def alignmol(mol):
masses = []
coordinates = [a.coords for a in mol.atoms]
totalMass = 0
for atom in mol:
m = 1
if options.useweights:
m = atom.atomicmass
masses.append(m)
totalMass += m
coordinates = numpy.array(coordinates)
masses = numpy.array(masses)
trans = -numpy.sum(coordinates * masses[:, numpy.newaxis],
axis=0) / totalMass
mol.OBMol.Translate(openbabel.vector3(*trans))
coordinates += trans
#this is shamelessly stolen from the mdanalysis package
inertia = calcI(masses, coordinates)
eigenval, eigenvec = eig(inertia)
# Sort
indices = numpy.argsort(eigenval)
# Return transposed in more logical form. See Issue 33.
principalAxes = eigenvec[:, indices].T
if det(principalAxes) < 0:
principalAxes = -principalAxes #remove reflection !!Is this correct?? Kabasch wiki says negate just one row, but this is Kabasch...
xrot = openbabel.double_array([1, 0, 0, 0, -1, 0, 0, 0, -1])
yrot = openbabel.double_array([-1, 0, 0, 0, 1, 0, 0, 0, -1])
zrot = openbabel.double_array([-1, 0, 0, 0, -1, 0, 0, 0, 1])
ident = openbabel.double_array([1, 0, 0, 0, 1, 0, 0, 0, 1])
rotmat = openbabel.double_array(principalAxes.flatten())
mol.OBMol.Rotate(rotmat)
coordinates = [a.coords for a in mol.atoms] #should be modified
(a, b) = calcSplitMoments(coordinates, 1)
if (a < b):
mol.OBMol.Rotate(xrot)
# print a,b
(a, b) = calcSplitMoments(coordinates, 0)
if (a < b):
mol.OBMol.Rotate(yrot)
# print a,b
return
def shiftAndCalculateReactionCoordinate(mol,nOfAtoms,reactionCoordinate,vector,h,coords=None): # this function is called many times
if coords==None:
tmp = openbabel.doubleArray_frompointer(mol.GetCoordinates())
coords = [ tmp[i] for i in xrange(3*nOfAtoms) ]
coords = addVec(coords,multVec(h,vector))
mol.SetCoordinates(openbabel.double_array(coords))
return reactionCoordinate(mol)
def separateFragments(pymol, dist=3.0):
mol = pymol.OBMol
nAtom = len(pymol.atoms)
unvisited = set(range(1, nAtom + 1))
q = deque([1])
fragments = [set()]
while q or unvisited:
if q:
curr = q.popleft()
unvisited.remove(curr)
fragments[-1].add(curr)
else:
curr = unvisited.pop()
fragments.append({curr})
atom = mol.GetAtom(curr)
for nbr in ob.OBAtomAtomIter(atom):
nbrNum = nbr.GetIdx()
if nbrNum in unvisited:
q.append(nbrNum)
coords = []
for atom in pymol:
coords.append(list(atom.coords))
nFragments = len(fragments)
delta = -(nFragments - 1) * dist / 2.0
for fragment in fragments:
for atomIdx in fragment:
x, y, z = coords[atomIdx - 1]
coords[atomIdx - 1] = [x + delta, y + delta, z + delta]
delta += dist
coords = [item for sublist in coords for item in sublist]
c_coords = ob.double_array(coords)
mol.SetCoordinates(c_coords)
def alignmol(mol):
masses = []
coordinates = [ a.coords for a in mol.atoms]
totalMass = 0
for atom in mol:
m = 1
if options.useweights:
m = atom.atomicmass
masses.append(m)
totalMass += m
coordinates = numpy.array(coordinates)
masses = numpy.array(masses)
trans = -numpy.sum(coordinates * masses[:, numpy.newaxis], axis=0) / totalMass
mol.OBMol.Translate(openbabel.vector3(*trans))
coordinates += trans
#this is shamelessly stolen from the mdanalysis package
inertia = calcI(masses, coordinates)
eigenval, eigenvec = eig(inertia)
# Sort
indices = numpy.argsort(eigenval)
# Return transposed in more logical form. See Issue 33.
principalAxes = eigenvec[:,indices].T
if det(principalAxes) < 0:
principalAxes = -principalAxes #remove reflection !!Is this correct?? Kabasch wiki says negate just one row, but this is Kabasch...
xrot = openbabel.double_array([1,0,0,0,-1,0,0,0,-1])
yrot = openbabel.double_array([-1,0,0,0,1,0,0,0,-1])
zrot = openbabel.double_array([-1,0,0,0,-1,0,0,0,1])
ident = openbabel.double_array([1,0,0,0,1,0,0,0,1])
rotmat = openbabel.double_array(principalAxes.flatten())
mol.OBMol.Rotate(rotmat)
coordinates = [ a.coords for a in mol.atoms] #should be modified
(a,b) = calcSplitMoments(coordinates, 1)
if(a < b):
mol.OBMol.Rotate(xrot)
# print a,b
(a,b) = calcSplitMoments(coordinates, 0)
if(a < b):
mol.OBMol.Rotate(yrot)
# print a,b
return
def set_xyz(x,coords):
"""
Parameters:
mol : Open babel mol object, or anything that can be converted to mol object with get_mol.
coords : One-d array of natom floats
"""
mol = get_mol(x)
mol.OBMol.SetCoordinates(openbabel.double_array(coords))
return mol
def rotate(mol, theta, phi):
m_theta = np.array([[1.0, 0.0, 0.0],
[0.0, math.cos(theta), -math.sin(theta)],
[0.0, math.sin(theta), math.cos(theta)]])
m_phi = np.array([[math.cos(phi), 0.0, math.sin(phi)],
[0.0, 1.0, 0.0],
[-math.sin(phi), 0.0, math.cos(phi)]])
m = np.dot(m_phi, m_theta)
m_list = list(itertools.chain(*m))
mol.Rotate(ob.double_array(m_list))
return mol
def shiftAndCalculateReactionCoordinate(
mol,
nOfAtoms,
reactionCoordinate,
vector,
h,
coords=None): # this function is called many times
if coords == None:
tmp = openbabel.doubleArray_frompointer(mol.GetCoordinates())
coords = [tmp[i] for i in xrange(3 * nOfAtoms)]
coords = addVec(coords, multVec(h, vector))
mol.SetCoordinates(openbabel.double_array(coords))
return reactionCoordinate(mol)
def AndersenIntegrator(self,mol,relevantCoordinates,ff,h,reactionCoordinate,timeStep,timeStep2,nuTimesTimeStep):
currCoords = self.coords[-1]
currVelocity = self.velocity[-1]
currAcc = self.acceleration[-1]
# calculating next position:
nextCoords = self.nOfAtomsX3*[0]
for i in xrange(self.nOfAtomsX3):
nextCoords[i] = currCoords[i] + timeStep*currVelocity[i] + currAcc[i]*timeStep2/2 # nie jestem pewien tego currAcc
for i in xrange(self.nOfAtomsX3):
currVelocity[i] = currVelocity[i] + 0.5*timeStep*currAcc[i] # that's the ACTUAL currentVelocity
mol.SetCoordinates( openbabel.double_array(nextCoords) )
energy = self.calculateGradU(ff,mol)
gradKsi = calcGrad(mol,relevantCoordinates,reactionCoordinate,h)
self.calculateZksi( gradKsi )
Zksi = self.Zksi[-1]
gradU = self.gradU[-1]
if Zksi==0: constraintLambda = 0
else: constraintLambda = (scalarTrippleProduct(self.invMasses,gradKsi,gradU)-calcVectorHessianVectorProduct(mol,reactionCoordinate,h,currVelocity)) / Zksi
###########################
#constraintLambda = 0 # if set to 0 it will be a simple Andersen dynamics simulation
###########################
currAcc = self.nOfAtomsX3*[0]
for i in xrange(self.nOfAtomsX3):
currAcc[i] = (-gradU[i] + constraintLambda*gradKsi[i])/self.masses[i] # TODO: upewnij sie, ze tu jest dzielenie przez mase
# second velocity half-step
for i in xrange(self.nOfAtomsX3):
currVelocity[i] = currVelocity[i] + 0.5*timeStep*currAcc[i] # that's the ACTUAL currentVelocity
# Andersen thermostat
for i in xrange(self.nOfAtoms):
if random.random()<nuTimesTimeStep:
for j in xrange(3): currVelocity[3*i+j] = random.gauss(0,self.AndersenSigmas[3*i+j])
self.setNonVelocityAtribute(self.coords,nextCoords)
self.setNonVelocityAtribute(self.acceleration,currAcc)
self.setNonVelocityAtribute(self.gradU,gradU)
self.velocity[3] = currVelocity
return energy
def make_structure(request):
def makeResidue(mol, idx, aaatoms):
res = mol.NewResidue()
res.SetNum(idx)
for atom in ob.OBMolAtomIter(mol):
if atom.GetIdx() not in aaatoms:
res.AddAtom(atom)
aminoacids = request.GET.getlist("as")
color = request.GET.get("rescol", "#3EC1CD")
mol = ob.OBMol()
conv = ob.OBConversion()
pattern = ob.OBSmartsPattern()
pattern.Init("[NX3][$([CX4H1]([*])),$([CX4H2])][CX3](=[OX1])[OX2]")
builder = ob.OBBuilder()
conv.SetInAndOutFormats("sdf", "svg")
conv.AddOption("d", ob.OBConversion.OUTOPTIONS)
conv.AddOption("b", ob.OBConversion.OUTOPTIONS, "none")
conv.ReadString(mol, str(Substrate.objects.get(pk=int(aminoacids[0])).structure))
pattern.Match(mol)
mollist = pattern.GetUMapList()[0]
oatom = mol.GetAtom(mollist[4])
catom = mol.GetAtom(mollist[2])
firstnatom = mol.GetAtom(mollist[0])
makeResidue(mol, 0, mollist)
i = 1
for aa in aminoacids[1:]:
mol2 = ob.OBMol()
conv.ReadString(mol2, str(Substrate.objects.get(pk=int(aa)).structure))
pattern.Match(mol2)
mollist = pattern.GetUMapList()[0]
makeResidue(mol2, i, mollist)
molnatoms = mol.NumAtoms()
mol += mol2
natom = mol.GetAtom(molnatoms + mol2.GetAtom(mollist[0]).GetIdx())
builder.Connect(mol, catom.GetIdx(), natom.GetIdx())
foatom = mol.GetAtom(molnatoms + mol2.GetAtom(mollist[4]).GetIdx())
catom = mol.GetAtom(molnatoms + mol2.GetAtom(mollist[2]).GetIdx())
mol.DeleteHydrogens(oatom)
mol.DeleteAtom(oatom)
natom.SetImplicitValence(3)
mol.DeleteHydrogens(natom)
mol.AddHydrogens(natom)
oatom = foatom
i += 1
nidx = firstnatom.GetIdx()
oidx = oatom.GetIdx()
builder.Build(mol)
natom = mol.GetAtom(nidx)
oatom = mol.GetAtom(oidx)
for res in ob.OBResidueIter(mol):
for atom in ob.OBResidueAtomIter(res):
for bond in ob.OBAtomBondIter(atom):
data = ob.OBPairData()
data.SetAttribute("color")
data.SetValue(color)
bond.CloneData(data)
mol.DeleteHydrogens()
gen2d = ob.OBOp.FindType("gen2d")
gen2d.Do(mol)
opp = oatom.GetY() - natom.GetY()
adj = oatom.GetX() - natom.GetX()
angle = abs(math.atan(opp / adj))
if opp > 0 and adj > 0:
pass
elif opp > 0 and adj < 0:
angle = math.pi - angle
elif opp < 0 and adj < 0:
angle = math.pi + angle
elif opp < 0 and adj > 0:
angle = 2 * math.pi - angle
angle = -angle
mol.Rotate(ob.double_array([math.cos(angle), -math.sin(angle), 0,
math.sin(angle), math.cos(angle), 0,
0, 0, 1]))
svg = conv.WriteString(mol)
# need to get rid of square aspect ratio
delstart = svg.find("width")
delend = svg.find("svg", delstart)
delend = svg.find("viewBox", delend)
svgend = svg.rfind("</g>")
svg = svg[0:delstart] + svg[delend:svgend]
return HttpResponse(svg, mimetype="image/svg+xml")
# generate .top and write
fcontent = gen_top(args.force_field,
os.path.splitext(args.dfrfile)[0] + ".itp")
with open("topology.top", "w") as f:
f.write(fcontent)
# get the molecule diameter
mol.OBMol.Center()
maxd = 0.0
for atom in mol:
x, y, z = atom.coords
r = sqrt(x * x + y * y + z * z)
if r > maxd:
maxd = r
# modify the unit cell and translate the molecule to the center of box
boxsize = maxd + 100.0
cell = openbabel.OBUnitCell()
cell.SetData(boxsize, boxsize, boxsize, 90.0, 90.0, 90.0)
mol.OBMol.CloneData(cell)
disp = boxsize / 2.0
arr = openbabel.vector3(openbabel.double_array([disp, disp, disp]))
mol.OBMol.Translate(arr)
# write .gro
mol.write("gro",
os.path.splitext(args.txtfile)[0] + ".gro",
overwrite=True)
def AndersenIntegrator(self, mol, relevantCoordinates, ff, h,
reactionCoordinate, timeStep, timeStep2,
nuTimesTimeStep):
currCoords = self.coords[-1]
currVelocity = self.velocity[-1]
currAcc = self.acceleration[-1]
# calculating next position:
nextCoords = self.nOfAtomsX3 * [0]
for i in xrange(self.nOfAtomsX3):
nextCoords[
i] = currCoords[i] + timeStep * currVelocity[i] + currAcc[
i] * timeStep2 / 2 # nie jestem pewien tego currAcc
for i in xrange(self.nOfAtomsX3):
currVelocity[i] = currVelocity[i] + 0.5 * timeStep * currAcc[
i] # that's the ACTUAL currentVelocity
mol.SetCoordinates(openbabel.double_array(nextCoords))
energy = self.calculateGradU(ff, mol)
gradKsi = calcGrad(mol, relevantCoordinates, reactionCoordinate, h)
self.calculateZksi(gradKsi)
Zksi = self.Zksi[-1]
gradU = self.gradU[-1]
if Zksi == 0: constraintLambda = 0
else:
constraintLambda = (
scalarTrippleProduct(self.invMasses, gradKsi, gradU) -
calcVectorHessianVectorProduct(mol, reactionCoordinate, h,
currVelocity)) / Zksi
###########################
#constraintLambda = 0 # if set to 0 it will be a simple Andersen dynamics simulation
###########################
currAcc = self.nOfAtomsX3 * [0]
for i in xrange(self.nOfAtomsX3):
currAcc[i] = (
-gradU[i] + constraintLambda * gradKsi[i]) / self.masses[
i] # TODO: upewnij sie, ze tu jest dzielenie przez mase
# second velocity half-step
for i in xrange(self.nOfAtomsX3):
currVelocity[i] = currVelocity[i] + 0.5 * timeStep * currAcc[
i] # that's the ACTUAL currentVelocity
# Andersen thermostat
for i in xrange(self.nOfAtoms):
if random.random() < nuTimesTimeStep:
for j in xrange(3):
currVelocity[3 * i + j] = random.gauss(
0, self.AndersenSigmas[3 * i + j])
self.setNonVelocityAtribute(self.coords, nextCoords)
self.setNonVelocityAtribute(self.acceleration, currAcc)
self.setNonVelocityAtribute(self.gradU, gradU)
self.velocity[3] = currVelocity
return energy
def align_ligand(dummies, ligand):
# fit dummy atoms of ligand to defined positions
log.info('Aligning ligand dummy atoms to desired dummy atoms...')
# 0.9 create local copy, as this function would otherwise modify the given ligand
aligned_ligand = openbabel.OBMol(ligand)
# 1.0 get dummy atoms from ligand
log.debug('... get dummy atoms of ligand')
ligand_dummies = get_dummies(ligand)
# 1.1 get translation vector from read-in position to origin
log.info('... determing translation vector from read-in to origin')
translation = ligand_dummies.Center(1)
## DEBUG
#obconversion = openbabel.OBConversion()
#obconversion.SetOutFormat("pdb")
#obconversion.WriteFile(ligand_dummies,"ligand_dummies_centered.pdb")
# 1.2 initialize OBAlign for alignment to final destination
log.info('... doing the alignment for dummy atoms')
aligner = openbabel.OBAlign(dummies, ligand_dummies)
success=aligner.Align()
if success == False:
return None, None
#log.info('... done.')
rmsd=aligner.GetRMSD()
log.debug('RMSD of alignment: ' + str(rmsd))
## 1.2.1 get Rotation Matrix for alignment
log.info('... determining the rotation matrix')
rotation_matrix = aligner.GetRotMatrix()
rot = openbabel.double_array([1,2,3,4,5,6,7,8,9])
rotation_matrix.GetArray(rot)
# .. only for debugging:
arewedebugging = log.getLogger()
if arewedebugging.isEnabledFor(logging.DEBUG):
log.debug('--- rotation matrix ---')
for i in range(0,9): log.debug(str(i)+ " : " + str(rot[i]))
# 1.3 generate positioning vector
## NB: centering would not work because of rotation!!
## update cooordinates to new value
aligner.UpdateCoords(ligand_dummies)
log.info('... generating positioning vector')
positioning = openbabel.vector3()
## calculate the vector for positioning to destination
n = 0
for atom in openbabel.OBMolAtomIter(ligand_dummies):
n += 1
positioning += atom.GetVector()
positioning /= n
# 1.4 move all ligand atoms to fit the pose the dummy atoms have been aligned to
## 1.4.1 generate inverted translation vector to translate ligand to origin
translation_to_origin = translation
translation_to_origin *= -1
## 1.4.2 generate inverted rotation matrix to reconstruct alignment results
rotation_inversion = rotation_matrix.transpose()
rot_inv = openbabel.double_array([1,2,3,4,5,6,7,8,9])
rotation_inversion.GetArray(rot_inv)
## 1.4.3 apply translation to origin, rotation, and translation to final destination
aligned_ligand.Translate(translation_to_origin)
aligned_ligand.Rotate(rot_inv)
aligned_ligand.Translate(positioning)
## 1.5 clean output ligand of dummy atoms, if desired
if remove_dummies:
log.info('Cleaning the ligand of unwanted dummies...')
_temp_atom = []
for atom in openbabel.OBMolAtomIter(aligned_ligand):
#aligned_ligand.AddResidue(atom.GetResidue())
#aligned_ligand.AddAtom(atom)
if atom.GetAtomicNum() == 0:
_temp_atom.append(atom)
for a in _temp_atom:
aligned_ligand.DeleteAtom(a)
#else:
#aligned_ligand = ligand
log.info('... returning the aligned ligand.')
return aligned_ligand, rmsd
print "x=%f; y=%f; z=%f" % (natom.GetX(), natom.GetY(), natom.GetZ())
print "x=%f; y=%f; z=%f" % (oatom.GetX(), oatom.GetY(), oatom.GetZ())
opp = oatom.GetY() - natom.GetY()
adj = oatom.GetX() - natom.GetX()
angle = abs(math.atan(opp / adj))
if opp > 0 and adj > 0:
pass
elif opp > 0 and adj < 0:
angle = math.pi - angle
elif opp < 0 and adj < 0:
angle = math.pi + angle
elif opp < 0 and adj > 0:
angle = 2 * math.pi - angle
print math.degrees(angle)
angle = -angle
mol.Rotate(ob.double_array([math.cos(angle), -math.sin(angle), 0,
math.sin(angle), math.cos(angle), 0,
0, 0, 1]))
svg = conv.WriteString(mol)
# need to get rid of square aspect ratio
delstart = svg.find("width")
delend = svg.find("svg", delstart)
delend = svg.find("viewBox", delend)
svgend = svg.rfind("</g>")
svg = svg[0:delstart] + svg[delend:svgend]
outf = file("test.svg", "w")
outf.write(svg)
outf.close()