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]

ghutchis

#!/usr/bin/env python

from __future__ import print_function

import sys
from cclib.parser import ccopen
import logging

def spectra(etens, etoscs, low = 0.5, high = 10.0, resolution = 0.01, smear = 0.04):
    """Return arrays of the energies and intensities of a Lorentzian-blurred spectrum"""

ghutchis

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 1a53e8cdd..bbf92481c 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -23,7 +23,7 @@ set (cpptests
     )
 set (alias_parts 1)
 set (automorphism_parts 1 2 3 4 5 6 7 8 9 10)
-set (builder_parts 1 2 3 4 5)
+set (builder_parts 1 2 3 4 5 6)

ghutchis

diff --git a/avogadro/qtgui/interfacescript.cpp b/avogadro/qtgui/interfacescript.cpp
index f0ad088..c0c2141 100644
--- a/avogadro/qtgui/interfacescript.cpp
+++ b/avogadro/qtgui/interfacescript.cpp
@@ -458,6 +458,14 @@ bool InterfaceScript::insertMolecule(QJsonObject& json,
   if (m_moleculeExtension == QLatin1String("None"))
     return true;
 
+  // insert the selected atoms
+  QJsonArray selectedList;

ghutchis

#!/usr/bin/env python

import sys, os

from openbabel import pybel

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

    filename, extension = os.path.splitext(argument)