bdrown

#Name: Project Table:Plane of Best Fit - PJH Lab
#Command: pythonrun calc_pbf.run
__doc__ = """
Performs plane of best fit analysis.
Calculates the average distance of all atoms in each molecule to the plane that
fits each structure. Plane fitting is performed by single value decomposition 
(SVD) using the Numpy package.
The script can also be run from the command line.
"""

JoaoRodrigues

#!/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

dwhswenson

#!/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)

JoaoRodrigues

Code now available at https://github.com/JoaoRodrigues/hydrophobic_moment with example usage and proper licensing.

greglandrum

PatWalters

#!/usr/bin/env python

import sys
from prody import *
from rdkit import Chem
from rdkit.Chem import AllChem
from io import StringIO
import pypdb

PatWalters

#!/usr/bin/env python

import sys
import os
from rdkit import Chem


def molecule_supplier_from_name(input_file_name):
    ext = os.path.splitext(input_file_name)[-1]
    if ext == ".smi":

greglandrum

greglandrum

greglandrum