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.

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.

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

schrodinger.protein.pdbname.recurse_neighbors(at: StructureAtom, residue_atoms: set[StructureAtom], atoms_to_assign: set[StructureAtom], excluded_atoms: set[StructureAtom]) → None

Recursively collect bonded neighbor atoms into residue_atoms, traversing the molecular graph outward from at. Neighbors are included only if they are in atoms_to_assign and not already in residue_atoms or excluded_atoms.

Parameters:

  • at – The atom from which to start traversal.

  • residue_atoms – The set of atoms collected so far; updated in place.

  • atoms_to_assign – The set of atoms eligible for assignment.

  • excluded_atoms – a set of atoms to exclude from traversal.

schrodinger.protein.pdbname.find_ace_cap_atoms(mol: Mol, rdk_idx_to_st_atom: dict[int, StructureAtom], atoms_to_assign: set[StructureAtom], backbone_atoms: set[StructureAtom]) → set[StructureAtom]

Find all ACE cap atoms in the given molecule.

Parameters:

  • mol – The RDKit Mol on which to search for ACE cap atoms.

  • rdk_idx_to_st_atom – A mapping from RDKit atom index to structure atom.

  • atoms_to_assign – The set of structure atoms to consider.

  • backbone_atoms – The set of backbone atoms in the molecule.

Returns:

The set of ACE cap atoms.

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 number of consecutive residues to be considered a backbone. By default, mono and dipeptides will be ignored.

schrodinger.protein.pdbname.renumber_residues(struct, chains, start_resnum=1)

Renumber all residues to have a unique residue number and have residue numbers that are contiguous.

Parameters:

  • struct (list[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.

schrodinger.protein.pdbname.process_structure(struct: Structure, renumber_chains: list[str] | str | None = None, assign_bond_orders: bool = False) → None

High-level PDB processing workflow: add hydrogens and assign PDB names, optionally renumbering the residues and assigning bond orders.

Parameters:

  • struct – structure to process; modified in-place.

  • renumber_chains – optional list of chain IDs to renumber, or the string “all” to renumber every chain.

  • assign_bond_orders – use this option when reading in a structure without bond orders, or when reading a PDB file with non-standard atom names that does not have CONNECT records for those atoms.