package jalview.ws.dbsources;
import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactMatrix;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
+import jalview.javascript.json.JSON;
import jalview.structure.StructureImportSettings;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.utils.UrlDownloadClient;
+import java.io.BufferedReader;
import java.io.File;
+import java.io.FileInputStream;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
+
+import org.jmol.adapter.readers.simple.JSONReader;
import com.stevesoft.pat.Regex;
@Override
public Regex getAccessionValidator()
{
- Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
validator.setIgnoreCase(true);
return validator;
}
return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v1.cif";
}
+ public static String getAlphaFoldPaeDownloadUrl(String id)
+ {
+ return "https://alphafold.ebi.ac.uk/files/" + id
+ + "-predicted_aligned_error_v1.json";
+ }
+
/*
* (non-Javadoc)
*
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
+ return getSequenceRecords(queries, null);
+ }
+
+ public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
+ throws Exception
+ {
AlignmentI pdbAlignment = null;
String chain = null;
String id = null;
if (!isValidReference(id))
{
System.err.println(
- "(AFClient) Ignoring invalid pdb query: '" + id + "'");
+ "(AFClient) Ignoring invalid alphafold query: '" + id + "'");
stopQuery();
return null;
}
String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+ if (retrievalUrl != null)
+ {
+ alphaFoldCif = retrievalUrl;
+ }
try
{
File tmpFile = File.createTempFile(id, ".cif");
+ Console.debug("Retrieving structure file for "+id+" from "+alphaFoldCif);
UrlDownloadClient.download(alphaFoldCif, tmpFile);
-
+
// may not need this check ?
file = tmpFile.getAbsolutePath();
if (file == null)
return null;
}
- pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, id, chain, getDbSource(),getDbVersion());
-
+ pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile,
+ id, chain, getDbSource(), getDbVersion());
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
{ id, ((chain == null) ? "' '" : chain) }));
}
+ // import PAE as contact matrix - assume this will work if there was a
+ // model
+ File pae = File.createTempFile(id, "pae_json");
+ String paeURL = getAlphaFoldPaeDownloadUrl(id);
+
+ if (retrievalUrl!=null) {
+ // manufacture the PAE url from a url like ...-model-vN.cif
+ paeURL = retrievalUrl.replace("model","predicted_aligned_error").replace(".cif",".json");
+ }
+ Console.debug("Downloading pae from " + paeURL
+ + " to " + pae.toString() + "");
+
+ try {
+ UrlDownloadClient.download(paeURL, pae);
+ if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
+ {
+ Console.warn("Couln't import contact matrix from " + paeURL
+ + " (stored in " + pae.toString() + ")");
+ }
+ } catch (Exception pae_ex) {
+ Console.debug("Couldn't download PAE",pae_ex);
+ }
+
} catch (Exception ex) // Problem parsing PDB file
{
stopQuery();
return pdbAlignment;
}
+ private boolean importPaeJSONAsContactMatrix(AlignmentI pdbAlignment,
+ File pae) throws Exception
+ {
+ FileInputStream pae_input = new FileInputStream(pae);
+
+ List<Object> pae_obj = (List<Object>) Platform
+ .parseJSON(pae_input);
+ if (pae_obj == null)
+ {
+ return false;
+ }
+ ContactMatrixI matrix = new PAEContactMatrix(
+ pdbAlignment.getSequenceAt(0), (Map<String, Object>)pae_obj.get(0));
+
+ pdbAlignment.getSequenceAt(0).addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
+ return true;
+ }
+
/**
- * general purpose structure importer - designed to yield alignment useful for transfer of annotation to associated sequences
+ * general purpose structure importer - designed to yield alignment useful for
+ * transfer of annotation to associated sequences
+ *
* @param alphaFoldCif
* @param tmpFile
* @param id
* @return
* @throws Exception
*/
- public static AlignmentI importDownloadedStructureFromUrl(String alphaFoldCif,
- File tmpFile, String id, String chain, String dbSource, String dbVersion) throws Exception
+ public static AlignmentI importDownloadedStructureFromUrl(
+ String alphaFoldCif, File tmpFile, String id, String chain,
+ String dbSource, String dbVersion) throws Exception
{
String file = tmpFile.getAbsolutePath();
// todo get rid of Type and use FileFormatI instead?
// dbentry.setMap()
pdbcs.addDBRef(dbentry);
// update any feature groups
- List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+ List<SequenceFeature> allsf = pdbcs.getFeatures()
+ .getAllFeatures();
List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
- if (allsf!=null && allsf.size()>0)
+ if (allsf != null && allsf.size() > 0)
{
- for (SequenceFeature f:allsf)
+ for (SequenceFeature f : allsf)
{
if (file.equals(f.getFeatureGroup()))
{
- f = new SequenceFeature(f, f.type, f.begin, f.end, id, f.score);
+ f = new SequenceFeature(f, f.type, f.begin, f.end, id,
+ f.score);
}
newsf.add(f);
}
@Override
public String getTestQuery()
{
- return "1QIP";
+ return "AF-O15552-F1";
}
@Override
public String getDbName()
{
- return "PDB"; // getDbSource();
+ return "ALPHAFOLD"; // getDbSource();
}
@Override
{
return new PDBFeatureSettings();
}
+
}
git://source.jalview.org / jalview.git / blobdiff