molecool_test

short description of molecool_test.

A Python package for analyzing and visualizing xyz files. For MolSSI Workshop Python Package development workshop.

Subpackages

• molecool_test.io
  • molecool_test.io.pdb
  • molecool_test.io.xyz

Submodules

• molecool_test.atom_data
• molecool_test.functions
• molecool_test.measure
• molecool_test.molecule
• molecool_test.visualize

Package Contents

Functions

calculate_distance(rA, rB)	Calculate the distance between two points.
calculate_angle(rA, rB, rC, degrees=False)
build_bond_list(coordinates, max_bond=1.5, min_bond=0)	Build a list of bonds in a set of coordinates based on a distance criteria.
calculate_molecular_mass(symbols)	Calculate the mass of a molecule.
calculate_center_of_mass(symbols, coordinates)	Calculate the center of mass of a molecule.
draw_molecule(coordinates, symbols, draw_bonds=None, save_location=None, dpi=300)
bond_histogram(bond_list, save_location=None, dpi=300, graph_min=0, graph_max=2)
open_pdb(file_location)	Open and read coordinates and atom symbols from a pdb file.
open_xyz(file_location)
write_xyz(file_location, symbols, coordinates)

Attributes

versions

molecool_test.calculate_distance(rA, rB)

Calculate the distance between two points.

Parameters

rA, rB (np.ndarray) – The coordinates of each point.

Returns

distance – The distance between the two points.

Return type

float

Examples

>>> r1 = np.array([0, 0, 0])
>>> r2 = np.array([0, 0.1, 0])
>>> calculate_distance(r1, r2)
0.1

molecool_test.calculate_angle(rA, rB, rC, degrees=False)

molecool_test.build_bond_list(coordinates, max_bond=1.5, min_bond=0)

Build a list of bonds in a set of coordinates based on a distance criteria.

Parameters

• coordinates (np.ndarray) – The coordinates of the atoms to analyze in an (natoms, ndim) array.

• max_bond (float, optional) – The maximum distance for two atoms to be considered bonded.

• min_bond (float, optional) – The minimum distance for two atoms to be considered bonded.

Returns

bonds – A dictionary containing bonded atoms with atom pairs as keys and the distance between the atoms as the value.

Return type

dict

molecool_test.calculate_molecular_mass(symbols)

Calculate the mass of a molecule.

Parameters

symbols (list) – A list of elements.

Returns

mass – The mass of the molecule

Return type

float

molecool_test.calculate_center_of_mass(symbols, coordinates)

Calculate the center of mass of a molecule.

The center of mass is weighted by each atom’s weight.

Parameters

• symbols (list) – A list of elements for the molecule

• coordinates (np.ndarray) – The coordinates of the molecule.

Returns

center_of_mass – The center of mass of the molecule.

Return type

np.ndarray

Notes

The center of mass is calculated with the formula

\[\vec{R}=\frac{1}{M} \sum_{i=1}^{n} m_{i}\vec{r_{}i}\]

molecool_test.draw_molecule(coordinates, symbols, draw_bonds=None, save_location=None, dpi=300)

molecool_test.bond_histogram(bond_list, save_location=None, dpi=300, graph_min=0, graph_max=2)

molecool_test.open_pdb(file_location)

Open and read coordinates and atom symbols from a pdb file.

The pdb file must specify the atom elements in the last column, and follow the conventions outlined in the PDB format specification.

Parameters

file_location (str) – The location of the pdb file to read in.

Returns

• coords (np.ndarray) – The coordinates of the pdb file.

• symbols (list) – The atomic symbols of the pdb file.

molecool_test.open_xyz(file_location)

molecool_test.write_xyz(file_location, symbols, coordinates)

molecool_test.versions