#!/usr/bin/env python3
"""Module containing the RenumberStructure class and the command line interface."""
import argparse
import json
from pathlib import Path
from typing import Optional
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_structure_utils.gro_lib.gro import Gro
from biobb_structure_utils.utils.common import PDB_SERIAL_RECORDS
[docs]
class RenumberStructure(BiobbObject):
"""
| biobb_structure_utils RenumberStructure
| Class to renumber atomic indexes from a 3D structure.
| Renumber atomic indexes from a 3D structure.
Args:
input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/cl3.noH.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
output_structure_path (str): Output structure file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/renum_cl3_noH.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
output_mapping_json_path (str): Output mapping json file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/cl3_output_mapping_json_path.json>`_. Accepted formats: json (edam:format_3464).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **renumber_residues** (*bool*) - (True) Residue code of the ligand to be removed.
* **renumber_residues_per_chain** (*bool*) - (True) Restart residue enumeration every time a new chain is detected.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
Examples:
This is a use example of how to use the building block from Python::
from biobb_structure_utils.utils.renumber_structure import renumber_structure
prop = {
'renumber_residues': True,
'renumber_residues_per_chain': True
}
renumber_structure(input_structure_path='/path/to/myInputStr.pdb',
output_structure_path='/path/to/newStructure.pdb',
output_mapping_json_path='/path/to/newMapping.json',
properties=prop)
Info:
* wrapped_software:
* name: In house
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_structure_path,
output_structure_path,
output_mapping_json_path,
properties=None,
**kwargs,
) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_structure_path": input_structure_path},
"out": {
"output_structure_path": output_structure_path,
"output_mapping_json_path": output_mapping_json_path,
},
}
# Properties specific for BB
self.renumber_residues = properties.get("renumber_residues", True)
self.renumber_residues_per_chain = properties.get(
"renumber_residues_per_chain", True
)
# Common in all BB
self.can_write_console_log = properties.get("can_write_console_log", True)
self.global_log = properties.get("global_log", None)
self.prefix = properties.get("prefix", None)
self.step = properties.get("step", None)
self.path = properties.get("path", "")
self.remove_tmp = properties.get("remove_tmp", True)
self.restart = properties.get("restart", False)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`RenumberStructure <utils.renumber_structure.RenumberStructure>` utils.renumber_structure.RenumberStructure object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Business code
extension = Path(
self.stage_io_dict["in"]["input_structure_path"]
).suffix.lower()
if extension.lower() == ".gro":
fu.log("GRO format detected, reenumerating atoms", self.out_log)
gro_st = Gro()
gro_st.read_gro_file(self.stage_io_dict["in"]["input_structure_path"])
residue_mapping, atom_mapping = gro_st.renumber_atoms(
renumber_residues=self.renumber_residues,
renumber_residues_per_chain=self.renumber_residues_per_chain,
)
gro_st.write_gro_file(self.stage_io_dict["out"]["output_structure_path"])
else:
fu.log("PDB format detected, reenumerating atoms", self.out_log)
atom_mapping = {}
atom_count = 0
residue_mapping = {}
residue_count = 0
with open(
self.stage_io_dict["in"]["input_structure_path"], "r"
) as input_pdb, open(
self.stage_io_dict["out"]["output_structure_path"], "w"
) as output_pdb:
for line in input_pdb:
record = line[:6].upper().strip()
if (
len(line) > 10 and record in PDB_SERIAL_RECORDS
): # Avoid MODEL, ENDMDL records and empty lines
# Renumbering atoms
pdb_atom_number = line[6:11].strip()
if not atom_mapping.get(
pdb_atom_number
): # ANISOU records should have the same numeration as ATOM records
atom_count += 1
atom_mapping[pdb_atom_number] = str(atom_count)
line = line[:6] + "{: >5d}".format(atom_count) + line[11:]
# Renumbering residues
if self.renumber_residues:
chain = line[21]
pdb_residue_number = line[22:26].strip()
if not residue_mapping.get(chain):
residue_mapping[chain] = {}
if self.renumber_residues_per_chain:
residue_count = 0
if not residue_mapping[chain].get(pdb_residue_number):
residue_count += 1
residue_mapping[chain][pdb_residue_number] = str(
residue_count
)
line = (
line[:22] + "{: >4d}".format(residue_count) + line[26:]
)
output_pdb.write(line)
with open(
self.stage_io_dict["out"]["output_mapping_json_path"], "w"
) as output_json:
output_json.write(
json.dumps({"residues": residue_mapping, "atoms": atom_mapping})
)
self.return_code = 0
##########
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def renumber_structure(
input_structure_path: str,
output_structure_path: str,
output_mapping_json_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Execute the :class:`RenumberStructure <utils.renumber_structure.RenumberStructure>` class and
execute the :meth:`launch() <utils.renumber_structure.RenumberStructure.launch>` method."""
return RenumberStructure(
input_structure_path=input_structure_path,
output_structure_path=output_structure_path,
output_mapping_json_path=output_mapping_json_path,
properties=properties,
**kwargs,
).launch()
[docs]
def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(
description="Renumber atoms and residues from a 3D structure.",
formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
)
parser.add_argument(
"-c",
"--config",
required=False,
help="This file can be a YAML file, JSON file or JSON string",
)
# Specific args of each building block
required_args = parser.add_argument_group("required arguments")
required_args.add_argument(
"-i", "--input_structure_path", required=True, help="Input structure file name"
)
required_args.add_argument(
"-o",
"--output_structure_path",
required=True,
help="Output structure file name",
)
required_args.add_argument(
"-j",
"--output_mapping_json_path",
required=True,
help="Output mapping json file name",
)
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
renumber_structure(
input_structure_path=args.input_structure_path,
output_structure_path=args.output_structure_path,
output_mapping_json_path=args.output_mapping_json_path,
properties=properties,
)
if __name__ == "__main__":
main()