Révision 4e82c425 modules/isolated.py
| b/modules/isolated.py | ||
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| 3 | 3 |
functions: |
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remove_C_linked_Hs: Removes hydrogens bonded to a carbon atom from a molecule. |
| 5 | 5 |
gen_confs: Generate a number of conformers in random orientations. |
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get_rmsd: Gets the rmsd matrix of the conformers in a rdkit mol object. |
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| 7 | 6 |
get_moments_of_inertia: Computes moments of inertia of the given conformers. |
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mmff_opt_confs: Optimizes the geometry of the given conformers and returns the |
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| 7 |
get_moments_of_inertia: Computes the moments of inertia of the given conformers. |
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pre_opt_confs: Optimizes the geometry of the given conformers and returns the |
|
| 9 | 9 |
new mol object and the energies of its conformers. |
| 10 | 10 |
run_isolated: directs the execution of functions to achieve the goal |
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""" |
| ... | ... | |
| 64 | 64 |
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def get_moments_of_inertia(mol: Chem.rdchem.Mol): |
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"""Computes the moments of inertia of the given conformers |
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"""Computes the moments of inertia of the given conformers.
|
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@param mol: rdkit mol object of the relevant molecule. |
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@return numpy array 2D: The inner array contains the moments of inertia for |
| ... | ... | |
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from modules.refinement import select_stable_confs |
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logger.info('Carrying out procedures for the isolated molecule.')
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# Read the molecule |
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rd_mol = adapt_format('rdkit', inp_vars['molec_file'],
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inp_vars['special_atoms']) |
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# Generate conformers |
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confs = gen_confs(rd_mol, inp_vars['num_conformers']) |
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# Pre-optimizes conformers |
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if inp_vars['pre_opt']: |
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confs, confs_ener = pre_opt_confs(confs, inp_vars['pre_opt']) |
| 152 | 155 |
else: |
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confs_ener = pre_opt_confs(confs, max_iters=0) |
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conf_list = confs_to_mol_list(confs) |
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# Calculates RMSD matrix of the conformers |
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rmsd_mtx = get_rmsd(conf_list) |
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confs_moi = get_moments_of_inertia(confs) |
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# Clusters the conformers and selects a representative |
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exemplars = clustering(rmsd_mtx) |
| 158 | 163 |
mol_list = confs_to_mol_list(confs, exemplars) |
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ase_atms_list = [rdkit_mol_to_ase_atoms(mol) for mol in mol_list] |
| ... | ... | |
| 162 | 167 |
"dockonsurf.inp" |
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logger.error(err_msg) |
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raise ValueError(err_msg) |
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# Runs the jobs. |
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run_calc('isolated', inp_vars, ase_atms_list)
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logger.info("Finished the procedures for the isolated molecule section. ")
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if inp_vars["batch_q_sys"]: |
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