CODEWITHSUNDEEP
pythonpython-3.xbioinformaticsbiopython
user11504554
user11504554

Reputation:

Is there a way to separate the chains belong to each Biological assembly in a PDB file?(python Script)

I want to separate the chain IDs which belong to specific Biological assemblies in a PDB file. As an Example PDB ID 1BRS has 3 Biological assemblies Biological assembly 1 : - chains A and D Biological assembly 2 : - Chains B and E Biological assembly 3 : - chains C and F

Is there a way (python Script) to get the Chain IDs separate which belong to each biological assembly as follows 1BRS_A:D 1BRS_B:E 1BRS_C:F No need to extract the chain coordinates. If I get the chain names, that will be enough. Thanks in advance

Upvotes: 0

Views: 772

Answers (2)

user11317114
user11317114

Reputation: 11

Thanks for the code! It works nicely with serveral assemblies. But if the entry has only a single assembly it does not recognize it properly. Updated it to this:

import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io.pdbx as pdbx
import json
ID = "3AV2"
#ID= "1BRS"
ID="2k6d"
#ID="1TBE"
ID="1HT2"
#ID="1HTI"
# Download structure
file_name = rcsb.fetch(ID, "pdbx", target_path=".")

# Read file
file = pdbx.PDBxFile()
file.read(file_name)

# Get 'entity_poly' category as dictionary
# to find out which chains are polymers
poly_chains = []
if isinstance(file["entity_poly"]["pdbx_strand_id"],str):
   poly_chains=file["entity_poly"]["pdbx_strand_id"].split(",")
else:
   for chain_list in file["entity_poly"]["pdbx_strand_id"]:
      poly_chains += chain_list.split(",")

biolAssemblyDict={}
if isinstance(file["pdbx_struct_assembly_gen"]["asym_id_list"],str):
    index=0
    asym_id_list=file["pdbx_struct_assembly_gen"]["asym_id_list"]
    chain_ids=asym_id_list.split(",")
    chain_ids = [chain_id for chain_id in chain_ids if chain_id in poly_chains]
    biolAssemblyDict[index+1]= ','.join(chain_ids)
else:
    # Get 'pdbx_struct_assembly_gen' category as dictionary
    for index,asym_id_list in enumerate(file["pdbx_struct_assembly_gen"]["asym_id_list"]):
        chain_ids = asym_id_list.split(",")
        #    print(chain_ids)
        # Filter chains that belong to a polymer
        chain_ids = [chain_id for chain_id in chain_ids if chain_id in poly_chains]
        biolAssemblyDict[index+1]= ','.join(chain_ids)
print(json.dumps(biolAssemblyDict,indent=4, sort_keys=True))

Upvotes: 0

Padix Key
Padix Key

Reputation: 970

The PDBx/mmCIF file format contains the information in the _pdbx_struct_assembly_gen category.

loop_
_pdbx_struct_assembly_gen.assembly_id 
_pdbx_struct_assembly_gen.oper_expression 
_pdbx_struct_assembly_gen.asym_id_list 
1 1 A,D,G,J 
2 1 B,E,H,K 
3 1 C,F,I,L

These files can be read e.g. with Biotite (https://www.biotite-python.org/), a package I am developing. The categories can be read in a dictionary-like manner:

import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io.pdbx as pdbx

ID = "1BRS"

# Download structure
file_name = rcsb.fetch(ID, "pdbx", target_path=".")

# Read file
file = pdbx.PDBxFile()
file.read(file_name)
# Get 'pdbx_struct_assembly_gen' category as dictionary
assembly_dict = file["pdbx_struct_assembly_gen"]
for asym_id_list in assembly_dict["asym_id_list"]:
    chain_ids = asym_id_list.split(",")
    print(f"{ID}_{':'.join(chain_ids)}")

The output is

1BRS_A:D:G:J
1BRS_B:E:H:K
1BRS_C:F:I:L

The chains G-L contain only water molecules.

EDIT:

To include only chain IDs that belong to a polymer, e.g. a protein or a nucleotide, you can use the entity_poly category:

loop_
_entity_poly.entity_id 
_entity_poly.type 
_entity_poly.nstd_linkage 
_entity_poly.nstd_monomer 
_entity_poly.pdbx_seq_one_letter_code 
_entity_poly.pdbx_seq_one_letter_code_can 
_entity_poly.pdbx_strand_id 
_entity_poly.pdbx_target_identifier 
1 'polypeptide(L)' no no 
;AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTS
GFRNSDRILYSSDWLIYKTTDHYQTFTKIR
;
;AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTS
GFRNSDRILYSSDWLIYKTTDHYQTFTKIR
;
A,B,C ? 
2 'polypeptide(L)' no no 
;KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAE
GADITIILS
;
;KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAE
GADITIILS
;
D,E,F ?

This is the updated Python code:

import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io.pdbx as pdbx

ID = "1BRS"

# Download structure
file_name = rcsb.fetch(ID, "pdbx", target_path=".")

# Read file
file = pdbx.PDBxFile()
file.read(file_name)

# Get 'entity_poly' category as dictionary
# to find out which chains are polymers
poly_chains = []
for chain_list in file["entity_poly"]["pdbx_strand_id"]:
    poly_chains += chain_list.split(",")

# Get 'pdbx_struct_assembly_gen' category as dictionary
for asym_id_list in file["pdbx_struct_assembly_gen"]["asym_id_list"]:
    chain_ids = asym_id_list.split(",")
    # Filter chains that belong to a polymer
    chain_ids = [chain_id for chain_id in chain_ids if chain_id in poly_chains]
    print(f"{ID}_{':'.join(chain_ids)}")

And this is the output:

1BRS_A:D
1BRS_B:E
1BRS_C:F

Upvotes: 2

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