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// BCAminoAcid.h
// BioCocoa
//
// Created by Koen van der Drift on Sat May 10 2003.
// Copyright (c) 2003-2009 The BioCocoa Project.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions
// are met:
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// 3. The name of the author may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
// NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
// THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
/*!
@header
@abstract Provides in-memory representations of amino acids.
*/
#import <Foundation/Foundation.h>
#import "BCSymbol.h"
/*!
@class BCAminoAcid
@abstract All amino acids are handled through this single class
@discussion This class provides in-memory representations of amino acids.
*/
@interface BCAminoAcid : BCSymbol
{
NSString *threeLetterCode;
float kyteDoolittleValue;
float hoppWoodsValue;
float pKaValue;
}
/*!
@method initAminoAcids
@abstract Used internaly to generate the full set of amino acid objects.
*/
+ (void) initAminoAcids;
/*!
@method objectForSavedRepresentation: (NSString *)aSymbol
@abstract Returns a BCAminoAcid object representing the amino acid submitted
@discussion all BC classes should implement a "savableRepresentation" and an
* "objectForSavedRepresentation" method to allow archiving/uncarchiving in
* .plist formatted files.
*/
+ (id) objectForSavedRepresentation: (NSString *)aSymbol;
/*!
@method aaPropertiesDict
@abstract Returns a singleton NSDictionary holding the information for an amino acid
*/
+ (NSMutableDictionary *) aaPropertiesDict;
/*!
@method symbolForChar: (unsigned char)symbol
@abstract Returns a BCAminoAcid item representing the amino acid submitted
*/
+ (id) symbolForChar: (unsigned char)symbol;
/*!
@method alanine
@abstract Obtains a reference to the single alanine representation
*/
+ (BCAminoAcid *) alanine;
/*!
@method arginine
@abstract Obtains a reference to the single arginine representation
*/
+ (BCAminoAcid *) arginine;
/*!
@method asparagine
@abstract Obtains a reference to the single asparagine representation
*/
+ (BCAminoAcid *) asparagine;
/*!
@method asparticacid
@abstract Obtains a reference to the single asparticacid representation
*/
+ (BCAminoAcid *) asparticacid;
/*!
@method cysteine
@abstract Obtains a reference to the single cysteine representation
*/
+ (BCAminoAcid *) cysteine;
/*!
@method glutamicacid
@abstract Obtains a reference to the single glutamicacid representation
*/
+ (BCAminoAcid *) glutamicacid;
/*!
@method glutamine
@abstract Obtains a reference to the single glutamine representation
*/
+ (BCAminoAcid *) glutamine;
/*!
@method glycine
@abstract Obtains a reference to the single glycine representation
*/
+ (BCAminoAcid *) glycine;
/*!
@method histidine
@abstract Obtains a reference to the single histidine representation
*/
+ (BCAminoAcid *) histidine;
/*!
@method isoleucine
@abstract Obtains a reference to the single isoleucine representation
*/
+ (BCAminoAcid *) isoleucine;
/*!
@method leucine
@abstract Obtains a reference to the single leucine representation
*/
+ (BCAminoAcid *) leucine;
/*!
@method lysine
@abstract Obtains a reference to the single lysine representation
*/
+ (BCAminoAcid *) lysine;
/*!
@method methionine
@abstract Obtains a reference to the single methionine representation
*/
+ (BCAminoAcid *) methionine;
/*!
@method phenylalanine
@abstract Obtains a reference to the single phenylalanine representation
*/
+ (BCAminoAcid *) phenylalanine;
/*!
@method proline
@abstract Obtains a reference to the single proline representation
*/
+ (BCAminoAcid *) proline;
/*!
@method serine
@abstract Obtains a reference to the single serine representation
*/
+ (BCAminoAcid *) serine;
/*!
@method threonine
@abstract Obtains a reference to the single threonine representation
*/
+ (BCAminoAcid *) threonine;
/*!
@method tryptophan
@abstract Obtains a reference to the single tryptophan representation
*/
+ (BCAminoAcid *) tryptophan;
/*!
@method tyrosine
@abstract Obtains a reference to the single tyrosine representation
*/
+ (BCAminoAcid *) tyrosine;
/*!
@method valine
@abstract Obtains a reference to the single valine representation
*/
+ (BCAminoAcid *) valine;
/*!
@method asx
@abstract Obtains a reference to the single asx amino acid representation
*/
+ (BCAminoAcid *) asx;
/*!
@method glx
@abstract Obtains a reference to the single glx amino acid representation
*/
+ (BCAminoAcid *) glx;
/*!
@method gap
@abstract Obtains a reference to the single gap amino acid representation
*/
+ (BCAminoAcid *) gap;
/*!
@method undefined
@abstract Obtains a reference to the single undefined amino acid representation
*/
+ (BCAminoAcid *) undefined;
/*!
@method threeLetterCode
@abstract Returns an NSString containg the three letter code for the amino acid
*/
- (NSString *)threeLetterCode;
- (float)kyteDoolittleValue;
- (void)setKyteDoolittleValue:(float)value;
- (float)hoppWoodsValue;
- (void)setHoppWoodsValue:(float)value;
- (float)pKaValue;
- (void)setpKaValue:(float)value;
@end
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