Code now available at https://github.com/JoaoRodrigues/hydrophobic_moment with example usage and proper licensing.
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#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. | |
""" |
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#!/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 |
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#!/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) |
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#!/usr/bin/env python | |
import sys | |
from prody import * | |
from rdkit import Chem | |
from rdkit.Chem import AllChem | |
from io import StringIO | |
import pypdb | |
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#!/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": |
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