Restraints

biobb_haddock/__init__.py

@@ -1,5 +1,5 @@
 from . import haddock
 
 name = "biobb_haddock"
-__all__ = ["haddock"]
+__all__ = ["haddock","haddock_restraints"]
 __version__ = "5.0.0"

biobb_haddock/haddock_restraints/__init__.py

@@ -0,0 +1,9 @@
+from . import (
+    haddock3_accessibility
+)
+
+name = "haddock_restraints"
+__all__ = [
+    "haddock3_accessibility",
+    "haddock3_actpass_to_ambig"
+]

biobb_haddock/haddock_restraints/haddock3_accessibility.py

@@ -0,0 +1,199 @@
+#!/usr/bin/env python3
+
+"""Module containing the haddock  class and the command line interface."""
+
+import argparse
+import glob
+import os
+import shutil
+from typing import Optional
+
+from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
+from biobb_common.tools.file_utils import launchlogger
+
+
+class Haddock3Accessibility(BiobbObject):
+    """
+    | biobb_haddock Haddock3Accessibility
+    | Wrapper class for the Haddock-Restraints Accessibility module.
+    | Haddock-Restraints Accessibility computes residues accessibility using freesasa included in the Haddock3 package.
+
+    Args:
+        input_pdb_path (str): Path to the input PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2aP_1F3G.pdb>`_. Accepted formats: pdb (edam:format_1476).
+        output_accessibility_path (str): Path to the output file with accessibility information. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/mol1_sasa.txt>`_. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), out (edam:format_2330).
+        output_actpass_path (str) (Optional): Path to the output file with active/passive residues to be used as haddock3 restraint information. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/mol1_haddock_actpass.txt>`_. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), out (edam:format_2330).
+        properties (dict - Python dictionary object containing the tool parameters, not input/output files):
+            * **chain** (*str*) - ("A") Chain to be used from the input PDB file.
+            * **cutoff** (*float*) - (0.4) Relative cutoff for sidechain accessibility.
+            * **probe_radius** (*float*) - (1.4) Probe radius for the accessibility calculation.
+            * **binary_path** (*str*) - ("haddock") Path to the haddock haddock executable binary.
+            * **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.
+            * **container_path** (*str*) - (None)  Path to the binary executable of your container.
+            * **container_image** (*str*) - (None) Container Image identifier.
+            * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
+            * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
+            * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
+            * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
+
+
+    Examples:
+        This is a use example of how to use the building block from Python::
+
+            from biobb_haddock.haddock_restraints.haddock3_accessibility import haddock3_accessibility
+            prop = { 'cutoff': 0.4 }
+            haddock3_accessibility(input_pdb_path='/path/to/mypdb.pdb',
+                       output_accessibility_path='/path/to/output_report.txt',
+                       properties=prop)
+
+    Info:
+        * wrapped_software:
+            * name: Haddock3-restraints
+            * version: 3.0.0
+            * license: Apache-2.0
+        * ontology:
+            * name: EDAM
+            * schema: http://edamontology.org/EDAM.owl
+    """
+
+    def __init__(
+        self,
+        input_pdb_path: str,
+        output_accessibility_path: str,
+        output_actpass_path: Optional[str] = None,
+        properties: Optional[dict] = None,
+        **kwargs,
+    ) -> None:
+        properties = properties or {}
+
+        # Call parent class constructor
+        super().__init__(properties)
+
+        # Input/Output files
+        self.io_dict = {
+            "in": {
+                "input_pdb_path": input_pdb_path,
+            },
+            "out": {
+                "output_accessibility_path": output_accessibility_path,
+                "output_actpass_path": output_actpass_path,
+            },
+        }
+
+        # Properties specific for BB
+        self.chain = properties.get("chain", "A")
+        self.cutoff = properties.get("cutoff", 0.4)
+        self.probe_radius = properties.get("probe_radius", 1.4)
+
+        # Properties specific for BB
+        self.binary_path = properties.get("binary_path", "haddock3-restraints")
+
+        # Check the properties
+        self.check_properties(properties)
+
+    @launchlogger
+    def launch(self) -> int:
+        """Execute the :class:`haddock <haddock.haddock.haddock>` object."""
+
+        # Setup Biobb
+        if self.check_restart():
+            return 0
+        self.stage_files()
+
+        # haddock3-restraints calc_accessibility 1UBQ.pdb --export_to_actpass
+        self.cmd = [self.binary_path, "calc_accessibility", self.stage_io_dict['in']['input_pdb_path']]
+
+        if self.io_dict["out"]["output_actpass_path"] is not None:
+            self.cmd.append("--export_to_actpass")
+
+        self.cmd.append("&>")
+        self.cmd.append(self.stage_io_dict['out']['output_accessibility_path'])
+
+        # Run Biobb block
+        self.run_biobb()
+
+        # Check chain
+        target_string = f"Chain {self.chain}"
+        found = False
+        with open(self.stage_io_dict['out']['output_accessibility_path'], 'r') as file:
+            for line in file:
+                if target_string in line:
+                    found = True
+
+        if found:
+            # Rename/Copy output file to the given output file name
+            file_name = os.path.basename(self.io_dict['in']['input_pdb_path'])
+            shutil.copyfile(f"{file_name[:-4]}_passive_{self.chain}.actpass", self.io_dict["out"]["output_actpass_path"])
+
+        else:
+            print(f"\nWARNING: Chain {self.chain} not found in input PDB file. Please check and modify the chain property accordingly.\n")
+
+        # Copy files to host
+        self.copy_to_host()
+
+        # Remove temporal files
+        self.tmp_files.extend([self.stage_io_dict["unique_dir"]])
+        actpass_files = glob.glob('*.actpass')
+        self.tmp_files.extend(actpass_files)
+        self.remove_tmp_files()
+
+        return self.return_code
+
+
+def haddock3_accessibility(
+    input_pdb_path: str,
+    output_accessibility_path: str,
+    output_actpass_path: Optional[str] = None,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
+    """Create :class:`haddock <haddock.haddock.haddock>` class and
+    execute the :meth:`launch() <haddock.haddock.haddock.launch>` method."""
+
+    return Haddock3Accessibility(
+        input_pdb_path=input_pdb_path,
+        output_accessibility_path=output_accessibility_path,
+        output_actpass_path=output_actpass_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
+
+
+haddock3_accessibility.__doc__ = Haddock3Accessibility.__doc__
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Wrapper of the haddock-restraints Accessibility module.",
+        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("--input_pdb_path", required=True)
+    required_args.add_argument("--output_accessibility_path", required=True)
+    parser.add_argument("--output_actpass_path", required=False)
+
+    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
+    haddock3_accessibility(
+        input_pdb_path=args.input_pdb_path,
+        output_accessibility_path=args.output_accessibility_path,
+        output_actpass_path=args.output_actpass_path,
+        properties=properties,
+    )
+
+
+if __name__ == "__main__":
+    main()

biobb_haddock/haddock_restraints/haddock3_actpass_to_ambig.py

@@ -0,0 +1,174 @@
+#!/usr/bin/env python3
+
+"""Module containing the haddock  class and the command line interface."""
+
+import argparse
+import glob
+import os
+import shutil
+from typing import Optional
+
+from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
+from biobb_common.tools.file_utils import launchlogger
+
+
+class Haddock3ActpassToAmbig(BiobbObject):
+    """
+    | biobb_haddock Haddock3ActpassToAmbig
+    | Wrapper class for the Haddock-Restraints active_passive_to_ambig module.
+    | Haddock-Restraints active_passive_to_ambig generates a corresponding ambig.tbl file to be used by HADDOCK from two given files containing active (in the first line) and passive (second line) residues.
+
+    Args:
+        input_actpass1_path (str): Path to the first input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/haddock_actpass.txt>`_. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), in (edam:format_2330), pass (edam:format_2330).
+        input_actpass2_path (str): Path to the second input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/haddock_actpass.txt>`_. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), in (edam:format_2330), pass (edam:format_2330).
+        output_tbl_path (str): Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/haddock_air.tbl>`_. Accepted formats: tbl (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).
+        properties (dict - Python dictionary object containing the tool parameters, not input/output files):
+            * **binary_path** (*str*) - ("haddock") Path to the haddock haddock executable binary.
+            * **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.
+            * **container_path** (*str*) - (None)  Path to the binary executable of your container.
+            * **container_image** (*str*) - (None) Container Image identifier.
+            * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
+            * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
+            * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
+            * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
+
+
+    Examples:
+        This is a use example of how to use the building block from Python::
+
+            from biobb_haddock.haddock_restraints.haddock3_actpass_to_ambig import haddock3_actpass_to_ambig
+            haddock3_actpass_to_ambig(
+                input_actpass1_path='/path/to/haddock_actpass1.txt',
+                input_actpass2_path='/path/to/haddock_actpass2.txt',
+                output_tbl_path='/path/to/output_AIR.tbl'
+            )
+
+    Info:
+        * wrapped_software:
+            * name: Haddock3-restraints
+            * version: 3.0.0
+            * license: Apache-2.0
+        * ontology:
+            * name: EDAM
+            * schema: http://edamontology.org/EDAM.owl
+    """
+
+    def __init__(
+        self,
+        input_actpass1_path: str,
+        input_actpass2_path: str,
+        output_tbl_path: str,
+        properties: Optional[dict] = None,
+        **kwargs,
+    ) -> None:
+        properties = properties or {}
+
+        # Call parent class constructor
+        super().__init__(properties)
+
+        # Input/Output files
+        self.io_dict = {
+            "in": {
+                "input_actpass1_path": input_actpass1_path,
+                "input_actpass2_path": input_actpass2_path,
+            },
+            "out": {
+                "output_tbl_path": output_tbl_path,
+            },
+        }
+
+        # Properties specific for BB
+        # self.chain = properties.get("chain", "A")
+
+        # Properties specific for BB
+        self.binary_path = properties.get("binary_path", "haddock3-restraints")
+
+        # Check the properties
+        self.check_properties(properties)
+
+    @launchlogger
+    def launch(self) -> int:
+        """Execute the :class:`haddock <haddock.haddock.haddock>` object."""
+
+        # Setup Biobb
+        if self.check_restart():
+            return 0
+        self.stage_files()
+
+        # haddock3-restraints active_passive_to_ambig haddock_actpass.txt
+        self.cmd = [self.binary_path, "active_passive_to_ambig", self.stage_io_dict['in']['input_actpass1_path'], self.stage_io_dict['in']['input_actpass2_path']]
+
+        self.cmd.append("&>")
+        self.cmd.append(self.stage_io_dict['out']['output_tbl_path'])
+
+        # Run Biobb block
+        self.run_biobb()
+
+        # Copy files to host
+        self.copy_to_host()
+
+        # Remove temporal files
+        self.tmp_files.extend([self.stage_io_dict["unique_dir"]])
+        self.remove_tmp_files()
+
+        return self.return_code
+
+
+def haddock3_actpass_to_ambig(
+    input_actpass1_path: str,
+    input_actpass2_path: str,
+    output_tbl_path: str,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
+    """Create :class:`haddock <haddock.haddock.haddock>` class and
+    execute the :meth:`launch() <haddock.haddock.haddock.launch>` method."""
+
+    return Haddock3ActpassToAmbig(
+        input_actpass1_path=input_actpass1_path,
+        input_actpass2_path=input_actpass2_path,
+        output_tbl_path=output_tbl_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
+
+
+haddock3_actpass_to_ambig.__doc__ = Haddock3ActpassToAmbig.__doc__
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Wrapper of the haddock-restraints active_passive_to_ambig module.",
+        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("--input_actpass1_path", required=True)
+    required_args.add_argument("--input_actpass2_path", required=True)
+    required_args.add_argument("--output_tbl_path", required=True)
+
+    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
+    haddock3_actpass_to_ambig(
+        input_actpass1_path=args.input_actpass1_path,
+        input_actpass2_path=args.input_actpass2_path,
+        output_tbl_path=args.output_tbl_path,
+        properties=properties,
+    )
+
+
+if __name__ == "__main__":
+    main()