<reponame>bioexcel/biobb_vs
#!/usr/bin/env python3

"""Module containing the BoxResidues class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import  settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_vs.utils.common import *


class BoxResidues(BiobbObject):
    """
    | biobb_vs BoxResidues
    | This class sets the center and the size of a rectangular parallelepiped box around a set of residues.
    | Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB. The residue identifiers that compose the selection (i.e. binding site) are provided by a property list.

    Args:
        input_pdb_path (str): PDB protein structure for which the box will be build. Its size and center will be set around the 'resid_list' property once mapped against this PDB. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box_residues.pdb>`_. Accepted formats: pdb (edam:format_1476).
        output_pdb_path (str): PDB including the annotation of the box center and size as REMARKs. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box_residues.pdb>`_. Accepted formats: pdb (edam:format_1476).
        properties (dic - Python dictionary object containing the tool parameters, not input/output files):
            * **resid_list** (*list*) - (None) List with all the residue numbers to form a cavity or binding site. Mandatory property.
            * **offset** (*float*) - (2.0) [0.1~1000|0.1] Extra distance (Angstroms) between the last residue atom and the box boundary.
            * **box_coordinates** (*bool*) - (False) Add box coordinates as 8 ATOM records.
            * **residue_offset** (*int*) - (0) [0~1000|1] Residue id offset.
            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.

    Examples:
        This is a use example of how to use the building block from Python::

            from biobb_vs.utils.box_residues import box_residues
            prop = { 
                'resid_list': [718, 743, 745, 762, 766, 796, 790, 791, 793, 794, 788],
                'offset': 2,
                'box_coordinates': True
            }
            box_residues(input_pdb_path='/path/to/myStructure.pdb', 
                        output_pdb_path='/path/to/newBox.pdb', 
                        properties=prop)

    Info:
        * wrapped_software:
            * name: In house using Biopython
            * version: >=1.76
            * license: Apache-2.0
        * ontology:
            * name: EDAM
            * schema: http://edamontology.org/EDAM.owl

    """

    def __init__(self, input_pdb_path, output_pdb_path, 
                properties=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_pdb_path": output_pdb_path } 
        }

        # Properties specific for BB
        self.resid_list = properties.get('resid_list', [])
        self.offset = float(properties.get('offset', 2.0))
        self.box_coordinates = float(properties.get('box_coordinates', False))
        self.residue_offset = properties.get('residue_offset', 0)
        self.properties = properties

        # Check the properties
        self.check_properties(properties)

    def check_data_params(self, out_log, err_log):
        """ Checks all the input/output paths and parameters """
        self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"],"input_pdb_path", self.out_log, self.__class__.__name__)
        self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"],"output_pdb_path", False, self.out_log, self.__class__.__name__)

    @launchlogger
    def launch(self) -> int:
        """Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` utils.box_residues.BoxResidues object."""

        # check input/output paths and parameters
        self.check_data_params(self.out_log, self.err_log)

        # Setup Biobb
        if self.check_restart(): return 0
        self.stage_files()

        # Parse structure
        fu.log('Loading input PDB structure %s' % (self.io_dict["in"]["input_pdb_path"]), self.out_log, self.global_log)
        structure_name = PurePath(self.io_dict["in"]["input_pdb_path"]).name
        parser      = Bio.PDB.PDBParser(QUIET = True)
        structPDB   = parser.get_structure(structure_name, self.io_dict["in"]["input_pdb_path"])

        if len(structPDB):
            structPDB = structPDB[0]

        ## Mapping residue structure into input structure

        fu.log('Mapping residue structure into input structure', self.out_log, self.global_log)

        # Listing residues to be selected from the residue structure
        residPDB_res_list = []
        for residPDB_res in self.resid_list:
            if self.residue_offset:
                residPDB_res_list.append((' ', residPDB_res+self.residue_offset, ' '))
            else:
                residPDB_res_list.append((' ', residPDB_res, ' '))

        selection_res_list   = []
        selection_atoms_num  = 0
        for struct_chain in structPDB:
            for struct_res in struct_chain:
                if struct_res.get_id() in residPDB_res_list:
                    selection_res_list.append(struct_res)
                    selection_atoms_num += len(struct_res.get_list())

        if len(selection_res_list) == 0:
            fu.log(self.__class__.__name__ + ': Cannot match any of the residues listed in [%s] into %s' % (', '.join(str(v) for v in self.resid_list), self.io_dict["in"]["input_pdb_path"]), self.out_log)
            raise SystemExit(self.__class__.__name__ + ': Cannot match any of the residues listed in [%s] into %s' % (', '.join(str(v) for v in self.resid_list), self.io_dict["in"]["input_pdb_path"]))
        elif len(selection_res_list) !=  len(residPDB_res_list):
            fu.log('Cannot match all the residues listed in %s into %s. Found %s out of %s' % (', '.join(str(v) for v in self.resid_list),self.io_dict["in"]["input_pdb_path"], len(selection_res_list),len(residPDB_res_list)), self.out_log)
        else:
            fu.log('Selection of residues successfully matched', self.out_log, self.global_log)

        ## Compute binding site box size

        # compute box center
        selection_box_center = sum(atom.coord for res in selection_res_list for atom in res.get_atoms()) / selection_atoms_num
        fu.log('Binding site center (Angstroms): %10.3f%10.3f%10.3f' % (selection_box_center[0],selection_box_center[1],selection_box_center[2]), self.out_log, self.global_log)

        # compute box size
        selection_coords_max = np.amax([atom.coord for res in selection_res_list for atom in res.get_atoms()],axis=0)
        selection_box_size   = selection_coords_max - selection_box_center
        if self.offset:
            selection_box_size = [c + self.offset for c in selection_box_size]
        fu.log('Binding site size (Angstroms):   %10.3f%10.3f%10.3f' % (selection_box_size[0],selection_box_size[1],selection_box_size[2]), self.out_log, self.global_log)

        # compute volume
        vol = np.prod(selection_box_size) * 2**3
        fu.log('Volume (cubic Angstroms): %.0f' % (vol), self.out_log, self.global_log)

        # add box details as PDB remarks
        remarks = "REMARK BOX CENTER:%10.3f%10.3f%10.3f" % (selection_box_center[0],selection_box_center[1],selection_box_center[2])
        remarks += " SIZE:%10.3f%10.3f%10.3f" % (selection_box_size[0],selection_box_size[1],selection_box_size[2])

        selection_box_coords_txt   = ""
        # add (optional) box coordinates as 8 ATOM records
        if self.box_coordinates:
            fu.log('Adding box coordinates', self.out_log, self.global_log)
            selection_box_coords_txt  = get_box_coordinates(selection_box_center,selection_box_size)

        with open(self.io_dict["out"]["output_pdb_path"], 'w') as f:
            f.seek(0, 0)
            f.write(remarks.rstrip('\r\n') + '\n' + selection_box_coords_txt)

        fu.log('Saving output PDB file (with box setting annotations): %s' % (self.io_dict["out"]["output_pdb_path"]), self.out_log, self.global_log)

        return 0

def box_residues(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int:
    """Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` class and
    execute the :meth:`launch() <utils.box_residues.BoxResidues.launch>` method."""

    return BoxResidues(input_pdb_path=input_pdb_path,
                output_pdb_path=output_pdb_path,
                properties=properties, **kwargs).launch()

def main():
    """Command line execution of this building block. Please check the command line documentation."""
    parser = argparse.ArgumentParser(description="Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
    parser.add_argument('--config', required=False, help='Configuration file')

    # Specific args of each building block
    required_args = parser.add_argument_group('required arguments')
    required_args.add_argument('--input_pdb_path', required=True, help='PDB protein structure for which the box will be build. Its size and center will be set around the \'resid_list\' property once mapped against this PDB. Accepted formats: pdb.')
    required_args.add_argument('--output_pdb_path', required=True, help='PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb.')

    args = parser.parse_args()
    args.config = args.config or "{}"
    properties = settings.ConfReader(config=args.config).get_prop_dic()

    # Specific call of each building block
    box_residues(input_pdb_path=args.input_pdb_path, 
                output_pdb_path=args.output_pdb_path, 
                properties=properties)

if __name__ == '__main__':
    main()

#!/usr/bin/env python3

"""Module containing the BoxResidues class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import  settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_vs.utils.common import *


class BoxResidues(BiobbObject):
    """
    | biobb_vs BoxResidues
    | This class sets the center and the size of a rectangular parallelepiped box around a set of residues.
    | Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB. The residue identifiers that compose the selection (i.e. binding site) are provided by a property list.

    Args:
        input_pdb_path (str): PDB protein structure for which the box will be build. Its size and center will be set around the 'resid_list' property once mapped against this PDB. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box_residues.pdb>`_. Accepted formats: pdb (edam:format_1476).
        output_pdb_path (str): PDB including the annotation of the box center and size as REMARKs. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box_residues.pdb>`_. Accepted formats: pdb (edam:format_1476).
        properties (dic - Python dictionary object containing the tool parameters, not input/output files):
            * **resid_list** (*list*) - (None) List with all the residue numbers to form a cavity or binding site. Mandatory property.
            * **offset** (*float*) - (2.0) [0.1~1000|0.1] Extra distance (Angstroms) between the last residue atom and the box boundary.
            * **box_coordinates** (*bool*) - (False) Add box coordinates as 8 ATOM records.
            * **residue_offset** (*int*) - (0) [0~1000|1] Residue id offset.
            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.

    Examples:
        This is a use example of how to use the building block from Python::

            from biobb_vs.utils.box_residues import box_residues
            prop = { 
                'resid_list': [718, 743, 745, 762, 766, 796, 790, 791, 793, 794, 788],
                'offset': 2,
                'box_coordinates': True
            }
            box_residues(input_pdb_path='/path/to/myStructure.pdb', 
                        output_pdb_path='/path/to/newBox.pdb', 
                        properties=prop)

    Info:
        * wrapped_software:
            * name: In house using Biopython
            * version: >=1.76
            * license: Apache-2.0
        * ontology:
            * name: EDAM
            * schema: http://edamontology.org/EDAM.owl

    """

    def __init__(self, input_pdb_path, output_pdb_path, 
                properties=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_pdb_path": output_pdb_path } 
        }

        # Properties specific for BB
        self.resid_list = properties.get('resid_list', [])
        self.offset = float(properties.get('offset', 2.0))
        self.box_coordinates = float(properties.get('box_coordinates', False))
        self.residue_offset = properties.get('residue_offset', 0)
        self.properties = properties

        # Check the properties
        self.check_properties(properties)

    def check_data_params(self, out_log, err_log):
        """ Checks all the input/output paths and parameters """
        self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"],"input_pdb_path", self.out_log, self.__class__.__name__)
        self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"],"output_pdb_path", False, self.out_log, self.__class__.__name__)

    @launchlogger
    def launch(self) -> int:
        """Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` utils.box_residues.BoxResidues object."""

        # check input/output paths and parameters
        self.check_data_params(self.out_log, self.err_log)

        # Setup Biobb
        if self.check_restart(): return 0
        self.stage_files()

        # Parse structure
        fu.log('Loading input PDB structure %s' % (self.io_dict["in"]["input_pdb_path"]), self.out_log, self.global_log)
        structure_name = PurePath(self.io_dict["in"]["input_pdb_path"]).name
        parser      = Bio.PDB.PDBParser(QUIET = True)
        structPDB   = parser.get_structure(structure_name, self.io_dict["in"]["input_pdb_path"])

        if len(structPDB):
            structPDB = structPDB[0]

        ## Mapping residue structure into input structure

        fu.log('Mapping residue structure into input structure', self.out_log, self.global_log)

        # Listing residues to be selected from the residue structure
        residPDB_res_list = []
        for residPDB_res in self.resid_list:
            if self.residue_offset:
                residPDB_res_list.append((' ', residPDB_res+self.residue_offset, ' '))
            else:
                residPDB_res_list.append((' ', residPDB_res, ' '))

        selection_res_list   = []
        selection_atoms_num  = 0
        for struct_chain in structPDB:
            for struct_res in struct_chain:
                if struct_res.get_id() in residPDB_res_list:
                    selection_res_list.append(struct_res)
                    selection_atoms_num += len(struct_res.get_list())

        if len(selection_res_list) == 0:
            fu.log(self.__class__.__name__ + ': Cannot match any of the residues listed in [%s] into %s' % (', '.join(str(v) for v in self.resid_list), self.io_dict["in"]["input_pdb_path"]), self.out_log)
            raise SystemExit(self.__class__.__name__ + ': Cannot match any of the residues listed in [%s] into %s' % (', '.join(str(v) for v in self.resid_list), self.io_dict["in"]["input_pdb_path"]))
        elif len(selection_res_list) !=  len(residPDB_res_list):
            fu.log('Cannot match all the residues listed in %s into %s. Found %s out of %s' % (', '.join(str(v) for v in self.resid_list),self.io_dict["in"]["input_pdb_path"], len(selection_res_list),len(residPDB_res_list)), self.out_log)
        else:
            fu.log('Selection of residues successfully matched', self.out_log, self.global_log)

        ## Compute binding site box size

        # compute box center
        selection_box_center = sum(atom.coord for res in selection_res_list for atom in res.get_atoms()) / selection_atoms_num
        fu.log('Binding site center (Angstroms): %10.3f%10.3f%10.3f' % (selection_box_center[0],selection_box_center[1],selection_box_center[2]), self.out_log, self.global_log)

        # compute box size
        selection_coords_max = np.amax([atom.coord for res in selection_res_list for atom in res.get_atoms()],axis=0)
        selection_box_size   = selection_coords_max - selection_box_center
        if self.offset:
            selection_box_size = [c + self.offset for c in selection_box_size]
        fu.log('Binding site size (Angstroms):   %10.3f%10.3f%10.3f' % (selection_box_size[0],selection_box_size[1],selection_box_size[2]), self.out_log, self.global_log)

        # compute volume
        vol = np.prod(selection_box_size) * 2**3
        fu.log('Volume (cubic Angstroms): %.0f' % (vol), self.out_log, self.global_log)

        # add box details as PDB remarks
        remarks = "REMARK BOX CENTER:%10.3f%10.3f%10.3f" % (selection_box_center[0],selection_box_center[1],selection_box_center[2])
        remarks += " SIZE:%10.3f%10.3f%10.3f" % (selection_box_size[0],selection_box_size[1],selection_box_size[2])

        selection_box_coords_txt   = ""
        # add (optional) box coordinates as 8 ATOM records
        if self.box_coordinates:
            fu.log('Adding box coordinates', self.out_log, self.global_log)
            selection_box_coords_txt  = get_box_coordinates(selection_box_center,selection_box_size)

        with open(self.io_dict["out"]["output_pdb_path"], 'w') as f:
            f.seek(0, 0)
            f.write(remarks.rstrip('\r\n') + '\n' + selection_box_coords_txt)

        fu.log('Saving output PDB file (with box setting annotations): %s' % (self.io_dict["out"]["output_pdb_path"]), self.out_log, self.global_log)

        return 0

def box_residues(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int:
    """Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` class and
    execute the :meth:`launch() <utils.box_residues.BoxResidues.launch>` method."""

    return BoxResidues(input_pdb_path=input_pdb_path,
                output_pdb_path=output_pdb_path,
                properties=properties, **kwargs).launch()

def main():
    """Command line execution of this building block. Please check the command line documentation."""
    parser = argparse.ArgumentParser(description="Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
    parser.add_argument('--config', required=False, help='Configuration file')

    # Specific args of each building block
    required_args = parser.add_argument_group('required arguments')
    required_args.add_argument('--input_pdb_path', required=True, help='PDB protein structure for which the box will be build. Its size and center will be set around the \'resid_list\' property once mapped against this PDB. Accepted formats: pdb.')
    required_args.add_argument('--output_pdb_path', required=True, help='PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb.')

    args = parser.parse_args()
    args.config = args.config or "{}"
    properties = settings.ConfReader(config=args.config).get_prop_dic()

    # Specific call of each building block
    box_residues(input_pdb_path=args.input_pdb_path, 
                output_pdb_path=args.output_pdb_path, 
                properties=properties)

if __name__ == '__main__':
    main()
#!/usr/bin/env python3 Module containing the BoxResidues class and the command line interface. | biobb_vs BoxResidues     | This class sets the center and the size of a rectangular parallelepiped box around a set of residues.     | Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB. The residue identifiers that compose the selection (i.e. binding site) are provided by a property list.      Args:         input_pdb_path (str): PDB protein structure for which the box will be build. Its size and center will be set around the 'resid_list' property once mapped against this PDB. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box_residues.pdb>`_. Accepted formats: pdb (edam:format_1476).         output_pdb_path (str): PDB including the annotation of the box center and size as REMARKs. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box_residues.pdb>`_. Accepted formats: pdb (edam:format_1476).         properties (dic - Python dictionary object containing the tool parameters, not input/output files):             * **resid_list** (*list*) - (None) List with all the residue numbers to form a cavity or binding site. Mandatory property.             * **offset** (*float*) - (2.0) [0.1~1000|0.1] Extra distance (Angstroms) between the last residue atom and the box boundary.             * **box_coordinates** (*bool*) - (False) Add box coordinates as 8 ATOM records.             * **residue_offset** (*int*) - (0) [0~1000|1] Residue id offset.             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.      Examples:         This is a use example of how to use the building block from Python::              from biobb_vs.utils.box_residues import box_residues             prop = {                  'resid_list': [718, 743, 745, 762, 766, 796, 790, 791, 793, 794, 788],                 'offset': 2,                 'box_coordinates': True             }             box_residues(input_pdb_path='/path/to/myStructure.pdb',                          output_pdb_path='/path/to/newBox.pdb',                          properties=prop)      Info:         * wrapped_software:             * name: In house using Biopython             * version: >=1.76             * license: Apache-2.0         * ontology:             * name: EDAM             * schema: http://edamontology.org/EDAM.owl # Call parent class constructor # Input/Output files # Properties specific for BB # Check the properties Checks all the input/output paths and parameters Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` utils.box_residues.BoxResidues object. # check input/output paths and parameters # Setup Biobb # Parse structure ## Mapping residue structure into input structure # Listing residues to be selected from the residue structure ## Compute binding site box size # compute box center # compute box size # compute volume # add box details as PDB remarks # add (optional) box coordinates as 8 ATOM records Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` class and     execute the :meth:`launch() <utils.box_residues.BoxResidues.launch>` method. Command line execution of this building block. Please check the command line documentation. # Specific args of each building block # Specific call of each building block