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)

ghutchis

ch3co2.sdf
  ChemDraw10291910202D

  4  3  0  0  0  0  0  0  0  0999 V2000
   -0.7145   -0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.6187    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0      
  2  3  1  0      

ghutchis

 OpenBabel10291910162D

  6  6  0  0  0  0  0  0  0  0999 V2000
   -0.8660   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7321   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7321    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8660    1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

ghutchis

#!/usr/bin/env python

from __future__ import print_function

import sys
import os
import math
import random

import pybel

ghutchis

git fetch origin # get tags
git checkout openbabel-3-0-0a1

cp -pr openbabel openbabel-3.0.0a1
cd openbabel-3.0.0a1
rm .travis.yml authors.txt
find . -name "*~" | xargs rm
find . -name ".git*" | xargs rm -r
(cd scripts/python/; rm -fr build)
(cd scripts/java/; rm -fr org)

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:]:

ghutchis

#!/usr/bin/env python

import sys
import os
import glob

import pybel
# don't need to reimport openbabel
ob = pybel.ob