def calculatePairWisePhiPsiRmsd( mol1, mol2, ranges='auto' ):
"""
Calculate a pairwise angular Phi,Psi rmsd between the models of mol1 and mol2
return result NTlistOfLists, pairwise1, pairwise2, pairwise12 tuple
"""
fitResidues1 = mol1.setResiduesFromRanges(ranges)
models1 = PhiPsiLists( mol1, fitResidues1 )
fitResidues2 = mol2.setResiduesFromRanges(ranges)
models2 = PhiPsiLists( mol2, fitResidues2 )
#print '>', ranges, models1, models2
l1 = len(models1)
l2 = len(models2)
if l1 == 0 or len(models1[0]) == 0 or l2 == 0 or len(models2[0]) == 0:
nTdebug(">calculatePairWisePhiPsiRmsd> returning None, %s %s %s", l1, l2, ranges)
return None, None, None, None
models = models1 + models2
result = NTlistOfLists(len(models), len(models), 0.0)
#nTmessage( '==> Calculating dihedral pairwise rmsds' )
for i in range(len(models)):
for j in range(i+1, len(models)):
#print '>>', i,j
r = models[i].calculateRMSD( models[j] )
if r == None:
nTdebug('calculatePairWisePhiPsiRmsd: error for %s and %s', models[i], models[j])
return None, None, None, None
else:
result[i][j] = r
result[j][i] = r
#end for
#end for
pairwise1 = NTlist()
for i in range(l1):
for j in range(i+1, l1):
pairwise1.append(result[i][j])
# print '1>', i,j
pairwise2 = NTlist()
for i in range(l1, l1+l2):
for j in range(i+1, l1+l2):
pairwise2.append(result[i][j])
# print '2>', i,j
pairwise12 = NTlist()
for i in range(l1):
for j in range(l1, l1+l2):
pairwise12.append(result[i][j])
# print '12>', i,j
# print len(pairwise1), len(pairwise2), len(pairwise12)
return ( result, pairwise1.average2(fmt='%6.2f +- %5.2f'),pairwise2.average2(fmt='%6.2f +- %5.2f'),
pairwise12.average2(fmt='%6.2f +- %5.2f') )
def calculatePairWiseRmsd( mol1, mol2, ranges=None ):
"""Calculate pairwise rmsd between mol1 and mol2
Optionally use ranges for the fitting
"""
#Use ranges routines to define fitAtoms ed
fitResidues1 = mol1.setResiduesFromRanges(ranges)
mol1.selectFitAtoms( fitResidues1, backboneOnly=True, includeProtons = False )
fitResidues2 = mol2.setResiduesFromRanges(ranges)
mol2.selectFitAtoms( fitResidues2, backboneOnly=True, includeProtons = False )
# mol2.superpose( ranges )
l1 = len(mol1.ensemble)
l2 = len(mol2.ensemble)
if ( l1 == 0 or len(mol1.ensemble[0].fitCoordinates) == 0
or l2 == 0 or len(mol2.ensemble[0].fitCoordinates) == 0
or len(mol1.ensemble[0].fitCoordinates) != len(mol2.ensemble[0].fitCoordinates)
):
nTdebug( ">calculatePairWiseRmsd> returning None, %s %s %s" , l1, l2, ranges)
return None, None, None, None
models = mol1.ensemble + mol2.ensemble
result = NTlistOfLists(len(models), len(models), 0.0)
nTmessage('==> Calculating pairwise rmsds %s %s', mol1, mol2)
for i in range(len(models)):
for j in range(i+1, len(models)):
result[i][j] = models[i].superpose( models[j] )
result[j][i] = result[i][j]
#end for
#end for
pairwise1 = NTlist()
for i in range(l1):
for j in range(i+1, l1):
pairwise1.append(result[i][j])
# print '1>', i,j
pairwise2 = NTlist()
for i in range(l1, l1+l2):
for j in range(i+1, l1+l2):
pairwise2.append(result[i][j])
# print '2>', i,j
pairwise12 = NTlist()
for i in range(l1):
for j in range(l1, l1+l2):
pairwise12.append(result[i][j])
# print '12>', i,j
# print len(pairwise1), len(pairwise2), len(pairwise12)
return ( result, pairwise1.average2(fmt='%6.2f +- %5.2f'),pairwise2.average2(fmt='%6.2f +- %5.2f'),
pairwise12.average2(fmt='%6.2f +- %5.2f'))