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sblivensbliven
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Merge branch 'itasser'
Add I-TASSER output format for Multiple Alignments
2 parents dbcf6f0 + 1467ce7 commit 7ecb81e

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java‎

Lines changed: 88 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,7 @@
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.Calc;
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import org.biojava.nbio.structure.StructureTools;
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import org.biojava.nbio.structure.align.client.StructureName;
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import org.biojava.nbio.structure.align.multiple.Block;
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import org.biojava.nbio.structure.align.multiple.BlockSet;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
@@ -669,7 +670,93 @@ public static List<Integer> getCorePositions(Block block){
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}
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return corePositions;
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}
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/**
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* Outputs a pairwise alignment in I-TASSER's 3D Format for target-template
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* alignment.
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* http://zhanglab.ccmb.med.umich.edu/I-TASSER/option4.html
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*
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* <p>The format is closely related to a standard PDB file, but contains only
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* CA atoms and adds two columns for specifying the alignment:
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*
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* <pre>
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ATOM 2001 CA MET 1 41.116 -30.727 6.866 129 THR
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ATOM 2002 CA ALA 2 39.261 -27.408 6.496 130 ARG
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ATOM 2003 CA ALA 3 35.665 -27.370 7.726 131 THR
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ATOM 2004 CA ARG 4 32.662 -25.111 7.172 132 ARG
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ATOM 2005 CA GLY 5 29.121 -25.194 8.602 133 ARG
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Column 1 -30: Atom & Residue records of query sequence.
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Column 31-54: Coordinates of atoms in query copied from corresponding atoms in template.
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Column 55-59: Corresponding residue number in template based on alignment
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Column 60-64: Corresponding residue name in template
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</pre>
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*
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* <p>Note that the output is a pairwise alignment. Other rows in the
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* MultipleAlignment will be ignored.
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*
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* <p>This method supports topology-independent alignments. The output will
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* have sequence order matching the query, but include atoms from the
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* template.
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*
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* @param alignment A <em>full</em> multiple alignment between proteins
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* @param queryIndex index of the query within the multiple alignment
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* @param templateIndex index of the template within the multiple alignment
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* @return The file contents as a string
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*/
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public static String to3DFormat(MultipleAlignment alignment, int queryIndex, int templateIndex) {
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List<Atom[]> atomArrays = alignment.getEnsemble().getAtomArrays();
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Atom[] queryAtoms = atomArrays.get(queryIndex);
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Atom[] templateAtoms = atomArrays.get(templateIndex);
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List<Block> blocks = alignment.getBlocks();
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sortBlocks(blocks, queryIndex);
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StringBuilder str = new StringBuilder();
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// Gather info about the template structure
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String tNameStr = alignment.getEnsemble().getStructureNames().get(templateIndex);
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StructureName tName = new StructureName(tNameStr);
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String tPdbId = tName.getPdbId();
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String tChain = tName.getChainId();
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if(tChain == null ) {
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// Use the chain of the first template block
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for(Integer i : blocks.get(0).getAlignRes().get(templateIndex)) {
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if(i!=null) {
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tChain = templateAtoms[ i ].getGroup().getChainId();
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break;
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}
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}
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}
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str.append(String.format("REMARK Template name:%s:%s\n",tPdbId,tChain));
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for(Block block : blocks) {
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List<Integer> qAlign = block.getAlignRes().get(queryIndex);
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List<Integer> tAlign = block.getAlignRes().get(templateIndex);
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for(int i=0;i<block.length();i++) {
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Integer qRes = qAlign.get(i);
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Integer tRes = tAlign.get(i);
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// skip gaps
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if(qRes == null || tRes == null)
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continue;
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// Get PDB-format ATOM records
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String qPDB = queryAtoms[qRes].toPDB();
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String tPDB = templateAtoms[tRes].toPDB();
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// merge the two records into 3D format
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str.append(qPDB.substring(0,30)); // up through coordinates
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str.append(tPDB.substring(30, 54)); // coordinates
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str.append(tPDB.substring(22, 27)); // residue number
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str.append(' ');
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str.append(tPDB.substring(17, 20));
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str.append('\n');
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}
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}
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return str.toString();
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}
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/**
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* Sort blocks so that the specified row is in sequential order.
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* The sort happens in place.

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