#!/usr/bin/env python

#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
XML I/O parser for the SMIRNOFF (SMIRKS Native Open Force Field) format.

.. codeauthor:: <NAME> <<EMAIL>>
.. codeauthor:: <NAME> <<EMAIL>>
.. codeauthor:: <NAME> <<EMAIL>>

"""

__all__ = [
    'ParameterIOHandler',
    'XMLParameterIOHandler',
]


#=============================================================================================
# GLOBAL IMPORTS
#=============================================================================================

import logging
import os

import xmltodict

from simtk import unit
from openforcefield.utils.utils import get_data_filename


#=============================================================================================
# CONFIGURE LOGGER
#=============================================================================================

logger = logging.getLogger(__name__)


#=============================================================================================
# QUANTITY PARSING UTILITIES
#=============================================================================================

def _ast_unit_eval(node):
    """
    Performs a safe algebraic syntax tree evaluation of a unit.

    This will likely be replaced by the native implementation in Pint
    if/when we'll switch over to Pint units.
    """
    import ast
    import operator as op

    operators = {ast.Add: op.add, ast.Sub: op.sub, ast.Mult: op.mul,
        ast.Div: op.truediv, ast.Pow: op.pow, ast.BitXor: op.xor,
        ast.USub: op.neg}

    if isinstance(node, ast.Num):  # <number>
        return node.n
    elif isinstance(node, ast.BinOp):  # <left> <operator> <right>
        return operators[type(node.op)](_ast_unit_eval(node.left), _ast_unit_eval(node.right))
    elif isinstance(node, ast.UnaryOp):  # <operator>( <operand> ) e.g., -1
        return operators[type(node.op)](_ast_unit_eval(node.operand))
    elif isinstance(node, ast.Name):
        # Check if this is a simtk unit.
        u = getattr(unit, node.id)
        if not isinstance(u, unit.Unit):
            raise ValueError('No unit named {} found in simtk.unit.'.format(node.id))
        return u
    else:
        raise TypeError(node)


#=============================================================================================
# Base ParameterIOHandler
#=============================================================================================


class ParameterIOHandler:
    """
    Base class for handling serialization/deserialization of SMIRNOFF ForceField objects
    """
    _FORMAT = None

    def __init__(self):
        """
        Create a new ParameterIOHandler.

        """
        pass
        #self._forcefield = forcefield

    def parse_file(self, filename):
        """

        Parameters
        ----------
        filename

        Returns
        -------

        """
        pass

    def parse_string(self, data):
        """
        Parse a SMIRNOFF force field definition in a seriaized format

        Parameters
        ----------
        data

        Returns
        -------

        """
        pass

    def to_file(self, filename, smirnoff_data):
        """
        Write the current forcefield parameter set to a file.

        Parameters
        ----------
        filename : str
            The filename to write to.
        smirnoff_data : dict
            A dictionary structured in compliance with the SMIRNOFF spec

        Returns
        -------

        """
        pass

    def to_string(self, smirnoff_data):
        """
        Render the forcefield parameter set to a string

        Parameters
        ----------
        smirnoff_data : dict
            A dictionary structured in compliance with the SMIRNOFF spec

        Returns
        -------
        str
        """
        pass


#=============================================================================================
# XML I/O
#=============================================================================================



class XMLParameterIOHandler(ParameterIOHandler):
    """
    Handles serialization/deserialization of SMIRNOFF ForceField objects from OFFXML format.
    """
    # TODO: Come up with a better keyword for format
    _FORMAT = 'XML'



    # TODO: Fix this
    def parse_file(self, source):
        """Parse a SMIRNOFF force field definition in XML format, read from a file.

        A ``ParseError`` is raised if the XML cannot be processed.

        Parameters
        ----------
        source : str or file-like obj
            File path of file-like obj specifying a SMIRNOFF force field definition in `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_.

        .. notes ::

           * New SMIRNOFF sections are handled independently, as if they were specified in the same file.
           * If a SMIRNOFF section that has already been read appears again, its definitions are appended to the end of the previously-read
             definitions if the sections are configured with compatible attributes; otherwise, an ``IncompatibleTagException`` is raised.
        """
        from pyexpat import ExpatError
        from openforcefield.typing.engines.smirnoff.forcefield import ParseError

        # this handles open file-like objects (and strings)
        try:
            smirnoff_data = self.parse_string(source)
            return smirnoff_data
        except ParseError:
            pass

        # This handles complete/local filenames
        try:
            # Check if the file exists in the data/forcefield directory
            data = open(source).read()
            smirnoff_data = xmltodict.parse(data, attr_prefix='')
            return smirnoff_data
        except ExpatError:
            pass
        except FileNotFoundError:
            pass

        # This handles nonlocal filenames
        try:
            # Check if the file exists in the data/forcefield directory
            temp_file = get_data_filename(os.path.join('forcefield', source))
            data = open(temp_file).read()
            smirnoff_data = self.parse_string(data)
            return smirnoff_data

        except Exception as e:
            # Fail with an error message about which file could not be read.
            # TODO: Also handle case where fallback to 'data' directory encounters problems,
            # but this is much less worrisome because we control those files.
            msg = str(e) + '\n'
            if hasattr(source, 'name'):
                filename = source.name
            else:
                filename = str(source)
            msg += "ForceField.loadFile() encountered an error reading file '%s'\n" % filename
            raise ParseError(msg)

    def parse_string(self, data):
        """Parse a SMIRNOFF force field definition in XML format.

        A ``ParseError`` is raised if the XML cannot be processed.

        Parameters
        ----------
        data : str
            A SMIRNOFF force field definition in `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_.

        """
        from pyexpat import ExpatError
        from openforcefield.typing.engines.smirnoff.forcefield import ParseError

        # Parse XML file
        try:
            smirnoff_data = xmltodict.parse(data, attr_prefix='')
            return smirnoff_data
        except ExpatError as e:
            raise ParseError(e)

    def to_file(self, filename, smirnoff_data):
        """Write the current forcefield parameter set to a file, autodetecting the type from the extension.

        Parameters
        ----------
        filename : str
            The name of the file to be written.
            The `.offxml` file extension must be present.
        smirnoff_data : dict
            A dict structured in compliance with the SMIRNOFF data spec.

        """
        xml_string = self.to_string(smirnoff_data)
        (basename, extension) = os.path.splitext(filename)
        if extension == '.offxml':
            with open(filename, 'wb') as of:
                of.write(xml_string)
        else:
            msg = "Cannot export forcefield parameters to file '{}'\n".format(
                filename)
            msg += 'Export to extension {} not implemented yet.\n'.format(
                extension)
            msg += "Supported choices are: ['.offxml']"
            raise NotImplementedError(msg)

    def to_string(self, smirnoff_data):
        """
        Write the current forcefield parameter set to an XML string.

        Parameters
        ----------
        smirnoff_data : dict
            A dictionary structured in compliance with the SMIRNOFF spec

        Returns
        -------
        serialized_forcefield : str
            XML String representation of this forcefield.

        """
        def prepend_all_keys(d, char='@'):
            """
            Modify a dictionary in-place, prepending a specified string to each key
            that doesn't refer to a value that is list or dict.

            Parameters
            ----------
            d : dict
                Hierarchical dictionary to traverse and modify keys
            char : string, optional. Default='@'
                String to prepend onto each applicable dictionary key

            """
            if isinstance(d, dict):
                for key in list(d.keys()):
                    if isinstance(d[key], list) or isinstance(d[key], dict):
                        prepend_all_keys(d[key])
                    else:
                        new_key = char + key
                        d[new_key] = d[key]
                        del d[key]
                        prepend_all_keys(d[new_key])
            elif isinstance(d, list):
                for item in d:
                    prepend_all_keys(item)

        prepend_all_keys(smirnoff_data['SMIRNOFF'])
        print(smirnoff_data)
        print()
        return xmltodict.unparse(smirnoff_data, pretty=True)

    def to_xml(self, smirnoff_data):
        """Render the forcefield parameter set to XML.

        Returns
        -------
        smirnoff_data : dict
            A dictionary structures in comliance with the SMIRNOFF data spec.
        """
        return self.to_string(smirnoff_data)

    # # TODO: Do we need this? Should we use built-in dict-based serialization?
    # def __getstate__(self):
    #     """Serialize to XML.
    #     """
    #     return self.to_xml()
    #
    # # TODO: Do we need this? Should we use built-in dict-based serialization?
    # def __setstate__(self, state):
    #     """Deserialize from XML.
    #     """
    #     self._initialize()
    #     self.parse_xml(state)

#!/usr/bin/env python

#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
XML I/O parser for the SMIRNOFF (SMIRKS Native Open Force Field) format.

.. codeauthor:: <NAME> <<EMAIL>>
.. codeauthor:: <NAME> <<EMAIL>>
.. codeauthor:: <NAME> <<EMAIL>>

"""

__all__ = [
    'ParameterIOHandler',
    'XMLParameterIOHandler',
]


#=============================================================================================
# GLOBAL IMPORTS
#=============================================================================================

import logging
import os

import xmltodict

from simtk import unit
from openforcefield.utils.utils import get_data_filename


#=============================================================================================
# CONFIGURE LOGGER
#=============================================================================================

logger = logging.getLogger(__name__)


#=============================================================================================
# QUANTITY PARSING UTILITIES
#=============================================================================================

def _ast_unit_eval(node):
    """
    Performs a safe algebraic syntax tree evaluation of a unit.

    This will likely be replaced by the native implementation in Pint
    if/when we'll switch over to Pint units.
    """
    import ast
    import operator as op

    operators = {ast.Add: op.add, ast.Sub: op.sub, ast.Mult: op.mul,
        ast.Div: op.truediv, ast.Pow: op.pow, ast.BitXor: op.xor,
        ast.USub: op.neg}

    if isinstance(node, ast.Num):  # <number>
        return node.n
    elif isinstance(node, ast.BinOp):  # <left> <operator> <right>
        return operators[type(node.op)](_ast_unit_eval(node.left), _ast_unit_eval(node.right))
    elif isinstance(node, ast.UnaryOp):  # <operator>( <operand> ) e.g., -1
        return operators[type(node.op)](_ast_unit_eval(node.operand))
    elif isinstance(node, ast.Name):
        # Check if this is a simtk unit.
        u = getattr(unit, node.id)
        if not isinstance(u, unit.Unit):
            raise ValueError('No unit named {} found in simtk.unit.'.format(node.id))
        return u
    else:
        raise TypeError(node)


#=============================================================================================
# Base ParameterIOHandler
#=============================================================================================


class ParameterIOHandler:
    """
    Base class for handling serialization/deserialization of SMIRNOFF ForceField objects
    """
    _FORMAT = None

    def __init__(self):
        """
        Create a new ParameterIOHandler.

        """
        pass
        #self._forcefield = forcefield

    def parse_file(self, filename):
        """

        Parameters
        ----------
        filename

        Returns
        -------

        """
        pass

    def parse_string(self, data):
        """
        Parse a SMIRNOFF force field definition in a seriaized format

        Parameters
        ----------
        data

        Returns
        -------

        """
        pass

    def to_file(self, filename, smirnoff_data):
        """
        Write the current forcefield parameter set to a file.

        Parameters
        ----------
        filename : str
            The filename to write to.
        smirnoff_data : dict
            A dictionary structured in compliance with the SMIRNOFF spec

        Returns
        -------

        """
        pass

    def to_string(self, smirnoff_data):
        """
        Render the forcefield parameter set to a string

        Parameters
        ----------
        smirnoff_data : dict
            A dictionary structured in compliance with the SMIRNOFF spec

        Returns
        -------
        str
        """
        pass


#=============================================================================================
# XML I/O
#=============================================================================================



class XMLParameterIOHandler(ParameterIOHandler):
    """
    Handles serialization/deserialization of SMIRNOFF ForceField objects from OFFXML format.
    """
    # TODO: Come up with a better keyword for format
    _FORMAT = 'XML'



    # TODO: Fix this
    def parse_file(self, source):
        """Parse a SMIRNOFF force field definition in XML format, read from a file.

        A ``ParseError`` is raised if the XML cannot be processed.

        Parameters
        ----------
        source : str or file-like obj
            File path of file-like obj specifying a SMIRNOFF force field definition in `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_.

        .. notes ::

           * New SMIRNOFF sections are handled independently, as if they were specified in the same file.
           * If a SMIRNOFF section that has already been read appears again, its definitions are appended to the end of the previously-read
             definitions if the sections are configured with compatible attributes; otherwise, an ``IncompatibleTagException`` is raised.
        """
        from pyexpat import ExpatError
        from openforcefield.typing.engines.smirnoff.forcefield import ParseError

        # this handles open file-like objects (and strings)
        try:
            smirnoff_data = self.parse_string(source)
            return smirnoff_data
        except ParseError:
            pass

        # This handles complete/local filenames
        try:
            # Check if the file exists in the data/forcefield directory
            data = open(source).read()
            smirnoff_data = xmltodict.parse(data, attr_prefix='')
            return smirnoff_data
        except ExpatError:
            pass
        except FileNotFoundError:
            pass

        # This handles nonlocal filenames
        try:
            # Check if the file exists in the data/forcefield directory
            temp_file = get_data_filename(os.path.join('forcefield', source))
            data = open(temp_file).read()
            smirnoff_data = self.parse_string(data)
            return smirnoff_data

        except Exception as e:
            # Fail with an error message about which file could not be read.
            # TODO: Also handle case where fallback to 'data' directory encounters problems,
            # but this is much less worrisome because we control those files.
            msg = str(e) + '\n'
            if hasattr(source, 'name'):
                filename = source.name
            else:
                filename = str(source)
            msg += "ForceField.loadFile() encountered an error reading file '%s'\n" % filename
            raise ParseError(msg)

    def parse_string(self, data):
        """Parse a SMIRNOFF force field definition in XML format.

        A ``ParseError`` is raised if the XML cannot be processed.

        Parameters
        ----------
        data : str
            A SMIRNOFF force field definition in `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_.

        """
        from pyexpat import ExpatError
        from openforcefield.typing.engines.smirnoff.forcefield import ParseError

        # Parse XML file
        try:
            smirnoff_data = xmltodict.parse(data, attr_prefix='')
            return smirnoff_data
        except ExpatError as e:
            raise ParseError(e)

    def to_file(self, filename, smirnoff_data):
        """Write the current forcefield parameter set to a file, autodetecting the type from the extension.

        Parameters
        ----------
        filename : str
            The name of the file to be written.
            The `.offxml` file extension must be present.
        smirnoff_data : dict
            A dict structured in compliance with the SMIRNOFF data spec.

        """
        xml_string = self.to_string(smirnoff_data)
        (basename, extension) = os.path.splitext(filename)
        if extension == '.offxml':
            with open(filename, 'wb') as of:
                of.write(xml_string)
        else:
            msg = "Cannot export forcefield parameters to file '{}'\n".format(
                filename)
            msg += 'Export to extension {} not implemented yet.\n'.format(
                extension)
            msg += "Supported choices are: ['.offxml']"
            raise NotImplementedError(msg)

    def to_string(self, smirnoff_data):
        """
        Write the current forcefield parameter set to an XML string.

        Parameters
        ----------
        smirnoff_data : dict
            A dictionary structured in compliance with the SMIRNOFF spec

        Returns
        -------
        serialized_forcefield : str
            XML String representation of this forcefield.

        """
        def prepend_all_keys(d, char='@'):
            """
            Modify a dictionary in-place, prepending a specified string to each key
            that doesn't refer to a value that is list or dict.

            Parameters
            ----------
            d : dict
                Hierarchical dictionary to traverse and modify keys
            char : string, optional. Default='@'
                String to prepend onto each applicable dictionary key

            """
            if isinstance(d, dict):
                for key in list(d.keys()):
                    if isinstance(d[key], list) or isinstance(d[key], dict):
                        prepend_all_keys(d[key])
                    else:
                        new_key = char + key
                        d[new_key] = d[key]
                        del d[key]
                        prepend_all_keys(d[new_key])
            elif isinstance(d, list):
                for item in d:
                    prepend_all_keys(item)

        prepend_all_keys(smirnoff_data['SMIRNOFF'])
        print(smirnoff_data)
        print()
        return xmltodict.unparse(smirnoff_data, pretty=True)

    def to_xml(self, smirnoff_data):
        """Render the forcefield parameter set to XML.

        Returns
        -------
        smirnoff_data : dict
            A dictionary structures in comliance with the SMIRNOFF data spec.
        """
        return self.to_string(smirnoff_data)

    # # TODO: Do we need this? Should we use built-in dict-based serialization?
    # def __getstate__(self):
    #     """Serialize to XML.
    #     """
    #     return self.to_xml()
    #
    # # TODO: Do we need this? Should we use built-in dict-based serialization?
    # def __setstate__(self, state):
    #     """Deserialize from XML.
    #     """
    #     self._initialize()
    #     self.parse_xml(state)

#!/usr/bin/env python #============================================================================================= # MODULE DOCSTRING #============================================================================================= XML I/O parser for the SMIRNOFF (SMIRKS Native Open Force Field) format.  .. codeauthor:: <NAME> <<EMAIL>> .. codeauthor:: <NAME> <<EMAIL>> .. codeauthor:: <NAME> <<EMAIL>> #============================================================================================= # GLOBAL IMPORTS #============================================================================================= #============================================================================================= # CONFIGURE LOGGER #============================================================================================= #============================================================================================= # QUANTITY PARSING UTILITIES #============================================================================================= Performs a safe algebraic syntax tree evaluation of a unit.      This will likely be replaced by the native implementation in Pint     if/when we'll switch over to Pint units. # <number> # <left> <operator> <right> # <operator>( <operand> ) e.g., -1 # Check if this is a simtk unit. #============================================================================================= # Base ParameterIOHandler #============================================================================================= Base class for handling serialization/deserialization of SMIRNOFF ForceField objects Create a new ParameterIOHandler. #self._forcefield = forcefield Parameters         ----------         filename          Returns         ------- Parse a SMIRNOFF force field definition in a seriaized format          Parameters         ----------         data          Returns         ------- Write the current forcefield parameter set to a file.          Parameters         ----------         filename : str             The filename to write to.         smirnoff_data : dict             A dictionary structured in compliance with the SMIRNOFF spec          Returns         ------- Render the forcefield parameter set to a string          Parameters         ----------         smirnoff_data : dict             A dictionary structured in compliance with the SMIRNOFF spec          Returns         -------         str #============================================================================================= # XML I/O #============================================================================================= Handles serialization/deserialization of SMIRNOFF ForceField objects from OFFXML format. # TODO: Come up with a better keyword for format # TODO: Fix this Parse a SMIRNOFF force field definition in XML format, read from a file.          A ``ParseError`` is raised if the XML cannot be processed.          Parameters         ----------         source : str or file-like obj             File path of file-like obj specifying a SMIRNOFF force field definition in `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_.          .. notes ::             * New SMIRNOFF sections are handled independently, as if they were specified in the same file.            * If a SMIRNOFF section that has already been read appears again, its definitions are appended to the end of the previously-read              definitions if the sections are configured with compatible attributes; otherwise, an ``IncompatibleTagException`` is raised. # this handles open file-like objects (and strings) # This handles complete/local filenames # Check if the file exists in the data/forcefield directory # This handles nonlocal filenames # Check if the file exists in the data/forcefield directory # Fail with an error message about which file could not be read. # TODO: Also handle case where fallback to 'data' directory encounters problems, # but this is much less worrisome because we control those files. Parse a SMIRNOFF force field definition in XML format.          A ``ParseError`` is raised if the XML cannot be processed.          Parameters         ----------         data : str             A SMIRNOFF force field definition in `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_. # Parse XML file Write the current forcefield parameter set to a file, autodetecting the type from the extension.          Parameters         ----------         filename : str             The name of the file to be written.             The `.offxml` file extension must be present.         smirnoff_data : dict             A dict structured in compliance with the SMIRNOFF data spec. Write the current forcefield parameter set to an XML string.          Parameters         ----------         smirnoff_data : dict             A dictionary structured in compliance with the SMIRNOFF spec          Returns         -------         serialized_forcefield : str             XML String representation of this forcefield. Modify a dictionary in-place, prepending a specified string to each key             that doesn't refer to a value that is list or dict.              Parameters             ----------             d : dict                 Hierarchical dictionary to traverse and modify keys             char : string, optional. Default='@'                 String to prepend onto each applicable dictionary key Render the forcefield parameter set to XML.          Returns         -------         smirnoff_data : dict             A dictionary structures in comliance with the SMIRNOFF data spec. # # TODO: Do we need this? Should we use built-in dict-based serialization? # def __getstate__(self): #     """Serialize to XML. #     """ #     return self.to_xml() # # # TODO: Do we need this? Should we use built-in dict-based serialization? # def __setstate__(self, state): #     """Deserialize from XML. #     """ #     self._initialize() #     self.parse_xml(state)