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‎_wikis/BioJava:CookBook3:ModFinder.md‎

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@@ -15,28 +15,26 @@ part of them.
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Example: identify and print all preloaded modifications from a structure
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------------------------------------------------------------------------
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<java> void identifyAndPrintModfications(Structure struc) {
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<java> Set<ModifiedCompound> identifyAllModfications(Structure struc) {
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`   ProteinModificationIdentifier parser = new ProteinModificationIdentifier();`
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`   parser.identify(struc);`
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`   Set`<ModifiedCompound>` mcs = parser.getIdentifiedModifiedCompound();`
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`   for (ModifiedCompound mc : mcs) {`
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`       System.out.println(mc.toString());`
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`   }`
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`   return mcs;`
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} </java>
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Example: identify phosphorylation sites in a structure
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------------------------------------------------------
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<java> List<PDBResidueNumber> identifyPhosphosites(Structure struc) {
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<java> List<ResidueNumber> identifyPhosphosites(Structure struc) {
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`   List`<PDBResidueNumber>` phosphosites = new ArrayList`<Integer>`();`
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`   List`<ResidueNumber>` phosphosites = new ArrayList`<ResidueNumber>`();`
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`   ProteinModificationIdentifier parser = new ProteinModificationIdentifier();`
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`   parser.identify(struc, ProteinModification.getByKeyword("phosphoprotein"));`
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`   parser.identify(struc, ProteinModificationRegistry.getByKeyword("phosphoprotein"));`
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`   Set`<ModifiedCompound>` mcs = parser.getIdentifiedModifiedCompound();`
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`   for (ModifiedCompound mc : mcs) {`
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`       Set`<StructureGroup>` groups = mc.getGroups(ComponentType.AMINOACID);`
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`       Set`<StructureGroup>` groups = mc.getGroups(true);`
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`       for (StructureGroup group : groups) {`
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`           phosphosites.add(group.getPDBResidueNumber());`
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`       }`
@@ -45,6 +43,41 @@ Example: identify phosphorylation sites in a structure
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} </java>
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Demo code to run the above methods
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----------------------------------
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<java> import org.biojava.bio.structure.ResidueNumber; import
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org.biojava.bio.structure.Structure; import
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org.biojava.bio.structure.io.PDBFileReader; import
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org.biojava3.protmod.structure.ProteinModificationIdentifier;
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public static void main(String[] args) {
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`   try {`
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`       PDBFileReader reader = new PDBFileReader();`
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`       reader.setAutoFetch(true);`
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`       // identify all modificaitons from PDB:1CAD and print them`
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`       String pdbId = "1CAD";`
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`       Structure struc = reader.getStructureById(pdbId);`
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`       Set`<ModifiedCompound>` mcs = identifyAllModfications(struc)`
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`       for (ModifiedCompound mc : mcs) {`
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`           System.out.println(mc.toString());`
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`       }`
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`       // identify all phosphosites from PDB:3MVJ and print them`
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`       String pdbId = "3MVJ";`
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`       Structure struc = reader.getStructureById(pdbId);`
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`       List`<ResidueNumber>` psites = identifyPhosphosites(struc);`
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`       for (ResidueNumber psite : psites) {`
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`           System.out.println(psite.toString());`
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`       }`
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`   } catch(Exception e) {`
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`       e.printStackTrace();`
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`   }`
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} </java>
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See also
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--------
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‎_wikis/BioJava:CookBook3:ModFinder.mediawiki‎

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==Example: identify and print all preloaded modifications from a structure==
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<java>
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void identifyAndPrintModfications(Structure struc) {
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ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
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parser.identify(struc);
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Set<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
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for (ModifiedCompound mc : mcs) {
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System.out.println(mc.toString());
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}
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Set<ModifiedCompound> identifyAllModfications(Structure struc) {
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ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
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parser.identify(struc);
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Set<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
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return mcs;
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}
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</java>
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==Example: identify phosphorylation sites in a structure==
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<java>
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List<PDBResidueNumber> identifyPhosphosites(Structure struc) {
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List<PDBResidueNumber> phosphosites = new ArrayList<Integer>();
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ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
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parser.identify(struc, ProteinModification.getByKeyword("phosphoprotein"));
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Set<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
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for (ModifiedCompound mc : mcs) {
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Set<StructureGroup> groups = mc.getGroups(ComponentType.AMINOACID);
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for (StructureGroup group : groups) {
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phosphosites.add(group.getPDBResidueNumber());
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}
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}
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return phosphosites;
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List<ResidueNumber> identifyPhosphosites(Structure struc) {
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List<ResidueNumber> phosphosites = new ArrayList<ResidueNumber>();
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ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
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parser.identify(struc, ProteinModificationRegistry.getByKeyword("phosphoprotein"));
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Set<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
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for (ModifiedCompound mc : mcs) {
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Set<StructureGroup> groups = mc.getGroups(true);
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for (StructureGroup group : groups) {
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phosphosites.add(group.getPDBResidueNumber());
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}
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}
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return phosphosites;
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}
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</java>
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==Demo code to run the above methods==
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<java>
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import org.biojava.bio.structure.ResidueNumber;
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import org.biojava.bio.structure.Structure;
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import org.biojava.bio.structure.io.PDBFileReader;
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import org.biojava3.protmod.structure.ProteinModificationIdentifier;
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public static void main(String[] args) {
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try {
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PDBFileReader reader = new PDBFileReader();
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reader.setAutoFetch(true);
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// identify all modificaitons from PDB:1CAD and print them
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String pdbId = "1CAD";
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Structure struc = reader.getStructureById(pdbId);
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Set<ModifiedCompound> mcs = identifyAllModfications(struc)
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for (ModifiedCompound mc : mcs) {
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System.out.println(mc.toString());
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}
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// identify all phosphosites from PDB:3MVJ and print them
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String pdbId = "3MVJ";
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Structure struc = reader.getStructureById(pdbId);
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List<ResidueNumber> psites = identifyPhosphosites(struc);
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for (ResidueNumber psite : psites) {
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System.out.println(psite.toString());
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}
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} catch(Exception e) {
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e.printStackTrace();
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}
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}
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</java>
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