Structure
AtomsAndBonds(parent_molecule_object)
¶
A class for adding and deleting atoms and bonds
Initializes the pymolecule.AtomsAndBonds class.
| PARAMETER | DESCRIPTION |
|---|---|
parent_molecule_object
|
The pymolecule.Molecule object associated with this class.
|
parent_molecule = parent_molecule_object
instance-attribute
¶
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=np.array([0.0, 0.0, 0.0]))
¶
Adds an atom.
| PARAMETER | DESCRIPTION |
|---|---|
record_name
|
An optional string, the record name of the atom. "ATOM" is the default.
DEFAULT:
|
serial
|
An optional int, the serial field of the atom. 1 is the default.
DEFAULT:
|
name
|
An optional string, the name of the atom. "X" is the default.
DEFAULT:
|
resname
|
An optional string, the resname of the atom. "XXX" is the default.
DEFAULT:
|
chainid
|
An optional string, chainid of the atom. "X" is the default.
DEFAULT:
|
resseq
|
An optional int, the resseq field of the atom. 1 is the default.
DEFAULT:
|
occupancy
|
An optional float, the occupancy of the atom. 0.0 is the default.
DEFAULT:
|
tempfactor
|
An optional float, the tempfactor of the atom. 0.0 is the default.
DEFAULT:
|
charge
|
An optional string, the charge of the atom. "" is the default.
DEFAULT:
|
element
|
An optional string, the element of the atom. "X" is the default.
DEFAULT:
|
coordinates
|
An optional np.array, the (x, y, z) coordinates of the atom. np.array([0.0, 0.0, 0.0]) is the default.
DEFAULT:
|
add_bond(index1, index2, order=1)
¶
Adds a bond.
| PARAMETER | DESCRIPTION |
|---|---|
index1
|
An int, the index of the first atom of the bonded pair.
|
index2
|
An int, the index of the second atom of the bonded pair.
|
order
|
An optional int, the order of the bond. 1 by default.
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.
| PARAMETER | DESCRIPTION |
|---|---|
remove_old_bond_data
|
An optional boolean, whether or not to discard old bond data before adding in bonds determined by distance. True by default.
DEFAULT:
|
delete_excessive_bonds
|
An optional boolean, whether or not to check for and delete excessive bonds. True by default.
DEFAULT:
|
delete_atom(index)
¶
Deletes an atom.
| PARAMETER | DESCRIPTION |
|---|---|
index
|
An int, the index of the atom to delete.
|
delete_bond(index1, index2)
¶
Deletes a bond.
| PARAMETER | DESCRIPTION |
|---|---|
index1
|
An int, the index of the first atom of the bonded pair.
|
index2
|
An int, the index of the second atom of the bonded pair.
|
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.
| PARAMETER | DESCRIPTION |
|---|---|
atom_index
|
An int, the index of the atom of interest.
|
the_element
|
A string specifying the desired element of the neighbor.
|
| RETURNS | DESCRIPTION |
|---|---|
|
An int, the index of the first neighbor atom of the specified element. If no such neighbor exists, returns -1. |
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.
| PARAMETER | DESCRIPTION |
|---|---|
atom_index
|
An int, the index of the atom of interest.
|
the_element
|
A string describing the element of the neighbors to be counted.
|
| RETURNS | DESCRIPTION |
|---|---|
|
An int, the number of neighboring atoms of the specified element. |