__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.

"""
Module to 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

class CrystalError(Exception):
    pass

def wrap_line(line):
    output = ''
    for i in range(0, len(line), 80):
        output = 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):
    """
    This class exists 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):
        # 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):
        """Returns 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):
    def __init__(self, residues = ''):
        self.data = []
        if isinstance(residues, str):
            residues = residues.replace('*', ' ')
            residues = residues.strip()
            elements = residues.split()
            self.data = map(Hetero, 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 = ''
        i = 0
        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):
        """Returns 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):
    def __init__(self, data = {}):
        # Enforcestorage
        if not isinstance(data, dict):
            raise CrystalError('Crystal must be a dictionary')
        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 = ''
        keys = self.data.keys()
        keys.sort()
        for key in keys:
            output = output + '%s : %s\n' % (key, self.data[ key ])
        return output

    def __str__(self):
        output = ''
        keys = self.data.keys()
        keys.sort()
        for key in keys:
            output = 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()