def test_superimpose():
from mglutil.math.rigidFit import RigidfitBodyAligner
rigidfitAligner = RigidfitBodyAligner()
refCoords=[[0,0,0] , [1,0,0], [0,1,0], [0,0,1]]
mobCoords=[[10,0,0] , [11,0,0], [10,1,0], [10,0,1]]
rigidfitAligner.setRefCoords(refCoords)
rigidfitAligner.rigidFit(mobCoords)
rmsd=rigidfitAligner.rmsdAfterSuperimposition(mobCoords)
assert diff(rmsd, 0.0 )
def test_superimpose():
from mglutil.math.rigidFit import RigidfitBodyAligner
rigidfitAligner = RigidfitBodyAligner()
refCoords = [[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1]]
mobCoords = [[10, 0, 0], [11, 0, 0], [10, 1, 0], [10, 0, 1]]
rigidfitAligner.setRefCoords(refCoords)
rigidfitAligner.rigidFit(mobCoords)
rmsd = rigidfitAligner.rmsdAfterSuperimposition(mobCoords)
assert diff(rmsd, 0.0)
class SuperImposeAtomsCommand(MVCommand):
def onAddCmdToViewer(self):
self.rigidfitAligner = RigidfitBodyAligner()
def doit(self, refAtoms, mobAtoms):
"""
The SuperImposeAtomsCommand takes two set of Atoms of the same length
compute the rotation and translation matrices to superimpose the
mobAtoms onto the refAtoms using rigidFit module and then transform the
corresponding geometry.
"""
refCoords = refAtoms.coords
mobCoords = mobAtoms.coords
self.rigidfitAligner.setRefCoords(refCoords)
# Nothing can be done if the two sets of coords are not of the same
# size
if not len(refCoords) == len(mobCoords):
print " ERROR: Cannot perform the superimposition because the 2 \
mv.lsets of Atoms are not of the same length"
return
# Get the rotation and the translation ysing mglutil.math.rigidFit
self.rigidfitAligner.rigidFit(mobCoords)
#rotation, translation= rigidFit.rigid_fit( refCoords, inCoords)
rotMat = Numeric.identity(4).astype('f')
rotMat[:3,:3] = self.rigidfitAligner.rotationMatrix
rotMat = Numeric.reshape(rotMat, (16,))
transMat = Numeric.array(self.rigidfitAligner.translationMatrix)
# transform the geometry representing the atoms only if a gui has been
# created:
if not self.vf.hasGui:
return
# Transform the mob geometry
mobMol = mobAtoms.top.uniq()[0]
mob = mobMol.geomContainer.masterGeom
self.vf.transformObject('rotation', mob.fullName, matrix=tuple(rotMat))
self.vf.transformObject('translation', mob.fullName, matrix=tuple(transMat))
def __call__(self, refAtoms, mobAtoms, **kw):
"""
None <- superimposeAtoms(refAtoms, mobAtoms, **kw)
"""
if not kw.has_key('redraw'): kw['redraw'] = 1
apply(self.doitWrapper, (refAtoms, mobAtoms), kw)
class SuperImposeAtomsCommand(MVCommand):
def onAddCmdToViewer(self):
self.rigidfitAligner = RigidfitBodyAligner()
def doit(self, refAtoms, mobAtoms):
"""
The SuperImposeAtomsCommand takes two set of Atoms of the same length
compute the rotation and translation matrices to superimpose the
mobAtoms onto the refAtoms using rigidFit module and then transform the
corresponding geometry.
"""
refCoords = refAtoms.coords
mobCoords = mobAtoms.coords
self.rigidfitAligner.setRefCoords(refCoords)
# Nothing can be done if the two sets of coords are not of the same
# size
if not len(refCoords) == len(mobCoords):
print " ERROR: Cannot perform the superimposition because the 2 \
mv.lsets of Atoms are not of the same length"
return
# Get the rotation and the translation ysing mglutil.math.rigidFit
self.rigidfitAligner.rigidFit(mobCoords)
#rotation, translation= rigidFit.rigid_fit( refCoords, inCoords)
rotMat = Numeric.identity(4).astype('f')
rotMat[:3,:3] = self.rigidfitAligner.rotationMatrix
rotMat = Numeric.reshape(rotMat, (16,))
transMat = Numeric.array(self.rigidfitAligner.translationMatrix)
# transform the geometry representing the atoms only if a gui has been
# created:
#if not self.vf.hasGui:
# return
# Transform the mob geometry
mobMol = mobAtoms.top.uniq()[0]
mob = mobMol.geomContainer.masterGeom
self.vf.transformObject('rotation', mob.fullName, matrix=tuple(rotMat))
self.vf.transformObject('translation', mob.fullName, matrix=tuple(transMat))
def __call__(self, refAtoms, mobAtoms, **kw):
"""
None <- superimposeAtoms(refAtoms, mobAtoms, **kw)
"""
if not kw.has_key('redraw'): kw['redraw'] = 1
apply(self.doitWrapper, (refAtoms, mobAtoms), kw)
def doit(self, refAtoms, mobAtoms, updateGeom=True, showRMSD=True):
"""
The SuperImposeAtomsCommand takes two set of Atoms of the same length
compute the rotation and translation matrices to superimpose the
mobAtoms onto the refAtoms using rigidFit module and then transform the
corresponding geometry.
updateGeom = True : transform the masterGeom of mobAtoms.
showRMSD = True : print and return RMSD
"""
if refAtoms is None or mobAtoms is None: return
assert isinstance(refAtoms, TreeNodeSet)
assert isinstance(mobAtoms, TreeNodeSet)
refAtoms = refAtoms.findType(Atom)
mobAtoms = mobAtoms.findType(Atom)
# validate the inputs
if len(refAtoms) !=len(mobAtoms):
print "The two atomSet are not of equal length"
return
if len(refAtoms) < 3 :
print "At least three atoms are needed for superimposition"
return
refCoords = refAtoms.coords
mobCoords = mobAtoms.coords
rigidfitAligner = RigidfitBodyAligner()
rigidfitAligner.setRefCoords(refCoords)
rigidfitAligner.rigidFit(mobCoords)
if updateGeom:
rotMat = Numeric.identity(4).astype('d')
rotMat[:3,:3] = rigidfitAligner.rotationMatrix
transMat = Numeric.array(rigidfitAligner.translationMatrix)
rotMat[3,:3] = transMat
#print rotMat # the matrix
mGeom = mobAtoms[0].top.geomContainer.masterGeom
mGeom.SetRotation(Numeric.reshape(rotMat, (16,)).astype('f'))
mGeom.viewer.Redraw()
if showRMSD:
rmsd=rigidfitAligner.rmsdAfterSuperimposition(mobCoords)
print "RMSD = ", rmsd
return rmsd
else:
return
def doit(self, refAtoms, mobAtoms, updateGeom=True, showRMSD=True):
"""
The SuperImposeAtomsCommand takes two set of Atoms of the same length
compute the rotation and translation matrices to superimpose the
mobAtoms onto the refAtoms using rigidFit module and then transform the
corresponding geometry.
updateGeom = True : transform the masterGeom of mobAtoms.
showRMSD = True : print and return RMSD
"""
if refAtoms is None or mobAtoms is None: return
assert isinstance(refAtoms, TreeNodeSet)
assert isinstance(mobAtoms, TreeNodeSet)
refAtoms = refAtoms.findType(Atom)
mobAtoms = mobAtoms.findType(Atom)
# validate the inputs
if len(refAtoms) != len(mobAtoms):
print "The two atomSet are not of equal length"
return
if len(refAtoms) < 3:
print "At least three atoms are needed for superimposition"
return
refCoords = refAtoms.coords
mobCoords = mobAtoms.coords
rigidfitAligner = RigidfitBodyAligner()
rigidfitAligner.setRefCoords(refCoords)
rigidfitAligner.rigidFit(mobCoords)
if updateGeom:
rotMat = Numeric.identity(4).astype('d')
rotMat[:3, :3] = rigidfitAligner.rotationMatrix
transMat = Numeric.array(rigidfitAligner.translationMatrix)
rotMat[3, :3] = transMat
#print rotMat # the matrix
mGeom = mobAtoms[0].top.geomContainer.masterGeom
mGeom.SetRotation(Numeric.reshape(rotMat, (16, )).astype('f'))
mGeom.viewer.Redraw()
if showRMSD:
rmsd = rigidfitAligner.rmsdAfterSuperimposition(mobCoords)
print "RMSD = ", rmsd
return rmsd
else:
return
class SuperimposeAtomsCommand(MVCommand):
def onAddCmdToViewer(self):
self.rigidfitAligner = RigidfitBodyAligner()
def doit(self, refAtoms, mobAtoms):
"""
The SuperImposeAtomsCommand takes two set of Atoms of the same length
compute the rotation and translation matrices to superimpose the
mobAtoms onto the refAtoms using rigidFit module and then transform the
corresponding geometry.
"""
refCoords = refAtoms.coords
mobCoords = mobAtoms.coords
self.rigidfitAligner.setRefCoords(refCoords)
# Nothing can be done if the two sets of coords are not of the same
# size
if not len(refCoords) == len(mobCoords):
print " ERROR: Cannot perform the superimposition because the 2 \
mv.lsets of Atoms are not of the same length"
return
# Get the rotation and the translation ysing mglutil.math.rigidFit
self.rigidfitAligner.rigidFit(mobCoords)
#rotation, translation= rigidFit.rigid_fit( refCoords, inCoords)
rotMat = Numeric.identity(4).astype('d')
rotMat[:3,:3] = self.rigidfitAligner.rotationMatrix
transMat = Numeric.array(self.rigidfitAligner.translationMatrix)
# transform the geometry representing the atoms only if a gui has been
# created:
if not self.vf.hasGui:
return
# build the geometry name:
mobMol = mobAtoms.top.uniq()[0]
mob = mobMol.geomContainer.masterGeom
#gName = 'root|'+ mobMol[0].name
vi = self.vf.GUI.VIEWER
oldCurrent = vi.currentObject
vi.SetCurrentObject(mob)
# transform only the given geometry.
if vi.redirectTransformToRoot == 1:
old = vi.redirectTransformToRoot
vi.TransformRootOnly(0)
else:
old = 0
# apply the rotation to the masterGeom of the inMol
mob.SetRotation(Numeric.reshape(rotMat, (16,)))
# apply the translation to the masterGeom of the inMol
mob.SetTranslation(transMat)
## refMol = refAtoms.top.uniq()[0]
## refmg = refMol.geomContainer.masterGeom
## refmg = refAtoms.top.uniq()[0].geomContainer.masterGeom
## mat = refmg.GetMatrix(refmg)
## tmat = Numeric.transpose(mat)
## rot, trans, scale = refmg.Decompose4x4(Numeric.reshape(tmat, (16,)))
## rot_1 = refmg.rotation
## trans_1 = refmg.translation
## print 'rot',rot
## print 'trans',trans
## print 'rot_1',rot_1
## print 'trans_1',trans_1
## mobPivot = list(mob.pivot)
## mobPivot.append(1.)
## transfo = Numeric.identity(4).astype('d')
## transfo[:3,:3] = rotMat[:3,:3]
## transfo[3, :3] = transMat
## hc = Numeric.array(mobPivot)
## tPivot = Numeric.dot(hc, transfo)
## print tPivot[:3]
## mob.SetPivot(tPivot[:3])
#self.vf.centerOnNodes(refMol)
#mob.ConcatRotationRelative(Numeric.reshape(rot, (16,)))
#mob.ConcatTranslation(trans_1)
if old == 1:
vi.TransformRootOnly(1)
vi.SetCurrentObject(oldCurrent)
# Not sure to put that here ?
# Need to concatenate with the transformation of the reference molecule
# to have the two molecule aligned:
# - Get the transformatiom matrix of the ref molecule and decompose it
## refmg = refAtoms.top.uniq()[0].geomContainer.masterGeom
## mat = refmg.GetMatrix(refmg)
## tmat = Numeric.transpose(mat)
## rot, trans, scale = refmg.Decompose4x4(Numeric.reshape(tmat, (16,)))
## self.vf.transformObject('rot', gName, rot)
## self.vf.transformObject('tra', gName, trans)
## #self.vf.transformObject('sca', gName, scale)
def __call__(self, refAtoms, mobAtoms, **kw):
"""
None <- superimposeAtoms(refAtoms, mobAtoms, **kw)
"""
if not kw.has_key('redraw'): kw['redraw'] = 1
apply(self.doitWrapper, (refAtoms, mobAtoms), kw)
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
print("NO REF COORDS!!!")
raise Exception(
'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 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)
# break the bond
if verbose: print "receptor atom for ligand attachment in residue %s is %s" %(resP.full_name(),otherAt.full_name())
otherAt.bonds.remove(b)
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
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
class SuperimposeAtomsCommand(MVCommand):
def onAddCmdToViewer(self):
self.rigidfitAligner = RigidfitBodyAligner()
def doit(self, refAtoms, mobAtoms):
"""
The SuperImposeAtomsCommand takes two set of Atoms of the same length
compute the rotation and translation matrices to superimpose the
mobAtoms onto the refAtoms using rigidFit module and then transform the
corresponding geometry.
"""
refCoords = refAtoms.coords
mobCoords = mobAtoms.coords
self.rigidfitAligner.setRefCoords(refCoords)
# Nothing can be done if the two sets of coords are not of the same
# size
if not len(refCoords) == len(mobCoords):
print " ERROR: Cannot perform the superimposition because the 2 \
mv.lsets of Atoms are not of the same length"
return
# Get the rotation and the translation ysing mglutil.math.rigidFit
self.rigidfitAligner.rigidFit(mobCoords)
#rotation, translation= rigidFit.rigid_fit( refCoords, inCoords)
rotMat = Numeric.identity(4).astype('d')
rotMat[:3, :3] = self.rigidfitAligner.rotationMatrix
transMat = Numeric.array(self.rigidfitAligner.translationMatrix)
# transform the geometry representing the atoms only if a gui has been
# created:
#if not self.vf.hasGui:
# return
# build the geometry name:
mobMol = mobAtoms.top.uniq()[0]
mob = mobMol.geomContainer.masterGeom
#gName = 'root|'+ mobMol[0].name
if not self.vf.hasGui:
vi = self.vf.GUI.VIEWER
oldCurrent = vi.currentObject
vi.SetCurrentObject(mob)
# transform only the given geometry.
if vi.redirectTransformToRoot == 1:
old = vi.redirectTransformToRoot
vi.TransformRootOnly(0)
else:
old = 0
# apply the rotation to the masterGeom of the inMol
mob.SetRotation(Numeric.reshape(rotMat, (16, )))
# apply the translation to the masterGeom of the inMol
mob.SetTranslation(transMat)
## refMol = refAtoms.top.uniq()[0]
## refmg = refMol.geomContainer.masterGeom
## refmg = refAtoms.top.uniq()[0].geomContainer.masterGeom
## mat = refmg.GetMatrix(refmg)
## tmat = Numeric.transpose(mat)
## rot, trans, scale = refmg.Decompose4x4(Numeric.reshape(tmat, (16,)))
## rot_1 = refmg.rotation
## trans_1 = refmg.translation
## print 'rot',rot
## print 'trans',trans
## print 'rot_1',rot_1
## print 'trans_1',trans_1
## mobPivot = list(mob.pivot)
## mobPivot.append(1.)
## transfo = Numeric.identity(4).astype('d')
## transfo[:3,:3] = rotMat[:3,:3]
## transfo[3, :3] = transMat
## hc = Numeric.array(mobPivot)
## tPivot = Numeric.dot(hc, transfo)
## print tPivot[:3]
## mob.SetPivot(tPivot[:3])
#self.vf.centerOnNodes(refMol)
#mob.ConcatRotationRelative(Numeric.reshape(rot, (16,)))
#mob.ConcatTranslation(trans_1)
if not self.vf.hasGui:
if old == 1:
vi.TransformRootOnly(1)
vi.SetCurrentObject(oldCurrent)
# Not sure to put that here ?
# Need to concatenate with the transformation of the reference molecule
# to have the two molecule aligned:
# - Get the transformatiom matrix of the ref molecule and decompose it
## refmg = refAtoms.top.uniq()[0].geomContainer.masterGeom
## mat = refmg.GetMatrix(refmg)
## tmat = Numeric.transpose(mat)
## rot, trans, scale = refmg.Decompose4x4(Numeric.reshape(tmat, (16,)))
## self.vf.transformObject('rot', gName, rot)
## self.vf.transformObject('tra', gName, trans)
## #self.vf.transformObject('sca', gName, scale)
def __call__(self, refAtoms, mobAtoms, **kw):
"""
None <- superimposeAtoms(refAtoms, mobAtoms, **kw)
"""
if not kw.has_key('redraw'): kw['redraw'] = 1
apply(self.doitWrapper, (refAtoms, mobAtoms), kw)
refAtoms = get_atoms(refMol, reflist, names_to_use, verbose)
refCoords = refAtoms.coords #or refMol.chains.residues.atoms.get('backbone').coords
#check that there are some
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 "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
