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

#!/usr/bin/env python

import sys
import os

import cclib
from cclib.parser import ccopen

from rdkit import Chem
try:

ghutchis

#!/usr/bin/python

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

class Connection:

ghutchis

from __future__ import annotations

from typing import List, Optional

from pydantic import BaseModel, Field

# todo:
# - double-check open-spin systems
# - other suggestions

ghutchis

diff --git a/src/formats/formats.cmake b/src/formats/formats.cmake
index c94c8def2..70ee7d81c 100644
--- a/src/formats/formats.cmake
+++ b/src/formats/formats.cmake
@@ -77,6 +77,7 @@ endif(MSVC OR HAVE_REGEX_H)
 if(WITH_JSON)
   set(formats_json
     chemdoodlejsonformat
+    chemicaljsonformat
     pubchemjsonformat

ghutchis

#!/usr/bin/env python

import sys, os, math, random

from openbabel import pybel
from openbabel import openbabel as ob

colors = [ [ 0, 0, 0 ], # Du
            [0.75, 0.75, 0.75], # H
            [0.85, 1.00, 1.00], # He

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

from openbabel import openbabel as ob
from openbabel import pybel

# syntax:
# molml.py [files]