def testOBMolSeparatePreservesAtomOrder(self):
"""Originally Separate() preserved DFS order rather
than atom order"""
# First test
smi = "C123.F3.Cl2.Br1"
mol = pybel.readstring("smi", smi)
atomicnums = [atom.OBAtom.GetAtomicNum() for atom in mol]
mols = mol.OBMol.Separate()
new_atomicnums = [
atom.OBAtom.GetAtomicNum() for atom in pybel.Molecule(mols[0])
]
for x, y in zip(atomicnums, new_atomicnums):
self.assertEqual(x,
y) # check that the atoms have not been permuted
# Second test
xyz = """6
examples/water_dimer.xyz
O 0.12908 -0.26336 0.64798
H 0.89795 0.28805 0.85518
H 0.10833 -0.20468 -0.33302
O 0.31020 0.07569 -2.07524
H 0.64083 -0.57862 -2.71449
H -0.26065 0.64232 -2.62218
"""
mol = pybel.readstring("xyz", xyz)
mols = mol.OBMol.Separate()
allatoms = pybel.Molecule(mols[0]).atoms + pybel.Molecule(
mols[1]).atoms
for idx, atom in enumerate(allatoms):
xcoord = atom.OBAtom.GetX()
orig_xcoord = mol.OBMol.GetAtom(idx + 1).GetX()
self.assertEqual(xcoord, orig_xcoord)
def copyMolecule(molecule):
'''Takes a pybel molecule as input.
Effectively returns a deep copy of the pybel molecule submitted'''
#using copy.deepcopy didnt return a usable molecule
newmolecule = pb.Molecule(pb.ob.OBMol(
molecule.OBMol)) #converts pybel into OpenBabel and back
return newmolecule
def getSmiles(mol):
'''
This function returns the SMILES string for a molecule
'''
a = BabelMolAdaptor(mol)
pba = pb.Molecule(a.openbabel_mol)
return pba.write("can").split()[0]
def layout(p):
"""Calculate points positions for depiction of Pharmacophore p using OpenBabel."""
if not isinstance(p, Pharmacophore):
raise TypeError("Expected Pharmacophore object, got %s instead" %
type(p).__name__)
positions = np.zeros((p.numnodes, 2))
m = pybel.Molecule(ob.OBMol())
for i in range(p.numnodes):
m.OBMol.NewAtom()
idx = p.numnodes + 1
for i in range(p.numnodes):
for j in range(i):
if p.edges[i, j] > 0:
tmp = int(math.ceil(p.edges[i, j])) - 1
prev = i + 1
# add invisible atoms to get right distance
for k in range(tmp):
atom = m.OBMol.NewAtom(idx)
atom.SetHyb(1)
m.OBMol.AddBond(prev, idx, 1)
prev = idx
idx += 1
m.OBMol.AddBond(prev, j + 1, 1)
m.draw(show=False, update=True)
for i in range(p.numnodes):
positions[i][0] = m.atoms[i].coords[0]
positions[i][1] = m.atoms[i].coords[1]
return positions
def average_properties(smiles):
"""
Calculate all relevant properties for a given molecule averaged across conformers
:param mol: input molecule smiles
:type mol: openbabel.OBMol
:return: dictionary of properties
:rtype dict
..todo: remove reliance on pybel
"""
mol = smiles_to_ob(smiles)
mols = run_confab(mol)
num_confs = mols.NumConformers()
globs = np.empty(num_confs)
# pbfs = np.empty(num_confs)
for i in range(num_confs):
mols.SetConformer(i)
pymol = pybel.Molecule(mols)
# calculate properties
globs[i] = calc_glob(pymol)
# pbfs[i] = calc_pbf(pymol)
data = {
'rotatable_bonds': rotatable_bonds(pymol),
'globularity': np.mean(globs),
'primary_amine': has_primary_amine(pymol),
# 'pbf': np.mean(pbfs)
}
return data
def restore_site_properties(self, site_property="ff_map", filename=None):
"""
Restore the site properties for the final packed molecule.
Args:
site_property (str):
filename (str): path to the final packed molecule.
Returns:
Molecule
"""
# only for pdb
if not self.control_params["filetype"] == "pdb":
raise
filename = filename or self.control_params["output"]
bma = BabelMolAdaptor.from_file(filename, "pdb")
pbm = pb.Molecule(bma._obmol)
assert len(pbm.residues) == sum([x["number"] for x in self.param_list])
packed_mol = self.convert_obatoms_to_molecule(
pbm.residues[0].atoms, residue_name=pbm.residues[0].name,
site_property=site_property)
for resid in pbm.residues[1:]:
mol = self.convert_obatoms_to_molecule(
resid.atoms, residue_name=resid.name, site_property=site_property)
for site in mol:
packed_mol.append(site.species_and_occu, site.coords,
properties=site.properties)
return packed_mol
def json_to_pybel(data, center=True):
"""Converts python data structure to pybel.Molecule.
This will infer bond data if not specified.
Args:
data: The loaded json data of a molecule, as a Python object
center: (Optional) Centers the coordinates of the outputted molecule
Returns:
An instance of `pybel.Molecule`
"""
obmol = ob.OBMol()
obmol.BeginModify()
for atom in data["atoms"]:
obatom = obmol.NewAtom()
obatom.SetAtomicNum(table.GetAtomicNum(str(atom["element"])))
obatom.SetVector(*atom["location"])
if "charge" in atom:
obatom.SetPartialCharge(atom["charge"])
# If there is no bond data, try to infer them
if "bonds" not in data or not data["bonds"]:
obmol.ConnectTheDots()
obmol.PerceiveBondOrders()
# Otherwise, use the bonds in the data set
else:
for bond in data["bonds"]:
if "atoms" not in bond:
continue
obmol.AddBond(bond["atoms"][0] + 1, bond["atoms"][1] + 1,
bond["order"])
obmol.EndModify()
if center:
obmol.Center()
return pybel.Molecule(obmol)
def getFormula(self):
"""
Return the molecular formula for the molecule.
"""
import pybel
mol = pybel.Molecule(self.toOBMol())
return mol.formula
def test_primary_amine_benzenesulfonamide():
mol = calc_props.smiles_to_ob("O=S(C1=CC=CC=C1)(N)=O")
pymol = pybel.Molecule(mol)
primary_amine_smarts = calc_props.FUNCTIONAL_GROUP_TO_SMARTS[
"primary_amine"]
assert_equals(calc_props.has_functional_group(pymol, primary_amine_smarts),
False)
def _write_input(self, input_dir="."):
"""
Write the packmol input file to the input directory.
Args:
input_dir (string): path to the input directory
"""
with open(os.path.join(input_dir, self.input_file), 'wt', encoding="utf-8") as inp:
for k, v in six.iteritems(self.control_params):
inp.write('{} {}\n'.format(k, self._format_param_val(v)))
# write the structures of the constituent molecules to file and set
# the molecule id and the corresponding filename in the packmol
# input file.
for idx, mol in enumerate(self.mols):
a = BabelMolAdaptor(mol)
pm = pb.Molecule(a.openbabel_mol)
filename = os.path.join(
input_dir, '{}.{}'.format(
idx, self.control_params["filetype"])).encode("ascii")
pm.write(self.control_params["filetype"], filename=filename,
overwrite=True)
inp.write("\n")
inp.write(
"structure {}.{}\n".format(
os.path.join(input_dir, str(idx)),
self.control_params["filetype"]))
for k, v in six.iteritems(self.param_list[idx]):
inp.write(' {} {}\n'.format(k, self._format_param_val(v)))
inp.write('end structure\n')
def test_primary_amine_methylethyl_ketone_oxime():
mol = calc_props.smiles_to_ob("CC/C(C)=N/O")
pymol = pybel.Molecule(mol)
primary_amine_smarts = calc_props.FUNCTIONAL_GROUP_TO_SMARTS[
"primary_amine"]
assert_equals(calc_props.has_functional_group(pymol, primary_amine_smarts),
False)
def test_primary_amine_1_benzylguanidine():
mol = calc_props.smiles_to_ob("NC(NCC1=CC=CC=C1)=N")
pymol = pybel.Molecule(mol)
primary_amine_smarts = calc_props.FUNCTIONAL_GROUP_TO_SMARTS[
"primary_amine"]
assert_equals(calc_props.has_functional_group(pymol, primary_amine_smarts),
False)
def main():
commandLineParser = argparse.ArgumentParser(description="Docking Results Ranking to Three Dimensions: takes \
a table generated by DRranker.py and builds a file \
with the coordinates of the docked molecules")
commandLineParser.add_argument("rankingFile", help="file generated by DRranker.py")
commandLineParser.add_argument("outputFile", help="output filename")
commandLineParser.add_argument("-r", "--lowest-ranking", dest="lowestRanking", default=1, type=int, help="Last ranking level to be processed. Default: 1")
commandLineParser.add_argument("-f", "--output-format", dest="outputFormat", default="sdf", help="Format of the file to be written. It must be a openbabel supported output format. Deafult: sdf")
options = commandLineParser.parse_args()
(ranking,basenames) = processRanking(options.rankingFile, options.lowestRanking)
for (basename,coordFile) in basenames:
try:
mols = pybel.readfile("sdf", coordFile)
except:
print("Can't open " + coordFile, file=sys.stderr)
exit()
for mol in mols:
if (mol.title,basename) in ranking:
ranking[(mol.title,basename)] = pybel.Molecule(pybel.ob.OBMol(mol.OBMol))
out = pybel.Outputfile(filename=options.outputFile, format=options.outputFormat, overwrite=True)
for (molname,basename) in list(ranking.keys()):
mol = ranking[(molname,basename)]
mol.title += "_" + basename
out.write(mol)
out.close()
def test_primary_amine_imine():
mol = calc_props.smiles_to_ob("CC1=CC(=CC=C1)N=CC2=CC=CC=C2")
pymol = pybel.Molecule(mol)
primary_amine_smarts = calc_props.FUNCTIONAL_GROUP_TO_SMARTS[
"primary_amine"]
assert_equals(calc_props.has_functional_group(pymol, primary_amine_smarts),
False)
def testStereo(self):
data = [
("FC[C@@](Br)(Cl)I", [((2, 3, 4, 5, 6), None, "C[C@@](Br)(Cl)I"),
((2, 3, 4, 5), None, "CC(Br)Cl"),
((1, 2, 3, 4, 5, 6), (4, ), "FCC(Br)Cl.I")]),
("[C@@H](Br)(Cl)I", [((1, 2, 3), None, "C(Br)Cl"),
((1, 2, 3, 4), (2, ), "C(Br)Cl.I")]),
("C[C@@H]1CO1", [
((2, 3, 4), None, "C1CO1"),
]),
("F/C=C/I", [((1, 2, 3, 4), None, "F/C=C/I"),
((1, 2, 3), None, "FC=C"),
((1, 2, 3, 4), (0, ), "F.C=CI"),
((1, 2, 3, 4), (1, ), "FC.CI")]),
]
for smi, d in data:
mol = pybel.readstring("smi", smi)
for a, b, ans in d:
nmol = ob.OBMol()
bv = self.createBitVec(7, a)
bondbv = None if b is None else self.createBitVec(5, b)
ok = mol.OBMol.CopySubstructure(nmol, bv, bondbv)
self.assertTrue(ok)
if "@" not in ans and "/" not in ans:
self.assertFalse(nmol.GetData(ob.StereoData))
self.assertEqual(
pybel.Molecule(nmol).write("smi").rstrip(), ans)
def get_zmatrix_template(parser):
"""Make a zmatrix from the original geometry.
Parameters
----------
parser : object
Parser object from vetee.
Returns
-------
zmatrix : str
The zmatrix (gzmat format) for the parser
molecule. Will be used to combine with
dihedral angles.
"""
# from vetee
obmol = openbabel.OBMol()
# add coordinates for each atom
for atom in parser.coords:
obatom = openbabel.OBAtom()
atomicnum = vetee.gaussian_options.periodic_table(atom[0])
obatom.SetAtomicNum(atomicnum)
obatom.SetVector(atom[1], atom[2], atom[3])
obmol.AddAtom(obatom)
# set charge, multiplicity, and comments (title)
obmol.SetTotalCharge(parser.charge)
obmol.SetTotalSpinMultiplicity(parser.multip)
if parser.comments is not None:
obmol.SetTitle(parser.comments)
# convert the obmol to a pybel Molecule
pybelmol = pybel.Molecule(obmol)
# generate a zmatrix string using the obmol input
zmatrix = pybelmol.write("gzmat")
return zmatrix
def loadcdxml(cdxml):
import pybel
obconv = openbabel.OBConversion() # ob Class
obmol = openbabel.OBMol() # ob Class
obconv.SetInFormat('cdxml') # ob Method to set cdxml
obconv.ReadFile(obmol, cdxml) # ob Method to reaad cdxml into a OBMol()
obmol.NumAtoms()
idx_list = []
atno_list = []
for idx in range(obmol.NumAtoms()):
if obmol.GetAtom(idx + 1).GetAtomicNum() == 26:
idx_list.append(idx)
atno_list.append(obmol.GetAtom(idx + 1).GetAtomicNum())
obmol.GetAtom(idx + 1).SetAtomicNum(14)
pymol = pybel.Molecule(obmol)
pymol.make3D()
pymol.localopt()
for i in range(len(idx_list)):
idx = idx_list[i]
atno = atno_list[i]
obmol.GetAtom(idx + 1).SetAtomicNum(atno)
fname = re.sub(r'.cdxml', '.xyz', cdxml) # file name for the new xyz
obconv.WriteFile(obmol, fname)
return fname
def insert_solvents(coll):
names = """THF
monoglyme
Dimethylacetamide
propylene carbonate
ethylene carbonate
dimethylcarbonate
DMSO
ACN
Diethylcarbonate
propyl glyme
ethyl glyme
ethyl diglyme
diglyme
Butyldiglyme
tetraglyme
Pentaethylene glycol diethyl ether
Tetraethylene glycol diethyl ether
Tetraethylene glycol dibutyl ether
Butyldiglyme"""
for n in names.split("\n"):
response = requests.get(
"http://cactus.nci.nih.gov/chemical/structure/{}/file?format=xyz".
format(n))
if response.status_code == 200:
xyz = XYZ.from_string(response.text)
clean_mol = xyz.molecule
bb = BabelMolAdaptor(clean_mol)
pbmol = pb.Molecule(bb.openbabel_mol)
smiles = pbmol.write("smi").split()[0]
can = pbmol.write("can").split()[0]
inchi = pbmol.write("inchi")
svg = pbmol.write("svg")
d = {"molecule": clean_mol.as_dict()}
comp = clean_mol.composition
d["pretty_formula"] = comp.reduced_formula
d["formula"] = comp.formula
d["composition"] = comp.as_dict()
d["elements"] = list(comp.as_dict().keys())
d["nelements"] = len(comp)
d["charge"] = clean_mol.charge
d["spin_multiplicity"] = clean_mol.spin_multiplicity
d["smiles"] = smiles
d["can"] = can
d["inchi"] = inchi
# d["names"] = get_nih_names(smiles)
d["svg"] = svg
d["xyz"] = str(xyz)
d["tags"] = ["Solvents"]
coll.update(
{
"inchi": inchi,
"charge": clean_mol.charge,
"spin_multiplicity": clean_mol.spin_multiplicity
}, {"$set": d},
upsert=True)
else:
print("{} not found.\n".format(n))
def canonicalize(lig):
"""Get the canonical atom order for the ligand."""
atomorder = None
# Get canonical atom order
lig = pybel.ob.OBMol(lig.OBMol)
for bond in pybel.ob.OBMolBondIter(lig):
if bond.GetBondOrder() != 1:
bond.SetBondOrder(1)
lig.DeleteData(pybel.ob.StereoData)
lig = pybel.Molecule(lig)
testcan = lig.write(format='can')
try:
pybel.readstring('can', testcan)
reference = pybel.readstring('can', testcan)
except IOError:
testcan, reference = '', ''
if testcan != '':
reference.removeh()
isomorphs = get_isomorphisms(
reference,
lig) # isomorphs now holds all isomorphisms within the molecule
if not len(isomorphs) == 0:
smi_dict = {}
smi_to_can = isomorphs[0]
for x in smi_to_can:
smi_dict[int(x[1]) + 1] = int(x[0]) + 1
atomorder = [smi_dict[x + 1] for x in range(len(lig.atoms))]
else:
atomorder = None
return atomorder
def singleTorsion(self, torsionLevel):
if torsionLevel == len(self.torsionList_):
self.printCurrentTorsion()
mymol = pybel.Molecule(self.myOBMol_)
if self.checkGeometry(mymol):
#basename='c'+str(self.conformer_).zfill(self.spacePerConformer_)
basename = 'conf' + str(self.conformer_)
fullbasename = self.outDir_ + basename
outname = fullbasename + '.xyz'
self.baseNames_.append(basename)
self.xyzNames_.append(outname)
mymol.write('xyz', outname, overwrite=True)
self.conformer_ += 1
return
else:
torsion = self.torsionList_[torsionLevel]
IDs = torsion.IDs
angles = torsion.angles
atoms = [self.myOBMol_.GetAtom(IDs[i]) for i in range(0, 4)]
for angle in angles:
targetAngle = math.radians(angle)
self.myOBMol_.SetTorsion(atoms[0], atoms[1], atoms[2],
atoms[3], targetAngle)
realAngle = self.myOBMol_.GetTorsion(IDs[0], IDs[1], IDs[2],
IDs[3])
self.currentTorsion_[torsionLevel] = realAngle
self.currentTargetTorsion_[torsionLevel] = angle
self.singleTorsion(torsionLevel + 1)
def optg_c(self, steps=60, ff="mmff94", optimizer='cg'):
"""
Opt geometry by ff with constrained torsions
==============================================
defaut ff: mmff94, mmff94s seems to be
problematic, sometimes it
leads to weird geometries
steps: ff steps for constraint opt
"""
m = self.m #copy.copy( self.m )
# Define constraints
c = ob.OBFFConstraints()
#c.AddDistanceConstraint(1, 8, 10) # Angstroms
#c.AddAngleConstraint(1, 2, 3, 120.0) # Degrees
# constrain torsion only
torsions = self.get_all_torsions()
for torsion in torsions:
i, j, k, l = torsion
ang = torsions[torsion]
c.AddTorsionConstraint(i, j, k, l, ang) # Degrees
# Setup the force field with the constraints
obff = ob.OBForceField.FindForceField(ff)
obff.Setup(m, c)
obff.SetConstraints(c)
obff.ConjugateGradients(steps)
obff.GetCoordinates(m)
self.m = m
self.M = pb.Molecule(m)
self.coords = get_coords(m)
def optg(self, cparam=[False, 'slow'], ff="MMFF94", steps=2500):
""" geoemtry optimization
================
cparam: conformer parameters to be used
cparam = [False] -- no conformer generation
cparam = [True, algo, num_conf, N] -- gen confs and `N ff steps for each conf
"""
# ff opt
m = self.m
obff = ob.OBForceField.FindForceField(ff)
obff.Setup(m)
#obff.SteepestDescent(1200, 1.0e-4) # a quick cleanup before searching
obff.ConjugateGradients(600, 1.0e-3) # fast & coarse
if cparam[0]:
if cparam[1] in ['slow']:
obff.FastRotorSearch(True)
elif algo in ['slowest']:
nc, n = cparam[1:]
obff.WeightedRotorSearch(nc, n)
else:
print('unknow algo')
raise
obff.ConjugateGradients(steps, 1.0e-6) # fast & coarse
#obff.SteepestDescent(500, 1.0e-6) # slower &
obff.GetCoordinates(m)
self.m = m
self.M = pb.Molecule(m)
self.coords = get_coords(m)
def test_primary_amine_glycine():
mol = calc_props.smiles_to_ob("C(C(=O)O)N")
pymol = pybel.Molecule(mol)
primary_amine_smarts = calc_props.FUNCTIONAL_GROUP_TO_SMARTS[
"primary_amine"]
assert_equals(calc_props.has_functional_group(pymol, primary_amine_smarts),
True)
def testAtomMapsAfterCopying(self):
"""Copying a molecule should copy the atom maps"""
smi = "C[CH2:2]O[Cl:6]"
obmol = pybel.readstring("smi", smi).OBMol
copy = pybel.ob.OBMol(obmol)
copysmi = pybel.Molecule(copy).write("smi", opt={"a": True})
self.assertEqual(copysmi.rstrip(), smi)
def mol_to_pybel(mdtmol):
""" Translate a moldesign molecule object into a pybel molecule object.
Note:
The focus is on translating topology and biomolecular structure -
we don't translate any metadata.
Args:
mdtmol (moldesign.Molecule): molecule to translate
Returns:
pybel.Molecule: translated molecule
"""
import openbabel as ob
import pybel as pb
obmol = ob.OBMol()
obmol.BeginModify()
atommap = {}
resmap = {}
for atom in mdtmol.atoms:
obatom = obmol.NewAtom()
obatom.SetAtomicNum(atom.atnum)
atommap[atom] = obatom
pos = atom.position.value_in(u.angstrom)
obatom.SetVector(*pos)
if atom.residue and atom.residue not in resmap:
obres = obmol.NewResidue()
resmap[atom.residue] = obres
obres.SetChain(
str(atom.chain.pdbname)[0] if atom.chain.pdbname else 'Z')
obres.SetName(
str(atom.residue.pdbname) if atom.residue.pdbname else 'UNL')
obres.SetNum(
str(atom.residue.pdbindex) if atom.residue.pdbindex else 0)
else:
obres = resmap[atom.residue]
obres.AddAtom(obatom)
obres.SetHetAtom(obatom, not atom.residue.is_standard_residue)
obres.SetAtomID(obatom, str(atom.name))
obres.SetSerialNum(
obatom, mdt.utils.if_not_none(atom.pdbindex, atom.index + 1))
for atom in mdtmol.bond_graph:
a1 = atommap[atom]
for nbr, order in mdtmol.bond_graph[atom].items():
a2 = atommap[nbr]
if a1.GetIdx() > a2.GetIdx():
obmol.AddBond(a1.GetIdx(), a2.GetIdx(), order)
obmol.EndModify()
pbmol = pb.Molecule(obmol)
for atom in atommap:
idx = atommap[atom].GetIdx()
obatom = obmol.GetAtom(idx)
obatom.SetFormalCharge(int(atom.formal_charge.value_in(u.q_e)))
return pbmol
def cell_ffopt(ff, mol, frozenats):
### FORCE FIELD OPTIMIZATION ##
# INPUT
# - ff: force field to use, available MMFF94, UFF< Ghemical, GAFF
# - mol: mol3D to be ff optimized
# - connected: indices of connection atoms to metal
# - constopt: flag for constrained optimization
# OUTPUT
# - mol: force field optimized mol3D
metals = range(21, 31) + range(39, 49) + range(72, 81)
### check requested force field
ffav = 'mmff94, uff, ghemical, gaff, mmff94s' # force fields
if ff.lower() not in ffav:
print 'Requested force field not available. Defaulting to MMFF94'
ff = 'mmff94'
### convert mol3D to OBmol via xyz file, because AFTER/END option have coordinates
backup_mol = mol3D()
backup_mol.copymol3D(mol)
# print('bck ' + str(backup_mol.getAtom(0).coords()))
# print('mol_ibf ' + str(mol.getAtom(0).coords()))
mol.writexyz('tmp.xyz')
mol.OBmol = mol.getOBmol('tmp.xyz', 'xyzf')
os.remove('tmp.xyz')
### initialize constraints
constr = pybel.ob.OBFFConstraints()
### openbabel indexing starts at 1 ### !!!
# convert metals to carbons for FF
indmtls = []
mtlsnums = []
for iiat, atom in enumerate(mol.OBmol.atoms):
if atom.atomicnum in metals:
indmtls.append(iiat)
mtlsnums.append(atom.atomicnum)
atom.OBAtom.SetAtomicNum(19)
for cat in frozenats:
constr.AddAtomConstraint(cat + 1) # indexing babel
### set up forcefield
forcefield = pybel.ob.OBForceField.FindForceField(ff)
obmol = mol.OBmol.OBMol
forcefield.Setup(obmol, constr)
## force field optimize structure
forcefield.ConjugateGradients(2500)
forcefield.GetCoordinates(obmol)
mol.OBmol = pybel.Molecule(obmol)
# reset atomic number to metal
for i, iiat in enumerate(indmtls):
mol.OBmol.atoms[iiat].OBAtom.SetAtomicNum(mtlsnums[i])
mol.convert2mol3D()
en = forcefield.Energy()
# print(str(mol.OBmol.atoms[1].OBAtom.GetVector().GetZ()))
# print(str(forcefield.Validate()))
# print('mol_af ' + str(mol.getAtom(0).coords()))
# print('ff delta = ' + str(backup_mol.rmsd(mol)))
del forcefield, constr, obmol
return mol, en
def json_to_pybel(data):
"""Converts a python data structure to pybel.Molecule.
The data structure is a plain python object of the form:
```
{
"atoms": [{"location": [0, 0, 0], "element": "H", "label": "H1",
"charge": 0}, ...],
"bonds": [{"source": 0, "target": 0, "order": 1}, ...],
"unitcell": [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
}
```
It is referred to as "json" because this data structure is intended to
be read from and written to json files or databases.
As RASPA makes no use of bond information, this field is ignored.
The labels are stripped and replaced with "MOF_{element}", in accordance
with the CrystalGenerator forcefield notation. Therefore, labels are also
ignored.
Args:
data: the molecule, as a python object
Returns:
An instance of `pybel.Molecule`
"""
if not PYBEL_LOADED:
raise ImportError("Open Babel not installed.")
table = pybel.ob.OBElementTable()
if "building_blocks" in data:
data["atoms"] = [a for bb in data["building_blocks"]
for a in bb["atoms"]]
obmol = pybel.ob.OBMol()
obmol.BeginModify()
for atom in data["atoms"]:
obatom = obmol.NewAtom()
obatom.SetAtomicNum(table.GetAtomicNum(str(atom["element"])))
obatom.SetVector(*atom["location"])
uc = pybel.ob.OBUnitCell()
uc.SetData(*(pybel.ob.vector3(*v) for v in data["unitcell"]))
uc.SetSpaceGroup("P1")
obmol.CloneData(uc)
obmol.EndModify()
mol = pybel.Molecule(obmol)
# Add partial charges
if "charge" in data["atoms"][0]:
mol.OBMol.SetPartialChargesPerceived()
for atom, pyatom in zip(data["atoms"], mol.atoms):
pyatom.OBAtom.SetPartialCharge(atom["charge"])
return mol
def test_rb_basic():
# DNM
mol = calc_props.smiles_to_ob(
"CC(C1=CC(C(C)=CC(N2C)=O)=C2C3=C1N4CO3)=CC4=O")
pymol = pybel.Molecule(mol)
assert_equals(calc_props.rotatable_bonds(pymol), 0)
# Ribocil C
mol = calc_props.smiles_to_ob(
"C1CC(CN(C1)CC2=CN(C=N2)C3=NC=CC=N3)C4=NC(=O)C=C(N4)C5=CC=CS5")
pymol = pybel.Molecule(mol)
assert_equals(calc_props.rotatable_bonds(pymol), 5)
# Triphenylphosphine
mol = calc_props.smiles_to_ob("C1(P(C2=CC=CC=C2)C3=CC=CC=C3)=CC=CC=C1")
pymol = pybel.Molecule(mol)
assert_equals(calc_props.rotatable_bonds(pymol), 3)
def mol_from_pymatgen(mol: Molecule):
"""
Args:
mol(Molecule)
"""
mol = pybel.Molecule(BabelMolAdaptor(mol).openbabel_mol)
mol.make3D()
return mol
def Clone(self):
tmp = Molecule()
tmp.title = self.title
tmp.obmol = openbabel.OBMol(self.obmol)
tmp.pybel_mol = pybel.Molecule(tmp.obmol)
tmp.smiles = self.smiles
tmp.inchi = self.inchi
return tmp