Molecule

Molecule()

Loads, saves, and manipulates molecular models. The main pymolecule class.

Initializes the variables of the Molecule class.

atoms_and_bonds = AtomsAndBonds(self) instance-attribute

geometry = Geometry(self) instance-attribute

information = Information(self) instance-attribute

io = FileIO(self) instance-attribute

manipulation = Manipulation(self) instance-attribute

other_molecule = OtherMolecules(self) instance-attribute

selections = Selections(self) instance-attribute

__is_number(s)

Determines whether or not a string represents a number.

PARAMETER	DESCRIPTION
s	A string (e.g., "5.4").

RETURNS	DESCRIPTION
	A boolean, whether or not the string can be represented by a float.

numpy_structured_array_remove_field(narray, field_names)

Removes a specific field name from a structured numpy array.

PARAMETER	DESCRIPTION
narray	A structured numpy array.
field_names	A list of strings, where each string is one of the field names of narray.

RETURNS	DESCRIPTION
	A structured numpy array identical to narray, but with the field names in field_names removed.

Selections(parent_molecule_object)

A class for selecting atoms

Initializes the pymolecule.Selections class.

PARAMETER	DESCRIPTION
parent_molecule_object	The pymolecule.Molecule object associated with this class.

parent_molecule = parent_molecule_object instance-attribute

copy()

Returns an exact copy (pymolecule.Molecule) of this Molecule object. Undo points are NOT copied.

RETURNS	DESCRIPTION
	A pymolecule.Molecule, containing to the same atomic information as this pymolecule.Molecule object.

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

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

PARAMETER	DESCRIPTION
selection	A np.array containing the indices of the atoms in the user-defined selection.
serial_reindex	An optional boolean, whether or not to reindex the atom serial fields. Default is True. DEFAULT: True
resseq_reindex	An optional boolean, whether or not to reindex the atom resseq fields. Default is False. DEFAULT: False

RETURNS	DESCRIPTION
	A pymolecule.Molecule object containing the atoms of the user-defined selection.

get_chain_selections()

Identifies the atom selections of each chain.

RETURNS	DESCRIPTION
	A dictionary. The keys of the dictionary correspond to the chainids, and the values are np.array objects containing the indices of the associated chain atoms.

get_molecule_from_selection(selection)

Creates a Molecule from a user-defined atom selection.

PARAMETER	DESCRIPTION
selection	A np.array containing the indices of the atoms in the user-defined selection.

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

get_residue_selections()

Identifies the atom selections of each residue.

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

get_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.

RETURNS	DESCRIPTION
	A python list of np.array objects containing the indices of the atoms belonging to each molecule of the composite pymolecule.Molecule object.

invert_selection(selection)

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

PARAMETER	DESCRIPTION
selection	A np.array containing the indices of the user-defined selection.

RETURNS	DESCRIPTION
	A np.array containing the indices of all atoms that are not in the user-defined seleciton.

select_all()

Selects all the atoms in a pymolecule.Molecule object.

RETURNS	DESCRIPTION
	A np.array containing the indices of all atoms in the pymolecule.Molecule object.

select_all_atoms_bound_to_selection(selection)

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

PARAMETER	DESCRIPTION
selection	A np.array containing the indices of the user-specified selection.

RETURNS	DESCRIPTION
	A np.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.

PARAMETER

DESCRIPTION

selection_criteria

An dictionary, where the keys correspond to keys in the self.parent_molecule.information.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	DESCRIPTION
	A np.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 pymolecule.Molecule object actually contains multiple physically distinct molecules that are not bound to each other via covalent bonds.

PARAMETER	DESCRIPTION
selection	A np.array containing the indices of the user-defined selection.

RETURNS	DESCRIPTION
	A np.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.

PARAMETER	DESCRIPTION
bounding_box	A 2x3 np.array containing the minimum and maximum points of the bounding box. Example: np.array([[min_x, min_y, min_z], [max_x, max_y, max_z]]).

RETURNS	DESCRIPTION
	A np.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.

PARAMETER	DESCRIPTION
selection	A np.array containing the indices of the user-defined selection.

RETURNS	DESCRIPTION
	A np.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.

PARAMETER	DESCRIPTION
selection	A np.array containing the indices of the user-defined selection.
cutoff	A float, the distance cutoff (in Angstroms).

RETURNS	DESCRIPTION
	A np.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.

PARAMETER	DESCRIPTION
root_atom_index	An int, the index of the first atom in the branch (the "root").
directionality_atom_index	An int, the index of the second atom in the branch, used to establish directionality

RETURNS	DESCRIPTION
	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.

PARAMETER	DESCRIPTION
other_mol	A pymolecule.Molecule object of the other molecule.
cutoff	A float, the user-defined distance cutoff in Angstroms.
pairwise_comparison	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. DEFAULT: True

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