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lafitalafita
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Format and improve SS support
1 parent 52f41f4 commit aeb2344

15 files changed

Lines changed: 770 additions & 615 deletions

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‎biojava-structure/src/main/java/demo/DemoLoadSecStruc.java‎

Lines changed: 39 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -21,60 +21,63 @@
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package demo;
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import java.io.IOException;
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import java.util.List;
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import org.biojava.nbio.structure.Chain;
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import org.biojava.nbio.structure.Group;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.secstruc.DSSPParser;
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import org.biojava.nbio.structure.secstruc.SecStrucInfo;
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import org.biojava.nbio.structure.secstruc.SecStrucTools;
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/**
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* Demonstration of how to load a Structure with the SS information,
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* either from the PDB file annotation (Author's assignment) or from
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* the DSSP file in the PDB servers (DSSP assignment).
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* Demonstration of how to load a Structure with the SS information, either from
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* the PDB file annotation (Author's assignment) or from the DSSP file in the
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* PDB servers (DSSP assignment).
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*
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* @author Aleix Lafita
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*
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*/
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public class DemoLoadSecStruc {
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public static void main(String[] args)
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throws IOException, StructureException {
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String pdbID = "5pti";
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FileParsingParameters params = new FileParsingParameters();
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//Only change needed to the normal Structure loading
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params.setParseSecStruc(true); //this is false as DEFAULT
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53-
AtomCache cache = new AtomCache();
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cache.setFileParsingParams(params);
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cache.setUseMmCif(false);
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public static void main(String[] args) throws IOException,
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StructureException {
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//The loaded Structure contains the SS assigned by Author
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Structure s = cache.getStructure(pdbID);
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//If the more detailed DSSP prediction is required call this
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DSSPParser.fetch(pdbID, s, true);
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String pdbID = "5pti";
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//Print the assignment residue by residue
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System.out.println("Residue assignment: ");
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for (Chain c : s.getChains()) {
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for (Group g: c.getAtomGroups()){
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// Only change needed to the DEFAULT Structure loading
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FileParsingParameters params = new FileParsingParameters();
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params.setParseSecStruc(true);
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68-
if (g.hasAminoAtoms()){
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AtomCache cache = new AtomCache();
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cache.setFileParsingParams(params);
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SecStrucInfo ss =
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(SecStrucInfo) g.getProperty(Group.SEC_STRUC);
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// Use PDB format, because SS cannot be parsed from mmCIF yet
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cache.setUseMmCif(false);
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System.out.println(c.getChainID() +
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" " + g.getResidueNumber() + " "
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+ g.getPDBName() + " -> " + ss);
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}
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}
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}
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}
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// The loaded Structure contains the SS assigned by Author (simple)
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Structure s = cache.getStructure(pdbID);
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// Print the Author's assignment (from PDB file)
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System.out.println("Author's assignment: ");
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List<SecStrucInfo> ssi = SecStrucTools.getSecStrucInfo(s);
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for (SecStrucInfo ss : ssi) {
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System.out.println(ss.getGroup().getChain().getChainID() + " "
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+ ss.getGroup().getResidueNumber() + " "
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+ ss.getGroup().getPDBName() + " -> " + ss.toString());
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}
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// If the more detailed DSSP prediction is required call this
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DSSPParser.fetch(pdbID, s, true);
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// Print the assignment residue by residue
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System.out.println("DSSP assignment: ");
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ssi = SecStrucTools.getSecStrucInfo(s);
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for (SecStrucInfo ss : ssi) {
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System.out.println(ss.getGroup().getChain().getChainID() + " "
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+ ss.getGroup().getResidueNumber() + " "
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+ ss.getGroup().getPDBName() + " -> " + ss.toString());
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}
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}
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}

‎biojava-structure/src/main/java/demo/DemoSecStrucPred.java‎

Lines changed: 33 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -20,36 +20,37 @@
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*/
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public class DemoSecStrucPred {
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public static void main(String[] args)
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throws IOException, StructureException {
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String pdbID = "5pti";
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AtomCache cache = new AtomCache();
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//Load structure without any SS assignment
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Structure s = cache.getStructure(pdbID);
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//Predict and assign the SS of the Structure
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SecStrucPred ssp = new SecStrucPred();
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ssp.predict(s, true);
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//Print the DSSP output
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System.out.println("******DSSP output: ");
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System.out.println(ssp.printDSSP());
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//Print the FASTA sequence of SS
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System.out.println("\n******FASTA output: ");
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System.out.println(ssp.printFASTA());
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//Print the Helix Summary
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System.out.println("\n******Helix Summary: ");
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System.out.println(ssp.printHelixSummary());
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//Obtain and print the SS elements of the Structure
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List<SecStrucElement> sse = SecStrucTools.getSSE(s);
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System.out.println("\n******SecStrucElements: ");
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for (SecStrucElement e : sse) System.out.println(e);
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}
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public static void main(String[] args) throws IOException,
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StructureException {
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26+
String pdbID = "5pti";
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28+
AtomCache cache = new AtomCache();
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// Load structure without any SS assignment
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Structure s = cache.getStructure(pdbID);
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// Predict and assign the SS of the Structure
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SecStrucPred ssp = new SecStrucPred();
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ssp.predict(s, true);
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// Print the DSSP output
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System.out.println("******DSSP output: ");
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System.out.println(ssp.printDSSP());
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// Print the FASTA sequence of SS
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System.out.println("\n******FASTA output: ");
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System.out.println(ssp.printFASTA());
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// Print the Helix Summary
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System.out.println("\n******Helix Summary: ");
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System.out.println(ssp.printHelixSummary());
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// Obtain and print the SS elements of the Structure
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List<SecStrucElement> sse = SecStrucTools.getSecStrucElements(s);
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System.out.println("\n******SecStrucElements: ");
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for (SecStrucElement e : sse)
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System.out.println(e);
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}
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}

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