def convert_sdfs_to_PDBs(contnrs, output_folder):
"""This will convert every conformer into a PDB file, which is saved in
the output_folder.
:param contnrs: A list of containers (MolContainer.MolContainer).
:type contnrs: list
:param output_folder: The name of the output folder.
:type output_folder: str
"""
# Go through each container.
for contnr in contnrs:
contnr.add_container_properties()
# Get the molecule name and associated variants.
name = contnr.name
mols = contnr.mols
# Got through the variants.
for i, m in enumerate(mols):
pdb_file = "{}{}__input{}__variant{}.pdb".format(
output_folder + os.sep,
Utils.slug(name),
contnr.contnr_idx_orig + 1,
i + 1,
)
# Get the conformers into the rdkit_mol object.
m.load_conformers_into_rdkit_mol()
mol = m.rdkit_mol
if mol == None:
continue
else:
# Write conformers to a PDB file.
Chem.MolToPDBFile(mol, pdb_file, flavor=32)
# Add header to PDB file with original SMILES and final SMILES
printout = "REMARK Original SMILES string: {}\nREMARK Final SMILES string: {}\n".format(
m.orig_smi, m.standardize_smiles()
)
with open(pdb_file) as f:
printout = printout + f.read()
with open(pdb_file, "w") as f:
f.write(printout)
printout = ""
def save_to_sdf(contnrs, params, separate_output_files, output_folder):
"""Saves the 3D models to the disk as an SDF file.
:param contnrs: A list of containers (MolContainer.MolContainer).
:type contnrs: list
:param params: The parameters.
:type params: dict
:param separate_output_files: Whether save each molecule to a different
file.
:type separate_output_files: bool
:param output_folder: The output folder.
:type output_folder: str
"""
# Save an empty molecule with the parameters.
if separate_output_files == False:
w = Chem.SDWriter(output_folder + os.sep + "gypsum_dl_success.sdf")
else:
w = Chem.SDWriter(output_folder + os.sep + "gypsum_dl_params.sdf")
m = Chem.Mol()
m.SetProp("_Name", "EMPTY MOLECULE DESCRIBING GYPSUM-DL PARAMETERS")
for param in params:
m.SetProp(param, str(params[param]))
w.write(m)
if separate_output_files == True:
w.flush()
w.close()
# Also save the file or files containing the output molecules.
Utils.log("Saving molecules associated with...")
for i, contnr in enumerate(contnrs):
# Add the container properties to the rdkit_mol object so they get
# written to the SDF file.
contnr.add_container_properties()
# Let the user know which molecule you're on.
Utils.log("\t" + contnr.orig_smi)
# Save the file(s).
if separate_output_files == True:
# sdf_file = "{}{}__{}.pdb".format(output_folder + os.sep, slug(name), conformer_counter)
sdf_file = "{}{}__input{}.sdf".format(
output_folder + os.sep,
Utils.slug(contnr.name),
contnr.contnr_idx_orig + 1,
)
w = Chem.SDWriter(sdf_file)
# w = Chem.SDWriter(output_folder + os.sep + "output." + str(i + 1) + ".sdf")
for m in contnr.mols:
m.load_conformers_into_rdkit_mol()
w.write(m.rdkit_mol)
if separate_output_files == True:
w.flush()
w.close()
if separate_output_files == False:
w.flush()
w.close()
