def computeNormalMode(self,) :
if self.anm is None :
return
if self.gammaStructure:
self.gamma = prody.GammaStructureBased(self.ca_model)
self.anm.buildHessian(self.ca_model, gamma=self.gamma, cutoff=self.cutoff)
self.anm.calcModes()
#extrapole
self.bb_anm, self.bb_atoms = prody.extrapolateModel(self.anm, self.ca_model, self.model.select(self.conf))#self.conf))
self.nbMode = self.anm.getNumOfModes()
def computeNormalMode(self, ):
if self.anm is None:
return
if self.gammaStructure:
self.gamma = prody.GammaStructureBased(self.ca_model)
self.anm.buildHessian(self.ca_model,
gamma=self.gamma,
cutoff=self.cutoff)
self.anm.calcModes()
#extrapole
self.bb_anm, self.bb_atoms = prody.extrapolateModel(
self.anm, self.ca_model,
self.model.select(self.conf)) #self.conf))
self.nbMode = self.anm.getNumOfModes()
def applyMode(self, idMode):
if idMode > self.nbMode:
return
#sample?should gave 10
#or should I use traverseMode
#should I redo the extrapolation ?
self.bb_anm, self.bb_atoms = prody.extrapolateModel(
self.anm, self.ca_model,
self.model.select(self.conf)) #self.conf))
self.nbMode = self.anm.getNumOfModes()
if self.sample == "sample":
ensemble = prody.sampleModes(self.bb_anm[idMode],
self.bb_atoms,
n_confs=self.nbconf,
rmsd=self.rmsd)
elif self.sample == "traverse":
ensemble = prody.traverseMode(self.bb_anm[idMode],
self.bb_atoms,
n_steps=int(self.nbconf / 2),
rmsd=self.rmsd)
coords = ensemble.getCoordsets()
nC = len(coords) #should beequal to nbconf
self.pmvmodel.allAtoms.setConformation(0)
if self.first:
self.oricoords = numpy.array(self.pmvmodel.allAtoms._coords[:])
self.first = False
else:
self.pmvmodel.allAtoms._coords = self.oricoords.tolist()
#self.pmvmodel.allAtoms._coords = numpy.concatenate(([oricoords,],coords),axis=0)
#if a gui is available shoud update it
#use current sel
for i, c in enumerate(coords):
if self.conf == "ca":
if len(c) != len(self.pmvmodel.allAtoms.get("CA").coords):
return
self.pmvmodel.allAtoms.get("CA").addConformation(c[:])
elif self.conf == "protein and ca":
self.pmvmodel.chains.residues.get("aminoacids").atoms.get(
"CA").addConformation(c[:])
elif self.conf == "protein":
self.pmvmodel.chains.residues.get(
"aminoacids").atoms.addConformation(c[:])
#self.pmvmodel.allAtoms.get("aminoacids").addConformation(c[:])
else: #all
if len(c) != len(self.pmvmodel.allAtoms.coords):
return
self.pmvmodel.allAtoms.addConformation(c[:])
def applyMode(self,idMode):
if idMode > self.nbMode:
return
#sample?should gave 10
#or should I use traverseMode
#should I redo the extrapolation ?
self.bb_anm, self.bb_atoms = prody.extrapolateModel(self.anm, self.ca_model, self.model.select(self.conf))#self.conf))
self.nbMode = self.anm.getNumOfModes()
if self.sample == "sample" :
ensemble = prody.sampleModes(self.bb_anm[idMode], self.bb_atoms, n_confs=self.nbconf, rmsd=self.rmsd)
elif self.sample == "traverse" :
ensemble = prody.traverseMode(self.bb_anm[idMode], self.bb_atoms, n_steps=int(self.nbconf/2), rmsd=self.rmsd)
coords=ensemble.getCoordsets()
nC = len(coords) #should beequal to nbconf
self.pmvmodel.allAtoms.setConformation(0)
if self.first:
self.oricoords = numpy.array(self.pmvmodel.allAtoms._coords[:])
self.first = False
else :
self.pmvmodel.allAtoms._coords = self.oricoords.tolist()
#self.pmvmodel.allAtoms._coords = numpy.concatenate(([oricoords,],coords),axis=0)
#if a gui is available shoud update it
#use current sel
for i,c in enumerate(coords):
if self.conf == "ca" :
if len(c) != len(self.pmvmodel.allAtoms.get("CA").coords):
return
self.pmvmodel.allAtoms.get("CA").addConformation(c[:])
elif self.conf == "protein and ca" :
self.pmvmodel.chains.residues.get("aminoacids").atoms.get("CA").addConformation(c[:])
elif self.conf == "protein" :
self.pmvmodel.chains.residues.get("aminoacids").atoms.addConformation(c[:])
#self.pmvmodel.allAtoms.get("aminoacids").addConformation(c[:])
else :#all
if len(c) != len(self.pmvmodel.allAtoms.coords):
return
self.pmvmodel.allAtoms.addConformation(c[:])
