def obatom_to_smina_type(self, ob_atom):
"""Original author: Constantin schneider"""
atomic_number = ob_atom.atomicnum
num_to_name = {1: 'HD', 6: 'A', 7: 'NA', 8: 'OA', 16: 'SA'}
# Default fn returns True, otherwise inspect atom properties
condition_fns = defaultdict(lambda: lambda: True)
condition_fns.update({
6: ob_atom.OBAtom.IsAromatic,
7: ob_atom.OBAtom.IsHbondAcceptor,
16: ob_atom.OBAtom.IsHbondAcceptor
})
# Get symbol
ename = openbabel.GetSymbol(atomic_number)
# Do we need to adjust symbol?
if condition_fns[atomic_number]():
ename = num_to_name.get(atomic_number, ename)
atype = self.string_to_smina_type(ename)
h_bonded = False
hetero_bonded = False
for neighbour in openbabel.OBAtomAtomIter(ob_atom.OBAtom):
if neighbour.GetAtomicNum() == 1:
h_bonded = True
elif neighbour.GetAtomicNum() != 6:
hetero_bonded = True
return self.adjust_smina_type(atype, h_bonded, hetero_bonded)
def testReadingMassDifferenceInMolfiles(self):
"""Previously we were rounding incorrectly when reading the mass diff"""
template = """
OpenBabel02181811152D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 %2s %2d 0 0 0 0 0 0 0 0 0 0 0
M END
"""
# Positive test cases:
# These are the BIOVIA Draw answers for the first 50 elements for
# a mass diff of 1
answers = [2,5,8,10,12,13,15,17,20,21,24,25,28,29,32,33,36,41,40,41,46,49,52,53,56,57,60,60,65,66,71,74,76,80,81,85,86,89,90,92,94,97,99,102,104,107,109,113,116,120,123]
for idx, answer in enumerate(answers):
elem = idx + 1
molfile = template % (ob.GetSymbol(elem), 1)
mol = pybel.readstring("mol", molfile).OBMol
iso = mol.GetAtom(1).GetIsotope()
self.assertEqual(answer, iso)
# Also test D and T - BIOVIA Draw ignores the mass diff
for elem, answer in zip("DT", [2, 3]):
molfile = template % (elem, 1)
mol = pybel.readstring("mol", molfile).OBMol
iso = mol.GetAtom(1).GetIsotope()
self.assertEqual(answer, iso)
# Negative test cases:
# Test error message for out-of-range values
for value in [5, -4]:
molfile = template % ("C", value)
mol = pybel.readstring("mol", molfile).OBMol
iso = mol.GetAtom(1).GetIsotope()
self.assertEqual(0, iso)
def print_table(self):
""" print the explicit table of all the terms for used to calculate complexity"""
seq = ['di', 'ei', 'si', 'Vi', 'bi', 'complexity']
atom_list = [str(x) for x in list(self._equivalents.keys())]
atom_symbols = [
self.mol.GetAtom(x).GetAtomicNum()
for x in self._equivalents.keys()
]
atom_symbols = [ob.GetSymbol(x) for x in atom_symbols]
atom_names = [
"%s-%s" % (x[0], x[1]) for x in zip(atom_symbols, atom_list)
]
print("\t", "\t".join(atom_names))
print("---------" * len(atom_symbols))
for prop in seq:
if prop == 'complexity':
string = 'cmplx'
else:
string = prop
print("%s\t" % string, end=' ')
for i in self._equivalents.keys():
if prop == 'complexity':
print("%2.2f\t" % self._indices[i][prop], end=' ')
else:
print("%1.1f\t" % self._indices[i][prop], end=' ')
print("")
print("---------" * len(atom_symbols))
print("SMILES : %s" % self._smiles)
print("Name : %s" % (self.mol.GetTitle()))
print("Intrinsic complexity : %2.2f" % self._intrinsic_complexity)
print("Complexity/atom : %2.2f" %
(self._intrinsic_complexity / len(self._indices)))
print("=========" * len(atom_symbols))
def testWhetherAllElementsAreSupported(self):
"""Check whether a new element has been correctly added"""
N = 0
while ob.GetSymbol(N+1):
N += 1
# Is the symbol parsed?
symbol = ob.GetSymbol(N)
self.assertEqual(N, ob.GetAtomicNum(symbol))
# Has an exact mass been set?
self.assertNotEqual(0.0, ob.GetExactMass(N))
# Has the symbol been added to the SMILES parser?
numatoms = pybel.readstring("smi", "[%s]" % symbol).OBMol.NumAtoms()
self.assertEqual(numatoms, 1)
# Check whether the element is available as a constant
self.assertEqual(N, getattr(ob, ob.GetName(N)))
self.assertTrue(N > 100)
def type_str(self, at):
"""Return a Dreiding type string representing the AtomType at"""
if OB_version == 3:
elsym = ob.GetSymbol(at.atomic_num)
elif OB_version == 2:
elsym = ob.etab.GetSymbol(at.atomic_num)
else:
raise Exception("Unknown openbabel version")
ts = "%s" % elsym
if len(ts) == 1:
ts += "_"
if at.atomic_num == 1 and at.hbond:
ts += "_HB"
if elsym not in ["H", "F", "Cl", "Br", "I", "Na", "Ca", "Fe", "Zn"]:
# Need hybridization
if at.is_resonant:
ts += "R"
elif elsym == "O":
ts += "%d" % (at.num_bonds + 1)
else:
ts += "%d" % (at.num_bonds - 1)
return ts
def make_g09(name, conf, nproc=4, mem=1900, queue='marc2'):
queue_choices = ['marc2', 'slurm', 'condor', 'none']
if queue not in queue_choices:
print("queue %s not known. Using queue 'none'.")
queue = 'none'
radius_dict = {'I': 1.98}
sumFCharge = 0
com_crds = ''
com_opt = ''
com_esp = ''
com_basis = ''
lelement_list = list()
helement_list = list()
has_user_basisset = False
for atm in ob.OBMolAtomIter(conf):
atm_number = atm.GetAtomicNum()
element = ob.GetSymbol(atm_number)
if atm_number > 35:
if not element in helement_list:
helement_list.append(element)
has_user_basisset = True
else:
if not element in lelement_list:
lelement_list.append(element)
sumFCharge += atm.GetFormalCharge()
com_crds += ' '
com_crds += element
com_crds += ' '
crds = [atm.GetX(), atm.GetY(), atm.GetZ()]
for crd in crds:
if crd > 0.:
com_crds += " "
com_crds += '%5.10f ' % crd
com_crds += '\n'
if queue in ['none', 'slurm']:
com_opt += '%%nproc=%d\n' % nproc
com_opt += '%%mem=%dMB\n' % mem
com_opt += '%%chk=%s.chk\n' % name
if has_user_basisset:
com_opt += '#B3LYP/GenECP 5d 7f pseudo=read '
else:
com_opt += '#B3LYP/6-31G* '
com_opt += 'Integral=(Grid=UltraFine) freq Opt pop=none\n'
com_opt += '\n'
com_opt += 'Optimization for %s\n' % name
com_opt += '\n'
com_opt += '%d 1\n' % int(sumFCharge)
com_opt += com_crds
com_opt += '\n'
if has_user_basisset:
for element in helement_list:
com_basis += '%s ' % element
com_basis += '0\n'
com_basis += 'sdd\n'
com_basis += '****\n'
for element in lelement_list:
com_basis += '%s ' % element
com_basis += '0\n'
com_basis += '6-31G*\n'
com_basis += '****\n'
com_basis += '\n'
for element in helement_list:
com_basis += '%s ' % element
com_basis += '0\n'
com_basis += 'sdd\n'
com_basis += '\n'
com_opt += com_basis
com_opt += '\n'
if queue in ['none', 'slurm']:
com_opt += '%%nproc=%d\n' % nproc
com_opt += '%%mem=%dMB\n' % mem
com_esp += '%%chk=%s.chk\n' % name
if has_user_basisset:
com_esp += '#HF/GenECP 5d 7f pseudo=read '
else:
com_esp += '#HF/6-31G* '
com_esp += 'Geom=AllCheck Guess=Read Pop=(MK,ReadRadii) '
com_esp += 'Integral=(Grid=UltraFine) iop(6/33=2)\n'
com_esp += '\n'
com_esp += com_basis
if has_user_basisset:
for element in helement_list:
com_esp += '%s %f\n' % (element, radius_dict[element])
com_esp += '\n'
return com_opt, com_esp
import h5py
import numpy as np
import os, sys
#imports the functions from the data packer used to put the data read from the 0509.sdf
#file into the h5py file format
from torchani.data._pyanitools import datapacker
#script takes an sdf file as argument
count = 0
outputFile = datapacker(sys.argv[2])
goodElements = set([1, 6, 7, 8, 9, 16, 17])
for mymol in pb.readfile(
"sdf", sys.argv[1]): #loops to get all molucules in the sdf file
a = mymol.atoms
mymolElements = set([a.atomicnum for a in mymol.atoms])
if bool(mymolElements - goodElements) == False:
coordinates = np.array([a.coords for a in mymol.atoms])
species = [ob.GetSymbol(a.atomicnum) for a in mymol.atoms]
smiles = mymol.write().split()[0]
outputFile.store_data('%s_%d' % (mymol.title, count),
coordinates=[coordinates],
species=species,
smiles=list(smiles),
energies=[0])
count += 1
#cleanup
outputFile.cleanup()
print('molecule count = ' + str(count))
def symbol(self):
return ob.GetSymbol(self.GetAtomicNum())