xyz-py 0.0.13

A package for manipulating xyz files and chemical structures

xyz-py

xyz-py is a python module for working with and manipulating chemical structures.

Installation

For convenience, xyz-py is available on PyPI and so can be installed using pip

pip install xyz-py

Functionality

To use the functions included in xyz-py, first import it into your python file

import xyz_py as xyzp

and then call them as

xyzp.function_name(arguments)

To find information on any of the functions included in xyz-py, use the help command from within a python environment, e.g.

help(xyzp.function_name)

List of functions

A brief descriptions of functions:

load_xyz

Loads labels and coordinates from xyz file

save_xyz

Save labels and coordinates to xyz file

remove_numbers

Remove indexing numbers from a set of atomic labels

add_numbers

Add indexing numbers to a set of atomic labels

count_elements

Count number of each element in a list of elements

formstr_to_formdict

Converts formula string into dictionary of {atomic label:quantity} pairs

formdict_to_formstr

Converts dictionary of {atomic label:quantity} pairs into a single formula string

contains_metal

Returns 1 if metal found in formula string else returns a 0

combine_xyz

Combines two sets of labels and coordinates

get_neighborlist

Calculate ASE neighbourlist with cutoffs

get_adjacency

Calculate adjacency matrix using ASE neighbourlist

get_bonds

Calculate and save list of atoms between which there is a bond using ASE. Only unique bonds are saved.

get_angles

Calculate and save list of atoms between which there is an angle using ASE. Only unique angles are saved.

get_dihedrals

Calculate and save list of atoms between which there is a dihedral using ASE. Only unique dihedrals are saved.

lab_to_num

Convert atomic label to atomic number

num_to_lab

Convert atomic number to atomic label

reflect_coords

Reflect coordinates through XY plane

remove_broken

Removes structures from coordinates which do not match user provided formulae

calculate_rmsd

Calculates RMSD (root mean square deviation) between two structures

rotate_coords

Rotates coordinates by alpha, beta, gamma using the zyz convention

minimise_rmsd

Minimises RMSD between two structures by rotating one onto the other