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add smiles and mol block input field to .db file #31

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merged 1 commit into from
Apr 18, 2024
Merged

add smiles and mol block input field to .db file #31

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22 changes: 15 additions & 7 deletions easydock/database.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
from copy import deepcopy
from functools import partial
from multiprocessing import Pool
from typing import Optional
from typing import Optional, Union
import yaml
from easydock import read_input
from easydock.preparation_for_docking import mol_is_3d
Expand Down Expand Up @@ -37,8 +37,10 @@ def create_db(db_fname, args, args_to_save=(), config_args_to_save=('protein', '
(
id TEXT,
stereo_id TEXT,
smi_input TEXT,
smi TEXT {'UNIQUE' if unique_smi else ''},
smi_protonated TEXT,
source_mol_block_input TEXT,
source_mol_block TEXT,
source_mol_block_protonated TEXT,
docking_score REAL,
Expand Down Expand Up @@ -158,29 +160,35 @@ def get_isomers(mol, max_stereoisomers=1):

MolBlock = str
Smi = str
def generate_init_data(mol_input: tuple[Chem.Mol, str], max_stereoisomers: int, prefix: str) -> list[list[str, tuple[str, int, Smi, Optional[MolBlock]]]]:
def generate_init_data(mol_input: tuple[Chem.Mol, str], max_stereoisomers: int, prefix: str) -> list[list[str, tuple[str, int, Union[Smi, MolBlock], Smi, Optional[MolBlock]]]]:
salt_remover = SaltRemover()
mol, mol_name = mol_input

mol_input = mol
smi_input = Chem.MolToSmiles(mol, isomericSmiles=True)

if len(Chem.GetMolFrags(mol, asMols=False, sanitizeFrags=False)) > 1:
mol = salt_remover.StripMol(mol, dontRemoveEverything=True)
if len(Chem.GetMolFrags(mol, asMols=False, sanitizeFrags=False)) > 1:
sys.stderr.write(f'EASYDOCK Warning: molecule {mol.GetProp("_Name")} was skipped, because it has multiple components which could not be fixed by SaltRemover\n')
return None
if mol_is_3d(mol):
return [['mol', (mol_name, None, None, Chem.MolToMolBlock(mol_input), None)]]
else:
return [['smi', (mol_name, None, smi_input, None)]]
sys.stderr.write(f'EASYDOCK Warning: molecule {mol.GetProp("_Name")}, salts were sripped\n')

if prefix:
mol_name = f'{prefix}-{mol_name}'
if mol_is_3d(mol):
smi = Chem.MolToSmiles(mol, isomericSmiles=True)
return [['mol', (mol_name, 0, smi, Chem.MolToMolBlock(mol))]]
return [['mol', (mol_name, 0, smi, Chem.MolToMolBlock(mol_input), Chem.MolToMolBlock(mol))]]

else:
isomer_list = []
isomers = get_isomers(mol, max_stereoisomers)
for stereo_id, stereo_mol in enumerate(isomers):
smi = Chem.MolToSmiles(stereo_mol, isomericSmiles=True)
isomer_list.append(['smi', (mol_name, stereo_id, smi)])
isomer_list.append(['smi', (mol_name, stereo_id, smi_input, smi)])
return isomer_list


Expand All @@ -203,8 +211,8 @@ def init_db(db_fname: str, input_fname: str, ncpu: int, max_stereoisomers=1, pre
elif input_format == 'mol':
data_mol.append(data)

cur.executemany(f'INSERT INTO mols (id, stereo_id, smi) VALUES(?, ?, ?)', data_smi)
cur.executemany(f'INSERT INTO mols (id, stereo_id, smi, source_mol_block) VALUES(?, ?, ?, ?)', data_mol)
cur.executemany(f'INSERT INTO mols (id, stereo_id, smi_input, smi) VALUES(?, ?, ?, ?)', data_smi)
cur.executemany(f'INSERT INTO mols (id, stereo_id, smi, source_mol_block_input, source_mol_block) VALUES(?, ?, ?, ?, ?)', data_mol)
conn.commit()


Expand Down