"""
Provides a class for reading CHARMM-style files. The key component to these
files is that the ! character is a comment character and everything after ! is
ignored.

This file is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of Biological
Structures at Stanford, funded under the NIH Roadmap for Medical Research,
grant U54 GM072970. See https://simtk.org.  This code was originally part of
the ParmEd program and was ported for use with OpenMM.

Copyright (c) 2014 the Authors

Author: Jason M. Swails
Contributors:
Date: April 18, 2014

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from simtk.openmm.app.internal.charmm.exceptions import CharmmFileError

class CharmmFile(object):
    """
    A CHARMM file that recognizes the "!" character as a 'comment' token. It
    can be iterated over and generally treated like a file object, but only
    spits out strings that have been truncated at its first comment character.
    
    There is currently no way to recognize a ! as a _non_ comment character,
    since allowing an escape character does not seem to be common practice and
    would likely introduce negative performance implications.
    """

    def __init__(self, fname, mode='r'):
        self.closed = False
        if mode not in ('r', 'w'):
            raise ValueError('Cannot open CharmmFile with mode "%s"' % mode)
        if mode == 'r':
            self.status = 'OLD'
        else:
            self.status = 'NEW'
        try:
            self._handle = open(fname, mode)
        except IOError, e:
            raise CharmmFileError(str(e))
        self.line_number = 0

    def write(self, *args, **kwargs):
        return self._handle.write(*args, **kwargs)

    def __iter__(self):
        # Iterate over the file
        for line in self._handle:
            try:
                idx = line.index('!')
                end = '\n'
            except ValueError:
                # There is no comment...
                idx = None
                end = ''
            yield line[:idx] + end

    def readline(self):
        self.line_number += 1
        line = self._handle.readline()
        try:
            idx = line.index('!')
            end = '\n'
        except ValueError:
            idx = None
            end = ''
        return line[:idx] + end

    def readlines(self):
        return [line for line in self]

    def read(self):
        return ''.join(self.readlines())

    def close(self):
        self._handle.close()
        self.closed = True

    def rewind(self):
        """ Return to the beginning of the file """
        self._handle.seek(0)

    def __del__(self):
        try:
            self.closed or self._handle.close()
        except AttributeError:
            # It didn't make it out of the constructor
            pass

# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

class CharmmStreamFile(object):
    """
    The stream file is broken down into sections of commands delimited by the
    strings:
        read <section> <options>
        ....
        ....
        end
    This object provides iterators over those sections and a file-like API for
    dealing with the text.
    """
    def __init__(self, fname):
        self.lines = CharmmFile(fname, 'r').readlines()
        self.line_number = 0

    def __iter__(self):
        return iter(self.lines)

    def rewind(self):
        """ Return to the beginning of the file """
        self.line_number = 0

    def next_section(self):
        """
        Fast-forwards the file to the next CHARMM command section

        Returns: (str, list)
            - The first string is the line defining the section that's being
              returned
            - The list is a list of all lines contained in the section
              excluding the "read <blah>" and "end" lines.

        Notes:
            The line pointer will be set to the line defining the 
        """
        lines = []
        while self.line_number < len(self.lines):
            line = self.lines[self.line_number].strip()
            if line[:4].lower() == 'read':
                title = line.strip()
                self.line_number += 1
                line = self.lines[self.line_number]
                while line and not line.strip().lower().startswith('end'):
                    lines.append(line)
                    self.line_number += 1
                    line = self.lines[self.line_number]
                return title, lines
            self.line_number += 1
        # No sections left
        return None, None

    def __del__(self):
        pass
