__init__.py

# Copyright 2002 by Katharine Lindner.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Represent the NDB Atlas structure (a minimal subset of PDB format).

Hetero, Crystal and Chain exist to represent the NDB Atlas structure.  Atlas
is a minimal subset of the PDB format.  Heteo supports a 3 alphameric code.
The NDB web interface is located at http://ndbserver.rutgers.edu/NDB/index.html
"""

import copy
from functools import reduce

from Bio._py3k import map
from Bio._py3k import basestring


class CrystalError(Exception):
    pass


def wrap_line(line):
    output = ''
    for i in range(0, len(line), 80):
        output += '%s\n' % line[i: i + 80]
    return output


def validate_key(key):
    if not isinstance(key, str):
        raise CrystalError('chain requires a string label')
    if len(key) != 1:
        raise CrystalError('chain label should contain one letter')


class Hetero(object):
    """Class to support the PDB hetero codes.

    Supports only the 3 alphameric code.
    The annotation is available from http://alpha2.bmc.uu.se/hicup/
    """

    def __init__(self, data):
        """Initialize the class."""
        # Enforce string storage
        if not isinstance(data, str):
            raise CrystalError('Hetero data must be an alphameric string')
        if data.isalnum() == 0:
            raise CrystalError('Hetero data must be an alphameric string')
        if len(data) > 3:
            raise CrystalError('Hetero data may contain up to 3 characters')
        if len(data) < 1:
            raise CrystalError('Hetero data must not be empty')

        self.data = data[:].lower()

    def __eq__(self, other):
        return self.data == other.data

    def __ne__(self, other):
        """Return true iff self is not equal to other."""
        return not self.__eq__(other)

    def __repr__(self):
        return "%s" % self.data

    def __str__(self):
        return "%s" % self.data

    def __len__(self):
        return len(self.data)


class Chain(object):
    """Class representing a sequence of Hetero elements."""

    def __init__(self, residues=''):
        """Initialize the class."""
        self.data = []
        if isinstance(residues, str):
            residues = residues.replace('*', ' ')
            residues = residues.strip()
            elements = residues.split()
            self.data = [Hetero(x) for x in elements]
        elif isinstance(residues, list):
            for element in residues:
                if not isinstance(element, Hetero):
                    raise CrystalError('Text must be a string')
            for residue in residues:
                self.data.append(residue)
        elif isinstance(residues, Chain):
            for residue in residues:
                self.data.append(residue)
        self.validate()

    def validate(self):
        data = self.data
        for element in data:
            self.validate_element(element)

    def validate_element(self, element):
        if not isinstance(element, Hetero):
            raise TypeError

    def __str__(self):
        output = ''
        for element in self.data:
            output = output + '%s ' % element
        output = output.strip()
        output = wrap_line(output)
        return output

    def __eq__(self, other):
        if len(self.data) != len(other.data):
            return 0
        ok = reduce(lambda x, y: x and y, map(lambda x, y: x == y, self.data, other.data))
        return ok

    def __ne__(self, other):
        """Return true iff self is not equal to other."""
        return not self.__eq__(other)

    def __len__(self):
        return len(self.data)

    def __getitem__(self, index):
        if isinstance(index, int):
            return self.data[index]
        elif isinstance(index, slice):
            return self.__class__(self.data[index])
        else:
            raise TypeError

    def __setitem__(self, index, value):
        if isinstance(index, int):
            try:
                self.validate_element(value)
            except TypeError:
                value = Hetero(value.lower())
            self.data[index] = value
        elif isinstance(index, slice):
            if isinstance(value, Chain):
                self.data[index] = value.data
            elif isinstance(value, type(self.data)):
                self.data[index] = value
            elif isinstance(value, basestring):
                self.data[index] = Chain(value).data
            else:
                raise TypeError
        else:
            raise TypeError

    def __delitem__(self, index):
        del self.data[index]

    def __contains__(self, item):
        try:
            self.validate_element(item)
        except TypeError:
            item = Hetero(item.lower())
        return item in self.data

    def append(self, item):
        try:
            self.validate_element(item)
        except TypeError:
            item = Hetero(item.lower())
        self.data.append(item)

    def insert(self, i, item):
        try:
            self.validate_element(item)
        except TypeError:
            item = Hetero(item.lower())
        self.data.insert(i, item)

    def remove(self, item):
        item = Hetero(item.lower())
        self.data.remove(item)

    def count(self, item):
        try:
            self.validate_element(item)
        except TypeError:
            item = Hetero(item.lower())
        return self.data.count(item)

    def index(self, item):
        try:
            self.validate_element(item)
        except TypeError:
            item = Hetero(item.lower())
        return self.data.index(item)

    def __add__(self, other):
        if isinstance(other, Chain):
            return self.__class__(self.data + other.data)
        elif isinstance(other, str):
            return self.__class__(self.data + Chain(other).data)
        else:
            raise TypeError

    def __radd__(self, other):
        if isinstance(other, Chain):
            return self.__class__(other.data + self.data)
        elif isinstance(other, str):
            return self.__class__(Chain(other).data + self.data)
        else:
            raise TypeError

    def __iadd__(self, other):
        if isinstance(other, Chain):
            self.data += other.data
        elif isinstance(other, str):
            self.data += Chain(other).data
        else:
            raise TypeError
        return self


class Crystal(object):
    """Represents a dictionary of labeled chains from the same structure."""

    def __init__(self, data=None):
        """Initialize the class."""
        # Enforcestorage
        if not isinstance(data, dict):
            raise CrystalError('Crystal must be a dictionary')
        if data is None:
            self.data = {}
        else:
            self.data = data
        self.fix()

    def fix(self):
        data = self.data
        for key in data:
            element = data[key]
            if isinstance(element, Chain):
                pass
            elif isinstance(element, str):
                data[key] = Chain(element)
            else:
                raise TypeError

    def __repr__(self):
        output = ''
        for key in sorted(self.data):
            output += '%s : %s\n' % (key, self.data[key])
        return output

    def __str__(self):
        output = ''
        for key in sorted(self.data):
            output += '%s : %s\n' % (key, self.data[key])
        return output

    def tostring(self):
        return self.data

    def __len__(self):
        return len(self.data)

    def __getitem__(self, key):
        return self.data[key]

    def __setitem__(self, key, item):
        if isinstance(item, Chain):
            self.data[key] = item
        elif isinstance(item, str):
            self.data[key] = Chain(item)
        else:
            raise TypeError

    def __delitem__(self, key):
        del self.data[key]

    def clear(self):
        self.data.clear()

    def copy(self):
        return copy.copy(self)

    def keys(self):
        return self.data.keys()

    def items(self):
        return self.data.items()

    def values(self):
        return self.data.values()

    def __contains__(self, value):
        return value in self.data

    def has_key(self, key):
        return key in self.data

    def get(self, key, failobj=None):
        return self.data.get(key, failobj)

    def setdefault(self, key, failobj=None):
        if key not in self.data:
            self.data[key] = failobj
        return self.data[key]

    def popitem(self):
        return self.data.popitem()