JALVIEW_ANNOTATION
HIDE_INSERTIONS
-STRUCTMODEL c4n58A_ c4n58A_.1.pdb 1 54 48 143 <b>PDB Header: </b>Hyrolase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Pectocin m2<br> <b>PDB Title: </b>Crystal structure of pectocin m2 at 1.86 amgtroms
-STRUCTMODEL d1a70a_ d1a70a_.2.pdb 1 71 48 144 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1offa_ d1offa_.3.pdb 1 73 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1frra_ d1frra_.4.pdb 0.999 62 49 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1pfda_ d1pfda_.5.pdb 0.999 70 48 143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1frda_ d1frda_.6.pdb 0.999 50 48 143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1fxia_ d1fxia_.7.pdb 0.999 62 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1gaqb_ d1gaqb_.8.pdb 0.999 71 48 144 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1iuea_ d1iuea_.9.pdb 0.999 48 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1awda_ d1awda_.10.pdb 0.999 68 50 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1wria_ d1wria_.11.pdb 0.999 59 49 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d1czpa_ d1czpa_.12.pdb 0.999 64 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d2cjoa_ d2cjoa_.13.pdb 0.999 63 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL d4fxca_ d4fxca_.14.pdb 0.999 64 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL c4itkA_ c4itkA_.15.pdb 0.999 57 50 142 <b>PDB Header: </b>Electron transport<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Apoferredoxin <br><b>PDB Title: </b>The structure of c.reinhardtii ferredoxin 2
-STRUCTMODEL c1krhA_ c1krhA_.16.pdb 0.999 25 48 142 <b>PDB Header: </b>Oxidoreductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Benzoate 1,2-deoxygenase reductase <br> <b>PDB Title: </b>X-ray structure of benzoate deoxygenate reductase
-STRUCTMODEL d1krha3 d1krha3.17.pdb 0.999 24 48 143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins
-STRUCTMODEL d1jq4a_ d1jq4a_.18.pdb 0.999 29 47 138 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins
-STRUCTMODEL c4wqmA_ c4wqmA_.19.pdb 0.999 28 49 144 <b>PDB header: </b>Oxidoreductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Toluene-4-monooxygenase electron transfer component<br><b>PDB Title: </b>Structure of the toluene 4-monooxygenase nah oxidoreductase t4mof,2 k270s k271s variant
-STRUCTMODEL c2piaA_ c2piaA_.20.pdb 0.999 22 1 136 <b>PDB header: </b>Reductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Phthalate deoxygenase reductase<br><b>PDB Title: </b>Phthalate deoxygenate reductase: a modular structure for2 electron transfer from pyridine nucleotides to [2fe-2s]
\ No newline at end of file
+STRUCTMODEL c4n58A_ c4n58A_.1.pdb c4n58A_.1.fasta 1 54 48 143 <b>PDB Header: </b>Hyrolase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Pectocin m2<br> <b>PDB Title: </b>Crystal structure of pectocin m2 at 1.86 amgtroms
+STRUCTMODEL d1a70a_ d1a70a_.2.pdb d1a70a_.2.fasta 1 71 48 144 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1offa_ d1offa_.3.pdb d1offa_.3.fasta 1 73 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1frra_ d1frra_.4.pdb d1frra_.4.fasta 0.999 62 49 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1pfda_ d1pfda_.5.pdb d1pfda_.5.fasta 0.999 70 48 143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1frda_ d1frda_.6.pdb d1frda_.6.fasta 0.999 50 48 143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1fxia_ d1fxia_.7.pdb d1fxia_.7.fasta 0.999 62 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1gaqb_ d1gaqb_.8.pdb d1gaqb_.8.fasta 0.999 71 48 144 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1iuea_ d1iuea_.9.pdb d1iuea_.9.fasta 0.999 48 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1awda_ d1awda_.10.pdb d1awda_.10.fasta 0.999 68 50 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1wria_ d1wria_.11.pdb d1wria_.11.fasta 0.999 59 49 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d1czpa_ d1czpa_.12.pdb d1czpa_.12.fasta 0.999 64 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d2cjoa_ d2cjoa_.13.pdb d2cjoa_.13.fasta 0.999 63 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL d4fxca_ d4fxca_.14.pdb d4fxca_.14.fasta 0.999 64 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL c4itkA_ c4itkA_.15.pdb c4itkA_.15.fasta 0.999 57 50 142 <b>PDB Header: </b>Electron transport<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Apoferredoxin <br><b>PDB Title: </b>The structure of c.reinhardtii ferredoxin 2
+STRUCTMODEL c1krhA_ c1krhA_.16.pdb c1krhA_.16.fasta 0.999 25 48 142 <b>PDB Header: </b>Oxidoreductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Benzoate 1,2-deoxygenase reductase <br> <b>PDB Title: </b>X-ray structure of benzoate deoxygenate reductase
+STRUCTMODEL d1krha3 d1krha3.17.pdb d1krha3.17.fasta 0.999 24 48 143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins
+STRUCTMODEL d1jq4a_ d1jq4a_.18.pdb d1jq4a_.18.fasta 0.999 29 47 138 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins
+STRUCTMODEL c4wqmA_ c4wqmA_.19.pdb c4wqmA_.19.fasta 0.999 28 49 144 <b>PDB header: </b>Oxidoreductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Toluene-4-monooxygenase electron transfer component<br><b>PDB Title: </b>Structure of the toluene 4-monooxygenase nah oxidoreductase t4mof,2 k270s k271s variant
+STRUCTMODEL c2piaA_ c2piaA_.20.pdb c2piaA_.20.fasta 0.999 22 1 136 <b>PDB header: </b>Reductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Phthalate deoxygenase reductase<br><b>PDB Title: </b>Phthalate deoxygenate reductase: a modular structure for2 electron transfer from pyridine nucleotides to [2fe-2s]
\ No newline at end of file
String templateId = getPhyreResultTable().getValueAt(row,
templateColIndex).toString();
String structureFile = phyre2ResultDirectory + templateId;
+ String fastaMapping = phyre2ResultDirectory
+ + templateId.replaceAll(".pdb", ".fasta");
+ // System.out.println("structure file >>>>> " + structureFile);
+ // System.out.println("fasta mapping >>>>> " + fastaMapping);
pdbEntriesToView[count++] = new AssociateStructureFileWithSeq()
.associateStructureWithSeq(structureFile,
DataSourceType.FILE, selectedSequence, true,
Desktop.instance);
- ssm.registerPhyre2Template(structureFile);
+ ssm.registerPhyre2Template(structureFile, fastaMapping);
}
final StructureSelectionManager ssm = ap
{
boolean failedtoadd = true;
// expect
- // STRUCTMODEL <TemplateSeqId> <TemplateFileName> <Confidence> <%.I.D>
+ // STRUCTMODEL <TemplateSeqId> <ModelFile> <FastaMappingFile>
+ // <Confidence> <%.I.D>
// <MatchStart> <MatchEnd> <Coverage> [<Other Information>]
if (st.hasMoreTokens()) {
refSeq = al.findName(refSeqId = st.nextToken());
else
{
String tempId = st.nextToken();
+ String fastaMapping = st.nextToken();
String confidence = 100 * Double.valueOf(st.nextToken()) + "";
String pid = st.nextToken();
String alignRange = st.nextToken() + "-" + st.nextToken();
String otherInfo = st.hasMoreTokens() ? st.nextToken() : "";
String coverage = "";
- if (add_structmodel(al, refSeq, tempId, alignRange, coverage,
+ if (add_structmodel(al, refSeq, tempId, fastaMapping,
+ alignRange, coverage,
confidence, pid, otherInfo))
{
failedtoadd = false;
if (failedtoadd)
{
System.err
- .println("Need <TemplateSeqId> <TemplateFileName> <Confidence> <%.I.D> <MatchStart> <MatchEnd> <Coverage> [<Other Information>] as tab separated fields after"
+ .println("Need <TemplateSeqId> <ModelFile> <FastaMappingFile> <Confidence> <%.I.D> <MatchStart> <MatchEnd> <Coverage> [<Other Information>] as tab separated fields after"
+ STRUCTMODEL
+ ".\nNote: other information could be provided in html format ");
} else {
* @return true if model and sequence was added
*/
private boolean add_structmodel(AlignmentI al, SequenceI refSeq,
- String tempId, String aRange, String coverage, String confidence,
+ String modelFile, String fastaFile, String aRange,
+ String coverage, String confidence,
String pid, String otherInfo)
{
String warningMessage = null;
boolean added = false;
try {
- String pdbFile = baseUri + tempId;
- PDBEntry phyre2PDBEntry = new PDBEntry(tempId, null, Type.FILE,
- pdbFile);
- refSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ String structureModelFile = resolveAbsolute(modelFile);
+ String fastaMappingFile = resolveAbsolute(fastaFile);
+ // System.out.println("Model File >> " + fastaMappingFile);
+ // System.out.println("Fasta File >> " + structureModelFile);
+ PDBEntry phyre2PDBEntry = new PDBEntry(modelFile, null, Type.FILE,
+ structureModelFile);
String phyre2ModelDesc = generatePhyre2InfoHTMLTable(aRange,
coverage, confidence, pid, otherInfo);
- refSeq.setDescription(phyre2ModelDesc);
+ phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
+ refSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
- ssm.registerPhyre2Template(pdbFile);
+ ssm.registerPhyre2Template(structureModelFile, fastaMappingFile);
added = true;
} catch (Exception x)
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.gff.GffConstants;
}
}
sb.append("</i>");
+
+ for (PDBEntry pdb : ds.getAllPDBEntries())
+ {
+ if (pdb != null && pdb.getProperty("PHYRE2_MODEL_INFO") != null)
+ {
+ sb.append(pdb.getProperty("PHYRE2_MODEL_INFO"));
+ }
+ }
return maxWidth;
}
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashMap;
+import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
- private List<String> phyre2ModelTemplates = new ArrayList<String>();
+ private Map<String, String> phyre2ModelTemplates = new Hashtable<String, String>();
/**
* @return true if will try to use external services for processing secondary
setProgressBar(MessageManager
.getString("status.obtaining_mapping_with_phyre2_template_alignment"));
StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
- .getStructureMapping(seq, pdbFile, " ");
+ .getStructureMapping(seq, pdbFile,
+ getPhyre2FastaFileFor(pdbFile), " ");
seqToStrucMapping.add(phyre2ModelMapping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
return pdb;
}
- public void registerPhyre2Template(String phyre2Template)
+ public void registerPhyre2Template(String phyre2Template,
+ String fastaMappingFile)
{
- phyre2ModelTemplates.add(phyre2Template);
+ phyre2ModelTemplates.put(phyre2Template, fastaMappingFile);
}
/**
{
return false;
}
- return (phyre2ModelTemplates.contains(structureFile));
+ return phyre2ModelTemplates.get(structureFile) != null
+ && !phyre2ModelTemplates.get(structureFile).isEmpty();
+ }
+
+ public String getPhyre2FastaFileFor(String structureFile)
+ {
+ return phyre2ModelTemplates.get(structureFile);
}
private final static String PATH_SEPARATOR = File.separator;
+ private String fastaMappingFile;
+
public Phyre2Client(StructureFile structureFile)
{
this.structureFile = structureFile;
}
+ public StructureMapping getStructureMapping(SequenceI seq,
+ String pdbFile, String fMappingFile, String chain)
+ {
+ this.fastaMappingFile = fMappingFile;
+ return getStructureMapping(seq, pdbFile, chain);
+ }
+
@Override
public StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String chain)
private String getFastaMappingFile()
{
- File phyre2ModelFile = new File(structureFile.getDataName());
- String phyre2ModelResultDir = phyre2ModelFile.getParent();
- String modelId = structureFile.getId().substring(0,
- structureFile.getId().lastIndexOf(".pdb"));
- return phyre2ModelResultDir + PATH_SEPARATOR + modelId + ".fasta";
+ return fastaMappingFile;
}
@Override
output.append(NEWLINE).append(NEWLINE);
}
float pid = (float) matchedSeqCount / seqRes.length() * 100;
- // if (pid < SiftsSettings.getFailSafePIDThreshold())
- // {
- // throw new Exception(">>> Low PID detected for Phyre2 mapping...");
- // }
output.append("Length of alignment = " + seqRes.length()).append(
NEWLINE);
output.append(new Format("Percentage ID = %2.2f").form(pid));
git://source.jalview.org / jalview.git / commitdiff