#!/usr/bin/env python3

"""Module containing the LeapSolvate class and the command line interface."""
import argparse
import shutil, re
from pathlib import Path, PurePath
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_amber.leap.common import *

class LeapSolvate(BiobbObject):
    """
    | biobb_amber LeapSolvate
    | Wrapper of the `AmberTools (AMBER MD Package) leap tool <https://ambermd.org/AmberTools.php>`_ module.
    | Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package.

    Args:
        input_pdb_path (str): Input 3D structure PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/structure.leap.pdb>`_. Accepted formats: pdb (edam:format_1476).
        input_lib_path (str) (Optional): Input ligand library parameters file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.lib>`_. Accepted formats: lib (edam:format_3889), zip (edam:format_3987).
        input_frcmod_path (str) (Optional): Input ligand frcmod parameters file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.frcmod>`_. Accepted formats: frcmod (edam:format_3888), zip (edam:format_3987).
        input_params_path (str) (Optional): Additional leap parameter files to load with loadAmberParams Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/frcmod.ionsdang_spce.txt>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987).
        input_source_path (str) (Optional): Additional leap command files to load with source Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/leaprc.water.spce.txt>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987).
        output_pdb_path (str): Output 3D structure PDB file matching the topology file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.solv.pdb>`_. Accepted formats: pdb (edam:format_1476).
        output_top_path (str): Output topology file (AMBER ParmTop). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.solv.top>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
        output_crd_path (str): Output coordinates file (AMBER crd). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.solv.crd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878).
        properties (dic - Python dictionary object containing the tool parameters, not input/output files):
            * **forcefield** (*list*) - (["protein.ff14SB","DNA.bsc1","gaff"]) Forcefield to be used for the structure generation. Values: protein.ff14SB, protein.ff19SB, DNA.bsc1, DNA.OL15, RNA.OL3, gaff.
            * **water_type** (*str*) - ("TIP3PBOX") Water molecule parameters to be used for the topology. Values: POL3BOX, QSPCFWBOX, SPCBOX, SPCFWBOX, TIP3PBOX, TIP3PFBOX, TIP4PBOX, TIP4PEWBOX, OPCBOX, OPC3BOX, TIP5PBOX.
            * **box_type** (*str*) - ("truncated_octahedron") Type for the MD system box. Values: cubic, truncated_octahedron.
            * **ions_type** (*str*) - ("ionsjc_tip3p") Ions type. Values: ionsjc_tip3p, ionsjc_spce, ionsff99_tip3p, ions_charmm22, ionsjc_tip4pew, None.
            * **neutralise** (*bool*) - ("False") Energetically neutralise the system adding the necessary counterions.
            * **iso** (*bool*) - ("False") Make the box isometric.
            * **positive_ions_number** (*int*) - (0) Number of additional positive ions to include in the system box.
            * **negative_ions_number** (*int*) - (0) Number of additional negative ions to include in the system box.
            * **positive_ions_type** (*str*) - ("Na+") Type of additional positive ions to include in the system box. Values: Na+,K+.
            * **negative_ions_type** (*str*) - ("Cl-") Type of additional negative ions to include in the system box. Values: Cl-.
            * **distance_to_molecule** (*float*) - ("8.0") Size for the MD system box -in Angstroms-, defined such as the minimum distance between any atom originally present in solute and the edge of the periodic box is given by this distance parameter.
            * **closeness** (*float*) - ("1.0") How close, in Å, solvent ATOMs may come to solute ATOMs.
            * **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_amber.leap.leap_solvate import leap_solvate
            prop = {
                'forcefield': ['protein.ff14SB'],
                'water_type': 'TIP3PBOX',
                'box_type': 'truncated_octahedron',
                'neutralise' : True
            }
            leap_solvate(input_pdb_path='/path/to/structure.pdb',
                          output_pdb_path='/path/to/newStructure.pdb',
                          output_top_path='/path/to/newTopology.top',
                          output_crd_path='/path/to/newCoordinates.crd',
                          properties=prop)

    Info:
        * wrapped_software:
            * name: AmberTools tLeap
            * version: >20.9
            * license: LGPL 2.1
        * ontology:
            * name: EDAM
            * schema: http://edamontology.org/EDAM.owl

    """

    def __init__(self, input_pdb_path: str, output_pdb_path: str,
    output_top_path: str, output_crd_path: str,
    input_lib_path: str = None, input_frcmod_path: str = None,
    input_params_path: str = None, input_source_path: str = None,
    properties: dict = None, **kwargs):

        properties = properties or {}

        # Call parent class constructor
        super().__init__(properties)

        # Input/Output files
        self.io_dict = {
            'in': { 'input_pdb_path': input_pdb_path,
                    'input_lib_path': input_lib_path,
                    'input_frcmod_path': input_frcmod_path,
                    'input_params_path': input_params_path,
                    'input_source_path': input_source_path
            },
            'out': {    'output_pdb_path': output_pdb_path,
                        'output_top_path': output_top_path,
                        'output_crd_path': output_crd_path }
        }

        # # Ligand Parameter lists
        # self.ligands_lib_list = []
        # if input_lib_path:
        #     self.ligands_lib_list.append(input_lib_path)
        #
        # self.ligands_frcmod_list = []
        # if input_frcmod_path:
        #     self.ligands_frcmod_list.append(input_frcmod_path)

        # Properties specific for BB
        self.properties = properties
        self.forcefield = properties.get('forcefield', ["protein.ff14SB","DNA.bsc1","gaff"])
        self.water_type = properties.get('water_type', "TIP3PBOX")
        self.box_type = properties.get('box_type', "truncated_octahedron")
        self.ions_type = properties.get('ions_type', "ionsjc_tip3p")
        self.neutralise = properties.get('neutralise', False)
        self.iso = properties.get('iso', False)
        self.positive_ions_number = properties.get('positive_ions_number', 0)
        self.positive_ions_type = properties.get('positive_ions_type', "Na+")
        self.negative_ions_number = properties.get('negative_ions_number', 0)
        self.negative_ions_type = properties.get('negative_ions_type', "Cl-")
        self.distance_to_molecule = properties.get('distance_to_molecule', 8.0)
        self.closeness = properties.get('closeness', 1.0)

        # Check the properties
        self.check_properties(properties)

    def check_data_params(self, out_log, err_log):
        """ Checks input/output paths correctness """

        # Check input(s)
        self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", False, out_log, self.__class__.__name__)
        self.io_dict["in"]["input_lib_path"] = check_input_path(self.io_dict["in"]["input_lib_path"], "input_lib_path", True, out_log, self.__class__.__name__)
        self.io_dict["in"]["input_frcmod_path"] = check_input_path(self.io_dict["in"]["input_frcmod_path"], "input_frcmod_path", True, out_log, self.__class__.__name__)
        #self.io_dict["in"]["input_params_path"] = check_input_path(self.io_dict["in"]["input_params_path"], "input_params_path", True, out_log, self.__class__.__name__)
        #self.io_dict["in"]["input_source_path"] = check_input_path(self.io_dict["in"]["input_source_path"], "input_source_path", True, out_log, self.__class__.__name__)

        # Check output(s)
        self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"],"output_pdb_path", False, out_log, self.__class__.__name__)
        self.io_dict["out"]["output_top_path"] = check_output_path(self.io_dict["out"]["output_top_path"],"output_top_path", False, out_log, self.__class__.__name__)
        self.io_dict["out"]["output_crd_path"] = check_output_path(self.io_dict["out"]["output_crd_path"],"output_crd_path", False, out_log, self.__class__.__name__)

    @launchlogger
    def launch(self):
        """Launches the execution of the LeapSolvate module."""

        # 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()

        # Creating temporary folder
        self.tmp_folder = fu.create_unique_dir()
        fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)

        # Leap configuration (instructions) file
        instructions_file = str(PurePath(self.tmp_folder).joinpath("leap.in"))

        box_command = "solvateOct"
        if self.box_type == "cubic":
            box_command = "solvateBox"

        # Forcefield
        #source_ff_command = "source leaprc." + self.forcefield

        # Water Type
        # leaprc.water.tip4pew, tip4pd, tip3p, spceb, spce, opc, fb4, fb3
        # Values: POL3BOX, QSPCFWBOX, SPCBOX, SPCFWBOX, TIP3PBOX, TIP3PFBOX, TIP4PBOX, TIP4PEWBOX, OPCBOX, OPC3BOX, TIP5PBOX.
        source_wat_command = "source leaprc.water.tip3p"
        if self.water_type == "TIP4PEWBOX":
            source_wat_command = "leaprc.water.tip4pew"
        if self.water_type == "TIP4PBOX":
            source_wat_command = "leaprc.water.tip4pd"
        if re.match(r"SPC", self.water_type):
            source_wat_command = "source leaprc.water.spce"
        if re.match(r"OPC", self.water_type):
            source_wat_command = "source leaprc.water.opc"

        # Counterions
        ions_command = ""
        if self.neutralise:
            ions_command = ions_command + "addions mol " + self.negative_ions_type + " 0 \n"
            ions_command = ions_command + "addions mol " + self.positive_ions_type + " 0 \n"

        if self.negative_ions_number != 0:
            ions_command = ions_command + "addions mol " + self.negative_ions_type + " " + str(self.negative_ions_number) + " \n"
        if self.positive_ions_number != 0:
            ions_command = ions_command + "addions mol " + self.positive_ions_type + " " + str(self.positive_ions_number) + " \n"

        ligands_lib_list = []
        if self.io_dict['in']['input_lib_path'] is not None:
            if self.io_dict['in']['input_lib_path'].endswith('.zip'):
                ligands_lib_list = fu.unzip_list(self.io_dict['in']['input_lib_path'], dest_dir=self.tmp_folder, out_log=self.out_log)
            else:
                ligands_lib_list.append(self.io_dict['in']['input_lib_path'])

        ligands_frcmod_list = []
        if self.io_dict['in']['input_frcmod_path'] is not None:
            if self.io_dict['in']['input_frcmod_path'].endswith('.zip'):
                ligands_frcmod_list = fu.unzip_list(self.io_dict['in']['input_frcmod_path'], dest_dir=self.tmp_folder, out_log=self.out_log)
            else:
                ligands_frcmod_list.append(self.io_dict['in']['input_frcmod_path'])

        amber_params_list = []
        if self.io_dict['in']['input_params_path'] is not None:
            if self.io_dict['in']['input_params_path'].endswith('.zip'):
                amber_params_list = fu.unzip_list(self.io_dict['in']['input_params_path'], dest_dir=self.tmp_folder, out_log=self.out_log)
            else:
                amber_params_list.append(self.io_dict['in']['input_params_path'])

        leap_source_list = []
        if self.io_dict['in']['input_source_path'] is not None:
            if self.io_dict['in']['input_source_path'].endswith('.zip'):
                leap_source_list = fu.unzip_list(self.io_dict['in']['input_source_path'], dest_dir=self.tmp_folder, out_log=self.out_log)
            else:
                leap_source_list.append(self.io_dict['in']['input_source_path'])

        with open(instructions_file, 'w') as leapin:
                # Forcefields loaded by default:
                # Protein: ff14SB (PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA)
                #leapin.write("source leaprc.protein.ff14SB \n")
                # DNA: parmBSC1 (ParmBSC1 (ff99 + bsc0 + bsc1) for DNA. Ivani et al. Nature Methods 13: 55, 2016)
                #leapin.write("source leaprc.DNA.bsc1 \n")
                # Ligands: GAFF (General Amber Force field, J. Comput. Chem. 2004 Jul 15;25(9):1157-74)
                #leapin.write("source leaprc.gaff \n")

                # Forcefields loaded from input forcefield property
                for t in self.forcefield:
                    leapin.write("source leaprc.{}\n".format(t))

                # Additional Leap commands
                for leap_commands in leap_source_list:
                    leapin.write("source " + leap_commands + "\n")

                # Ions Type
                if self.ions_type != "None":
                    leapin.write("loadamberparams frcmod." + self.ions_type + "\n")

                # Additional Amber parameters
                for amber_params in amber_params_list:
                    leapin.write("loadamberparams " + amber_params + "\n")

                # Water Model loaded from input water_model property
                leapin.write(source_wat_command + " \n")

                # Ligand(s) libraries (if any)
                for amber_lib in ligands_lib_list:
                    leapin.write("loadOff " + amber_lib + "\n")
                for amber_frcmod in ligands_frcmod_list:
                    leapin.write("loadamberparams " + amber_frcmod + "\n")

                # Loading PDB file
                leapin.write("mol = loadpdb " + self.io_dict['in']['input_pdb_path'] + " \n")

                # Generating box + adding water molecules
                leapin.write(box_command + " mol " + self.water_type + " " + str(self.distance_to_molecule) + " " + str(self.closeness))
                leapin.write(" iso \n") if self.iso else leapin.write("\n")

                # Adding counterions
                leapin.write(ions_command)

                # Saving output PDB file, coordinates and topology
                leapin.write("savepdb mol " + self.io_dict['out']['output_pdb_path'] + " \n")
                leapin.write("saveAmberParm mol " + self.io_dict['out']['output_top_path'] + " " + self.io_dict['out']['output_crd_path'] + "\n")
                leapin.write("quit \n");

        # Command line
        self.cmd = ['tleap ',
               '-f', instructions_file
               ]

        # Run Biobb block
        self.run_biobb()

        # Copy files to host
        self.copy_to_host()

        # Saving octahedron box with all decimals in PDB file. Needed for the add_ions BB.

        # Getting octahedron box from generated crd file
        with open(self.io_dict['out']['output_crd_path'], "r") as file:
            for line in file:
                pass

        # Adding box as a first line in the generated pdb file with OCTBOX tag
        octbox = "OCTBOX " + line
        with open(self.io_dict['out']['output_pdb_path'], 'r+') as f:
            content = f.read()
            f.seek(0, 0)
            f.write(octbox + content)

        # remove temporary folder(s)
        if self.remove_tmp:
            self.tmp_files.append(self.tmp_folder)
            self.tmp_files.append("leap.log")
            self.remove_tmp_files()

        return self.return_code

def leap_solvate(input_pdb_path: str, output_pdb_path: str,
           output_top_path: str, output_crd_path: str,
           input_lib_path: str = None, input_frcmod_path: str = None,
           input_params_path: str = None, input_source_path: str = None,
           properties: dict = None, **kwargs) -> int:
    """Create :class:`LeapSolvate <leap.leap_solvate.LeapSolvate>`leap.leap_solvate.LeapSolvate class and
    execute :meth:`launch() <leap.leap_solvate.LeapSolvate.launch>` method"""

    return LeapSolvate( input_pdb_path=input_pdb_path,
                        input_lib_path=input_lib_path,
                        input_frcmod_path=input_frcmod_path,
                        input_params_path=input_params_path,
                        input_source_path=input_source_path,
                        output_pdb_path=output_pdb_path,
                        output_top_path=output_top_path,
                        output_crd_path=output_crd_path,
                        properties=properties).launch()

def main():
    parser = argparse.ArgumentParser(description='Generating and solvating a system box for an AMBER MD system. using tLeap program from AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
    parser.add_argument('--config', required=False, help='Configuration file')

    # Specific args
    required_args = parser.add_argument_group('required arguments')
    required_args.add_argument('--input_pdb_path', required=True, help='Input 3D structure PDB file. Accepted formats: pdb.')
    required_args.add_argument('--input_lib_path', required=False, help='Input ligand library parameters file. Accepted formats: lib, zip.')
    required_args.add_argument('--input_frcmod_path', required=False, help='Input ligand frcmod parameters file. Accepted formats: frcmod, zip.')
    required_args.add_argument('--input_params_path', required=False, help='Additional leap parameter files to load with loadAmberParams Leap command. Accepted formats: leapin, in, txt, zip.')
    required_args.add_argument('--input_source_path', required=False, help='Additional leap command files to load with source Leap command. Accepted formats: leapin, in, txt, zip.')
    required_args.add_argument('--output_pdb_path', required=True, help='Output 3D structure PDB file matching the topology file. Accepted formats: pdb.')
    required_args.add_argument('--output_top_path', required=True, help='Output topology file (AMBER ParmTop). Accepted formats: top.')
    required_args.add_argument('--output_crd_path', required=True, help='Output coordinates file (AMBER crd). Accepted formats: crd.')

    args = parser.parse_args()
    config = args.config if args.config else None
    properties = settings.ConfReader(config=config).get_prop_dic()

    # Specific call
    leap_solvate(    input_pdb_path=args.input_pdb_path,
                    input_lib_path=args.input_lib_path,
                    input_frcmod_path=args.input_frcmod_path,
                    input_params_path=args.input_params_path,
                    input_source_path=args.input_source_path,
                    output_pdb_path=args.output_pdb_path,
                    output_top_path=args.output_top_path,
                    output_crd_path=args.output_crd_path,
                    properties=properties)

if __name__ == '__main__':
    main()
