Révision 5c70d6c6
| b/modules/isolated.py | ||
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"""Functions to generate the conformers to be adsorbed and the most stable one. |
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functions. |
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functions: |
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remove_C_linked_Hs: Removes hydrogens bonded to a carbon atom from a molecule. |
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gen_confs: Generate a number of different conformers in random orientations. |
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run_isolated: directs the execution of functions to achieve the goal |
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""" |
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logger = logging.getLogger('DockOnSurf')
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def remove_C_linked_Hs(mol): |
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"""Removes hydrogens bonded to a carbon atom from a rdkit mol object. |
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@param mol: rdkit mol object of the molecule with hydrogens |
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@return: rdkit mol object of the molecule without hydrogens linked to carbon |
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atoms. |
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The functions removes the hydrogens bonded to C atoms while keeping the |
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ones bonded to heteroatoms. |
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""" |
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from rdkit import Chem |
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mol = Chem.RWMol(mol) |
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rev_atm_idxs = [atom.GetIdx() for atom in reversed(mol.GetAtoms())] |
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for atm_idx in rev_atm_idxs: |
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atom = mol.GetAtomWithIdx(atm_idx) |
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if atom.GetAtomicNum() != 1: |
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continue |
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for neigh in atom.GetNeighbors(): |
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if neigh.GetAtomicNum() == 6: |
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mol.RemoveAtom(atom.GetIdx()) |
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return mol |
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def gen_confs(mol, num_confs, rms_thld): |
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"""Generate a number of different conformers in random orientations. |
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|
| ... | ... | |
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""" |
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from rdkit.Chem import AllChem as Chem |
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logger.info('Generating Conformers')
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conf_ids = Chem.EmbedMultipleConfs(mol, numConfs=num_confs, |
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numThreads=0) |
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conf_ids = Chem.EmbedMultipleConfs(mol, numConfs=num_confs, numThreads=0) |
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for conf in conf_ids: |
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Chem.UFFOptimizeMolecule(mol, confId=conf) # TODO: Do we want this? |
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for conf1 in conf_ids: # TODO parallelize |
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for conf2 in conf_ids[conf1+1:]: |
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Chem.UFFOptimizeMolecule(mol, confId=conf) # TODO: Do we want this? |
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Chem.AlignMolConformers(mol) |
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mol_wo_Hs = remove_C_linked_Hs(mol) |
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for conf1 in conf_ids: |
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for conf2 in conf_ids[conf1 + 1:]: |
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try: |
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rms = Chem.GetConformerRMS(mol, conf1, conf2) |
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rms = Chem.GetBestRMS(mol_wo_Hs, mol_wo_Hs, prbId=conf2, |
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refId=conf1) |
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except ValueError: |
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continue |
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else: |
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if rms <= rms_thld: |
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mol.RemoveConformer(conf2) |
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logger.info(f'Generated {len(mol)} different conformers')
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return mol # TODO: mol indices |
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for i, conf in enumerate(mol.GetConformers()): |
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conf.SetId(i) |
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logger.info(f'Generated {len(mol.GetConformers())} different conformers')
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return mol |
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def run_isolated(inp_vars): |
Formats disponibles : Unified diff