janash

language: python

# turn off sudo
sudo: false

# python versions to be tested
matrix:
  include:
    - python: 2.7
    - python: 3.5

janash

# .readthedocs.yml

version: 2

build:
  image: latest

python:
  version: 3.7
  install:

janash

"""
molecule.py
A python package for the MolSSI Software Summer School.

Contains a molecule class
"""

import numpy as np

def calculate_distance(rA, rB):

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# .readthedocs.yml

version: 2

build:
  image: latest

python:
  version: 3.6
  install:

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def calculate_molecular_mass(symbols):
   """Calculate the mass of a molecule.
   
   Parameters
   ----------
   symbols : list
       A list of elements.
   
   Returns
   -------

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def 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

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import numpy as np

for atom1 in atoms:
    for atom2 in atoms:
        a1 = atoms.index(atom1)
        a2 = atoms.index(atom2)
        coor1 = coordinates[a1]
        coor2 = coordinates[a2]
        distance = np.sqrt(np.sum((coor1-coor2)**2))
        if 0 < distance <= 1.5:

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def read_xyz(filepath):
    """
    Reads coordinates from an xyz file.
    
    Parameters
    ----------
    filepath : str
       The path to the xyz file to be processed.
       
    Returns

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def rdf(values, max_value, bin_size,num_particles, box_length):
    """
    Calculate the radial distribution function for a set of particles.
    
    Parameters
    ----------
    values : list
        A list of particle particle distances.
    max_value : float
        The maximum value to consider for the calculation.

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def rdf(values, n_bins, max_value, num_particles, box_length):
    """
    Compute the RDF for a set of values
    
    Parameters
    -----------
    values : np.ndarray
        The distance values to compute the RDF for.
        
    n_bins : int