Loading deepchem/utils/vina_utils.py +8 −228 Original line number Diff line number Diff line """ This file contains utilities to work with autodock vina. This file contains deprecated utilities to work with autodock vina. """ from typing import List, Optional, Tuple import numpy as np from deepchem.utils.typing import RDKitMol from deepchem.utils.pdbqt_utils import pdbqt_to_pdb from deepchem.utils.docking_utils import write_vina_conf, load_docked_ligands, prepare_inputs import warnings import functools Loading @@ -20,7 +16,8 @@ def deprecated(func): def new_func(*args, **kwargs): warnings.simplefilter('always', DeprecationWarning) # turn off filter warnings.warn( "Call to deprecated function {}. Please use the corresponding function in deepchem.utils.docking_utils.".format(func.__name__), "Call to deprecated function {}. Please use the corresponding function in deepchem.utils.docking_utils.". format(func.__name__), category=DeprecationWarning, stacklevel=2) warnings.simplefilter('default', DeprecationWarning) # reset filter Loading @@ -29,224 +26,7 @@ def deprecated(func): return new_func @deprecated def write_vina_conf(protein_filename: str, ligand_filename: str, centroid: np.ndarray, box_dims: np.ndarray, conf_filename: str, num_modes: int = 9, exhaustiveness: int = None) -> None: """Writes Vina configuration file to disk. Autodock Vina accepts a configuration file which provides options under which Vina is invoked. This utility function writes a vina configuration file which directs Autodock vina to perform docking under the provided options. Parameters ---------- protein_filename: str Filename for protein ligand_filename: str Filename for the ligand centroid: np.ndarray A numpy array with shape `(3,)` holding centroid of system box_dims: np.ndarray A numpy array of shape `(3,)` holding the size of the box to dock conf_filename: str Filename to write Autodock Vina configuration to. num_modes: int, optional (default 9) The number of binding modes Autodock Vina should find exhaustiveness: int, optional The exhaustiveness of the search to be performed by Vina """ with open(conf_filename, "w") as f: f.write("receptor = %s\n" % protein_filename) f.write("ligand = %s\n\n" % ligand_filename) f.write("center_x = %f\n" % centroid[0]) f.write("center_y = %f\n" % centroid[1]) f.write("center_z = %f\n\n" % centroid[2]) f.write("size_x = %f\n" % box_dims[0]) f.write("size_y = %f\n" % box_dims[1]) f.write("size_z = %f\n\n" % box_dims[2]) f.write("num_modes = %d\n\n" % num_modes) if exhaustiveness is not None: f.write("exhaustiveness = %d\n" % exhaustiveness) @deprecated def load_docked_ligands( pdbqt_output: str) -> Tuple[List[RDKitMol], List[float]]: """This function loads ligands docked by autodock vina. Autodock vina writes outputs to disk in a PDBQT file format. This PDBQT file can contain multiple docked "poses". Recall that a pose is an energetically favorable 3D conformation of a molecule. This utility function reads and loads the structures for multiple poses from vina's output file. Parameters ---------- pdbqt_output: str Should be the filename of a file generated by autodock vina's docking software. Returns ------- Tuple[List[rdkit.Chem.rdchem.Mol], List[float]] Tuple of `molecules, scores`. `molecules` is a list of rdkit molecules with 3D information. `scores` is the associated vina score. Notes ----- This function requires RDKit to be installed. """ try: from rdkit import Chem except ModuleNotFoundError: raise ImportError("This function requires RDKit to be installed.") lines = open(pdbqt_output).readlines() molecule_pdbqts = [] scores = [] current_pdbqt: Optional[List[str]] = None for line in lines: if line[:5] == "MODEL": current_pdbqt = [] elif line[:19] == "REMARK VINA RESULT:": words = line.split() # the line has format # REMARK VINA RESULT: score ... # There is only 1 such line per model so we can append it scores.append(float(words[3])) elif line[:6] == "ENDMDL": molecule_pdbqts.append(current_pdbqt) current_pdbqt = None else: # FIXME: Item "None" of "Optional[List[str]]" has no attribute "append" current_pdbqt.append(line) # type: ignore molecules = [] for pdbqt_data in molecule_pdbqts: pdb_block = pdbqt_to_pdb(pdbqt_data=pdbqt_data) mol = Chem.MolFromPDBBlock(str(pdb_block), sanitize=False, removeHs=False) molecules.append(mol) return molecules, scores @deprecated def prepare_inputs(protein: str, ligand: str, replace_nonstandard_residues: bool = True, remove_heterogens: bool = True, remove_water: bool = True, add_hydrogens: bool = True, pH: float = 7.0, optimize_ligand: bool = True, pdb_name: Optional[str] = None) -> Tuple[RDKitMol, RDKitMol]: """This prepares protein-ligand complexes for docking. Autodock Vina requires PDB files for proteins and ligands with sensible inputs. This function uses PDBFixer and RDKit to ensure that inputs are reasonable and ready for docking. Default values are given for convenience, but fixing PDB files is complicated and human judgement is required to produce protein structures suitable for docking. Always inspect the results carefully before trying to perform docking. Parameters ---------- protein: str Filename for protein PDB file or a PDBID. ligand: str Either a filename for a ligand PDB file or a SMILES string. replace_nonstandard_residues: bool (default True) Replace nonstandard residues with standard residues. remove_heterogens: bool (default True) Removes residues that are not standard amino acids or nucleotides. remove_water: bool (default True) Remove water molecules. add_hydrogens: bool (default True) Add missing hydrogens at the protonation state given by `pH`. pH: float (default 7.0) Most common form of each residue at given `pH` value is used. optimize_ligand: bool (default True) If True, optimize ligand with RDKit. Required for SMILES inputs. pdb_name: Optional[str] If given, write sanitized protein and ligand to files called "pdb_name.pdb" and "ligand_pdb_name.pdb" Returns ------- Tuple[RDKitMol, RDKitMol] Tuple of `protein_molecule, ligand_molecule` with 3D information. Note ---- This function requires RDKit and OpenMM to be installed. Read more about PDBFixer here: https://github.com/openmm/pdbfixer. Examples -------- >>> p, m = prepare_inputs('3cyx', 'CCC') >>> p.GetNumAtoms() 1415 >>> m.GetNumAtoms() 11 >>> p, m = prepare_inputs('3cyx', 'CCC', remove_heterogens=False) >>> p.GetNumAtoms() 1720 """ try: from rdkit import Chem from rdkit.Chem import AllChem from pdbfixer import PDBFixer from simtk.openmm.app import PDBFile except ModuleNotFoundError: raise ImportError( "This function requires RDKit and OpenMM to be installed.") if protein.endswith('.pdb'): fixer = PDBFixer(protein) else: fixer = PDBFixer(url='https://files.rcsb.org/download/%s.pdb' % (protein)) if ligand.endswith('.pdb'): m = Chem.MolFromPDBFile(ligand) else: m = Chem.MolFromSmiles(ligand, sanitize=True) # Apply common fixes to PDB files if replace_nonstandard_residues: fixer.findMissingResidues() fixer.findNonstandardResidues() fixer.replaceNonstandardResidues() if remove_heterogens and not remove_water: fixer.removeHeterogens(True) if remove_heterogens and remove_water: fixer.removeHeterogens(False) if add_hydrogens: fixer.addMissingHydrogens(pH) PDBFile.writeFile(fixer.topology, fixer.positions, open('tmp.pdb', 'w')) p = Chem.MolFromPDBFile('tmp.pdb', sanitize=True) # Optimize ligand if optimize_ligand: m = Chem.AddHs(m) # need hydrogens for optimization AllChem.EmbedMolecule(m) AllChem.MMFFOptimizeMolecule(m) if pdb_name: Chem.rdmolfiles.MolToPDBFile(p, '%s.pdb' % (pdb_name)) Chem.rdmolfiles.MolToPDBFile(m, 'ligand_%s.pdb' % (pdb_name)) return (p, m) # These functions have moved to deepchem.utils_docking_utils write_vina_conf = deprecated(write_vina_conf) load_docked_ligands = deprecated(load_docked_ligands) prepare_inputs = deprecated(prepare_inputs) Loading
deepchem/utils/vina_utils.py +8 −228 Original line number Diff line number Diff line """ This file contains utilities to work with autodock vina. This file contains deprecated utilities to work with autodock vina. """ from typing import List, Optional, Tuple import numpy as np from deepchem.utils.typing import RDKitMol from deepchem.utils.pdbqt_utils import pdbqt_to_pdb from deepchem.utils.docking_utils import write_vina_conf, load_docked_ligands, prepare_inputs import warnings import functools Loading @@ -20,7 +16,8 @@ def deprecated(func): def new_func(*args, **kwargs): warnings.simplefilter('always', DeprecationWarning) # turn off filter warnings.warn( "Call to deprecated function {}. Please use the corresponding function in deepchem.utils.docking_utils.".format(func.__name__), "Call to deprecated function {}. Please use the corresponding function in deepchem.utils.docking_utils.". format(func.__name__), category=DeprecationWarning, stacklevel=2) warnings.simplefilter('default', DeprecationWarning) # reset filter Loading @@ -29,224 +26,7 @@ def deprecated(func): return new_func @deprecated def write_vina_conf(protein_filename: str, ligand_filename: str, centroid: np.ndarray, box_dims: np.ndarray, conf_filename: str, num_modes: int = 9, exhaustiveness: int = None) -> None: """Writes Vina configuration file to disk. Autodock Vina accepts a configuration file which provides options under which Vina is invoked. This utility function writes a vina configuration file which directs Autodock vina to perform docking under the provided options. Parameters ---------- protein_filename: str Filename for protein ligand_filename: str Filename for the ligand centroid: np.ndarray A numpy array with shape `(3,)` holding centroid of system box_dims: np.ndarray A numpy array of shape `(3,)` holding the size of the box to dock conf_filename: str Filename to write Autodock Vina configuration to. num_modes: int, optional (default 9) The number of binding modes Autodock Vina should find exhaustiveness: int, optional The exhaustiveness of the search to be performed by Vina """ with open(conf_filename, "w") as f: f.write("receptor = %s\n" % protein_filename) f.write("ligand = %s\n\n" % ligand_filename) f.write("center_x = %f\n" % centroid[0]) f.write("center_y = %f\n" % centroid[1]) f.write("center_z = %f\n\n" % centroid[2]) f.write("size_x = %f\n" % box_dims[0]) f.write("size_y = %f\n" % box_dims[1]) f.write("size_z = %f\n\n" % box_dims[2]) f.write("num_modes = %d\n\n" % num_modes) if exhaustiveness is not None: f.write("exhaustiveness = %d\n" % exhaustiveness) @deprecated def load_docked_ligands( pdbqt_output: str) -> Tuple[List[RDKitMol], List[float]]: """This function loads ligands docked by autodock vina. Autodock vina writes outputs to disk in a PDBQT file format. This PDBQT file can contain multiple docked "poses". Recall that a pose is an energetically favorable 3D conformation of a molecule. This utility function reads and loads the structures for multiple poses from vina's output file. Parameters ---------- pdbqt_output: str Should be the filename of a file generated by autodock vina's docking software. Returns ------- Tuple[List[rdkit.Chem.rdchem.Mol], List[float]] Tuple of `molecules, scores`. `molecules` is a list of rdkit molecules with 3D information. `scores` is the associated vina score. Notes ----- This function requires RDKit to be installed. """ try: from rdkit import Chem except ModuleNotFoundError: raise ImportError("This function requires RDKit to be installed.") lines = open(pdbqt_output).readlines() molecule_pdbqts = [] scores = [] current_pdbqt: Optional[List[str]] = None for line in lines: if line[:5] == "MODEL": current_pdbqt = [] elif line[:19] == "REMARK VINA RESULT:": words = line.split() # the line has format # REMARK VINA RESULT: score ... # There is only 1 such line per model so we can append it scores.append(float(words[3])) elif line[:6] == "ENDMDL": molecule_pdbqts.append(current_pdbqt) current_pdbqt = None else: # FIXME: Item "None" of "Optional[List[str]]" has no attribute "append" current_pdbqt.append(line) # type: ignore molecules = [] for pdbqt_data in molecule_pdbqts: pdb_block = pdbqt_to_pdb(pdbqt_data=pdbqt_data) mol = Chem.MolFromPDBBlock(str(pdb_block), sanitize=False, removeHs=False) molecules.append(mol) return molecules, scores @deprecated def prepare_inputs(protein: str, ligand: str, replace_nonstandard_residues: bool = True, remove_heterogens: bool = True, remove_water: bool = True, add_hydrogens: bool = True, pH: float = 7.0, optimize_ligand: bool = True, pdb_name: Optional[str] = None) -> Tuple[RDKitMol, RDKitMol]: """This prepares protein-ligand complexes for docking. Autodock Vina requires PDB files for proteins and ligands with sensible inputs. This function uses PDBFixer and RDKit to ensure that inputs are reasonable and ready for docking. Default values are given for convenience, but fixing PDB files is complicated and human judgement is required to produce protein structures suitable for docking. Always inspect the results carefully before trying to perform docking. Parameters ---------- protein: str Filename for protein PDB file or a PDBID. ligand: str Either a filename for a ligand PDB file or a SMILES string. replace_nonstandard_residues: bool (default True) Replace nonstandard residues with standard residues. remove_heterogens: bool (default True) Removes residues that are not standard amino acids or nucleotides. remove_water: bool (default True) Remove water molecules. add_hydrogens: bool (default True) Add missing hydrogens at the protonation state given by `pH`. pH: float (default 7.0) Most common form of each residue at given `pH` value is used. optimize_ligand: bool (default True) If True, optimize ligand with RDKit. Required for SMILES inputs. pdb_name: Optional[str] If given, write sanitized protein and ligand to files called "pdb_name.pdb" and "ligand_pdb_name.pdb" Returns ------- Tuple[RDKitMol, RDKitMol] Tuple of `protein_molecule, ligand_molecule` with 3D information. Note ---- This function requires RDKit and OpenMM to be installed. Read more about PDBFixer here: https://github.com/openmm/pdbfixer. Examples -------- >>> p, m = prepare_inputs('3cyx', 'CCC') >>> p.GetNumAtoms() 1415 >>> m.GetNumAtoms() 11 >>> p, m = prepare_inputs('3cyx', 'CCC', remove_heterogens=False) >>> p.GetNumAtoms() 1720 """ try: from rdkit import Chem from rdkit.Chem import AllChem from pdbfixer import PDBFixer from simtk.openmm.app import PDBFile except ModuleNotFoundError: raise ImportError( "This function requires RDKit and OpenMM to be installed.") if protein.endswith('.pdb'): fixer = PDBFixer(protein) else: fixer = PDBFixer(url='https://files.rcsb.org/download/%s.pdb' % (protein)) if ligand.endswith('.pdb'): m = Chem.MolFromPDBFile(ligand) else: m = Chem.MolFromSmiles(ligand, sanitize=True) # Apply common fixes to PDB files if replace_nonstandard_residues: fixer.findMissingResidues() fixer.findNonstandardResidues() fixer.replaceNonstandardResidues() if remove_heterogens and not remove_water: fixer.removeHeterogens(True) if remove_heterogens and remove_water: fixer.removeHeterogens(False) if add_hydrogens: fixer.addMissingHydrogens(pH) PDBFile.writeFile(fixer.topology, fixer.positions, open('tmp.pdb', 'w')) p = Chem.MolFromPDBFile('tmp.pdb', sanitize=True) # Optimize ligand if optimize_ligand: m = Chem.AddHs(m) # need hydrogens for optimization AllChem.EmbedMolecule(m) AllChem.MMFFOptimizeMolecule(m) if pdb_name: Chem.rdmolfiles.MolToPDBFile(p, '%s.pdb' % (pdb_name)) Chem.rdmolfiles.MolToPDBFile(m, 'ligand_%s.pdb' % (pdb_name)) return (p, m) # These functions have moved to deepchem.utils_docking_utils write_vina_conf = deprecated(write_vina_conf) load_docked_ligands = deprecated(load_docked_ligands) prepare_inputs = deprecated(prepare_inputs)
