Structural alignments between two chains (3.4) can be computed with class MTPairwiseStrxAlignment.
|* 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|
|-(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|
|-(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|
|+(MTPairwiseStrxAlignment*)alignmentBetweenChain: (MTChain*)chain1 andChain:(MTChain*)chain2||creates a new instance working on chain1 and chain2 (3.4)|
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. "
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