/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
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.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
import jalview.ws.utils.UrlDownloadClient;
/**
* @author JimP
*
*/
public class EBIAlfaFold extends EbiFileRetrievedProxy
{
private static final String SEPARATOR = "|";
private static final String COLON = ":";
private static final int PDB_ID_LENGTH = 4;
private static String AF_VERSION = "3";
public EBIAlfaFold()
{
super();
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
@Override
public String getAccessionSeparator()
{
return null;
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
@Override
public Regex getAccessionValidator()
{
Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
validator.setIgnoreCase(true);
return validator;
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
@Override
public String getDbSource()
{
return "ALPHAFOLD";
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
@Override
public String getDbVersion()
{
return "1";
}
public static String getAlphaFoldCifDownloadUrl(String id, String vnum)
{
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, String vnum)
{
if (vnum == null || vnum.length() == 0)
{
vnum = AF_VERSION;
}
return "https://alphafold.ebi.ac.uk/files/" + id
+ "-predicted_aligned_error_v" + vnum + ".json";
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
@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 (queries.indexOf(COLON) > -1)
{
chain = queries.substring(queries.indexOf(COLON) + 1);
id = queries.substring(0, queries.indexOf(COLON));
}
else
{
id = queries;
}
if (!isValidReference(id))
{
System.err.println(
"(AFClient) Ignoring invalid alphafold query: '" + id + "'");
stopQuery();
return null;
}
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);
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());
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
throw new Exception(MessageManager.formatMessage(
"exception.no_pdb_records_for_chain", new String[]
{ id, ((chain == null) ? "' '" : chain) }));
}
// done during structure retrieval
// retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl);
} catch (Exception ex) // Problem parsing PDB file
{
stopQuery();
throw (ex);
}
return pdbAlignment;
}
/**
* 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.error("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
{
List