Metadata-Version: 2.1
Name: xyz-py
Version: 0.0.9
Summary: A package for manipulating xyz files and chemical structures
Home-page: https://gitlab.com/jonkragskow/xyz_py
Author: Jon Kragskow
Author-email: jonkragskow@gmail.com
License: UNKNOWN
Project-URL: Bug Tracker, https://gitlab.com/jonkragskow/xyz_py/issues
Description: # xyz-py
        
        `xyz-py` is a python module for working with and manipulating chemical structures. 
        
        # Installation
        
        For convenience, `xyz-py` is available on [PyPI](https://pypi.org/project/xyz-py/) 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
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
