schrodinger.protein.pdbname module¶
Uses SMARTS matching to set PDB atom and residue names for a structure. Also re-numbers residues, and optionally adds bond orders.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.protein.pdbname.
find_oxt_atom
(atoms)¶ Given a list of atom objects, returns the OT atom (oxygen of the -COOH) bound to the C-termini atom of the group. If no such atom is found, None is returned.
TODO: Extend to include other termini atoms.
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schrodinger.protein.pdbname.
find_n1_atom
(atoms)¶ Given a list of atoms, returns the N1 atom (N-terminus backbone nitrogen). If no such atom is found, None is returned. This function only works when the atom pdbname is properly named.
Parameters: atoms (list[schrodinger.structure._StructureAtom]) – List of atoms in which to find N1 Returns: The N1 atom Return type: schrodinger.structure._StructureAtom
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schrodinger.protein.pdbname.
recurse_neighbors
(at, residue_atoms, atoms_to_assign, labeled_atoms, backbone_atoms)¶
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schrodinger.protein.pdbname.
assign_pdb_names
(st, *, selected_residues=None, rename_residues=True, rename_atoms=True, resolve_his=False, backbone_detection_size=3)¶ Assign PDB residue and/or atom names to struct. This is based on substructure definitions for standard residues.
Notes:
- Only residues attached to a backbone chain will be assigned names.
- An attempt will be made to identify side chains for amino acids and
peptoids not in the patterns list. These will be labeled “UNK “.
- PDB atom names for multiple Hydrogens attached to the same heavy atom
will not follow the pro-R numbering rule, but instead H numbers will follow atom index order.
Parameters: - st (schrodinger.Structure) – structure on which to work.
- selected_residues (list or None) – The list of Structure._Residue objects on which the assigning will take place. If None, all the structure will be used
- rename_residues (bool) – Whether to assign PDB residue names.
- rename_atoms (bool) – Whether to assign PDB atom names.
- resolve_his (bool) – Whether HIS residues should be resolved into HID, HIE or HIP.
- backbone_detection_size (int) – minimum numner of consecutive residues to be considered a backbone. By default, mono and dipeptides will be ignored.
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schrodinger.protein.pdbname.
renumber_residues
(struct, chains)¶ Renumber all residues to have a unique residue number and have residue numbers that are contiguous.
Parameters: - struct (list[schrodinger.structure.Structure]) – The structure to operate on. This structure is modified in-place.
- chains (list or 'all') – A list of chains to renumber, or the string ‘all’ if all chains should be fixed.
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schrodinger.protein.pdbname.
process_structure
(struct, renumber_chains=None, assign_bond_orders=False)¶