Bio-Python Module for doing Chop stuff

BioPythonModules.py

# Using BioPython Doing All the Manipulations
##
import numpy as np
from Bio.PDB import *
from Bio.KDTree import KDTree
import pandas as pd
import warnings
from Bio import BiopythonWarning
warnings.simplefilter('ignore', BiopythonWarning)


def DeleteClashes(prot, memb):
    '''
    - Deleting The Overlapping residues between two models 
    - Meant for Protein and Membrane system but can be used 
      for membrane systems too
    - Deletion happens in place 
    '''
    prot_atoms = [at for at in prot.get_atoms()]
    memb_atoms = [at for at in memb.get_atoms()]
    prot_coos = np.array([at.coord for at in prot_atoms], np.float)
    memb_coos = np.array([at.coord for at in memb_atoms], np.float)
    clashes = []
    atom_kdtree = KDTree(3)
    atom_kdtree.set_coords(memb_coos)
    for p in range(len(prot_coos)):
        atom_kdtree.search(prot_coos[p], 1.500)
        res = list(atom_kdtree.get_indices())
        clashes = clashes + res
    del_res = [memb_atoms[c].get_parent().get_id()[1] for c in clashes]
    del_res = list(set(del_res))
    for p in range(len(del_res)):
        for chain in memb[0]:
            if chain.has_id(del_res[p]):
                chain.detach_child((' ', del_res[p], ' '))
    return None


def Struct2DF(prot):
    '''
    - Creates a pandas dataframe from BIO.PDB object
    '''
    prot_atoms = [at for at in prot.get_atoms()]
    prot_coos = np.array([at.coord for at in prot_atoms], np.float)
    f3 = pd.DataFrame(prot_coos, columns=['X', 'Y', 'Z'])
    f3['res_name'] = [at.get_parent().get_resname() for at in prot_atoms]
    f3['res_id'] = [at.get_parent().get_id()[1] for at in prot_atoms]
    f3['atom_name'] = [at.get_id() for at in prot_atoms]
    return f3


def Displace(prot, disp_vec):
    '''
    - Displace all atoms in model by values in DispVec
    '''
    for chain in prot[0]:
        for res in chain:
            for atom in res:
                old = atom.coord
                atom.set_coord(old - disp_vec)
    return None