rdworks 0.74.1

Chained Workflow built on RDKit

RDWORKS

Rdworks is inspired by pandas. Many rdworks functions work like pandas and can be chained into a workflow.

Installation

$ pip install rdworks

# or build from the source
$ pip install git+https://github.com/sunghunbae/rdworks.git

# or if you use uv package/project manager
$ uv add rdworks

Usage

Process Compound Library

from rdworks import MolLibr

# initialize the library
libr = MolLibr(drug_smiles[:5], drug_names[:5])
libr = MolLibr([Chem.MolFromSmiles(_) for _ in drug_smiles[5:10]], drug_names[5:10])
libr = MolLibr([Mol(smi, name) for smi, name in zip(drug_smiles[10:15], drug_names[10:15])])

# libr will be changed by +=, -=, &= operators
libr += other_libr

# remove redundant compounds
libr_unique = libr.unique()

# select compounds satisfying ZINC druglike rules
drug_like_libr = libr.drop("~ZINC_druglike") 

# select compounds CNS compliant
cns_compliant_libr = libr.drop("~CNS") 
cns_compliant_libr = libr.drop("CNS", invert=True)

# select compounds compliant to a custom rule defined in a xml file
custom_rule_compliant_libr = libr.drop(custom_rul_xml_path, invert=True)

# select neural network potential applicable compounds
ani_2x_applicable_libr = libr.nnp_ready("ANI-2x", progress=False)

# select compounds similar to query with a threshold
sim = libr.similar(query_Mol, threshold=0.2)

Complete Stereoisomers

from rdworks import Mol, MolLibr
from rdworks.complete import complete_stereoisomers

mol = Mol(cmpd.smiles)
stereoisomers = complete_stereoisomers(mol)

Complete Tautomers

m = Mol("Oc1c(cccc3)c3nc2ccncc12", "tautomer")
libr = complete_tautomers(m)
assert libr.count() == 3
expected_names = ["tautomer.1", "tautomer.2", "tautomer.3"]
names = [_.name for _ in libr]
assert names == expected_names
expected_canonical_smiles = [
    "O=c1c2c[nH]ccc-2nc2ccccc12",
    "O=c1c2ccccc2[nH]c2ccncc12",
    "Oc1c2ccccc2nc2ccncc12",
]
canonical_smiles = [_.smiles for _ in libr]
difference = set(expected_canonical_smiles) - set(canonical_smiles)
assert len(difference) == 0

Generate Conformer

from rdworks import Mol
from batchopt import BatchOptimizer


mol = Mol(smiles, name)
mol = mol.make_confs(n=n, method='ETKDG') # optimize with MMFF94
mol = mol.optimize_confs()
# remove similar conformers (RMSD <0.3) [and stereo-flipped conformers by default]
mol = mol.drop_confs(similar=True, similar_rmsd=0.3)
mol = mol.optimize_confs(calculator=BatchOptimizer, batchsize_atoms=16384)
mol = mol.sort_confs().rename()
mol = mol.align_confs().cluster_confs(sort='energy')

Serialize/deserialize Molecule or Conformer

Mol and Conf objects have serialize() and deserialize() functions to exchange and reproduce the exact objects.

from rdworks import Conf


mol_serialized = mol.serialize()
lowest_energy_conf_serialized = mol.confs[0].serialize() 
# lowest energy conformer
# serialized conformer is regular string can be easily exchanged
conf = Conf().deserialize(lowest_energy_conf_serialized)

Profile Torsion Angle Energies

from batchopt import BatchSinglePointer


conf = conf.calculate_sp_torsion_energies(
        calculator = BatchSinglePointer,
        torsion_angle_idx = torsion_angle_idx,
        simplify = simplify,
        interval = interval,
        water = water,
        batchsize_atoms = batchsize_atoms,
    )
results = conf.serialize()

Generate Microstates

Microstates are molecular states that have defined protonation states. A molecule exists as an ensemble of microstates at a given pH condition.

import logging
import math
import numpy as np
from rdworks import State, StateNetwork


logger = logging.getLogger(__name__)
original_state = State(smiles=smiles)
num_ionizable_sites = len(original_state.sites)
logger.info(f"found {num_ionizable_sites} ionizable sites.")
state_net = StateNetwork()

if num_ionizable_sites > 6:
    state_net.build(smiles=smiles,
                    max_formal_charge=3,
                    protomer_rule='simple',
                    tautomer_rule=None)
else:
    state_net.build(smiles=smiles,
                    max_formal_charge=3,
                    protomer_rule='default',
                    tautomer_rule=None)

state_ens = state_net.get_state_ensemble()
logger.info(f'generated {state_ens.size()} microstates.')

Calculate Microstate Population with External dG Predictor

from unipka.deltaG import UniMolFreeEnergy


dG_dict = dG_predictor.predict([st.smiles for st in state_ens])

# set state energies via Uni-pKa model
# Uni-pka model specific variable for pH dependent deltaG
# Training might be conducted with a dataset in which raw pKa values
# were subtracted by the mean value (TRANSLATE_PH), 6.504894871171601.
dG = [dG_dict[st.smiles] for st in state_ens]
state_ens.set_energies(dG, ref_ph=6.504894871171601)

ph_values = np.linspace(-2, 16, 180)
p = state_ens.get_population(ph_values, C=math.log(10), beta=1.0)
state_ens = state_ens.trim(p, threshold=0.05)

# representative state(s) at pH 7.4, a subset of state_ens
ph_74 = np.array([7.4])
p_74 = state_ens.get_population(ph_74)
# p_74.shape == (self.size(), pH.shape[0] or number of pH)
ph74_pop = {state_idx: p.item() for state_idx, p in enumerate(p_74)}
dictdata = {
    'ensemble' : state_ens.serialize(), # str
    'ph74_pop' : ph74_pop, # dict
    }