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#! /usr/bin/env python |
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# |
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# Copyright (C) 2016 Rich Lewis <[email protected]> |
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# License: 3-clause BSD |
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""" |
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# skchem.features.descriptors.constitutional |
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Constitutional features for scikit-chem. |
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""" |
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from collections import OrderedDict |
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from functools import partial |
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from rdkit.Chem import rdMolDescriptors, rdmolops, Descriptors |
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from .caching import cache, requires_h_filled, requires_h_depleted |
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from .fundamentals import bond_order_adjacency_matrix |
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def molecular_weight(mol): |
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""" The molecular weight. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return rdMolDescriptors.CalcExactMolWt(mol) |
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@requires_h_filled |
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def average_molecular_weight(mol): |
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""" Average molecular weight of atoms. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return molecular_weight(mol) / len(mol.atoms) |
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def sum_van_der_waals_volume(mol): |
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""" The sum of the Van der Waals volume. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return mol.atoms.van_der_waals_volume.sum() |
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def sum_electronegativity(mol): |
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""" The sum of the Sanderson electronegativities. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return mol.atoms.sanderson_electronegativity.sum() |
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def sum_ionisation_energy(mol): |
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""" The sum of the first ionisation energies. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return mol.atoms.ionisation_energy.sum() |
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def sum_polarisability(mol): |
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""" The sum of the polarisabilities. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return mol.atoms.polarisability.sum() |
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def mean_van_der_waals_volume(mol): |
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""" The mean of the Van der Waals volume. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return mol.atoms.van_der_waals_volume.sum() |
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def mean_electronegativity(mol): |
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""" The mean of the Sanderson electronegativity. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return mol.atoms.sanderson_electronegativity.mean() |
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def mean_ionisation_energy(mol): |
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""" The mean of the first ionisation energies. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return mol.atoms.ionisation_energy.mean() |
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def mean_polarisability(mol): |
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""" The mean of the polarizabilities. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return mol.atoms.polarisability.mean() |
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@requires_h_depleted |
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def graph_density(mol): |
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""" The graph density of the h-depleted graph. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return 2 * len(mol.bonds) / (len(mol.atoms) * (len(mol.atoms) - 1)) |
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def n_atoms(mol): |
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""" The number of atoms. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return len(mol.atoms) |
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@requires_h_filled |
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def n_hyd(mol): |
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""" The number of hydrogen atoms. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return sum(mol.atoms.atomic_number == 1) |
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@requires_h_depleted |
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def n_atom(mol, symbol='C'): |
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""" The number of atoms of symbol *s*. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return sum(mol.atoms.symbol == symbol) |
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@requires_h_filled |
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def fract_atom(mol, symbol='C'): |
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""" The fraction of atoms of symbol *s*. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return sum(mol.atoms.symbol == symbol) / len(mol.atoms) |
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def n_halo(mol): |
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# TODO: memoize |
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""" The number of halogens. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return sum(n_atom(mol, s) for s in ('F', 'Cl', 'Br', 'I')) |
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@requires_h_filled |
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def fract_halo(mol): |
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""" The fraction of halogens. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return n_halo(mol) / len(mol.atoms) |
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def n_hetero(mol): |
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""" The number of heteroatoms. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return rdMolDescriptors.CalcNumHeteroatoms(mol) |
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def n_heavy(mol): |
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""" The number of heavy atoms. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return mol.GetNumHeavyAtoms() |
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def n_terminal(mol): |
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""" The number of heavy atoms. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return mol.atoms.is_terminal.sum() |
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@requires_h_filled |
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def n_bonds(mol): |
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""" The number of bonds. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return len(mol.bonds) |
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@requires_h_depleted |
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def n_bonds_non_h(mol): |
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""" The number of bonds between atoms other than hydrogen. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return len(mol.bonds) |
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@requires_h_depleted |
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def n_bonds_multiple(mol): |
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""" The number of multiple bonds. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return (mol.bonds.order > 1).sum() |
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@requires_h_depleted |
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def sum_of_conventional_bond_orders(mol): |
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""" The sum of conventional bond orders (h-depleted). |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return mol.bonds.order.sum() |
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def n_rotatable_bonds(mol): |
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""" The number of rotatable bonds. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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int |
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""" |
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return rdMolDescriptors.CalcNumRotatableBonds(mol) |
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@requires_h_depleted |
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def fract_rotatable_bonds(mol): |
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# TODO: memoize |
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""" The fraction of rotatable bonds. |
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Args: |
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mol (skchem.Mol): |
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The molecule for which to calculate the descriptor. |
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Returns: |
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float |
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""" |
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return n_rotatable_bonds(mol) / n_bonds(mol) |
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@requires_h_depleted |
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def n_bond_order(mol, order=1): |
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""" The number of bonds of order *i*. |
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Args: |
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mol (skchem.Mol): |
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|
|
The molecule for which to calculate the descriptor. |
426
|
|
|
|
427
|
|
|
order (int): |
428
|
|
|
The order of bonds. |
429
|
|
|
Returns: |
430
|
|
|
int |
431
|
|
|
""" |
432
|
|
|
return (mol.bonds.order == order).sum() |
433
|
|
|
|
434
|
|
|
|
435
|
1 |
|
def fract_c_hybrid(mol, h_state='SP3'): |
436
|
|
|
|
437
|
|
|
""" The fraction of carbons that are in a certain hybridization state. |
438
|
|
|
|
439
|
|
|
Args: |
440
|
|
|
mol (skchem.Mol): |
441
|
|
|
The molecule for which to calculate the descriptor. |
442
|
|
|
|
443
|
|
|
h_state (str): |
444
|
|
|
The hybridization state for which to measure the fraction. |
445
|
|
|
Returns: |
446
|
|
|
float |
447
|
|
|
""" |
448
|
|
|
|
449
|
|
|
carbs = mol.atoms.atomic_number == 6 |
450
|
|
|
return (mol.atoms.hybridization_state == h_state)[carbs].sum() / carbs.sum() |
451
|
|
|
|
452
|
|
|
|
453
|
1 |
|
def n_disconnected(mol): |
454
|
|
|
|
455
|
|
|
""" The number of disconnected fragments in the mol. |
456
|
|
|
|
457
|
|
|
Args: |
458
|
|
|
mol (skchem.Mol): |
459
|
|
|
The molecule for which to calculate the descriptor. |
460
|
|
|
|
461
|
|
|
Returns: |
462
|
|
|
int |
463
|
|
|
""" |
464
|
|
|
|
465
|
|
|
return len(rdmolops.GetMolFrags(mol)) |
466
|
|
|
|
467
|
|
|
|
468
|
1 |
|
def total_charge(mol): |
469
|
|
|
|
470
|
|
|
""" The total charge of the molecule. |
471
|
|
|
|
472
|
|
|
Args: |
473
|
|
|
mol (skchem.Mol): |
474
|
|
|
The molecule for which to calculate the descriptor. |
475
|
|
|
|
476
|
|
|
Returns: |
477
|
|
|
float |
478
|
|
|
""" |
479
|
|
|
|
480
|
|
|
return mol.atoms.formal_charge.sum() |
481
|
|
|
|
482
|
|
|
|
483
|
1 |
|
def n_hba(mol): |
484
|
|
|
|
485
|
|
|
""" The number of h bond acceptors. |
486
|
|
|
|
487
|
|
|
Args: |
488
|
|
|
mol (skchem.Mol): |
489
|
|
|
The molecule for which to calculate the descriptor. |
490
|
|
|
|
491
|
|
|
Returns: |
492
|
|
|
float |
493
|
|
|
""" |
494
|
|
|
return rdMolDescriptors.CalcNumHBA(mol) |
495
|
|
|
|
496
|
|
|
|
497
|
1 |
|
def n_hba(mol): |
|
|
|
|
498
|
|
|
|
499
|
|
|
""" The number of h bond donors. |
500
|
|
|
|
501
|
|
|
Args: |
502
|
|
|
mol (skchem.Mol): |
503
|
|
|
The molecule for which to calculate the descriptor. |
504
|
|
|
|
505
|
|
|
Returns: |
506
|
|
|
float |
507
|
|
|
""" |
508
|
|
|
return rdMolDescriptors.CalcNumHBD(mol) |
509
|
|
|
|
510
|
|
|
|
511
|
1 |
|
def n_radical_electrons(mol): |
512
|
|
|
|
513
|
|
|
""" The number of radical electrons. |
514
|
|
|
|
515
|
|
|
Args: |
516
|
|
|
mol (skchem.Mol): |
517
|
|
|
The molecule for which to calculate the descriptor. |
518
|
|
|
|
519
|
|
|
Returns: |
520
|
|
|
float |
521
|
|
|
""" |
522
|
|
|
return Descriptors.NumRadicalElectrons(mol) |
523
|
|
|
|
524
|
|
|
|
525
|
1 |
|
def n_valence_electrons(mol): |
526
|
|
|
|
527
|
|
|
""" The number of valence electrons. |
528
|
|
|
|
529
|
|
|
Args: |
530
|
|
|
mol (skchem.Mol): |
531
|
|
|
The molecule for which to calculate the descriptor. |
532
|
|
|
|
533
|
|
|
Returns: |
534
|
|
|
float |
535
|
|
|
""" |
536
|
|
|
|
537
|
|
|
return Descriptors.NumValenceElectrons(mol) |
538
|
|
|
|
539
|
|
|
|
540
|
1 |
|
def heavy_atom_mol_wt(x): |
|
|
|
|
541
|
|
|
|
542
|
|
|
""" The molecular weight of only heavy atoms. |
543
|
|
|
|
544
|
|
|
Args: |
545
|
|
|
mol (skchem.Mol): |
546
|
|
|
The molecule for which to calculate the descriptor. |
547
|
|
|
|
548
|
|
|
Returns: |
549
|
|
|
float |
550
|
|
|
""" |
551
|
|
|
|
552
|
|
|
return rdMolDescriptors.CalcExactMolWt(x, True) |
553
|
|
|
|
554
|
|
|
|
555
|
1 |
|
def n_hbd_lipinski(x): |
|
|
|
|
556
|
|
|
|
557
|
|
|
""" The number of hydrogen bond donors according to Lipinski.""" |
558
|
|
|
|
559
|
|
|
return rdMolDescriptors.CalcNumLipinskiHBD(x) |
560
|
|
|
|
561
|
|
|
|
562
|
1 |
|
def n_hba_lipinski(x): |
|
|
|
|
563
|
|
|
|
564
|
|
|
""" The number of hydrogen bond acceptors according to Lipinski.""" |
565
|
|
|
|
566
|
|
|
return rdMolDescriptors.CalcNumLipinskiHBA(x) |
567
|
|
|
|
568
|
|
|
|
569
|
1 |
|
@requires_h_depleted |
570
|
1 |
|
def n_paths(mol, length=1): |
571
|
|
|
|
572
|
|
|
""" The number of paths of length *l*. """ |
573
|
|
|
|
574
|
|
|
return len(rdmolops.FindAllPathsOfLengthN(mol, length)) |
575
|
|
|
|
576
|
|
|
|
577
|
1 |
|
DESCRIPTORS = OrderedDict(( |
578
|
|
|
('mol_wt', molecular_weight), |
579
|
|
|
('avg_mol_wt', average_molecular_weight), |
580
|
|
|
('sum_vdw_vol', sum_van_der_waals_volume), |
581
|
|
|
('sum_eneg', sum_electronegativity), |
582
|
|
|
('sum_pol', sum_polarisability), |
583
|
|
|
('sum_ion_energy', sum_ionisation_energy), |
584
|
|
|
('mean_vdw_vol', mean_van_der_waals_volume), |
585
|
|
|
('mean_eneg', mean_electronegativity), |
586
|
|
|
('mean_pol', mean_polarisability), |
587
|
|
|
('mean_ion_energy', mean_ionisation_energy), |
588
|
|
|
('graph_density', graph_density), |
589
|
|
|
('n_atoms', n_atoms), |
590
|
|
|
('n_term', n_terminal), |
591
|
|
|
('n_bonds', n_bonds), |
592
|
|
|
('n_bonds_non_h', n_bonds_non_h), |
593
|
|
|
('n_bonds_mult', n_bonds_multiple), |
594
|
|
|
('sum_bond_order', sum_of_conventional_bond_orders), |
595
|
|
|
('n_rot_bonds', n_rotatable_bonds), |
596
|
|
|
('fract_rot_bonds', fract_rotatable_bonds), |
597
|
|
|
('n_hyd', n_hyd), |
598
|
|
|
('n_halo', n_halo), |
599
|
|
|
('n_heavy', n_heavy), |
600
|
|
|
('n_hetero', n_hetero), |
601
|
|
|
('n_hba', n_hba), |
602
|
|
|
('n_atoms', n_atoms), |
603
|
|
|
('fract_halo', fract_halo), |
604
|
|
|
('n_disconn', n_disconnected), |
605
|
|
|
('total_charge', total_charge), |
606
|
|
|
('n_rad', n_radical_electrons), |
607
|
|
|
('n_val', n_valence_electrons), |
608
|
|
|
('heavy_mol_wt', heavy_atom_mol_wt), |
609
|
|
|
('n_hbd_lip', n_hbd_lipinski), |
610
|
|
|
('n_hba_lib', n_hba_lipinski) |
611
|
|
|
)) |
612
|
|
|
|
613
|
1 |
|
SYMBOLS = ('C', 'N', 'O', 'P', 'S', 'F', 'Cl', 'Br', 'I', 'B') |
614
|
1 |
|
HYBRIDS = ('SP3', 'SP2', 'SP') |
615
|
|
|
|
616
|
1 |
|
DESCRIPTORS.update(('fract_c_{}'.format(hybrid), partial(fract_c_hybrid, |
617
|
|
|
h_state=hybrid)) |
618
|
|
|
for hybrid in HYBRIDS) |
619
|
|
|
|
620
|
1 |
|
DESCRIPTORS.update((('n_{}'.format(symbol), partial(n_atom, symbol=symbol)) |
621
|
|
|
for symbol in SYMBOLS)) |
622
|
|
|
|
623
|
1 |
|
DESCRIPTORS.update((('n_{}'.format(symbol), partial(fract_atom, symbol=symbol)) |
624
|
|
|
for symbol in ('H', 'C', 'N', 'O'))) |
625
|
|
|
|
626
|
1 |
|
DESCRIPTORS.update((('n_bond_{}'.format(order), partial(n_bond_order, |
627
|
|
|
order=order)) |
|
|
|
|
628
|
|
|
for order in (1, 1.5, 2, 3))) |
629
|
|
|
|
630
|
1 |
|
DESCRIPTORS.update((('n_paths_{}'.format(length), partial(n_paths, length=length)) |
631
|
|
|
for length in range(1, 7))) |
632
|
|
|
|
This can be caused by one of the following:
1. Missing Dependencies
This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands.
2. Missing __init__.py files
This error could also result from missing
__init__.py
files in your module folders. Make sure that you place one file in each sub-folder.