2. The AtomsAndBonds Class

2.1. Rationale of the AtomsAndBonds functions

The functions within the AtomsAndBonds framework all involve the addition, deletion, and manipulation of individual atoms and their bonds within the molecular framework.

2.1.1. Other Classes

To make modifications to the coordinate set of all atoms, use the functions within the Manipulation class. To look at groups of atoms with similar properties, use the functions within the Selections class.

2.2. Function Definitions

class scoria.AtomsAndBonds.AtomsAndBonds(parent_molecule_object)

A class for adding and deleting atoms and bonds. Subclass to the scoria.Molecule class.

add_atom(record_name='ATOM', serial=1, name='X', resname='XXX', chainid='X', resseq=1, occupancy=0.0, tempfactor=0.0, charge='', element='X', coordinates=array([ 0., 0., 0.]), autoindex=True)

Adds an atom.

Should be called via the wrapper function add_atom().

Parameters:
  • record_name (str) – An optional string, the record name of the atom. “ATOM” is the default.
  • serial (int) – An optional int, the serial field of the atom. 1 is the default.
  • name (str) – An optional string, the name of the atom. ‘X’ is the default.
  • resname (str) – An optional string, the resname of the atom. ‘XXX’ is the default.
  • chainid (str) – An optional string, chainid of the atom. ‘X’ is the default.
  • resseq (int) – An optional int, the resseq field of the atom. 1 is the default.
  • occupancy (float) – An optional float, the occupancy of the atom. 0.0 is the default.
  • tempfactor (float) – An optional float, the tempfactor of the atom. 0.0 is the default.
  • charge (str) – An optional string, the charge of the atom. ‘’ is the default.
  • element (str) – An optional string, the element of the atom. ‘X’ is the default.
  • coordinates (numpy.array) – An optional numpy.array, the (x, y, z) coordinates of the atom. numpy.array([0.0, 0.0, 0.0]) is the default.
add_bond(index1, index2, order=1)

Adds a bond.

Should be called via the wrapper function add_bond().

Parameters:
  • index1 (int) – An int, the index of the first atom of the bonded pair.
  • index2 (int) – An int, the index of the second atom of the bonded pair.
  • order (int) – An optional int, the order of the bond. 1 by default.
create_bonds_by_distance(remove_old_bond_data=True, delete_excessive_bonds=True)

Determines which atoms are bound to each other based on their proximity.

Requires the numpy and scipy libraries.

Should be called via the wrapper function create_bonds_by_distance().

Parameters:
  • remove_old_bond_data (bool) – An optional boolean, whether or not to discard old bond data before adding in bonds determined by distance. True by default.
  • delete_excessive_bonds (bool) – An optional boolean, whether or not to check for and delete excessive bonds. True by default.
delete_atom(index)

Deletes an atom.

Should be called via the wrapper function delete_atom().

Parameters:index (int) – An int, the index of the atom to delete.
delete_bond(index1, index2)

Deletes a bond.

Should be called via the wrapper function delete_bond().

Parameters:
  • index1 (int) – An int, the index of the first atom of the bonded pair.
  • index2 (int) – An int, the index of the second atom of the bonded pair.
get_index_of_first_bond_partner_of_element(atom_index, the_element)

For a given atom of interest, returns the index of the first neighbor of a specified element.

Requires the numpy and scipy.spatial libraries.

Should be called via the wrapper function get_index_of_first_bond_partner_of_element().

Parameters:
  • atom_index (int) – An int, the index of the atom of interest.
  • the_element (str) – A string specifying the desired element of the neighbor.
Returns:

An int, the index of the first neighbor atom of the specified element. If no such neighbor exists, returns -1.
Return type:

int
get_number_of_bond_partners_of_element(atom_index, the_element)

Counts the number of atoms of a given element bonded to a specified atom of interest.

Requires the numpy library.

Should be called via the wrapper function get_number_of_bond_partners_of_element().

Parameters:
  • atom_index (int) – An int, the index of the atom of interest.
  • the_element (str) – A string describing the element of the neighbors to be counted.
Returns:

An int, the number of neighboring atoms of the specified element.
Return type:

int