxValue: %s', keys, minValue, maxValue)
if path==None:
stream = sys.stdout
else:
stream = open( path, 'w')
#end if
fprintf(stream, 'Console off\n')
fprintf(stream, 'ColorRes All, Gray\n')
fprintf(stream, 'PropRes All, -999\n')
if reverseColorScheme:
fprintf(stream, 'ColorPar Property Min,red,%f\n', minValue)
fprintf(stream, 'ColorPar Property Max,blue,%f\n', maxValue)
else:
fprintf(stream, 'ColorPar Property Min,blue,%f\n', minValue)
fprintf(stream, 'ColorPar Property Max,red,%f\n', maxValue)
for p in projects:
for res in p.molecule.allResidues():
value = getDeepByKeysOrAttributes(res, *keys)
# if res.has_key(property) and res[property] != None and not isNaN(res[property]):
if value != None and not isNaN(value):
fprintf(stream, 'PropRes object %d Residue %d, %.4f\n', p.id+1, res.resNum, value)
#end for
fprintf(stream, 'ColorAll Property\n')
fprintf(stream, 'Console on\n')
if path:
stream.close()