ghutchis

#!/usr/bin/env python

import sys, os

from openbabel import openbabel as ob
from openbabel import pybel

# syntax:
# molml.py [files]

ghutchis

  auto graph = m_molecule->graph();

  for (Index i = 0; i < m_molecule->atomCount(); ++i)
  {
    // print the symbol for the atom
    Core::Atom atom = m_molecule->atom(i);
    std::string atomType = Core::Elements::symbol(atom.atomicNumber());
    std::cout << "Atom " << atomType << " (" << i << ")" << std::endl;

    // check neighbors

ghutchis

#!/usr/bin/env python

import sys
import json
import subprocess

# example molecule for testing
water = {
"chemicalJson": 1,
"atoms": {

ghutchis

#!/usr/bin/python

import json
import socket
import struct
import glob
import tempfile
import os
import time

ghutchis

element_symbols = [
  "Xx", "H", "He", "Li", "Be", "B", "C", "N", "O", "F",
  "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K",
  "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu",
  "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y",
  "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In",
  "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr",
  "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm",
  "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au",

ghutchis

#!/usr/bin/env python

import sys
import os

import cclib
from cclib.parser import ccopen

from rdkit import Chem
try:

ghutchis

#!/usr/bin/env python

from __future__ import print_function

import sys
import os
import math
import random

import pybel

ghutchis

#!/usr/bin/python

import json
import socket
import struct
import glob
import tempfile
import os

class Connection:

ghutchis

# Calculate nConf20 - from https://pubs.acs.org/doi/10.1021/acs.jcim.6b00565
# Jerome G. P. Wicker and Richard I. Cooper  J. Chem. Inf. Model. 2016 56(12) pp. 2347-2352
# reformatted for Python3 by Geoffrey R. Hutchison https://hutchison.chem.pitt.edu 

from collections import OrderedDict
import fileinput

import numpy as np

from rdkit import Chem

ghutchis

#!/usr/bin/env python

import sys, os

import pybel
ob = pybel.ob

# read through multiple files on command-line
for argument in sys.argv[1:]: