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Scripts in this repo

Rosetta

default.enzdes.flags

By Justin Siegel

A default flags file for use with RosettaScripts.

submit.bash

High-powered submission script for use on Epiphany.

Scripts for working with PDB files

pdb_parser.py

By Andrew Leaver-Fay, Morgan Nance, and Steve Bertolani

A full-featured PDB parser.

For working with scorefiles

scores.py

By Morgan Nance and Steve Bertolani

# example usage 
from score import ScoreFile
from pandas import read_csv

data = read_csv("score.sc",delim_whitespace=True,header=0) # Note, the header may not be the first line
     
sf = ScoreFile(data)
lowest_pdb = sf.return_lowest_energy_tag(tag="score") # You can put in any valid scorefile tag from the header
     
print "The lowest energy pdb file is %s" %lowest_pdb

enzdes_score.py

By Alex Carlin

A module for reading and filtering EnzDes-style scorefiles.

# example use
from core import enzdes_score

sf = enzdes_score.read_scorefile('tests/enzdes.sc')
lowest10 = lowest_by_percent(sf, percent=0.33)

pose.py

By Alex Carlin

A minimal PDB parser. Usage

from core import pose
mypdb = pose.from_pdb('tests/1sny.pdb')

Data analysis

mm.py

By Wai Shun Mak and Alex Carlin

Fits assay data to Michaelis-Menten models.

  • Generates statistics for linear, Michaelis-Menten, and Michaelis-Menten with substrate inhibition

  • Generates diagnostic plots

bfactor.py

Color PBDs in PyMOL, useful for looking at the effects of a lot of mutations.

APIs

HMMER API

By Steve Bertolani

Python API for HMMER.

Experimental/robots/oligos/ordering

makeoligo.py

Makes oligos for Kunkel mutagenesis.

kinetic_assay.py

Example kinetic assay for use on Transcriptic.

  • Use with mm.py above to automate kinetic characterization of mutants

Database

atom_types.py

Atom types reference

amino_acid.py

Chemical information and translation dictionaries

  • one-letter to three letter ('A' → 'ala')
  • three-letter to one-letter ('ALA' → 'A')
  • freely mix & match case

ecoli_codon.py

Reference of E. coli favored codon use for making mutagenic oligos