*/
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.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()
{
- return 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";
}
/*
@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;
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");
+ 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;
}
- // todo get rid of Type and use FileFormatI instead?
- FileFormatI fileFormat = FileFormat.MMCif;
- pdbAlignment = new FormatAdapter().readFile(tmpFile,
- DataSourceType.FILE, fileFormat);
- if (pdbAlignment != null)
- {
- List<SequenceI> toremove = new ArrayList<SequenceI>();
- for (SequenceI pdbcs : pdbAlignment.getSequences())
- {
- String chid = null;
- // Mapping map=null;
- for (PDBEntry pid : pdbcs.getAllPDBEntries())
- {
- if (pid.getFile() == file)
- {
- chid = pid.getChainCode();
-
- }
- }
- if (chain == null || (chid != null && (chid.equals(chain)
- || chid.trim().equals(chain.trim())
- || (chain.trim().length() == 0 && chid.equals("_")))))
- {
- // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
- // TODO: suggest simplify naming to 1qip|A as default name defined
- pdbcs.setName(id + SEPARATOR + pdbcs.getName());
- // Might need to add more metadata to the PDBEntry object
- // like below
- /*
- * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
- * entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable());
- * entry.getProperty().put("chains", pdbchain.id + "=" +
- * sq.getStart() + "-" + sq.getEnd());
- * sq.getDatasetSequence().addPDBId(entry);
- */
- // Add PDB DB Refs
- // We make a DBRefEtntry because we have obtained the PDB file from
- // a
- // verifiable source
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping
- // information
- DBRefEntry dbentry = new DBRefEntry(getDbSource(),
- getDbVersion(), (chid == null ? id : id + chid));
- // dbentry.setMap()
- pdbcs.addDBRef(dbentry);
- }
- else
- {
- // mark this sequence to be removed from the alignment
- // - since it's not from the right chain
- toremove.add(pdbcs);
- }
- }
- // now remove marked sequences
- for (SequenceI pdbcs : toremove)
- {
- pdbAlignment.deleteSequence(pdbcs);
- if (pdbcs.getAnnotation() != null)
- {
- for (AlignmentAnnotation aa : pdbcs.getAnnotation())
- {
- pdbAlignment.deleteAnnotation(aa);
- }
- }
- }
- }
+ 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) }));
}
-
- // 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);
- UrlDownloadClient.download(paeURL, pae);
- if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
- {
- Cache.log.debug("Couln't import contact matrix from " + paeURL
- + " (stored in " + pae.toString() + ")");
- }
+ retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl);
} catch (Exception ex) // Problem parsing PDB file
{
return pdbAlignment;
}
- private boolean importPaeJSONAsContactMatrix(AlignmentI pdbAlignment,
- File pae) throws Exception
+ /**
+ * 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);
+ }
+
+ }
+
+ /**
+ * 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
+ *
+ * @param alphaFoldCif
+ * @param tmpFile
+ * @param id
+ * @param chain
+ * @param dbSource
+ * @param dbVersion
+ * @return
+ * @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?
+ FileFormatI fileFormat = FileFormat.MMCif;
+ AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile,
+ DataSourceType.FILE, fileFormat);
+ if (pdbAlignment != null)
+ {
+ List<SequenceI> toremove = new ArrayList<SequenceI>();
+ for (SequenceI pdbcs : pdbAlignment.getSequences())
+ {
+ String chid = null;
+ // Mapping map=null;
+ for (PDBEntry pid : pdbcs.getAllPDBEntries())
+ {
+ if (pid.getFile() == file)
+ {
+ chid = pid.getChainCode();
+
+ }
+ }
+ if (chain == null || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim())
+ || (chain.trim().length() == 0 && chid.equals("_")))))
+ {
+ // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+ // TODO: suggest simplify naming to 1qip|A as default name defined
+ pdbcs.setName(id + SEPARATOR + pdbcs.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+ * entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable());
+ * entry.getProperty().put("chains", pdbchain.id + "=" +
+ * sq.getStart() + "-" + sq.getEnd());
+ * sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from
+ // a
+ // verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ // information
+ if (dbSource != null)
+ {
+ DBRefEntry dbentry = new DBRefEntry(dbSource,
+
+ dbVersion, (chid == null ? id : id + chid));
+ // dbentry.setMap()
+ pdbcs.addDBRef(dbentry);
+ // update any feature groups
+ List<SequenceFeature> allsf = pdbcs.getFeatures()
+ .getAllFeatures();
+ List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
+ if (allsf != null && allsf.size() > 0)
+ {
+ for (SequenceFeature f : allsf)
+ {
+ if (file.equals(f.getFeatureGroup()))
+ {
+ f = new SequenceFeature(f, f.type, f.begin, f.end, id,
+ f.score);
+ }
+ newsf.add(f);
+ }
+ pdbcs.setSequenceFeatures(newsf);
+ }
+ }
+ }
+ else
+ {
+ // mark this sequence to be removed from the alignment
+ // - since it's not from the right chain
+ toremove.add(pdbcs);
+ }
+ }
+ // now remove marked sequences
+ for (SequenceI pdbcs : toremove)
+ {
+ pdbAlignment.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+ {
+ pdbAlignment.deleteAnnotation(aa);
+ }
+ }
+ }
+ }
+ return pdbAlignment;
+ }
+
/*
* (non-Javadoc)
*
{
return new PDBFeatureSettings();
}
+
}
git://source.jalview.org / jalview.git / blobdiff