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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.
"""
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 string, array, copy
from Bio.Seq import Seq
from Bio.Seq import MutableSeq
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( type( key ) != type( '' ) ):
raise CrystalError( 'chain requires a string label' )
if( len( key ) != 1 ):
raise CrystalError( 'chain label should contain one letter' )
class Error( Exception ):
"""
"""
def __init__( self ):
pass
class CrystalError( Error ):
"""
message - description of error
"""
def __init__( self, message ):
self.message = message
class Hetero:
"""
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( type(data) != type("") ):
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:
def __init__(self, residues = '' ):
self.data = []
if( type( residues ) == type( '' ) ):
residues = residues.replace( '*', ' ' )
residues = residues.strip()
elements = residues.split()
self.data = map( Hetero, elements )
elif( type( residues ) == type( [] ) ):
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, i): return self.data[i]
def __setitem__(self, i, item):
try:
self.validate_element( item )
except TypeError:
item = Hetero( item.lower() )
self.data[i] = item
def __delitem__(self, i):
del self.data[i]
def __getslice__(self, i, j):
i = max(i, 0); j = max(j, 0)
return self.__class__(self.data[i:j])
def __setslice__(self, i, j, other):
i = max(i, 0); j = max(j, 0)
if isinstance(other, Chain):
self.data[i:j] = other.data
elif isinstance(other, type(self.data)):
self.data[i:j] = other
elif type( other ) == type( '' ):
self.data[ i:j ] = Chain( other ).data
else:
raise TypeError
def __delslice__(self, i, j):
i = max(i, 0); j = max(j, 0)
del self.data[i:j]
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 type( other ) == type( '' ):
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 type( other ) == type( '' ):
return self.__class__( Chain( other ).data + self.data )
else:
raise TypeError
def __iadd__(self, other):
if isinstance(other, Chain ):
self.data += other.data
elif type( other ) == type( '' ):
self.data += Chain( other ).data
else:
raise TypeError
return self
class Crystal:
def __init__(self, data = {} ):
# Enforcestorage
if( type( data ) != type( {} ) ):
raise CrystalError( 'Crystal must be a dictionary' )
self.data = data
self.fix()
def fix( self ):
data = self.data
for key in data.keys():
element = data[ key ]
if( isinstance( element, Chain ) ):
pass
elif type( element ) == type( '' ):
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 type( item ) == type( '' ):
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 has_key(self, key): return self.data.has_key(key)
def get(self, key, failobj=None):
return self.data.get(key, failobj)
def setdefault(self, key, failobj=None):
if not self.data.has_key(key):
self.data[key] = failobj
return self.data[key]
def popitem(self):
return self.data.popitem()
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