In [22]:

    

import numpy as np
import pandas as pd
from Bio.PDB.PDBParser import PDBParser


    

In [1]:

    

a = "/Users/weilu/Research/server/apr_2020/cornichon_cbd/chain_E/frags.mem"
with open(a) as f:
    b = f.readlines()
pdb_list = [c.split()[0].split("/")[-1].split(".")[0] for c in b[4:]]


    

In [23]:

    

a = "/Users/weilu/Research/server/apr_2020/cornichon_cbd//chain_E/fraglib/1deka.gro"


    

In [24]:

    

parser = PDBParser()
# all_atom_pdb_file = "/Users/weilu/Research/server/feb_2020/compare_side_chain_with_and_without/side_chain_run1/256b/4_0/crystal_structure.pdb"
structure = parser.get_structure("x", a)


    

In [27]:

    

list(structure.get_residues())


    

    
Out[27]:





[]

In [29]:

    

import sys
sys.path.insert(0, "/Users/weilu/openmmawsem/helperFunctions/")
from Pdb2GroLib import *


    

In [36]:

    

a = list(structure.get_residues())[0]


    

In [39]:

    

list(a.get_atoms())


    

    
Out[39]:





[<Atom O5'>,
 <Atom C5'>,
 <Atom C4'>,
 <Atom O4'>,
 <Atom C3'>,
 <Atom O3'>,
 <Atom C2'>,
 <Atom C1'>,
 <Atom N9>,
 <Atom C8>,
 <Atom N7>,
 <Atom C5>,
 <Atom C6>,
 <Atom N6>,
 <Atom N1>,
 <Atom C2>,
 <Atom N3>,
 <Atom C4>]

In [42]:

    

set()


    

    
Out[42]:





False

In [37]:

    

"CA" in a


    

    
Out[37]:





False

In [33]:

    

parser = PDBParser()
# all_atom_pdb_file = "/Users/weilu/Research/server/feb_2020/compare_side_chain_with_and_without/side_chain_run1/256b/4_0/crystal_structure.pdb"
structure = parser.get_structure("x", pdbFile)


    

    




/Users/weilu/anaconda3/envs/py36/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:92: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 3312.
  PDBConstructionWarning,
/Users/weilu/anaconda3/envs/py36/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:92: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 3313.
  PDBConstructionWarning,
/Users/weilu/anaconda3/envs/py36/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:92: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 3314.
  PDBConstructionWarning,
/Users/weilu/anaconda3/envs/py36/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:92: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 3331.
  PDBConstructionWarning,

In [35]:

    

list(structure.get_chains())


    

    
Out[35]:





[<Chain id=D>, <Chain id=E>, <Chain id=A>, <Chain id=B>]

In [32]:

    

pdbFile = "/Users/weilu/Research/server/apr_2020/cornichon_cbd/frag_in_cbd/pdbs/1AWC.pdb"
groFile = "/Users/weilu/Research/server/apr_2020/cornichon_cbd/frag_in_cbd/pdbs/1awcA.pdb"
chainID = "A"
Pdb2Gro(pdbFile, groFile, chainID.upper())


    

In [ ]:

    

def convert_all_atom_pdb_to_cbd_representation(all_atom_pdb_file, cbd_representation_file):
    # from a all atom pdb.
    # preserve N, CA, C, O, and place the CB at the center of mass of the side chain
    parser = PDBParser()
    # all_atom_pdb_file = "/Users/weilu/Research/server/feb_2020/compare_side_chain_with_and_without/side_chain_run1/256b/4_0/crystal_structure.pdb"
    structure = parser.get_structure("x", all_atom_pdb_file)

    x_com_dic = {}
    for res in structure.get_residues():
        chain = res.get_full_id()[2]
        resID = res.get_full_id()[3][1]
        x_com = get_side_chain_center_of_mass(res)
        x_com_dic[f"{chain}{resID}"] = x_com


    for res in structure.get_residues():
        chain = res.get_full_id()[2]
        resID = res.get_full_id()[3][1]
        x_com = x_com_dic[f"{chain}{resID}"]
        if res.resname == "GLY":
            continue
        res["CB"].set_coord(x_com)
    io = PDBIO()
    io.set_structure(structure)

    class CBDRepresentationSelect(Select):
        def accept_atom(self, atom):
            if atom.id in ["N", "CA", "C", "O", "CB", "H"]:
                return True
            else:
                return False
    # cbd_representation_file = "/Users/weilu/Research/server/feb_2020/compare_side_chain_with_and_without/side_chain_run1/256b/4_0/cbd_representation.pdb"
    io.save(cbd_representation_file, CBDRepresentationSelect())
    return True