"""
PDB molecular container
=======================

Molecular container for storing all contents of PDB files.
"""
import logging
import os
import propka.version
from propka.output import write_pka, print_header, print_result
from propka.conformation_container import ConformationContainer
from propka.lib import make_grid


_LOGGER = logging.getLogger(__name__)


class MolecularContainer:
    """Container for storing molecular contents of PDB files.

    TODO - this class name does not conform to PEP8 but has external use.
    We should deprecate and change eventually.


    .. versionchanged:: 3.4.0
       Removed :meth:`write_propka` and
       :meth:`additional_setup_when_reading_input_file` as reading and writing
       PROPKA input files is no longer supported.
    """

    def __init__(self, parameters, options=None):
        """Initialize molecular container.

        Args:
            parameters:  Parameters() object
            options:  options object
        """
        # printing out header before parsing input
        print_header()
        self.conformation_names = []
        self.conformations = {}
        self.options = options
        self.name = None
        try:
            version_class = getattr(propka.version, parameters.version)
            self.version = version_class(parameters)
        except AttributeError as err:
            print(err)
            errstr = 'Error: Version {0:s} does not exist'.format(
                parameters.version)
            raise Exception(errstr)

    def top_up_conformations(self):
        """Makes sure that all atoms are present in all conformations."""
        first = self.conformations[self.conformation_names[0]]
        for name in self.conformation_names[1:]:
            if len(self.conformations[name]) < len(first):
                self.conformations[name].top_up(first)

    def find_covalently_coupled_groups(self):
        """Find covalently coupled groups."""
        for name in self.conformation_names:
            self.conformations[name].find_covalently_coupled_groups()

    def find_non_covalently_coupled_groups(self):
        """Find non-covalently coupled groups."""
        verbose = self.options.display_coupled_residues
        for name in self.conformation_names:
            self.conformations[name].find_non_covalently_coupled_groups(
                verbose=verbose)

    def extract_groups(self):
        """Identify the groups needed for pKa calculation."""
        for name in self.conformation_names:
            self.conformations[name].extract_groups()

    def calculate_pka(self):
        """Calculate pKa values."""
        # calculate for each conformation
        for name in self.conformation_names:
            self.conformations[name].calculate_pka(
                self.version, self.options)
        # find non-covalently coupled groups
        self.find_non_covalently_coupled_groups()
        # find the average of the conformations
        self.average_of_conformations()
        # print out the conformation-average results
        print_result(self, 'AVR', self.version.parameters)

    def average_of_conformations(self):
        """Generate an average of conformations."""
        parameters = self.conformations[self.conformation_names[0]].parameters
        # make a new configuration to hold the average values
        avr_conformation = ConformationContainer(
            name='average', parameters=parameters, molecular_container=self)
        container = self.conformations[self.conformation_names[0]]
        for group in container.get_groups_for_calculations():
            # new group to hold average values
            avr_group = group.clone()
            # sum up all groups ...
            for name in self.conformation_names:
                group_to_add = self.conformations[name].find_group(group)
                if group_to_add:
                    avr_group += group_to_add
                else:
                    str_ = (
                        'Group {0:s} could not be found in '
                        'conformation {1:s}.'.format(
                            group.atom.residue_label, name))
                    _LOGGER.warning(str_)
            # ... and store the average value
            avr_group = avr_group / len(self.conformation_names)
            avr_conformation.groups.append(avr_group)
        # store information on coupling in the average container
        if len(list(filter(lambda c: c.non_covalently_coupled_groups,
                           self.conformations.values()))):
            avr_conformation.non_covalently_coupled_groups = True
        # store chain info
        avr_conformation.chains = self.conformations[
            self.conformation_names[0]].chains
        self.conformations['AVR'] = avr_conformation

    def write_pka(self, filename=None, reference="neutral",
                  direction="folding", options=None):
        """Write pKa information to a file.

        Args:
            filename:  file to write to
            reference:  reference state
            direction:  folding vs. unfolding
            options:  options object
        """
        if filename is None:
            filename = os.path.join('{0:s}.pka'.format(self.name))
        # if the display_coupled_residues option is true, write the results out
        # to an alternative pka file
        if self.options.display_coupled_residues:
            filename = os.path.join('{0:s}_alt_state.pka'.format(self.name))
        if (hasattr(self.version.parameters, 'output_file_tag')
                and len(self.version.parameters.output_file_tag) > 0):
            filename = os.path.join(
                '{0:s}_{1:s}.pka'.format(
                    self.name, self.version.parameters.output_file_tag))
        write_pka(
            self, self.version.parameters, filename=filename,
            conformation='AVR', reference=reference)

    def get_folding_profile(self, conformation='AVR', reference="neutral",
                            grid=[0., 14., 0.1]):
        """Get a folding profile.

        Args:
            conformation:  conformation to select
            reference:  reference state
            direction:  folding direction (folding)
            grid:  the grid of pH values [min, max, step_size]
            options:  options object
        Returns:
            TODO - figure out what these are
            1. profile
            2. opt
            3. range_80pct
            4. stability_range
        """
        # calculate stability profile
        profile = []
        for ph in make_grid(*grid):
            conf = self.conformations[conformation]
            ddg = conf.calculate_folding_energy(ph=ph, reference=reference)
            profile.append([ph, ddg])
        # find optimum
        opt = [None, 1e6]
        for point in profile:
            opt = min(opt, point, key=lambda v: v[1])
        # find values within 80 % of optimum
        range_80pct = [None, None]
        values_within_80pct = [p[0] for p in profile if p[1] < 0.8*opt[1]]
        if len(values_within_80pct) > 0:
            range_80pct = [min(values_within_80pct), max(values_within_80pct)]
        # find stability range
        stability_range = [None, None]
        stable_values = [p[0] for p in profile if p[1] < 0.0]
        if len(stable_values) > 0:
            stability_range = [min(stable_values), max(stable_values)]
        return profile, opt, range_80pct, stability_range

    def get_charge_profile(self, conformation='AVR', grid=[0., 14., .1]):
        """Get charge profile for conformation as function of pH.

        Args:
            conformation:  conformation to test
            grid:  grid of pH values [min, max, step]
        Returns:
            list of charge state values
        """
        charge_profile = []
        for ph in make_grid(*grid):
            conf = self.conformations[conformation]
            q_unfolded, q_folded = conf.calculate_charge(
                self.version.parameters, ph=ph)
            charge_profile.append([ph, q_unfolded, q_folded])
        return charge_profile

    def get_pi(self, conformation='AVR', grid=[0., 14., 1], *,
            precision: float = 1e-4):
        """Get the isoelectric points for folded and unfolded states.

        Args:
            conformation:  conformation to test
            grid:  grid of pH values [min, max, step]
            precision:  Compute pI up to this precision
        Returns:
            1. Folded state PI
            2. Unfolded state PI
        """
        conf = self.conformations[conformation]

        WHICH_UNFOLDED = 0
        WHICH_FOLDED = 1

        def pi(which, pH, min_, max_):
            charge = conf.calculate_charge(
                self.version.parameters, ph=pH)[which]
            if max_ - min_ > precision:
                if charge > 0.0:
                    min_ = pH
                else:
                    max_ = pH
                next_pH = (min_ + max_) / 2
                return pi(which, next_pH, min_, max_)
            return pH

        start = (grid[0] + grid[1]) / 2, grid[0], grid[1]

        return (
            pi(WHICH_FOLDED, *start),
            pi(WHICH_UNFOLDED, *start),
        )
