Class MTPairwiseStrxAlignment

Inherits from:

NSObject

Declared in:

../libmoltalk/MTPairwiseStrxAlignment.oh

Class Hierarchy

    NSObject
      |
      +---MTPairwiseStrxAlignment

Last modified:

06-Jun-2006 (../libmoltalk/MTPairwiseStrxAlignment.m)

Instance Variables

private MTChain *chain1

private MTChain *chain2

private NSMutableArray *positions

private BOOL calculated

private MTMatrix53 *transformation

private int f_gop, f_gep

private Class substitutionMatrix

Method Index

• commonly used methods
  

  -(NSString*)description

• readonly access
  

  -(NSArray*)alignmentPositions

  -(MTChain*)chain1

  -(MTChain*)chain2

  -(int)gep

  -(MTMatrix53*)getTransformation

  -(int)gop

• operations
  

  -(double)calculateRMSD

  -(int)countPairs

  -(int)countPairsMaxDistance:(double)dist

  -(int)countUngappedPairs

  -(void)optimize

  -(void)setGep:(int)p_gep

  -(void)setGop:(int)p_gop

• from superimposition
  

  -(void)deriveStructuralAlignment

• from sequence alignment
  

  -(void)globalSequenceInducedStructuralAlignment

• from sequence alignment
  

  -(void)localSequenceInducedStructuralAlignment

• input/output
  

  -(void)fromStreamAsTCoffee:(MTStream*)stream

  -(void)toStreamAsTCoffee:(MTStream*)stream name1:(NSString*)name1 name2:(NSString*)name2

• creation
  

  +(MTPairwiseStrxAlignment*)alignmentBetweenChain:(MTChain*)chain1 andChain:(MTChain*)chain2

Methods

+(MTPairwiseStrxAlignment*)alignmentBetweenChain:(MTChain*)p_chain1 andChain:(MTChain*)p_chain2

creation

-(NSArray*)alignmentPositions

-(double)calculateRMSD

-(MTChain*)chain1

readonly access

-(MTChain*)chain2

-(int)countPairs

-(int)countPairsMaxDistance:(double)dist

-(int)countUngappedPairs

-(void)deriveStructuralAlignment

given a superpositions of the class MTChain, derive the structural alignment using dynamic programming

-(NSString*)description

-(void)fromStreamAsTCoffee:(MTStream*)stream

input a pairwise sequence alignment from a stream and interpret as a T-Coffee library.
the library indicates the selection of residues pairs which will be included in the calculation of the transformation

-(int)gep

-(MTMatrix53*)getTransformation

-(void)globalSequenceInducedStructuralAlignment

compute the global (Needleman-Wunsch) alignment between the two class MTChain, derive the structural alignment based on the pairwise assignment

-(int)gop

-(void)localSequenceInducedStructuralAlignment

compute the local (Smith-Waterman) alignment between the two class MTChain, derive the structural alignment based on the pairwise assignment

-(void)optimize

-(void)setGep:(int)p_gep

-(void)setGop:(int)p_gop

operations

-(void)toStreamAsTCoffee:(MTStream*)stream name1:(NSString*)name1 name2:(NSString*)name2

output derived structural alignment from computed superposition as a T-Coffee library.