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# 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
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):
"""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):
"""This class represents a sequence of Hetero elements."""
def __init__(self, residues=''):
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):
"""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):
"""Represents a dictionary of labeled chains from the same structure."""
def __init__(self, data=None):
# 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()
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