MTPairwiseStrxAlignment

Structural alignments between two chains (3.4) can be computed with class MTPairwiseStrxAlignment.

Methods:

* read-only access
-(NSString*)description	returns textual representation
-(MTChain*)chain1	returns the first chain (3.4); this is the static chain
-(MTChain*)chain2	returns the second chain (3.4); this chain is matched onto the first chain
-(NSArray*)alignmentPositions	returns array of alignment positions (3.12)
-(MTMatrix53*)getTransformation	returns the calculated transformation (4.4) to match chain2 onto chain1
* compute structural alignment
-(void)globalSequenceInducedStructuralAlignment	computes the global sequence alignment (Needleman-Wunsch) between the two chains using the class MTPairwiseSequenceAlignment (3.11). The aligned pairs are selected and the transformation retained from their least-squares fit (3.13).
-(void)localSequenceInducedStructuralAlignment	same as the previous method but uses a local alignment (Smith-Waterman)
-(void)deriveStructuralAlignment	computes transformation from superimposed chains by selecting close residue pairs and retaining the transformation of their least-squares fit (3.13)
-(void)optimize	iteratively recomputes transformation from selecting residue pairs which have at most 3.5 A distance until no further progress is made
* analyze
-(double)calculateRMSD	calculates RMSD of structural alignment
-(int)countPairs	counts alignment positions in structural alignment
-(int)countUngappedPairs	counts aligned pairs only
-(int)countPairsMaxDistance: (double)dist	counts aligned pairs with distance below given distance
* input/output
-(void)fromStreamAsTCoffee: (MTStream*)stream	remakes structural alignment based on the pairwise information in the T_Coffee read from stream (5.1)
-(void)toStreamAsTCoffee: (MTStream*)stream name1:(NSString*)name1 name2:(NSString*)name2	writes structural alignment in T_Coffee library format to the given stream, explicitly name chain sequences
* creation
+(MTPairwiseStrxAlignment*)alignmentBetweenChain: (MTChain*)chain1 andChain:(MTChain*)chain2	creates a new instance working on chain1 and chain2 (3.4)

strxal := MTPairwiseStrxAlignment alignmentBetweenChain:chain1 andChain: chain2.     " create object. "

strxal deriveStructuralAlignment.     " from the given superimposition, derive the structural alignment. "

rmsd := strxal calculateRMSD.     " compute the RMSD (root mean square distance). "

alpairs := strxal countUngappedPairs.     " count all aligned pairs (was also the basis for the RMSD calculation). "

trafo := strxal getTransformation.

chain2 transformBy: trafo.     " transform the second chain by the computed transformation. "