def test_checker_nlimits(sdf=SDF_LIMIT_ATOMS):
try:
ch.check_limit_number_atoms(sdf, 100)
except ce.LigandSizeExceed:
assert True
else:
assert False
def _prepare_input_file(self, logger=None):
from rdkit import Chem
import rdkit.Chem.rdmolops as rd
self.parameters.input = "input.conf"
params = self.parameters
# Check input file
limit_atoms_ligand = 100
ch.check_limit_number_atoms(params.ligands, limit_atoms_ligand)
# Get core of the ligand
mol = Chem.MolFromPDBFile(params.core)
try:
ligand_core = rd.SplitMolByPDBResidues(mol)[params.residue]
except KeyError:
raise ce.MissResidueFlag("Missing residue flag to specify " +
"the ligand core residue name. " +
"i.e resname: 'LIG'")
# Get sdf full grown ligands
ligands_grown = Chem.SDMolSupplier(params.ligands, removeHs=False)
fragment_files = []
# For each full grown ligand create neutral fragment
with open(params.input, "w") as fout:
pass
for ligand in ligands_grown:
Chem.AssignAtomChiralTagsFromStructure(ligand)
try:
line, fragment = \
self._create_fragment_from_ligand(ligand,
ligand_core)
except Exception as e:
try:
line, fragment = \
self._create_fragment_from_ligand(ligand,
ligand_core,
substructure=False)
except Exception as e:
try:
# Try to fix symmetry
line, fragment = \
self._create_fragment_from_ligand(ligand,
ligand_core,
symmetry=True)
except Exception as e:
# Try with second substructure search
line, fragment = \
self._create_fragment_from_ligand(
ligand, ligand_core,
result=1, substructure=False)
logger.info(f"Ligand {fragment.file} preprocessed")
fragment_files.append(fragment.file)
with open(params.input, "a") as fout:
fout.write(line + "\n")
return fragment_files
def _prepare_input_file(self):
from rdkit import Chem
import rdkit.Chem.rdmolops as rd
import rdkit.Chem.rdchem as rc
import rdkit.Chem.AllChem as rp
self.input = "input.conf"
#Check input file
limit_atoms_ligand = 100
ch.check_limit_number_atoms(self.ligands, limit_atoms_ligand)
#Get core of the ligand
mol = Chem.MolFromPDBFile(self.core)
try:
ligand_core = rd.SplitMolByPDBResidues(mol)[self.residue]
except KeyError:
raise ce.MissResidueFlag(
"Missing residue flag to specify the ligand core residue name. i.e resname: 'LIG'"
)
#Get sdf full grown ligands
ligands_grown = Chem.SDMolSupplier(self.ligands, removeHs=False)
#For each full grown ligand create neutral fragment
self.fragments = []
lines = []
for ligand in ligands_grown:
try:
line, fragment = self._create_fragment_from_ligand(
ligand, ligand_core)
except Exception as e:
try:
# Try to fix simmetry
line, fragment = self._create_fragment_from_ligand(
ligand, ligand_core, simmetry=True)
except Exception as e:
try:
# Try with second substructure search
line, fragment = self._create_fragment_from_ligand(
ligand, ligand_core, result=1, substructure=False)
except Exception as e:
#Skip the ligand
print("Ligand Skipped")
print(e)
continue
lines.append(line)
self.fragments.append(fragment)
print(f"Ligand {fragment.file} preprocessed")
with open(self.input, "w") as fout:
fout.write(("\n").join(lines))