9. scoria.Selections module

class scoria.Selections.Selections(parent_molecule_object)

A class for selecting atoms. Subclass to the scoria.Molecule class.

get_molecule_from_selection(selection, serial_reindex=True, resseq_reindex=False)

Creates a scoria.Molecule from a user-defined atom selection.

Should be called via the wrapper function get_molecule_from_selection().

Parameters:

• selection (numpy.array) – A numpy.array containing the indices of the atoms in the user-defined selection.
• serial_reindex (bool) – An optional boolean, whether or not to reindex the atom serial fields. Default is True.
• resseq_reindex (bool) – An optional boolean, whether or not to reindex the atom resseq fields. Default is False.

Returns:

A scoria.Molecule object containing the atoms of the user-defined selection.

invert_selection(selection)

Inverts a user-defined selection (i.e., identifies all atoms that are not in the seleciton).

Should be called via the wrapper function invert_selection().

Parameters:selection (numpy.array) – A numpy.array containing the indices of the user-defined selection. Returns:A numpy.array containing the indices of all atoms that are not in the user-defined seleciton.

select_all()

Selects all the atoms in a scoria.Molecule object.

Should be called via the wrapper function select_all().

Returns:A numpy.array containing the indices of all atoms in the scoria.Molecule object.

select_all_atoms_bound_to_selection(selection)

Selects all the atoms that are bound to a user-specified selection.

Requires the numpy library.

Should be called via the wrapper function select_all_atoms_bound_to_selection().

Parameters:selection (numpy.array) – A numpy.array containing the indices of the user-specified selection. Returns:A numpy.array containing the indices of the atoms that are bound to the user-specified selection. Note that this new selection does not necessarily include the indices of the original user-specified selection.

select_atoms(selection_criteria)

Select a set of atoms based on user-specified criteria.

Should be called via the wrapper function select_atoms().

Parameters:selection_criteria (dict) – A dictionary, where the keys correspond to keys in the self.__parent_Information.Information.get_atom_information() structured numpy array, and the values are lists of acceptable matches. The selection is a logical “AND” between dictionary entries, but “OR” within the value lists themselves. For example: {‘atom’:[‘CA’, ‘O’], ‘chain’:’A’, ‘resname’:’PRO’} would select all atoms with the names CA or O that are located in the PRO residues of chain A. Returns:A numpy.array containing the indices of the atoms of the selection.

select_atoms_from_same_molecule(selection)

Selects all the atoms that belong to the same molecule as a user-defined selection, assuming that the scoria.Molecule object actually contains multiple physically distinct molecules that are not bound to each other via covalent bonds.

Requires the numpy library.

Should be called via the wrapper function select_atoms_from_same_molecule().

Parameters:selection (numpy.array) – A numpy.array containing the indices of the user-defined selection. Returns:A numpy.array containing the indices of the atoms belonging to the same molecules as the atoms of the user-defined selection.

select_atoms_in_bounding_box(bounding_box)

Selects all the atoms that are within a bounding box.

Requires the numpy library.

Should be called via the wrapper function select_atoms_in_bounding_box().

Parameters:bounding_box (numpy.array) – A 2x3 numpy.array containing the minimum and maximum points of the bounding box. Example: numpy.array( [[min_x, min_y, min_z], [max_x, max_y, max_z]] ). Returns:A numpy.array containing the indices of the atoms that are within the bounding box.

select_atoms_in_same_residue(selection)

Selects all atoms that are in the same residue as any of the atoms of a user-defined seleciton. Residues are considered unique if they have a unique combination of resname, resseq, and chainid fields.

Should be called via the wrapper function select_atoms_in_same_residue().

Parameters:selection (numpy.array) – A numpy.array containing the indices of the user-defined selection. Returns:A numpy.array containing the indices of all atoms in the same residue as any of the atoms of the user-defined selection.

select_atoms_near_other_selection(selection, cutoff)

Selects all atoms that are near the atoms of a user-defined selection.

Requires the numpy and scipy libraries.

Should be called via the wrapper function select_atoms_near_other_selection().

Parameters:

• selection (numpy.array) – A numpy.array containing the indices of the user-defined selection.
• cutoff (float) – A float, the distance cutoff (in Angstroms).

Returns:

A numpy.array containing the indices of all atoms near the user-defined selection, not including the atoms of the user-defined selection themselves.

select_branch(root_atom_index, directionality_atom_index)

Identify an isolated “branch” of a molecular model. Assumes the atoms with indices root_atom_index and directionality_atom_index are bound to one another and that the branch starts at root_atom_index one and “points” in the direction of directionality_atom_index.

Requires the numpy library.

Should be called via the wrapper function select_branch().

Parameters:

• root_atom_index (int) – An int, the index of the first atom in the branch (the “root”).
• directionality_atom_index (int) – An int, the index of the second atom in the branch, used to establish directionality

Returns:

A numpy array containing the indices of the atoms of the branch.

select_close_atoms_from_different_molecules(other_mol, cutoff, pairwise_comparison=True, terminate_early=False)

Effectively detects steric clashes between self and another pymolecule.Molecule.

Requires the numpy and scipy libraries.

Should be called via the wrapper function select_close_atoms_from_different_molecules().

Parameters:

• other_mol (pymolecule.Molecule) – A pymolecule.Molecule object of the other molecule.
• cutoff (float) – A float, the user-defined distance cutoff in Angstroms.
• pairwise_comparison (bool) – An optional boolean, whether or not to perform a simple pairwise distance comparison (if True) or to use a more sophisitcated method (if False). True by default.
• terminate_early (bool) – An optional boolean, whether or not to stop looking for steric clashes once one is found. False by default.

Returns:

A tuple containing two elements. The first is a numpy.array containing the indices of all nearby atoms from this pymolecule.Molecule object (self). The second is a numpy.array containing the indices of all nearby atoms from the other molecule.

selections_of_chains()

Identifies the atom selections of each chain.

Requires the numpy library.

Should be called via the wrapper function selections_of_chains().

Returns:A dictionary. The keys of the dictionary correspond to the chainids, and the values are numpy.array objects containing the indices of the associated chain atoms.

selections_of_constituent_molecules()

Identifies the indices of atoms belonging to separate molecules, assuming that the pymolecule.Molecule object actually contains multiple physically distinct molecules that are not bound to each other via covalent bonds.

Requires the numpy library.

Should be called via the wrapper function selections_of_constituent_molecules().

Returns:A python list of numpy.array objects containing the indices of the atoms belonging to each molecule of the composite pymolecule.Molecule object.

selections_of_residues()

Identifies the atom selections of each residue.

Requires the numpy library.

Should be called via the wrapper function selections_of_residues().

Returns:A dictionary. The keys of this dictionary correspond to the unique resname-resseq-chainid residue identifiers, and the values are numpy.array objects containing the indices of the associated residue atoms.