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I may be slow to respond. Busy writing proposals and teaching

Geoff Hutchison ghutchis

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I may be slow to respond. Busy writing proposals and teaching
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@ghutchis
ghutchis / crystals.txt
Created Aug 12, 2011
Crystal Structures
View crystals.txt
http://cst-www.nrl.navy.mil/lattice/
http://en.wikipedia.org/wiki/Category:Minerals_by_crystal_system
http://www.crystallography.net/
http://wwmm.ch.cam.ac.uk/crystaleye/
Zeolites: http://www.iza-structure.org/databases/
AlO
γ-, δ-, η-, θ-, and χ-aluminas
@ghutchis
ghutchis / gist:1201677
Created Sep 7, 2011
inorganic ligands
View gist:1201677
crown ethers
cryptands
pyridines
edta
eta2-ethylene
eta2-acetylene
eta4-c4
eta3-c3
eta3-allyl
eta7-c7
View gist:1320887
int numcartpershell[14] = {1, 3, 6, 10, 15, 21, 28, 36, 45, 55, 66, 78, 93, 107};
const char* map[14] = {"S\0", "P\0", "D\0", "F\0", "G\0", "H\0",
"I\0", "K\0", "L\0", "M\0", "N\0", "O\0", "Q\0", "R\0"};
View GZCGUPFRVQAUEE-SLPGGIOYSA-N.mol2
@<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
@ghutchis
ghutchis / molcsv.py
Created May 14, 2015
Print molecule "report" as a CSV file
View molcsv.py
#!/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)
View energies.py
#!/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
ghutchis / gsoc2017.md
Last active Mar 16, 2017
OpenChemistry in Google Summer of Code 2017
View gsoc2017.md

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

View piezo-dist.py
#!/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
ghutchis / readingList.py
Created May 11, 2017
Parse Safari Reading List using Python
View readingList.py
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
ghutchis / gwiddion-batch.py
Created Jun 30, 2017
Batch script through Igor AFM data
View gwiddion-batch.py
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