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

The 12 Steps of Grad School

by Geoff Hutchison (with thanks to Andrew Metz) http://hutchison.chem.pitt.edu/

1. Initial Optimism: (I will solve problem X and change the world!)
2. Pessimism: (Hmm, this problem is hard)
3. Apathy: (Meh, I’m getting okay results, but not great)
4. Delusion: (I’m not sure what’s going on - it’s complicated)
5. Cynicism: (Nobody can solve this..)
6. Procrastination: (Eh, it’s a multi-year project, one day won’t hurt)

ghutchis

#!/usr/bin/env python

import sys
import os
import glob

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

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

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

from __future__ import print_function

import sys
import os
import math
import random

import pybel

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

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

#!/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

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;