From c57165816d1a0896a22608112b489d115f72674a Mon Sep 17 00:00:00 2001 From: dp-yuanyn Date: Fri, 8 Mar 2024 16:35:06 +0800 Subject: [PATCH 1/3] doc:remove unidock_ad4 in README --- unidock/README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/unidock/README.md b/unidock/README.md index f07d304..5c378a0 100644 --- a/unidock/README.md +++ b/unidock/README.md @@ -58,7 +58,7 @@ make clang-format ### Using binary Please download the latest binary of Uni-Dock at the assets tab of [the Release page](https://github.com/dptech-corp/Uni-Dock/releases). -Executable `unidock` supports vina and vinardo scoring functions, and `unidock_ad4` supports ad4 scoring function. +Executable `unidock` to dock. After downloading, please make sure that the path to `unidock` is in your `PATH` environment variable. @@ -69,7 +69,11 @@ After downloading, please make sure that the path to `unidock` is in your `PATH` To launch a Uni-Dock job, the most important parameters are as follows: - `--receptor`: filepath of the receptor (PDBQT) + + (If you want to use `ad4` scoring function, you need to generate affinity maps first and use `--maps ` instead of `--receptor`. The method to generate maps is in [here](https://autodock-vina.readthedocs.io/en/latest/docking_basic.html#optional-generating-affinity-maps-for-autodock-ff)) + - `--gpu_batch`: filepath of the ligands to dock with GPU (PDBQT), enter multiple at a time, separated by spaces (" ") + - `--search_mode`: computational complexity, choose in \[*`fast`*, *`balance`*, and *`detail`*]. ***Advanced options*** From 08a1a38193e8d595a2b163059a935c8c4e2c79bc Mon Sep 17 00:00:00 2001 From: dp-yuanyn Date: Sat, 9 Mar 2024 15:06:34 +0800 Subject: [PATCH 2/3] fix:ligandprep skip failed cases --- unidock_tools/pyproject.toml | 4 +- .../unidock_tools/application/ligandprep.py | 43 +++++++++++++------ .../modules/ligand_prep/torsion_tree.py | 24 ++++------- .../modules/protein_prep/pdb2pdbqt.py | 1 - .../src/unidock_tools/utils/mol_group.py | 9 ++-- .../src/unidock_tools/utils/rdkit_helper.py | 6 +-- 6 files changed, 47 insertions(+), 40 deletions(-) diff --git a/unidock_tools/pyproject.toml b/unidock_tools/pyproject.toml index 7de19dc..77411ba 100644 --- a/unidock_tools/pyproject.toml +++ b/unidock_tools/pyproject.toml @@ -48,6 +48,6 @@ pythonVersion = "3.11" pythonPlatform = "Linux" reportMissingImports = false reportMissingModuleSource = false -reportMissingTypeStubs = false reportAttributeAccessIssue = false -reportIncompatibleMethodOverride = false \ No newline at end of file +reportIncompatibleMethodOverride = false +reportCallIssue = false \ No newline at end of file diff --git a/unidock_tools/src/unidock_tools/application/ligandprep.py b/unidock_tools/src/unidock_tools/application/ligandprep.py index 5c3462b..9625c65 100644 --- a/unidock_tools/src/unidock_tools/application/ligandprep.py +++ b/unidock_tools/src/unidock_tools/application/ligandprep.py @@ -3,10 +3,12 @@ import os from functools import partial from multiprocessing import Pool +import traceback import logging import argparse from rdkit import Chem +from unidock_tools.utils import read_ligand from unidock_tools.modules.ligand_prep import TopologyBuilder @@ -14,26 +16,37 @@ def iter_ligands(ligands: List[Path], batch_size: int = 1200, use_file_name: bool = False) -> Generator[List[Tuple[Chem.Mol, str]], None, None]: curr_mol_name_list = [] for ligand in ligands: - mols = list(Chem.SDMolSupplier(str(ligand), removeHs=False)) + mols = read_ligand(ligand) for i, mol in enumerate(mols): - if not use_file_name and mol.HasProp("_Name") and mol.GetProp("_Name").strip(): - name = mol.GetProp("_Name").strip() + if mol: + if not use_file_name and mol.HasProp("_Name") and mol.GetProp("_Name").strip(): + name = mol.GetProp("_Name").strip() + else: + name = f"{ligand.stem}_{i}" if len(mols) > 1 else ligand.stem + curr_mol_name_list.append((mol, name)) + if len(curr_mol_name_list) > batch_size: + yield curr_mol_name_list + curr_mol_name_list = [] else: - name = f"{ligand.stem}_{i}" if len(mols) > 1 else ligand.stem - curr_mol_name_list.append((mol, name)) - if len(curr_mol_name_list) > batch_size: - yield curr_mol_name_list - curr_mol_name_list = [] + logging.warning(f"read ligand file {ligand.stem} ind {i} error") if len(curr_mol_name_list) > 0: yield curr_mol_name_list return -def ligprep(mol_name_tup: Tuple[Chem.Mol, str], savedir: Path): +def ligprep(mol_name_tup: Tuple[Chem.Mol, str], savedir: Path, save_format: str = "sdf"): mol, name = mol_name_tup - tb = TopologyBuilder(mol) - tb.build_molecular_graph() - tb.write_sdf_file(os.path.join(savedir, f"{name}.sdf")) + try: + tb = TopologyBuilder(mol) + tb.build_molecular_graph() + if save_format == "sdf": + tb.write_sdf_file(os.path.join(savedir, f"{name}.sdf")) + elif save_format == "pdbqt": + tb.write_pdbqt_file(os.path.join(savedir, f"{name}.pdbqt")) + else: + logging.error(f"Invalid save format: {save_format}") + except: + logging.error(f"ligprep failed for {name}: {traceback.format_exc()}") def main(args: dict): @@ -52,9 +65,11 @@ def main(args: dict): continue ligands.append(Path(line.strip()).resolve()) + os.makedirs(Path(args["savedir"]).resolve(), exist_ok=True) for mol_name_tup_list in iter_ligands(ligands, args["batch_size"], args["use_file_name"]): with Pool(os.cpu_count()) as pool: - pool.map(partial(ligprep, savedir=args["savedir"]), mol_name_tup_list) + pool.map(partial(ligprep, savedir=args["savedir"], + save_format=args["save_format"]), mol_name_tup_list) def get_parser() -> argparse.ArgumentParser: @@ -65,6 +80,8 @@ def get_parser() -> argparse.ArgumentParser: help="A text file containing the path of ligand files in sdf format.") parser.add_argument("-sd", "--savedir", type=str, default="ligprep_results", help="Save directory. Default: 'MultiConfDock-Result'.") + parser.add_argument("-sf", "--save_format", type=str, default="sdf", + help="Ligprep result files format. Choose from ['sdf', 'pdbqt']. Default: 'sdf'.") parser.add_argument("-bs", "--batch_size", type=int, default=1200, help="Batch size for docking. Default: 1200.") parser.add_argument("-ufn", "--use_file_name", action="store_true", diff --git a/unidock_tools/src/unidock_tools/modules/ligand_prep/torsion_tree.py b/unidock_tools/src/unidock_tools/modules/ligand_prep/torsion_tree.py index 1c72329..f68594e 100644 --- a/unidock_tools/src/unidock_tools/modules/ligand_prep/torsion_tree.py +++ b/unidock_tools/src/unidock_tools/modules/ligand_prep/torsion_tree.py @@ -1,4 +1,4 @@ -from typing import Dict, Tuple +from typing import Dict, Tuple, Union import os import numpy as np import networkx as nx @@ -163,7 +163,7 @@ def build_molecular_graph(self): node_idx = 0 root_fragment = splitted_mol_list[root_fragment_idx] num_root_atoms = root_fragment.GetNumAtoms() - atom_info_list = [None] * num_root_atoms + atom_info_list = [dict()] * num_root_atoms for root_atom_idx in range(num_root_atoms): root_atom = root_fragment.GetAtomWithIdx(root_atom_idx) atom_info_dict = {} @@ -189,7 +189,7 @@ def build_molecular_graph(self): else: fragment = splitted_mol_list[fragment_idx] num_fragment_atoms = fragment.GetNumAtoms() - atom_info_list = [None] * num_fragment_atoms + atom_info_list = [dict()] * num_fragment_atoms for atom_idx in range(num_fragment_atoms): atom = fragment.GetAtomWithIdx(atom_idx) atom_info_dict = {} @@ -341,7 +341,7 @@ def _deep_first_search(self, node_idx): self.pdbqt_atom_line_list.append( self.pdbqt_end_branch_line_format.format('ENDBRANCH', parent_atom_idx, offspring_atom_idx)) - def write_pdbqt_file(self, out_file: str = ''): + def write_pdbqt_file(self, out_file: Union[str, bytes, os.PathLike]): self.pdbqt_remark_line_list = [] self.pdbqt_atom_line_list = [] @@ -383,7 +383,7 @@ def write_pdbqt_file(self, out_file: str = ''): for pdbqt_line in self.pdbqt_line_list: f.write(pdbqt_line) - def write_constraint_bpf_file(self, out_path: str = ''): + def write_constraint_bpf_file(self, out_path: Union[str, bytes, os.PathLike]): self.core_bpf_remark_line_list = [] self.core_bpf_atom_line_list = [] self.core_bpf_atom_line_format = '{:8.3f}\t{:8.3f}\t{:8.3f}\t{:6.2f}\t{:6.2f}\t{:3s}\t{:<2s}\n' @@ -452,7 +452,7 @@ def get_sdf_torsion_tree_info(self) -> Tuple[str, str, str, str]: return frag_info_str, frag_all_info_str, torsion_info_str, atom_info_str - def write_sdf_file(self, out_file: str = '', do_rigid_docking: bool = False): + def write_sdf_file(self, out_file: Union[str, bytes, os.PathLike], do_rigid_docking: bool = False): frag_info_str, frag_all_info_str, torsion_info_str, atom_info_str = self.get_sdf_torsion_tree_info() if do_rigid_docking: self.mol.SetProp("fragInfo", frag_all_info_str) @@ -460,13 +460,5 @@ def write_sdf_file(self, out_file: str = '', do_rigid_docking: bool = False): self.mol.SetProp("fragInfo", frag_info_str) self.mol.SetProp("torsionInfo", torsion_info_str) self.mol.SetProp("atomInfo", atom_info_str) - if out_file: - os.makedirs(os.path.dirname(os.path.abspath(out_file)), exist_ok=True) - with Chem.SDWriter(out_file) as writer: - writer.write(self.mol) - - -def generate_topology(mol: Chem.Mol, out_file: str = ''): - topology_builder = TopologyBuilder(mol) - topology_builder.build_molecular_graph() - topology_builder.write_pdbqt_file(out_file=out_file) \ No newline at end of file + with Chem.SDWriter(str(out_file)) as writer: + writer.write(self.mol) \ No newline at end of file diff --git a/unidock_tools/src/unidock_tools/modules/protein_prep/pdb2pdbqt.py b/unidock_tools/src/unidock_tools/modules/protein_prep/pdb2pdbqt.py index 28a4a17..e05959e 100644 --- a/unidock_tools/src/unidock_tools/modules/protein_prep/pdb2pdbqt.py +++ b/unidock_tools/src/unidock_tools/modules/protein_prep/pdb2pdbqt.py @@ -3,7 +3,6 @@ from math import isnan, isinf from rdkit import Chem from rdkit.Chem import AllChem -from rdkit.Chem.rdchem import BondType def get_pdbqt_atom_lines(mol: Chem.Mol, donors: List[int], acceptors: List[int]): diff --git a/unidock_tools/src/unidock_tools/utils/mol_group.py b/unidock_tools/src/unidock_tools/utils/mol_group.py index 6cc45a9..40144c1 100644 --- a/unidock_tools/src/unidock_tools/utils/mol_group.py +++ b/unidock_tools/src/unidock_tools/utils/mol_group.py @@ -57,7 +57,7 @@ def update_conf_props(self, conf_props: dict): self.conf_props.update(conf_props) def get_rdkit_mol_conf_with_props(self, conf_idx: int, props_list: List[str] = [], - exclude_props_list: List[str] = []): + exclude_props_list: List[str] = []) -> Chem.Mol: mol = copy.copy(self.mol_confs[conf_idx]) props = copy.deepcopy(self.get_props()) props.update({k:v[conf_idx] for k, v in self.get_conf_props().items()}) @@ -135,10 +135,9 @@ def write_sdf_by_idx(self, ) -> List[Path]: save_dir = make_tmp_dir(str(save_dir), False, False) - mol_confs_copy = [None] * len(self.mol_group[idx]) - for conf_idx in range(len(self.mol_group[idx])): - mol_conf_copy = self.mol_group[idx].get_rdkit_mol_conf_with_props(conf_idx, props_list, exclude_props_list) - mol_confs_copy[conf_idx] = mol_conf_copy + mol_confs_copy = [self.mol_group[idx].get_rdkit_mol_conf_with_props( + conf_idx, props_list, exclude_props_list) for conf_idx in range( + len(self.mol_group[idx]))] # save SDF files file_prefix = self.mol_group[idx].get_props()['file_prefix'] sdf_file_list = [] diff --git a/unidock_tools/src/unidock_tools/utils/rdkit_helper.py b/unidock_tools/src/unidock_tools/utils/rdkit_helper.py index 72bef13..a528689 100644 --- a/unidock_tools/src/unidock_tools/utils/rdkit_helper.py +++ b/unidock_tools/src/unidock_tools/utils/rdkit_helper.py @@ -32,12 +32,12 @@ def set_properties(mol: Chem.Mol, properties: dict): """ for key, value in properties.items(): try: - if isinstance(key, int): + if isinstance(value, int): mol.SetIntProp(key, value) - elif isinstance(key, float): + elif isinstance(value, float): mol.SetDoubleProp(key, value) else: - mol.SetProp(key, str(value)) + mol.SetProp(value, str(value)) except: logging.warning(f"set property {key} err: {traceback.format_exc()}") From 5c37f638f2bfe76dd62c779b550319a6e72b0cab Mon Sep 17 00:00:00 2001 From: dp-yuanyn Date: Sat, 9 Mar 2024 16:00:46 +0800 Subject: [PATCH 3/3] fix:write sdf set prop key name err --- .../application/unidock_pipeline.py | 1 + .../src/unidock_tools/utils/rdkit_helper.py | 2 +- .../inputs/unidock_pipeline/bigsdf/ligand.sdf | 1619 +++-------------- 3 files changed, 290 insertions(+), 1332 deletions(-) diff --git a/unidock_tools/src/unidock_tools/application/unidock_pipeline.py b/unidock_tools/src/unidock_tools/application/unidock_pipeline.py index fef4f69..74ed9eb 100644 --- a/unidock_tools/src/unidock_tools/application/unidock_pipeline.py +++ b/unidock_tools/src/unidock_tools/application/unidock_pipeline.py @@ -257,6 +257,7 @@ def main(args: dict): batch_size=int(args["batch_size"]), score_only=bool(args["score_only"]), local_only=bool(args["local_only"]), + props_list=["fragInfo", "torsionInfo", "atomInfo"], ) runner.save_results(save_dir=savedir) end_time = time.time() diff --git a/unidock_tools/src/unidock_tools/utils/rdkit_helper.py b/unidock_tools/src/unidock_tools/utils/rdkit_helper.py index a528689..9205431 100644 --- a/unidock_tools/src/unidock_tools/utils/rdkit_helper.py +++ b/unidock_tools/src/unidock_tools/utils/rdkit_helper.py @@ -37,7 +37,7 @@ def set_properties(mol: Chem.Mol, properties: dict): elif isinstance(value, float): mol.SetDoubleProp(key, value) else: - mol.SetProp(value, str(value)) + mol.SetProp(key, str(value)) except: logging.warning(f"set property {key} err: {traceback.format_exc()}") diff --git a/unidock_tools/tests/inputs/unidock_pipeline/bigsdf/ligand.sdf b/unidock_tools/tests/inputs/unidock_pipeline/bigsdf/ligand.sdf index 7920ec8..4a64532 100644 --- a/unidock_tools/tests/inputs/unidock_pipeline/bigsdf/ligand.sdf +++ b/unidock_tools/tests/inputs/unidock_pipeline/bigsdf/ligand.sdf @@ -1,1371 +1,328 @@ -CHEMBL417870 +1a RDKit 3D - 61 61 0 0 1 0 0 0 0 0999 V2000 - -0.5986 2.0910 0.8139 C 0 0 0 0 0 0 0 0 0 0 0 0 - -0.4414 0.5739 0.6943 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.8230 -0.0758 0.5942 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.6657 -1.5930 0.4747 C 0 0 0 0 0 0 0 0 0 0 0 0 - -3.0473 -2.2426 0.3745 C 0 0 0 0 0 0 0 0 0 0 0 0 - -2.8901 -3.7598 0.2550 C 0 0 1 0 0 0 0 0 0 0 0 0 - -2.2951 -4.1303 1.0897 H 0 0 0 0 0 0 0 0 0 0 0 0 - -4.2497 -4.4093 0.2799 C 0 0 0 0 0 0 0 0 0 0 0 0 - -4.7737 -4.7592 -0.7564 O 0 0 0 0 0 0 0 0 0 0 0 0 - -4.8834 -4.6013 1.4538 N 0 0 0 0 0 0 0 0 0 0 0 0 - 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