leelasd

This post examines the features of [R Markdown](http://www.rstudio.org/docs/authoring/using_markdown) 
using [knitr](http://yihui.name/knitr/) in Rstudio 0.96.
This combination of tools provides an exciting improvement in usability for 
[reproducible analysis](http://stats.stackexchange.com/a/15006/183).
Specifically, this post 
(1) discusses getting started with R Markdown and `knitr` in  Rstudio 0.96;
(2) provides a basic example of producing console output and plots using R Markdown;
(3) highlights several code chunk options such as caching and controlling how input and output is displayed;
(4) demonstrates use of standard Markdown notation as well as the extended features of formulas and tables; and 
(5) discusses the implications of R Markdown.

leelasd

#!/usr/bin/env ruby
# 
# This script is a wrapper around pandoc that uses pandoc's
# builtin citeproc support to generate a markdown bibliography
# from bibtex.
#
# Inspired by Jacob Barney's [bib2mkd][] script.
#
# [bib2mkd]: http://jmbarney.dyndns.org/?/linux/bib2mkd/
#

leelasd

Creating Whispernote's GitHub Project Page

Jekyll, GitHub's static site generator, and Bootstrap were used to create Whispernote's GitHub Project Page. This document shows how.

Project Goals

I wanted a stylish "brand" page for my project, and I wanted to reuse the README file I had created without a lot of copy/pasting. GitHub's Jekyll allowed me to essentially embed the file as a partial. What I got was really an enhanced README file (thanks to some jQuery and Bootstrap), which is exactly what I wanted.

gh-pages

leelasd

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# for chimera 1.4
from chimera import runCommand
import sys
rec_file = sys.argv[1]
basename = rec_file.split('/')[-1].split('.')[0]
#runCommand("open 0 receptor.pdb")
runCommand("open 0 %s"%rec_file)
runCommand("hbonds intramodel true distSlop 0.65 angleSlop 80 saveFile output/%s_hbonds.txt namingStyle serial"%basename)

leelasd

"""
Experimental wrapper to use Chimera's Python directly from console.

You can `import chimera` with no errors!

Usage
=====
1. Alias your /path/to/chimera/bin/python binary to something more user-friendly, like `chimerapy`.
2. Download these two files and put them together
3. Run `chimerapy -i chimera_cli.py`. (Tip: Realias `chimerapy` to this command).

leelasd

"""
dcdreporter.py: Outputs simulation trajectories in DCD format

This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.

Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman

leelasd

from __future__ import print_function
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit
from sys import stdout

pdb = app.PDBFile('water256_bulk_tip5p.pdb')
#pdb = app.PDBFile('a.pdb')
#pdb = app.PDBFile('water14_cluster.pdb')
boxDim = 19.3996888399961804/10.

leelasd

import openbabel
# Copyright 2009 TJ O'Donnell
class recap:
  # RECAP-Retrosynthetic Combinatorial Analysis Procedure
  # J. Chem. Inf. Comput. Sci. 1998, 38, 511-522
  def __init__(self, mol, minsize=5):
    self.mol = mol;
    # minimum allowed size (atom count) of fragment
    self.minsize = minsize;
    # bonded atom pairs populated by the apply method,

leelasd

import sys
from rdkit import Chem
from rdkit.Chem import AllChem, TorsionFingerprints
from rdkit.ML.Cluster import Butina


def gen_conformers(mol, numConfs=100, maxAttempts=1000, pruneRmsThresh=0.1, useExpTorsionAnglePrefs=True, useBasicKnowledge=True, enforceChirality=True):
	ids = AllChem.EmbedMultipleConfs(mol, numConfs=numConfs, maxAttempts=maxAttempts, pruneRmsThresh=pruneRmsThresh, useExpTorsionAnglePrefs=useExpTorsionAnglePrefs, useBasicKnowledge=useBasicKnowledge, enforceChirality=enforceChirality, numThreads=0)
	return list(ids)
	

leelasd