Define set_rdkit_ring_dihedrals and make test
#767
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## main #767 +/- ##
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+ Coverage 74.09% 74.12% +0.03%
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Files 101 101
Lines 28005 28038 +33
Branches 5860 5863 +3
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+ Hits 20751 20784 +33
Misses 5786 5786
Partials 1468 1468
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@JintaoWu98, what's the status of this PR? I don't see the new function being used, would you like to wait with it? |
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| return num_comb | |||
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| def plot_ring_torsion_angles(conformers, plot_path=None, tolerance=15): | |||
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| os.makedirs(plot_path) | ||
| try: | ||
| plt.savefig(ring_plot_path, bbox_inches='tight') | ||
| except FileNotFoundError: |
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| torsion_0_indexed = [[tor - 0 for tor in sub_torsion] for sub_torsion in torsion] | ||
| ring_length = len(torsion_0_indexed) | ||
| head = torsion_0_indexed[0][0] | ||
| for torsion in torsion_0_indexed: |
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| # Remove the bond to open the ring | ||
| rd_mol_noH = Chem.RWMol(rd_mol_noH) | ||
| rd_mol_noH.RemoveBond(atom_map[ring_head], atom_map[ring_tail]) |
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| rdMT.SetDihedralDeg(conf_noH, *torsion_noH, dihedral) | ||
| # Re-add the bond to close the ring | ||
| rd_mol_noH.AddBond( | ||
| atom_map[ring_head], atom_map[ring_tail], rd_mol.GetBondBetweenAtoms(ring_head, ring_tail).GetBondType() |
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| mol = b_mol if b_mol is not None else s_mol | ||
| _, rd_mol = converter.rdkit_conf_from_mol(mol, xyz_original) | ||
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| xyz_final = converter.set_rdkit_ring_dihedrals(rd_mol, ring_head, ring_tail, torsions, dihedrals) |
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| if plot_path is not None: | ||
| arc.plotter.plot_torsion_angles(torsion_angles, torsions_sampling_points, wells_dict=wells_dict, | ||
| plot_path=plot_path) | ||
| ring_angle_data = arc.plotter.plot_ring_torsion_angles(conformers=conformers, plot_path=plot_path) | ||
| # Process the ring angle data | ||
| if ring_angle_data: |
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This PR introduces a new helper function,
set_rdkit_ring_dihedrals, to theconverter.pymodule. This function allows for setting dihedral angles in a ring structure using RDKit, facilitating the manipulation of molecular conformations.