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leelasd

#!/usr/bin/env python

"""
Calculates a set of properties from a protein sequence:
    - hydrophobicity (according to a particular scale)
    - mean hydrophobic dipole moment assuming it is an alpha-helix.
    - total charge (at pH 7.4)
    - amino acid composition
    - discimination factor according to Rob Keller (IJMS, 2011)

leelasd

#!/usr/bin/env python

"""Sequence-based structural alignment of two proteins."""

import argparse
import pathlib

from Bio.PDB import FastMMCIFParser, MMCIFIO, PDBParser, PDBIO, Superimposer
from Bio.PDB.Polypeptide import is_aa

leelasd

#!/usr/bin/env python
# coding: utf-8

##########################################################################
# this script was generated by openmm-builder. to customize it further,
# you can save the file to disk and edit it with your favorite editor.
##########################################################################

# REQUIRES:
# * OpenMM (core dynamics)

leelasd

#!/bin/bash -x

# This script is for running the preparation workflow to create a pdb file that is compatible for parsing by openmm
# It reads in a pdb provided in the supplementary information from 10.1021/ja512751q always of the form:
# {target}_protein.pdb and runs pdb4amber and pdbfixer to generate a new pdb file with form {target}_protein_fixed.pdb


if [ $1 == "-h" ]; then
    echo "
        This script assumes that the first argument is an unprocessed pdb file of the form

leelasd