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Merged
sbliven merged 22 commits into from
Jul 22, 2015
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Extend structure alignment page with multiple alignments #5

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509057f
Adding basic alignmentcode page with MultipleStructureAlignment proposal
sbliven Jul 10, 2014
e60bfea
Explanation for AFPChain Data Model
lafita Jul 21, 2015
30a0202
Update references and section template
lafita Jul 21, 2015
f095f28
Explain MultipleAlignment object hierarchy
lafita Jul 21, 2015
ac15b5d
Include examples for the two data models
lafita Jul 21, 2015
fa0fae2
Change protein references to structure
lafita Jul 22, 2015
a45465c
Add figures for multiple GUI
lafita Jul 22, 2015
34a1a4d
Change multiple figures
lafita Jul 22, 2015
dd2b482
Describe the GUI for multiple alignments
lafita Jul 22, 2015
3e2f422
Update structure reference in README
lafita Jul 22, 2015
3118385
Update structure references in Structure modules
lafita Jul 22, 2015
9b6123b
Update first steps
lafita Jul 22, 2015
1990920
Update structure data model
lafita Jul 22, 2015
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Update caching
lafita Jul 22, 2015
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Update chemcomp.md
lafita Jul 22, 2015
77fc195
Update mmCIF explanation
lafita Jul 22, 2015
bed1234
Update SEQRES
lafita Jul 22, 2015
b1b8204
Explain utility methods for MSTA manipulation
lafita Jul 22, 2015
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Description of the MultipleMC algorithm
lafita Jul 22, 2015
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Footer script compatible with python 2.6
lafita Jul 22, 2015
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Merge remote-tracking branch 'origin/multiplealignment' into multiple…
lafita Jul 22, 2015
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lafita Jul 22, 2015
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Explain utility methods for MSTA manipulation
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lafita committed Jul 22, 2015
commit b1b82049d6381ecd3d135acb4d7ec905b0b157e0
24 changes: 22 additions & 2 deletions structure/alignment-data-model.md
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Expand Up @@ -15,6 +15,8 @@ Some of the important stored variables are:
* BlockRotationMatrix: rotation component of the superposition transformation.
* BlockShiftVector: translation component of the superposition transformation.

BioJava class: [org.biojava.bio.structure.align.model.AFPChain](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/model/AFPChain.html)

### The Optimal Alignment

The residue equivalencies of the alignment (EQRs) are described in the optimal
Expand Down Expand Up @@ -80,6 +82,8 @@ In addtition, the data structure is not limited in the number and types of score
it can store, because the scores are stored in a key:value fashion, as it will be
described later.

BioJava class: [org.biojava.bio.structure.align.multiple.MultipleAlignment](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/multiple/MultipleAlignment.html)

### Object Hierarchy

The biggest difference with `AFPChain` is that the `MultipleAlignment` data
Expand Down Expand Up @@ -167,8 +171,20 @@ on a `MultipleAlignment`:
double bsRMSD = alignment.getScore('bsRMSD');
```

Methods and names for some frequent scores are located in a util class called
`MultipleAlignmentScorer`.
### Manipulating Multiple Alignments

Some classes are designed to contain utility methods for manipulating a `MultipleAlignment` object.
The most important ones are ennumerated and briefly described below:

* [MultipleAlignmentScorer](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.html): contains frequent names for scores and methods to calculate them.

* [MultipleAlignmentTools](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.html): contains helper methods, such as sequence alignment calculation, transform atom arrays of the structures or calculate aligned residue distances between all structures.

* [MultipleAlignmentWriter](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.html): contains methods to generate different types of String outputs of the alignment, e.g. FASTA, XML, FatCat.

* [MultipleSuperimposer](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.html): interface for implementations that calculate the structure superpositions of the alignment. Some examples of implementations are the ReferenceSuperimposer (superimposes all the structures to a reference) and the CoreSuperimposer (only uses EQRs present in all structures, without gaps, to superimpose them).

* [MultipleAlignmentXMLParser](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.html): contains a method to create a `MultipleAlignment` object from an XML file representation.

### Overview

Expand Down Expand Up @@ -207,3 +223,7 @@ the first representation supports any number of structures, while the second is
only supporting pairwise alignments. However, the conversion can be done with some
lines of code if needed (instantiate a new `AFPChain` and copy one by one the
properties that can be represented from the `MultipleAlignment`.

===

Go back to [Chapter 8 : Structure Alignments](alignment.md).