ghutchis

include_directories(${CMAKE_CURRENT_BINARY_DIR})

avogadro_plugin(ResetView
  "Manipulate the view camera."
  ExtensionPlugin
  resetview.h
  ResetView
  "resetview.cpp"
  ""
)

ghutchis

#!/usr/bin/env python

from __future__ import print_function

import sys
import logging
import numpy as np
from cclib.io import ccopen
from nms import nmsgenerator
from masses import element_masses

ghutchis

Are you a student? Know a student?

Want to get paid to write open source chemistry code this summer?

Following up on a successful 2016 and 2017, the Open Chemistry "umbrella" group of open source chemistry projects is looking for student proposals for Google Summer of Code (https://summerofcode.withgoogle.com/how-it-works/)

Applications and proposals are due from March 12th until March 27th. Students who are selected are paid between $US 2400 and $US 6600 for completing their work (https://developers.google.com/open-source/gsoc/help/student-stipends#amounts).

Students can submit their own ideas or work on suggested projects (Avogadro, cclib, RDKit, 3Dmol.js, MSDK, NWChem, Open Babel, DeepChem, etc.) Ideas range from easy-to-use web repositories for computational chemistry, OpenMM and GPU enabled molecular mechanics, volumetric rendering, to advanced analytical methods for quantum chemistry. http://wiki.openchemistry.org/GSoC_Ideas_2018

ghutchis

import glob, sys
try:
  import gwy
except:
  print "You need to install Gwyddion first"
  sys.exit(0)

# Script adapted from the Gwyddion documentation
# http://gwyddion.net/documentation/user-guide-en/pygwy.html

ghutchis

import os
import plistlib
import requests

INPUT_FILE = os.path.join(os.environ['HOME'], 'Library/Safari/Bookmarks.plist')
OUTPUT_FILE = 'readinglist.txt'

# Load and parse the Bookmarks file
with open(INPUT_FILE, 'rb') as plist_file:
    plist = plistlib.load(plist_file)

ghutchis

#!/usr/bin/env python

import sys
import openbabel as ob
import pybel

for filename in sys.argv[1:]:
    mol = pybel.readfile("g09", filename).next()
    nitro = mol.atoms[0]
    amine = mol.atoms[0]

ghutchis

Are you a student? Know a student?

Want to get paid to write open source chemistry code this summer?

Following up on a successful 2016, the Open Chemistry "umbrella" group of open source chemistry projects is looking for student proposals for Google Summer of Code (https://summerofcode.withgoogle.com/how-it-works/)

Applications and proposals are due from March 20th until April 3rd. Students who are selected are paid between $US 2400 and $US 6600 for completing their work (https://developers.google.com/open-source/gsoc/help/student-stipends#amounts).

Students can submit their own ideas or work on suggested projects (Avogadro, cclib, RDKit, 3Dmol.js, MSDK, NWChem, Open Babel) Ideas range from easy-to-use web repositories for computational chemistry, OpenMM and GPU enabled molecular mechanics, volumetric rendering, to advanced analytical methods for quantum chemistry. http://wiki.openchemistry.org/GSoC_Ideas_2017

ghutchis

#!/usr/bin/env python

import sys
from cclib.io import ccopen
import logging

for filename in sys.argv[1:]:
    file = ccopen(filename)

    # Strip off common extensions

ghutchis

#!/usr/bin/env python

import sys, os

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

for argument in sys.argv[1:]:
    filename, extension = os.path.splitext(argument)

ghutchis

@<TRIPOS>MOLECULE
d-(+)-glucose
 24 23 0 0 0
SMALL
USER_CHARGES

@<TRIPOS>ATOM
      1 O          -3.9862   -0.0915   -0.4753 O.2     1  UNL11111   -0.4322
      2 C          -3.1086   -0.7606    0.0104 C.2     1  UNL11111    0.3255
      3 C          -1.9542   -0.0724    0.7328 C.3     1  UNL11111   -0.0217