name, ll = l.split()
ll.strip()
moving_mol = Read(name)[0]
indices = list(map(int, ll.split(',')))
moving_ats = AtomSet()
for i in indices:
new_atoms = moving_mol.allAtoms.get(lambda x: x.number == i)
if not len(new_atoms):
print("There is no atom in %s with number %d" % (name, i))
break
else:
moving_ats.append(new_atoms[0])
#moving_ats.append(moving_mol.allAtoms.get(lambda x: x.number==i)[0])
num_moving_ats = len(moving_ats)
if num_moving_ats != num_ref_ats:
print(
"Number of moving_ats (%d) does not match number of reference atoms (%d). Skipping %s"
% (num_moving_ats, num_ref_ats, name))
continue
#for i in indices: moving_ats.append(moving_mol.allAtoms[i-1])
RFA.rigidFit(moving_ats.coords)
newCoords = RFA.transformCoords(moving_mol.allAtoms.coords)
if not newCoords is None and newCoords.shape[1] != 3:
newCoords = newCoords[:, :3]
outputfilename = prefix + name
moving_mol.parser.write_with_new_coords(newCoords, outputfilename)
if verbose: print('wrote %s' % outputfilename)
# To execute this command type:
# superpose_molecules.py -d data_filename [-p prefix] -v
)
mobAtoms = get_atoms(mobMol, moblist, names_to_use, verbose)
mobCoords = mobAtoms.coords
if len(mobCoords) == 0:
print("NO MOB COORDS!!!")
raise Exception(
'Unable to superimpose because no mobile coordinates were specified!!!'
)
#check that moblist and reflist are of the same length
assert len(refCoords) == len(mobCoords)
rigidfitAligner.setRefCoords(refCoords)
rigidfitAligner.rigidFit(mobCoords)
#now rigidfitAligner has attributes 'rotationMatrix' and 'translationMatrix'
newCoords = rigidfitAligner.transformCoords(mobMol.allAtoms.coords)
#make sure the coordinates have the correct shape, ie (num_atoms, 3)
if not newCoords is None and newCoords.shape[1] != 3:
newCoords = newCoords[:, :3]
#newCoords is 2D Numeric array with dimensions num_atoms, and length of each coordinate
#if verbose: print "newCoords[0]=", newCoords[0]
# end by writing a file with the transformed coordinates:
#the parser of the moving molecule knows about all the input lines
# so use it to write a file with the new coords:
if outputfilename is None:
EXT = os.path.splitext(refMol.parser.filename)[1]
outputfilename = refMol.name + "_superimposed" + EXT
mobMol.parser.write_with_new_coords(newCoords, outputfilename)
if verbose: print("wrote ", outputfilename)
# To execute this command type:
rat3.bonds.remove(b)
if verbose: print "removed %s-%s bond from %s and from %s"%(b.atom1.name, b.atom2.name, otherAt.full_name(), rat3.full_name())
if bond_to_break is None:
print "unable to locate the bond to break in receptor residue %s: expected a bond from %s to an atom other than %s"%(resP.full_name(), rat3.name, rat2.name)
raise 'invalid input'
#setup for the superposition
ref_coords = ref_atoms.coords
lig_coords = lig_atoms.coords
#(1) create the tool
rigidfitAligner = RigidfitBodyAligner()
rigidfitAligner.setRefCoords(ref_coords)
rigidfitAligner.rigidFit(lig_coords)
#(2) get new coordinates for the moving atoms
# here all the ligand atoms move
new_coords = rigidfitAligner.transformCoords(lM.allAtoms.coords)
# get the correct shape for the coords (natoms,3)
#new_coords.shape
#(25, 4)
new_coords=new_coords[:,:3]
#(3) add the new to ligand
lM.allAtoms.addConformation(new_coords)
confNum = len(lM.allAtoms[0]._coords)-1
#(4) set the coordinates to use to the new ones
lM.allAtoms.setConformation(confNum)
if verbose: print "new coordinates added to ligand"
#add the ligand atoms other than at1 + at2 to the residue
#(1) get the atoms to add
atoms_to_adopt = lM.allAtoms[:]
#atoms_to_adopt = lM.allAtoms.get(lambda x: not x in lig_atoms)
indices = map(int, ll.split(','))
moving_ats = AtomSet()
for i in indices:
new_atoms = moving_mol.allAtoms.get(lambda x: x.number==i)
if not len(new_atoms):
print "There is no atom in %s with number %d" %(name, i)
break
else:
moving_ats.append(new_atoms[0])
#moving_ats.append(moving_mol.allAtoms.get(lambda x: x.number==i)[0])
num_moving_ats = len(moving_ats)
if num_moving_ats!=num_ref_ats:
print "Number of moving_ats (%d) does not match number of reference atoms (%d). Skipping %s" %(num_moving_ats,num_ref_ats,name)
continue
#for i in indices: moving_ats.append(moving_mol.allAtoms[i-1])
RFA.rigidFit(moving_ats.coords)
newCoords = RFA.transformCoords(moving_mol.allAtoms.coords)
if not newCoords is None and newCoords.shape[1]!=3:
newCoords=newCoords[:,:3]
outputfilename = prefix + name
moving_mol.parser.write_with_new_coords(newCoords,outputfilename)
if verbose: print 'wrote %s' %outputfilename
# To execute this command type:
# superpose_molecules.py -d data_filename [-p prefix] -v
if len(refCoords)==0:
print "NO REF COORDS!!!"
raise 'Unable to superimpose because no reference coordinates were specified!!!'
mobAtoms = get_atoms(mobMol, moblist, names_to_use, verbose)
mobCoords = mobAtoms.coords
if len(mobCoords)==0:
print "NO MOB COORDS!!!"
raise 'Unable to superimpose because no mobile coordinates were specified!!!'
#check that moblist and reflist are of the same length
assert len(refCoords)==len(mobCoords)
rigidfitAligner.setRefCoords(refCoords)
rigidfitAligner.rigidFit(mobCoords)
#now rigidfitAligner has attributes 'rotationMatrix' and 'translationMatrix'
newCoords = rigidfitAligner.transformCoords(mobMol.allAtoms.coords)
#make sure the coordinates have the correct shape, ie (num_atoms, 3)
if not newCoords is None and newCoords.shape[1]!=3:
newCoords=newCoords[:,:3]
#newCoords is 2D Numeric array with dimensions num_atoms, and length of each coordinate
#if verbose: print "newCoords[0]=", newCoords[0]
# end by writing a file with the transformed coordinates:
#the parser of the moving molecule knows about all the input lines
# so use it to write a file with the new coords:
if outputfilename is None:
EXT = os.path.splitext(refMol.parser.filename)[1]
outputfilename = refMol.name + "_superimposed"+ EXT
mobMol.parser.write_with_new_coords(newCoords, outputfilename)
if verbose: print "wrote ", outputfilename
# To execute this command type:
rat3.full_name())
if bond_to_break is None:
print "unable to locate the bond to break in receptor residue %s: expected a bond from %s to an atom other than %s" % (
resP.full_name(), rat3.name, rat2.name)
raise 'invalid input'
#setup for the superposition
ref_coords = ref_atoms.coords
lig_coords = lig_atoms.coords
#(1) create the tool
rigidfitAligner = RigidfitBodyAligner()
rigidfitAligner.setRefCoords(ref_coords)
rigidfitAligner.rigidFit(lig_coords)
#(2) get new coordinates for the moving atoms
# here all the ligand atoms move
new_coords = rigidfitAligner.transformCoords(lM.allAtoms.coords)
# get the correct shape for the coords (natoms,3)
#new_coords.shape
#(25, 4)
new_coords = new_coords[:, :3]
#(3) add the new to ligand
lM.allAtoms.addConformation(new_coords)
confNum = len(lM.allAtoms[0]._coords) - 1
#(4) set the coordinates to use to the new ones
lM.allAtoms.setConformation(confNum)
if verbose: print "new coordinates added to ligand"
#add the ligand atoms other than at1 + at2 to the residue
#(1) get the atoms to add
atoms_to_adopt = lM.allAtoms[:]
#atoms_to_adopt = lM.allAtoms.get(lambda x: not x in lig_atoms)
