From c756aff4f94576d38e1f65d58762c6f7554a68c3 Mon Sep 17 00:00:00 2001 From: Brian Kelley Date: Sat, 1 Nov 2025 01:28:52 -0400 Subject: [PATCH] [CONTRIB]: Freewilson now keeps the coordinates passed in (#8868) * Freewilson now keeps the coordinates passed in * Add better 3D reconstruction test --- Contrib/FreeWilson/data/cmet_ligands.sdf | 2867 ++++++++++++++++++++ Contrib/FreeWilson/freewilson.py | 135 +- Contrib/FreeWilson/test/test_freewilson.py | 43 +- 3 files changed, 3016 insertions(+), 29 deletions(-) create mode 100644 Contrib/FreeWilson/data/cmet_ligands.sdf diff --git a/Contrib/FreeWilson/data/cmet_ligands.sdf b/Contrib/FreeWilson/data/cmet_ligands.sdf new file mode 100644 index 000000000..0136744f9 --- /dev/null +++ b/Contrib/FreeWilson/data/cmet_ligands.sdf @@ -0,0 +1,2867 @@ +CHEMBL3402753_200 + 3D + Schrodinger Suite 2022-3. + 46 49 0 0 1 0 999 V2000 + 24.0334 34.0645 50.5646 C 0 0 0 0 0 0 + 23.6641 33.7796 52.0079 C 0 0 0 0 0 0 + 22.4301 33.2273 52.3426 C 0 0 0 0 0 0 + 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+> +-11.247 + +$$$$ diff --git a/Contrib/FreeWilson/freewilson.py b/Contrib/FreeWilson/freewilson.py index 41605eb15..d04daff8d 100644 --- a/Contrib/FreeWilson/freewilson.py +++ b/Contrib/FreeWilson/freewilson.py @@ -151,7 +151,7 @@ from rdkit.Chem import rdRGroupDecomposition as rgd logger = logging.getLogger("freewilson") -FreeWilsonPrediction = namedtuple("FreeWilsonPrediction", ['prediction', 'smiles', 'rgroups']) +FreeWilsonPrediction = namedtuple("FreeWilsonPrediction", ['prediction', 'smiles', 'rgroups', 'mol', 'is_training']) # match dummy atoms in a smiles string to extract atom maps dummypat = re.compile(r"\*:([0-9]+)") @@ -159,6 +159,7 @@ dummypat = re.compile(r"\*:([0-9]+)") # molzip doesn't handle some of the forms that the RGroupDecomposition # returns, this solves these issues. + def molzip_smi(smiles): """Fix a rgroup smiles for molzip, note that the core MUST come first in the smiles string, ala core.rgroup1.rgroup2 ... @@ -209,6 +210,59 @@ def molzip_smi(smiles): m.AddBond(oatom.GetIdx(), xatom.GetIdx(), Chem.BondType.SINGLE) return Chem.molzip(m) +def molzip_mols(mols): + """Fix a rgroup smiles for molzip, note that the core MUST come first + in the smiles string, ala core.rgroup1.rgroup2 ... + """ + if not mols: return Chem.RWMol() + + m = Chem.RWMol(mols[0]) + dupes = set() + for mol in mols[1:]: + s = Chem.MolToSmiles(mol) + if s.count("*") >= 1: + if s in dupes: + continue + else: + dupes.add(s) + + m.InsertMol(mol) + + frags = Chem.GetMolFrags(m) + core = frags[0] + atommaps = {} + counts = defaultdict(int) + for idx in core: + atommap = m.GetAtomWithIdx(idx).GetAtomMapNum() + if atommap: + atommaps[atommap] = idx + counts[atommap] += 1 + + next_atommap = max(atommaps) + 1 + add_atommap = [] + for fragment in frags[1:]: + for idx in fragment: + atommap = m.GetAtomWithIdx(idx).GetAtomMapNum() + if atommap: + count = counts[atommap] = counts[atommap] + 1 + if count > 2: + m.GetAtomWithIdx(idx).SetAtomMapNum(next_atommap) + add_atommap.append((atommaps[atommap], next_atommap)) + next_atommap += 1 + + for atomidx, atommap in add_atommap: + atom = m.GetAtomWithIdx(atomidx) + bonds = list(atom.GetBonds()) + if len(bonds) == 1: + oatom = bonds[0].GetOtherAtom(atom) + xatom = Chem.Atom(0) + idx = m.AddAtom(xatom) + xatom = m.GetAtomWithIdx(idx) + xatom.SetAtomMapNum(atommap) + m.AddBond(oatom.GetIdx(), xatom.GetIdx(), Chem.BondType.SINGLE) + + return Chem.molzip(m) + class RGroup: """FreeWilson RGroup @@ -219,13 +273,14 @@ class RGroup: idx - one-hot encoding for the rgroup """ - def __init__(self, smiles, rgroup, count, coefficient, idx=None): + def __init__(self, smiles, rgroup, count, coefficient, idx=None, mol=None): self.smiles = smiles # smiles for the sidechain (n.b. can be a core as well) self.rgroup = rgroup # rgroup Core, R1, R2,... self.count = count # num molecules with this rgruop self.coefficient = coefficient # ridge coefficient self.idx = idx # descriptor index self.dummies = tuple([int(x) for x in sorted(dummypat.findall(smiles))]) + self.mol = mol # Assemble some additive properties @@ -302,7 +357,11 @@ default_decomp_params.scoreMethod = rgd.RGroupScore.FingerprintVariance # we need to keep hydrogens so molzip will work default_decomp_params.removeHydrogensPostMatch = False - +class DecompEntry: + def __init__(self, mol): + self.mol = mol + self.smiles = Chem.MolToSmiles(mol) + def FWDecompose(scaffolds, mols, scores, decomp_params=default_decomp_params) -> FreeWilsonDecomposition: """ @@ -366,20 +425,24 @@ def FWDecompose(scaffolds, mols, scores, logger.error("No scaffolds matched the input molecules") return - decomposition = decomposer.GetRGroupsAsRows(asSmiles=True) - + #d = decomposer.GetRGroupsAsRows(asSmiles=True) + d = decomposer.GetRGroupsAsRows() + + decomposition = [ {rg: DecompEntry(m) for rg, m in row.items()} for row in d] + logger.info("Get unique rgroups...") blocker = rdBase.BlockLogs() rgroup_counts = defaultdict(int) num_reconstructed = 0 + for num_mols, (row, idx) in enumerate(zip(decomposition, matched_indices)): row_smiles = [] - for rgroup, smiles in row.items(): - row_smiles.append(smiles) - rgroup_counts[smiles] += 1 - if smiles not in rgroup_idx: - rgroup_idx[smiles] = len(rgroup_idx) - rgroups[rgroup].append(RGroup(smiles, rgroup, 0, 0)) + for rgroup, de in row.items(): + row_smiles.append(de.smiles) + rgroup_counts[de.smiles] += 1 + if de.smiles not in rgroup_idx: + rgroup_idx[de.smiles] = len(rgroup_idx) + rgroups[rgroup].append(RGroup(de.smiles, rgroup, 0, 0, mol=de.mol)) row['original_idx'] = idx reconstructed = ".".join(row_smiles) try: @@ -387,7 +450,8 @@ def FWDecompose(scaffolds, mols, scores, mol = molzip_smi(reconstructed) num_reconstructed += 1 except: - print("failed:", Chem.MolToSmiles(matched[num_mols]), reconstructed) + logging.error("failed reconstructing %s, %s", Chem.MolToSmiles(matched[num_mols]), + reconstructed) logger.info(f"Descriptor size {len(rgroup_idx)}") logger.info(f"Reconstructed {num_reconstructed} out of {num_mols}") @@ -401,9 +465,10 @@ def FWDecompose(scaffolds, mols, scores, row['molecule'] = mol descriptor = [0] * len(rgroup_idx) descriptors.append(descriptor) - for smiles in row.values(): - if smiles in rgroup_idx: - descriptor[rgroup_idx[smiles]] = 1 + for k, de in row.items(): + if k == "original_idx" or k == 'molecule': continue + if de.smiles in rgroup_idx: + descriptor[rgroup_idx[de.smiles]] = 1 assert len(descriptors) == len( matched_scores @@ -428,7 +493,8 @@ def FWDecompose(scaffolds, mols, scores, num_reconstructed) -def _enumerate(rgroups, fw, mw_filter=None, hvy_filter=None, pred_filter=None, mol_filter=None): +def _enumerate(rgroups, fw, mw_filter=None, hvy_filter=None, pred_filter=None, mol_filter=None, + keep_training_set=False): N = fw.N fitter = fw.fitter num_products = 1 @@ -450,6 +516,7 @@ def _enumerate(rgroups, fw, mw_filter=None, hvy_filter=None, pred_filter=None, m max_pred = -1e10 min_pred = 1e10 delta = num_products // 10 or 1 + for i, groups in tqdm(enumerate(itertools.product(*rgroups)), total=num_products): if i and i % delta == 0: logging.debug( @@ -466,7 +533,11 @@ def _enumerate(rgroups, fw, mw_filter=None, hvy_filter=None, pred_filter=None, m if tuple(descriptors) in fw.descriptors: in_training_set += 1 - continue + is_training = True + if not keep_training_set: + continue + else: + is_training = False min_mw = min(min_mw, mw) max_mw = max(max_mw, mw) @@ -487,13 +558,22 @@ def _enumerate(rgroups, fw, mw_filter=None, hvy_filter=None, pred_filter=None, m rejected_pred += 1 continue good_pred += 1 - smiles = set([g.smiles for g in groups]) # remove dupes - smi = ".".join(set([g.smiles for g in groups])) - try: - mol = molzip_smi(smi) - except: - rejected_bad += 1 - continue + + mols = [g.mol for g in groups] + if None in mols: + smiles = set([g.smiles for g in groups]) # remove dupes + smi = ".".join(set([g.smiles for g in groups])) + try: + mol = molzip_smi(smi) + except: + rejected_bad += 1 + continue + else: + try: + mol = molzip_mols(mols) + except: + rejected_bad += 1 + continue rejected = False if mol_filter and not mol_filter(mol): @@ -501,7 +581,7 @@ def _enumerate(rgroups, fw, mw_filter=None, hvy_filter=None, pred_filter=None, m continue out_smi = Chem.MolToSmiles(mol) - yield FreeWilsonPrediction(pred, out_smi, groups) + yield FreeWilsonPrediction(pred, out_smi, groups, mol, is_training) wrote += 1 logging.info( f"Wrote {wrote} results out of {num_products}\n\tIn Training set: {in_training_set}\n\tBad MW: {rejected_mw}\n\tBad Pred: {rejected_pred}\n\tBad Filters: {rejected_filters}\n\tBad smi: {rejected_bad}\n\tmin mw: {min_mw}\n\tmax mw: {max_mw}\n\tBad HVY: {rejected_hvy}\n\tBad Pred: {rejected_pred}\n\tBad Filters: {rejected_filters}\n\tBad smi: {rejected_bad}\n\tmin mw: {min_mw}\n\tmax mw: {max_mw}\n\tmin hvy: {min_hvy}\n\tmax hvy: {max_hvy}\n\t\n\tmin pred: {min_pred}\n\tmax pred: {max_pred}" @@ -509,7 +589,7 @@ def _enumerate(rgroups, fw, mw_filter=None, hvy_filter=None, pred_filter=None, m def FWBuild(fw: FreeWilsonDecomposition, pred_filter=None, mw_filter=None, hvy_filter=None, - mol_filter=None) -> Generator[FreeWilsonPrediction, None, None]: + mol_filter=None, keep_training_set=False) -> Generator[FreeWilsonPrediction, None, None]: """Enumerate the freewilson decomposition and return their predictions :param fw: FreeWilsonDecomposition generated from FWDecompose @@ -551,7 +631,8 @@ def FWBuild(fw: FreeWilsonDecomposition, pred_filter=None, mw_filter=None, hvy_f rgroups = [rgroup for key, rgroup in sorted(rgroups_no_cycles.items())] # core is always first for res in _enumerate(rgroups, fw, pred_filter=pred_filter, mw_filter=mw_filter, - hvy_filter=hvy_filter, mol_filter=mol_filter): + hvy_filter=hvy_filter, mol_filter=mol_filter, + keep_training_set=keep_training_set): yield res # iterate on rgroups with cycles diff --git a/Contrib/FreeWilson/test/test_freewilson.py b/Contrib/FreeWilson/test/test_freewilson.py index 9a5801eb3..7b7f14813 100644 --- a/Contrib/FreeWilson/test/test_freewilson.py +++ b/Contrib/FreeWilson/test/test_freewilson.py @@ -2,10 +2,20 @@ import csv import io import logging import os +import sys -import freewilson as fw +try: + import freewilson as fw +except: + path = os.path.abspath(os.curdir) + sys.path.insert(0, os.path.join(path, "..")) + import freewilson as fw + +import importlib +fw = importlib.reload(fw) from rdkit import Chem, rdBase +from rdkit.Chem import rdFMCS, rdMolAlign PATH = os.path.join(os.path.dirname(fw.__file__), 'data') assert os.path.exists(PATH), PATH @@ -33,7 +43,7 @@ def test_chembl(): with rdBase.BlockLogs(): free = fw.FWDecompose(scaffold, mols, scores) # let's make sure the r squared is decent - assert free.r2 > 0.8 + assert free.r2 > 0.8, str(free.r2) # assert we get something preds = list(fw.FWBuild(free)) @@ -68,3 +78,32 @@ def test_multicore(): decomp = fw.FWDecompose(scaffolds, mols, [1, 2, 3, 4, 5, 6]) s = io.StringIO() fw.predictions_to_csv(s, decomp, fw.FWBuild(decomp)) + +def test_fep_benchmark_3D(): + benchmark = os.path.join(PATH, "cmet_ligands.sdf") + mols = list(Chem.SDMolSupplier(benchmark, removeHs=False)) + smis = {Chem.MolToSmiles(m):m for m in mols if m} + assert smis + match = rdFMCS.FindMCS(mols) + + scores = [float(m.GetProp("r_exp_dg")) for m in mols] + with rdBase.BlockLogs(): + free = fw.FWDecompose(match.queryMol, mols, scores) + preds2 = list(fw.FWBuild(free, keep_training_set=True)) + assert preds2 + + count = 0 + found = 0 + # we use an rms of 0.7 because we are assembling rgroups from different + # ligands together which may not exactly align + for p in preds2: + if not p.is_training: continue + + smi = Chem.MolToSmiles(p.mol) + + count += 1 + if smi not in smis: continue + rms = rdMolAlign.GetBestRMS(smis[smi], p.mol) + assert rms < 0.7 + +