*/
package jalview.ws.dbsources;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import com.stevesoft.pat.Regex;
+
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.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeaturesI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
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;
-
/**
* @author JimP
*
private static final int PDB_ID_LENGTH = 4;
+ private static String AF_VERSION = "2";
+
public EBIAlfaFold()
{
super();
@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 "1";
}
- public static String getAlphaFoldCifDownloadUrl(String id)
+ public static String getAlphaFoldCifDownloadUrl(String id, String vnum)
{
- return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v1.cif";
+ if (vnum == null || vnum.length() == 0)
+ {
+ vnum = AF_VERSION;
+ }
+ return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v" + vnum
+ + ".cif";
}
- public static String getAlphaFoldPaeDownloadUrl(String id)
+ public static String getAlphaFoldPaeDownloadUrl(String id, String vnum)
{
+ if (vnum == null || vnum.length() == 0)
+ {
+ vnum = AF_VERSION;
+ }
return "https://alphafold.ebi.ac.uk/files/" + id
- + "-predicted_aligned_error_v1.json";
+ + "-predicted_aligned_error_v" + vnum + ".json";
}
/*
{
return getSequenceRecords(queries, null);
}
- public AlignmentI getSequenceRecords(String queries, String retrievalUrl) throws Exception
+
+ public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
+ throws Exception
{
AlignmentI pdbAlignment = null;
String chain = null;
stopQuery();
return null;
}
- String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+ String alphaFoldCif = getAlphaFoldCifDownloadUrl(id, AF_VERSION);
if (retrievalUrl != null)
{
alphaFoldCif = retrievalUrl;
try
{
File tmpFile = File.createTempFile(id, ".cif");
- Console.debug("Retrieving structure file for "+id+" from "+alphaFoldCif);
+ 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)
{
"exception.no_pdb_records_for_chain", new String[]
{ id, ((chain == null) ? "' '" : chain) }));
}
+ retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl);
- // 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() + "");
+ } catch (Exception ex) // Problem parsing PDB file
+ {
+ stopQuery();
+ throw (ex);
+ }
+ return pdbAlignment;
+ }
- try {
- UrlDownloadClient.download(paeURL, pae);
- if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
+ /**
+ * get an alphafold pAE for the given id, and add it to sequence 0 in
+ * pdbAlignment (assuming it came from structurefile parser).
+ *
+ * @param id
+ * @param pdbAlignment
+ * @param retrievalUrl
+ * - URL of .mmcif from EBI-AlphaFold - will be used to generate the
+ * pAE URL automatically
+ * @throws Exception
+ */
+ public static void retrieve_AlphaFold_pAE(String id,
+ AlignmentI pdbAlignment, String retrievalUrl) throws Exception
+ {
+ // 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, AF_VERSION);
+
+ 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);
+ FileInputStream pae_input = new FileInputStream(pae);
+
+ if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input))
{
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
+ } catch (Exception pae_ex)
{
- stopQuery();
- throw (ex);
+ Console.debug("Couldn't download PAE", pae_ex);
}
- return pdbAlignment;
+
}
- private boolean importPaeJSONAsContactMatrix(AlignmentI pdbAlignment,
- File pae) throws Exception
+ /**
+ * parses the given pAE matrix and adds it to sequence 0 in the given
+ * alignment
+ *
+ * @param pdbAlignment
+ * @param pae_input
+ * @return true if there was a pAE matrix added
+ * @throws Exception
+ */
+ public static boolean importPaeJSONAsContactMatrix(
+ AlignmentI pdbAlignment, InputStream pae_input) throws Exception
{
- FileInputStream pae_input = new FileInputStream(pae);
- List<Object> pae_obj = (List<Object>) Platform
- .parseJSON(pae_input);
+ 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),
+ (Map<String, Object>) pae_obj.get(0));
- pdbAlignment.getSequenceAt(0).addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
+ 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);
}
git://source.jalview.org / jalview.git / blobdiff