import java.io.File;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
+import org.json.simple.parser.ParseException;
+
import com.stevesoft.pat.Regex;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
private static final int PDB_ID_LENGTH = 4;
- private static String AF_VERSION = "2";
+ private static String AF_VERSION = "3";
public EBIAlfaFold()
{
* @param retrievalUrl
* - URL of .mmcif from EBI-AlphaFold - will be used to generate the
* pAE URL automatically
+ * @throws IOException
* @throws Exception
*/
public static void retrieve_AlphaFold_pAE(String id,
- AlignmentI pdbAlignment, String retrievalUrl) throws Exception
+ AlignmentI pdbAlignment, String retrievalUrl) throws IOException
{
// 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)
paeURL = retrievalUrl.replace("model", "predicted_aligned_error")
.replace(".cif", ".json");
}
+
+ File pae = null;
+ try
+ {
+ pae = File.createTempFile(id == null ? "af_pae" : id, "pae_json");
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
Console.debug("Downloading pae from " + paeURL + " to " + pae.toString()
+ "");
+ UrlDownloadClient.download(paeURL, pae);
+ addAlphaFoldPAEToSequence(pdbAlignment, pae, 0, null);
+ }
+ public static void addAlphaFoldPAEToSequence(AlignmentI pdbAlignment,
+ File pae, int index, String seqId)
+ {
+ FileInputStream pae_input = null;
try
{
- UrlDownloadClient.download(paeURL, pae);
- FileInputStream pae_input = new FileInputStream(pae);
+ pae_input = new FileInputStream(pae);
+ } catch (FileNotFoundException e)
+ {
+ Console.error(
+ "Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+ }
- if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input))
+ try
+ {
+ if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input, index,
+ seqId))
{
- Console.warn("Couln't import contact matrix from " + paeURL
- + " (stored in " + pae.toString() + ")");
+ Console.warn("Could not import contact matrix from '"
+ + pae.getAbsolutePath() + "'");
}
- } catch (Exception pae_ex)
+ } catch (IOException e1)
+ {
+ Console.error("Error when importing pAE file '"
+ + pae.getAbsolutePath() + "'", e1);
+ } catch (ParseException e2)
+ {
+ Console.error(
+ "Error when parsing pAE file '" + pae.getAbsolutePath() + "'",
+ e2);
+ }
+
+ }
+
+ public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
+ File pae, int index, String structId)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
{
- Console.error("Couldn't download PAE", pae_ex);
+ /*
+ ssm.setAddTempFacAnnot(showTemperatureFactor);
+ ssm.setProcessSecondaryStructure(showSecondaryStructure);
+ */
}
}
* @param pdbAlignment
* @param pae_input
* @return true if there was a pAE matrix added
+ * @throws ParseException
+ * @throws IOException
* @throws Exception
*/
public static boolean importPaeJSONAsContactMatrix(
- AlignmentI pdbAlignment, InputStream pae_input) throws Exception
+ AlignmentI pdbAlignment, InputStream pae_input)
+ throws IOException, ParseException
+ {
+ return importPaeJSONAsContactMatrix(pdbAlignment, pae_input, 0, null);
+ }
+
+ public static boolean importPaeJSONAsContactMatrix(
+ AlignmentI pdbAlignment, InputStream pae_input, int index,
+ String seqId) throws IOException, ParseException
{
List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
if (pae_obj == null)
{
+ Console.debug("JSON file did not parse properly.");
return false;
}
- ContactMatrixI matrix = new PAEContactMatrix(
- pdbAlignment.getSequenceAt(0),
+ SequenceI sequence = null;
+ /* debugging */
+ SequenceI[] seqs = pdbAlignment.getSequencesArray();
+ if (seqs == null)
+ Console.debug("******* sequences is null");
+ else
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ SequenceI s = seqs[i];
+ Console.debug("******* sequences[" + i + "]='" + s.getName() + "'");
+ }
+ }
+ /* end debug */
+ if (seqId == null)
+ {
+ int seqToGet = index > 0 ? index : 0;
+ sequence = pdbAlignment.getSequenceAt(seqToGet);
+ Console.debug("***** Got sequence at index " + seqToGet + ": "
+ + (sequence == null ? null : sequence.getName()));
+ }
+ if (sequence == null)
+ {
+ Console.debug("***** Looking for sequence with id '" + seqId + "'");
+
+ SequenceI[] sequences = pdbAlignment.findSequenceMatch(seqId);
+ if (sequences == null || sequences.length < 1)
+ {
+ Console.warn("Could not find sequence with id '" + seqId
+ + "' to attach pAE matrix to. Ignoring matrix.");
+ return false;
+ }
+ else
+ {
+ sequence = sequences[0]; // just use the first sequence with this seqId
+ }
+ }
+ ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) pae_obj.get(0));
- AlignmentAnnotation cmannot = pdbAlignment.getSequenceAt(0)
- .addContactList(matrix);
+ AlignmentAnnotation cmannot = sequence.addContactList(matrix);
pdbAlignment.addAnnotation(cmannot);
return true;
}
git://source.jalview.org / jalview.git / blobdiff