Adding basic alignmentcode page with MultipleStructureAlignment proposal

biojava · sbliven · Jul 22, 2015 · Jul 10, 2014 · Jul 21, 2015 · Jul 21, 2015
commit 509057f86a941aea061f927db18ec8d839c6061b
diff --git a/structure/alignment.md b/structure/alignment.md
@@ -53,7 +53,7 @@ The functionality to perform and visualize these alignments can of course be
 used also from your own code. Let's first have a look at the alignment
 algorithms.
 
-## The Alignment Algorithms
+## Pairwise Alignment Algorithms
 
 ### Combinatorial Extension (CE)
 
@@ -247,6 +247,10 @@ are available which are not exposed in the GUI, such as outputting results to a
 file in various formats.
 
 
+## See Also
+
+For details about performing alignments programatically, see [Structure Alignment in BioJava](alignmentcode.md)
+
 ## Acknowledgements
 
 Thanks to P. Bourne, Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute their algorithms.

diff --git a/structure/alignmentcode.md b/structure/alignmentcode.md
@@ -0,0 +1,40 @@
+Structure Alignment in BioJava
+===
+
+## Data Structures
+
+### Legacy AFPChain model
+
+Pairwise structure alignments are currently stored in the `AFPChain` class. The
+class functions as a bean, and contains many variables used internally by
+various alignment algorithms.
+
+### Proposed MultipleStructureAlignment data model
+
+This data structure introduces a more explicit model for storing structure
+alignments. It is more flexible than the AFPChain model, adding support for
+
+* Multiple alignments
+* Non-topological alignments, such as circular permutations
+* Mutable, while maintaining internal consistency
+
+A ***block*** is a series of aligned residues within a structure. A block must
+be a sequential alignment; the order of residues within the block should be
+strictly increasing. Blocks in the same alignment should be non-overlapping.
+Only aligned positions are specified in the block, but individual structures may
+have gaps and deletions at any position. A block corresponds most closely to a
+traditional, sequential multiple alignment with a row for each structure and a
+column for each aligned position.
+
+A ***match*** represents a set of blocks with a single global superposition.
+This superposition is stored in a ***pose***, which contains the affine
+transform required for the superposition.
+
+Finally, a `MultipleStructureAlignment` associates a set of Structures with one
+or more matches.
+
+### Examples
+
+A typical pairwise alignment would be a single match, a single pose, and a
+single block of two structures.
+