[compute_contacts] new option for optarg scheme="backbone", tests added #1832
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Hi 👋 @sukritsingh greetings from Berlin! |
sukritsingh
reviewed
Nov 14, 2023
mdtraj/geometry/contact.py
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| if scheme not in ['ca', 'closest', 'closest-heavy', 'sidechain', 'sidechain-heavy']: | ||
| raise ValueError('scheme must be one of [ca, closest, closest-heavy, sidechain, sidechain-heavy]') | ||
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| if scheme not in ['ca', 'closest', 'closest-heavy', 'sidechain', 'sidechain-heavy', "backbone"]: |
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Probably good to use single quotes here for backbone to keep it consistent with the rest of the options (looks like double quotes used)
sukritsingh
reviewed
Nov 14, 2023
mdtraj/geometry/contact.py
Outdated
| @@ -181,7 +184,7 @@ def compute_contacts(traj, contacts='all', scheme='closest-heavy', ignore_nonpro | |||
| distances = md.compute_distances(traj, atom_pairs, periodic=periodic) | |||
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| elif scheme in ['closest', 'closest-heavy', 'sidechain', 'sidechain-heavy']: | |||
| elif scheme in ['closest', 'closest-heavy', 'sidechain', 'sidechain-heavy', "backbone"]: | |||
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As above - change to single quotes
sukritsingh
reviewed
Nov 14, 2023
mdtraj/geometry/contact.py
Outdated
| @@ -192,6 +195,9 @@ def compute_contacts(traj, contacts='all', scheme='closest-heavy', ignore_nonpro | |||
| elif scheme == 'sidechain': | |||
| residue_membership = [[atom.index for atom in residue.atoms if atom.is_sidechain] | |||
| for residue in traj.topology.residues] | |||
| elif scheme == "backbone": | |||
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change to single quotes
sukritsingh
reviewed
Nov 14, 2023
| @@ -38,23 +38,27 @@ def test_contact_0(get_fn): | |||
| closest_heavy, closest_heavy_pairs = md.compute_contacts(pdb, contacts, scheme='closest-heavy') | |||
| sidechain, sidechain_pairs = md.compute_contacts(pdb, contacts, scheme='sidechain') | |||
| sidechain_heavy, sidechain_heavy_pairs = md.compute_contacts(pdb, contacts, scheme='sidechain-heavy') | |||
| backbone, backbone_pairs = md.compute_contacts(pdb,contacts,scheme="backbone") | |||
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change to single quotes
sukritsingh
reviewed
Nov 14, 2023
tests/test_contact.py
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| ref_ca = np.loadtxt(get_fn('cc_ca.dat')) | ||
| ref_closest = np.loadtxt(get_fn('cc_closest.dat')) | ||
| ref_closest_heavy = np.loadtxt(get_fn('cc_closest-heavy.dat')) | ||
| ref_sidechain = np.loadtxt(get_fn('cc_sidechain.dat')) | ||
| ref_sidechain_heavy = np.loadtxt(get_fn('cc_sidechain-heavy.dat')) | ||
| ref_backbone = np.loadtxt(get_fn("backbone.dat")) |
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maybe rename the file to cc_backbone.dat for consistency with the other filenames?
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This is a nice addition to the I added some minor comments/edits to keep things consistent with the rest of the code, but the rest of it looks good! |
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Adds option
scheme="backbone"for md.compute contactsAdds tests and one test file
backbone.datcreated like this: