Chimie Théorique » scripts_chimie4psmn » DockOnSurf

"""Functions to generate the conformers to be adsorbed and the most stable one.

functions:

remove_C_linked_Hs: Removes hydrogens bonded to a carbon atom from a molecule.

gen_confs: Generate a number of conformers in random orientations.

get_moments_of_inertia: Computes moments of inertia of the given conformers.

get_moments_of_inertia: Computes the moments of inertia of the given conformers.

pre_opt_confs: Optimizes the geometry of the given conformers and returns the

    new mol object and the energies of its conformers.

run_isolated: directs the execution of functions to achieve the goal

"""

import logging

import numpy as np

import rdkit.Chem.AllChem as Chem

logger = logging.getLogger('DockOnSurf')

def remove_C_linked_Hs(mol: Chem.rdchem.Mol):

    """Removes hydrogen atoms bonded to a carbon atom from a rdkit mol object.

    @param mol: rdkit mol object of the molecule with hydrogen atoms.

    @return: rdkit mol object of the molecule without hydrogen atoms linked to

    a carbon atom.

    The functions removes the hydrogen atoms bonded to carbon atoms while

    keeping the ones bonded to other atoms or non-bonded at all.

    """

    mol = Chem.RWMol(mol)

    rev_atm_idxs = [atom.GetIdx() for atom in reversed(mol.GetAtoms())]

    for atm_idx in rev_atm_idxs:

        atom = mol.GetAtomWithIdx(atm_idx)

        if atom.GetAtomicNum() != 1:

            continue

        for neigh in atom.GetNeighbors():

            if neigh.GetAtomicNum() == 6:

                mol.RemoveAtom(atom.GetIdx())

    return mol

def gen_confs(mol: Chem.rdchem.Mol, num_confs: int):

    """Generate conformers in random orientations.

    @param mol: rdkit mol object of the molecule to be adsorbed.

    @param num_confs: number of conformers to randomly generate.

    @return: mol: rdkit mol object containing the different conformers.

             rmsd_mtx: Matrix with the rmsd values of conformers.

    Using the rdkit library, conformers are randomly generated. If structures 

    are required to be local minima, ie. setting the 'local_min' value to 

    True, a geometry optimisation using UFF is performed.

    """

    logger.debug('Generating Conformers.')

    mol = Chem.AddHs(mol)

    Chem.EmbedMultipleConfs(mol, numConfs=num_confs, numThreads=0,

                            randomSeed=5817216)

    Chem.AlignMolConformers(mol)

    logger.info(f'Generated {len(mol.GetConformers())} conformers.')

    return mol

def get_moments_of_inertia(mol: Chem.rdchem.Mol):

    """Computes the moments of inertia of the given conformers.

    @param mol: rdkit mol object of the relevant molecule.

    @return numpy array 2D: The inner array contains the moments of inertia for

    the three principal axis of a given conformer. They are ordered by its value

    in ascending order. The outer tuple loops over the conformers.

    """

    from rdkit.Chem.Descriptors3D import PMI1, PMI2, PMI3

    return np.array([[PMI(mol, confId=conf) for PMI in (PMI1, PMI2, PMI3)]

                     for conf in range(mol.GetNumConformers())])

def pre_opt_confs(mol: Chem.rdchem.Mol, force_field='mmff', max_iters=2000):

    """Optimizes the geometry of the given conformers and returns the new mol

    object and the energies of its conformers.

    @param mol: rdkit mol object of the relevant molecule.

    @param force_field: Force Field to use for the pre-optimization.

    @param max_iters: Maximum number of geometry optimization iterations. With 0

    a single point energy calculation is performed and only the conformer

    energies are returned.

    @return mol: rdkit mol object of the optimized molecule.

    @return numpy.ndarray: Array with the energies of the optimized conformers.

    The MMFF and UFF force fields can be used for the geometry optimization in

    their rdkit implementation. With max_iters value set to 0, a single point

    energy calculation is performed and only the energies are returned. For

    values larger than 0, if the geometry does not converge for a certain

    conformer, the latter is removed from the list of conformers and its energy

    is not included in the returned list.

    """

    from rdkit.Chem.rdForceFieldHelpers import MMFFOptimizeMoleculeConfs, \

        UFFOptimizeMoleculeConfs

    init_num_confs = mol.GetNumConformers()

    if force_field == 'mmff':

        results = np.array(MMFFOptimizeMoleculeConfs(mol, numThreads=0,

                                                     maxIters=max_iters,

                                                     nonBondedThresh=10))

    elif force_field == 'uff':

        results = np.array(UFFOptimizeMoleculeConfs(mol, numThreads=0,

                                                    maxIters=max_iters,

                                                    vdwThresh=10))

    else:

        logger.error("force_field parameter must be 'MMFF' or 'UFF'")

        raise ValueError("force_field parameter must be 'MMFF' or 'UFF'")

    # Remove non-converged conformers if optimization is on, ie. maxIters > 0

    # return all conformers if optimization is switched off, ie. maxIters = 0

    if max_iters > 0:

        for i, conv in enumerate(results[:, 0]):

            if conv != 0:

                mol.RemoveConformer(i)

        for i, conf in enumerate(mol.GetConformers()):

            conf.SetId(i)

        if mol.GetNumConformers() < init_num_confs:

            logger.warning(f'Geometry optimization did not comverge for at'

                           f'least one conformer. Continuing with '

                           f'{mol.GetNumConformers()} converged conformers.')

        logger.info(f'Pre-optimized conformers with {force_field}.')

        return mol, np.array([res[1] for res in results if res[0] == 0])

    else:

        logger.info(f'Computed conformers energy with {force_field}.')

        return np.array([res[1] for res in results])

def run_isolated(inp_vars):

    """Directs the execution of functions to obtain the conformers to adsorb

    @param inp_vars: Calculation parameters from input file.

    @return:

    """

    from modules.formats import adapt_format, confs_to_mol_list, \

        rdkit_mol_to_ase_atoms, collect_confs

    from modules.clustering import clustering, get_rmsd

    from modules.calculation import run_calc, check_finished_calcs

    from modules.refinement import select_stable_confs

    logger.info('Carrying out procedures for the isolated molecule.')

    # Read the molecule

    rd_mol = adapt_format('rdkit', inp_vars['molec_file'],

                          inp_vars['special_atoms'])

    # Generate conformers

    confs = gen_confs(rd_mol, inp_vars['num_conformers'])

    # Pre-optimizes conformers

    if inp_vars['pre_opt']:

        confs, confs_ener = pre_opt_confs(confs, inp_vars['pre_opt'])

    else:

        confs_ener = pre_opt_confs(confs, max_iters=0)

    conf_list = confs_to_mol_list(confs)

    # Calculates RMSD matrix of the conformers

    rmsd_mtx = get_rmsd(conf_list)

    confs_moi = get_moments_of_inertia(confs)

    # Clusters the conformers and selects a representative

    exemplars = clustering(rmsd_mtx)

    mol_list = confs_to_mol_list(confs, exemplars)

    ase_atms_list = [rdkit_mol_to_ase_atoms(mol) for mol in mol_list]

    if len(ase_atms_list) == 0:

        err_msg = "No configurations were generated: Check the parameters in" \

                  "dockonsurf.inp"

        logger.error(err_msg)

        raise ValueError(err_msg)

    # Runs the jobs.

    run_calc('isolated', inp_vars, ase_atms_list)

    logger.info("Finished the procedures for the isolated molecule section. ")

    if inp_vars["batch_q_sys"]:

        finished_calcs, failed_calcs = check_finished_calcs('isolated',

                                                            inp_vars['code'])

        conf_list = collect_confs(finished_calcs, inp_vars['code'], 'isolated',

                              inp_vars['special_atoms'])

        most_stable_conf = select_stable_confs(conf_list, 0)[0]

        logger.info(f"Most stable conformers is {most_stable_conf.info['iso']},"

                    f" with a total energy of {most_stable_conf.info['energy']}"

                    f" eV.")