def _CDPLgenerateConformation(cdpl_mol):
'''
PRIVAT METHOD
configures a CDPL Molecule for conformation generation. \n
Input: \n
mol (CDPL BasicMolecule): a CDPL BasicMolecule \n
Return: \n
(CDPL BasicMolecule): the corresponding random conf. for the input BasicMolecule
'''
_CDPLconfigForConformation(
cdpl_mol
) #TODO What exactly should be in the config for the cmp generation?
cg = ConfGen.RandomConformerGenerator()
coords = Math.Vector3DArray()
i = 0
cg.strictMMFF94AtomTyping = False
ConfGen.prepareForConformerGeneration(cdpl_mol)
coords.resize(cdpl_mol.numAtoms, Math.Vector3D())
cg.setup(cdpl_mol)
if cg.generate(coords) != ConfGen.RandomConformerGenerator.SUCCESS:
log.error('! Conformer generation failed !')
return
Chem.set3DCoordinates(cdpl_mol, coords)
return cdpl_mol
def calcMeanPos(positions):
mean_pos = Math.Vector3D()
for pos in positions:
mean_pos += pos
mean_pos /= len(positions)
return mean_pos
def calcMSF(positions, mean_pos):
msf = 0.0
tmp = Math.Vector3D()
for pos in positions:
tmp.assign(pos)
tmp -= mean_pos
msf += Math.innerProd(tmp, tmp)
msf = msf / len(positions)
return msf
def calcAtomSetCentroid(atoms, conf_idx):
if len(atoms) == 1:
return Chem.getConformer3DCoordinates(atoms[0], conf_idx)
ctr = Math.Vector3D()
for atom in atoms:
ctr += Chem.getConformer3DCoordinates(atom, conf_idx)
ctr /= len(atoms)
return ctr
def calcLonePairPosition(atom, mol, coords):
lp_pos = Math.Vector3D()
atom_pos = coords[mol.getAtomIndex(atom)]
for nbr_atom in atom.atoms:
lp_pos -= coords[mol.getAtomIndex(nbr_atom)]
lp_pos -= atom_pos
lp_pos /= atom.getNumAtoms()
lp_pos += atom_pos
return lp_pos
def calcMaxFluct(positions, mean_pos):
max_fluct = 0.0
tmp = Math.Vector3D()
for pos in positions:
tmp.assign(pos)
tmp -= mean_pos
dev = Math.norm2(tmp)
if dev > max_fluct:
max_fluct = dev
return max_fluct
def process():
if len(sys.argv) < 4:
print >> sys.stderr, 'Usage:', sys.argv[
0], '[input.cdf] [output directory] [frame index]'
sys.exit(2)
print >> sys.stderr, '> Processing grid CDF-file:', sys.argv[1], '...'
index_frame = int(sys.argv[3])
grid_set = Grid.DRegularGridSet()
cdf_grid_reader = Grid.FileCDFDRegularGridSetReader(sys.argv[1])
print >> sys.stderr, '> Writing grid data for frame', index_frame, '...\n'
grid_set.clear()
if not cdf_grid_reader.read(index_frame, grid_set):
print '> No grid in file.'
sys.exit(2)
coord = Math.Vector3D()
for grid in grid_set:
int_descr = Grid.getName(grid)
out_fname = path.splitext(
path.basename(sys.argv[1])
)[0] + '_' + int_descr + '_frame_no_' + sys.argv[3] + '.kont'
out_path = path.join(sys.argv[2], out_fname)
kont_file = open(out_path, 'w')
index_mol = 0
grid_values = []
print '>', int_descr, 'grid'
for k in range(grid.getSize3()):
for i in range(grid.getSize1()):
for j in range(grid.getSize2()):
index_mol += 1
grid_values.append(grid(i, j, k))
grid.getCoordinates(i, j, k, coord)
kont_file.write(
"{:>7} {:>7.3f} {:>7.3f} {:>7.3f}\n".format(
index_mol, coord[0], coord[1], coord[2]))
kont_file.write("{:>8}\n".format(int_descr))
for txt in grid_values:
kont_file.write("{:>8.3f}\n".format(txt))
kont_file.close()
def makeRandomTranslation(self,
inplace: bool = True,
scalingFactor: float = 10) -> Math.Vector3DArray:
"""
:param inplace:
:param scalingFactor: Scales the randomly retrieved direction by this factor
:return:
"""
direction = Math.Vector3D()
direction.assign(np.random.rand(3) * scalingFactor)
translatedCoords = translate3DObject(self.getCoordinates(), direction)
if inplace:
Chem.set3DCoordinates(self, translatedCoords)
return translatedCoords
def process():
if len(sys.argv) < 3:
print >> sys.stderr, 'Usage:', sys.argv[
0], '[input.cdf] [output directory]'
sys.exit(2)
in_fname = path.splitext(path.basename(sys.argv[1]))[0]
mol = Chem.BasicMolecule()
cdf_reader = Chem.FileCDFMoleculeReader(sys.argv[1])
pvd_file = open(path.join(sys.argv[2], in_fname + '.pvd'), 'w')
Util.writePVDHeader(pvd_file)
print >> sys.stderr, '- Processing CDF-file:', sys.argv[1], '...'
if not cdf_reader.read(mol):
print '!! Could not read file'
sys.exit(2)
backbone_atoms = []
for atom in mol.atoms:
if Biomol.isPDBBackboneAtom(atom) and Biomol.getResidueAtomName(
atom) == 'C':
backbone_atoms.append(atom)
bond_list = []
for bond in mol.bonds:
if Biomol.getResidueCode(
bond.getAtom(0)) == 'HOH' or Biomol.getResidueCode(
bond.getAtom(1)) == 'HOH':
continue
if Chem.getType(bond.getAtom(0)) == Chem.AtomType.H or Chem.getType(
bond.getAtom(1)) == Chem.AtomType.H:
continue
bond_list.append(bond)
num_confs = Chem.getNumConformations(mol)
num_coords = len(bond_list) * 4 + (
len(backbone_atoms) * SPLINE_POINTS_PER_BB_ATOM - 1) * 2
bond_ctr = Math.Vector3D()
i = 0
while i < num_confs:
line_x_coords = numpy.ndarray(num_coords, numpy.float32)
line_y_coords = numpy.ndarray(num_coords, numpy.float32)
line_z_coords = numpy.ndarray(num_coords, numpy.float32)
atom_types = numpy.ndarray(num_coords, numpy.uint32)
spline_ctrl_points = numpy.ndarray((len(backbone_atoms), 3),
numpy.float32)
j = 0
for atom in backbone_atoms:
atom_pos = Chem.getConformer3DCoordinates(atom, i)
spline_ctrl_points[j, 0] = atom_pos(0)
spline_ctrl_points[j, 1] = atom_pos(1)
spline_ctrl_points[j, 2] = atom_pos(2)
j += 1
spline_pts = spline(spline_ctrl_points,
len(backbone_atoms) * SPLINE_POINTS_PER_BB_ATOM)
j = 0
k = 0
while k < (len(backbone_atoms) * SPLINE_POINTS_PER_BB_ATOM - 1):
line_x_coords[j] = spline_pts[0][k]
line_y_coords[j] = spline_pts[1][k]
line_z_coords[j] = spline_pts[2][k]
atom_types[j] = 0
j += 1
line_x_coords[j] = spline_pts[0][k + 1]
line_y_coords[j] = spline_pts[1][k + 1]
line_z_coords[j] = spline_pts[2][k + 1]
atom_types[j] = 0
j += 1
k += 1
for bond in bond_list:
atom1 = bond.getAtom(0)
atom2 = bond.getAtom(1)
atom1_pos = Chem.getConformer3DCoordinates(atom1, i)
atom2_pos = Chem.getConformer3DCoordinates(atom2, i)
atom1_type = Chem.getType(atom1)
atom2_type = Chem.getType(atom2)
bond_ctr.assign(atom1_pos)
bond_ctr += atom2_pos
bond_ctr *= 0.5
line_x_coords[j] = atom1_pos(0)
line_y_coords[j] = atom1_pos(1)
line_z_coords[j] = atom1_pos(2)
atom_types[j] = atom1_type
j += 1
line_x_coords[j] = bond_ctr(0)
line_y_coords[j] = bond_ctr(1)
line_z_coords[j] = bond_ctr(2)
atom_types[j] = atom1_type
j += 1
line_x_coords[j] = bond_ctr(0)
line_y_coords[j] = bond_ctr(1)
line_z_coords[j] = bond_ctr(2)
atom_types[j] = atom2_type
j += 1
line_x_coords[j] = atom2_pos(0)
line_y_coords[j] = atom2_pos(1)
line_z_coords[j] = atom2_pos(2)
atom_types[j] = atom2_type
j += 1
line_x_coords.resize(j)
line_y_coords.resize(j)
line_z_coords.resize(j)
atom_types.resize(j)
out_fname = in_fname + '_frame_no_' + str(i)
out_path = path.join(sys.argv[2], out_fname)
line_data = {'atom_type': atom_types}
print >> sys.stderr, '- Writing structure data for frame', i, '...'
if not pyevtk.hl.linesToVTK(out_path,
line_x_coords,
line_y_coords,
line_z_coords,
pointData=line_data):
print '!! Could not write output file'
sys.exit(2)
Util.writePVDEntry(pvd_file, i, out_fname, 'vtu')
i += 1
Util.writePVDFooter(pvd_file)
# calculate surface area for a single carbon atom
protein.getGaussianShape()
shapeFunc = protein.shapeFunc
carbonProteinIndex = None
for a in protein.atoms:
if Chem.getType(a) == 6:
carbonProteinIndex = protein.getAtomIndex(a)
break
surfAreaCarbonProtein = shapeFunc.calcSurfaceArea(carbonProteinIndex) # calculate the surface area contribution here?
# create a simple carbon molecule with coordinates
carbon = Chem.BasicMolecule()
cAtom = carbon.addAtom()
Chem.setType(cAtom, 6)
coords = Math.Vector3D()
coords.assign([1, 2, 3])
Chem.set3DCoordinates(cAtom, coords)
# calculate shape and surface area of carbon molecule
carbonShape, carbonShapeFunc = getGaussianShapeOfMolecule(carbon)
surfAreaCarbon = carbonShapeFunc.surfaceArea
# assert that contribution of carbon atom in protein is in fact the entire surface area of a single carbon
assert surfAreaCarbon == surfAreaCarbonProtein
# What am I missing here?
# Summing the surface area of all atoms in the protein yields the surface area of the protein. I find it hard to
# believe that all the atoms are surface atoms. Am I missing the VDW radius somehow and all atoms are in fact
# just points right now?
# for example:
def process():
if len(sys.argv) < 3:
print >> sys.stderr, 'Usage:', sys.argv[
0], '[input.cdf] [output directory]'
sys.exit(2)
in_fname = path.splitext(path.basename(sys.argv[1]))[0]
grid_set = Grid.DRegularGridSet()
cdf_reader = Grid.FileCDFDRegularGridSetReader(sys.argv[1])
pvd_file = open(path.join(sys.argv[2], in_fname + '.pvd'), 'w')
Util.writePVDHeader(pvd_file)
print >> sys.stderr, '- Processing grid CDF-file:', sys.argv[1], '...'
frame_no = 0
while True:
grid_set.clear()
if not cdf_reader.read(grid_set):
break
output_data = {}
grid_spacing = None
grid_origin = None
for grid in grid_set:
int_descr = Grid.getName(grid)
grid_values = numpy.ndarray(
(grid.getSize1(), grid.getSize2(), grid.getSize3()),
numpy.float32)
output_data[int_descr] = grid_values
for i in range(grid.getSize1()):
for j in range(grid.getSize2()):
for k in range(grid.getSize3()):
grid_values[i, j, k] = grid(i, j, k)
if not grid_spacing:
grid_spacing = (grid.getXStepSize(), grid.getYStepSize(),
grid.getZStepSize())
if not grid_origin:
grid_origin = Math.Vector3D()
grid.getCoordinates(0, 0, 0, grid_origin)
out_fname = in_fname + '_frame_no_' + str(frame_no)
out_path = path.join(sys.argv[2], out_fname)
print >> sys.stderr, '- Writing grid data for frame', frame_no, '...'
if not pyevtk.hl.imageToVTK(out_path,
origin=grid_origin,
spacing=grid_spacing,
pointData=output_data):
print '!! Could not write grid output file'
sys.exit(2)
Util.writePVDEntry(pvd_file, frame_no, out_fname, 'vti')
frame_no += 1
Util.writePVDFooter(pvd_file)
def process():
if len(sys.argv) < 4:
print >> sys.stderr, 'Usage:', sys.argv[
0], '[input topology-file] [input coordinates-file] [output CDF-file]'
sys.exit(2)
print >> sys.stderr, '- Processing topology-file', sys.argv[
1], 'and coordinates-file', sys.argv[2], '...'
u = MDAnalysis.Universe(sys.argv[1], sys.argv[2])
cdf_mol = Chem.BasicMolecule()
cdf_mol.reserveMemoryForAtoms(len(u.atoms))
cdf_mol.reserveMemoryForBonds(len(u.bonds))
print >> sys.stderr, '- Num. atoms:', len(u.atoms)
print >> sys.stderr, '- Num. bonds:', len(u.bonds)
num_frames = len(u.trajectory)
print >> sys.stderr, '- Num. frames:', num_frames
# construct atoms
print >> sys.stderr, '- Building atoms ...'
waters = {}
i = 0
for md_atom in u.atoms:
atom = cdf_mol.addAtom()
sym = MDAnalysis.topology.guessers.guess_atom_element(md_atom.name)
Chem.setSymbol(atom, sym.title())
Chem.setImplicitHydrogenCount(atom, 0)
Biomol.setChainID(atom, md_atom.segid)
if md_atom.resname == 'WAT':
Biomol.setResidueCode(atom, 'HOH')
else:
Biomol.setResidueCode(atom, md_atom.resname)
if Biomol.getResidueCode(atom) == 'HOH':
if md_atom.resid in waters:
waters[md_atom.resid].append(i)
else:
waters[md_atom.resid] = [i]
Biomol.setResidueSequenceNumber(atom, int(md_atom.resid))
Biomol.setResidueAtomName(atom, md_atom.name)
# fix positive charge on arginin nitrogen
if md_atom.resname == 'ARG' and md_atom.name == 'NH2':
Chem.setFormalCharge(atom, 1)
coords = []
for coord in md_atom.position:
coords.append(float(coord))
Chem.set3DCoordinates(atom, coords)
coords_array = Math.Vector3DArray()
coords_array.reserve(num_frames)
Chem.set3DCoordinatesArray(atom, coords_array)
Chem.setPEOECharge(atom, float(md_atom.charge))
i += 1
Chem.setAtomTypesFromSymbols(cdf_mol, True)
# construct bonds
print >> sys.stderr, '- Building bonds ...'
for md_bond in u.bonds:
cdf_mol.addBond(int(md_bond.atoms[0].index),
int(md_bond.atoms[1].index))
print >> sys.stderr, '- Building water atom bonds ...'
for water in waters.values():
if len(water) < 2:
continue
for atom_idx in water:
if Chem.getType(cdf_mol.atoms[atom_idx]) == Chem.AtomType.O:
if atom.numBonds > 1:
break
for atom_idx2 in water:
if Chem.getType(
cdf_mol.atoms[atom_idx2]) == Chem.AtomType.H:
cdf_mol.addBond(atom_idx, atom_idx2)
break
# make sane biomolecule
Chem.perceiveSSSR(cdf_mol, True)
Chem.setRingFlags(cdf_mol, True)
Chem.perceiveBondOrders(cdf_mol, True)
Chem.perceiveHybridizationStates(cdf_mol, True)
Chem.setAromaticityFlags(cdf_mol, True)
Chem.calcFormalCharges(cdf_mol, True)
# read timsteps and write cdf
print >> sys.stderr, '- Importing coordinates ...'
i = 0
traj_coords = []
atom_coords = Math.Vector3D()
for ts in u.trajectory:
print >> sys.stderr, '- Processing time step', i, '...'
for md_atom in u.atoms:
del traj_coords[:]
for coord in md_atom.position:
traj_coords.append(float(coord))
coords_array = Chem.get3DCoordinatesArray(
cdf_mol.getAtom(int(md_atom.index)))
atom_coords[0] = traj_coords[0]
atom_coords[1] = traj_coords[1]
atom_coords[2] = traj_coords[2]
coords_array.addElement(atom_coords)
i += 1
print >> sys.stderr, '- Writing output file:'
if not Chem.FileCDFMolecularGraphWriter(sys.argv[3]).write(cdf_mol):
print >> sys.stderr, '!! Could not write output file'
sys.exit(2)