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226 changes: 226 additions & 0 deletions
226
.../mutationhotspots/mutationhotspotsdetection/utils/structure/ContactMapFromSwissModel.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,226 @@ | ||
| /* | ||
| * To change this license header, choose License Headers in Project Properties. | ||
| * To change this template file, choose Tools | Templates | ||
| * and open the template in the editor. | ||
| */ | ||
| package org.cbioportal.mutationhotspots.mutationhotspotsdetection.utils.structure; | ||
|
|
||
| import com.fasterxml.jackson.databind.JsonNode; | ||
| import org.cbioportal.mutationhotspots.mutationhotspotsdetection.ContactMap; | ||
| import java.util.ArrayList; | ||
| import java.util.Collections; | ||
| import java.util.HashMap; | ||
| import java.util.HashSet; | ||
| import java.util.Iterator; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Set; | ||
| import org.biojava.nbio.structure.Atom; | ||
| import org.biojava.nbio.structure.Chain; | ||
| import org.biojava.nbio.structure.Group; | ||
| import org.biojava.nbio.structure.Structure; | ||
| import org.biojava.nbio.structure.StructureIO; | ||
| import org.biojava.nbio.structure.StructureTools; | ||
| import org.biojava.nbio.structure.contact.AtomContact; | ||
| import org.biojava.nbio.structure.contact.AtomContactSet; | ||
| import org.biojava.nbio.structure.contact.Pair; | ||
| import org.cbioportal.mutationhotspots.mutationhotspotsdetection.MutatedProtein; | ||
| import org.cbioportal.mutationhotspots.mutationhotspotsdetection.MutatedProtein3D; | ||
| import org.cbioportal.mutationhotspots.mutationhotspotsdetection.impl.MutatedProtein3DImpl; | ||
| import org.genomenexus.g2s.client.model.Alignment; | ||
| import org.genomenexus.g2s.client.model.ResidueMapping; | ||
| import com.fasterxml.jackson.databind.ObjectMapper; | ||
| import java.io.IOException; | ||
| import java.net.URL; | ||
| import java.util.logging.Level; | ||
| import java.util.logging.Logger; | ||
| import org.biojava.nbio.structure.io.PDBFileReader; | ||
|
|
||
| /** | ||
| * | ||
| * @author jgao | ||
| */ | ||
| public class ContactMapFromSwissModel implements ProteinStructureContactMapCalculator { | ||
|
|
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| ContactMapFromSwissModel() { | ||
|
|
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| } | ||
|
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| @Override | ||
| public Map<MutatedProtein3D, ContactMap> getContactMaps(MutatedProtein mutatedProtein, | ||
| double identpThreshold, double distanceThresholdClosestAtoms) { | ||
| Map<MutatedProtein3D, ContactMap> contactMaps = new HashMap<>(); | ||
|
|
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| String uniprotAcc = mutatedProtein.getUniprotAcc(); | ||
| if (uniprotAcc == null) { | ||
| return Collections.emptyMap(); | ||
| } | ||
|
|
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| List<Map<String, Object>> structures = readSwissModel(uniprotAcc); | ||
| for (Map<String, Object> structure : structures) { | ||
| Object obj = structure.get("identity"); | ||
| if (obj != null) { | ||
| double identity = Double.class.cast(obj); | ||
| if (identity < identpThreshold) { | ||
| continue; | ||
| } | ||
| } // if identity not available, still process | ||
|
|
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| obj = structure.get("template"); | ||
| if (obj == null) { | ||
| continue; | ||
| } | ||
| String[] template = String.class.cast(obj).split("\\."); | ||
| String pdbId = template[0]; | ||
| String chain = template[2]; | ||
|
|
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| obj = structure.get("coordinates"); | ||
| if (obj == null) { | ||
| continue; | ||
| } | ||
| String structureUrl = String.class.cast(obj); | ||
|
|
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| obj = structure.get("from"); | ||
| if (obj == null) { | ||
| continue; | ||
| } | ||
| int from = Integer.class.cast(obj); | ||
|
|
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| obj = structure.get("to"); | ||
| if (obj == null) { | ||
| continue; | ||
| } | ||
| int to = Integer.class.cast(obj); | ||
|
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| MutatedProtein3DImpl protein3D = new MutatedProtein3DImpl(mutatedProtein); | ||
| protein3D.setPdbId("swissmodel:"+pdbId); | ||
| protein3D.setPdbChain(chain); | ||
|
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| Map<Integer, Set<Integer>> pdbContactMap = getPdbContactMap(structureUrl, distanceThresholdClosestAtoms); | ||
|
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| ContactMap contactMap = getContactMap(pdbContactMap, from, to, mutatedProtein.getLength()); | ||
|
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| contactMaps.put(protein3D, contactMap); | ||
| } | ||
|
|
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| return contactMaps; | ||
| } | ||
|
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| private List<Map<String, Object>> readSwissModel(String uniprotAcc) { | ||
| List<Map<String, Object>> ret = new ArrayList<>(); | ||
|
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| ObjectMapper mapper = new ObjectMapper(); | ||
|
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| JsonNode root; | ||
| try { | ||
| URL url = new URL("https://swissmodel.expasy.org/repository/uniprot/"+uniprotAcc+".json?provider=swissmodel"); | ||
| root = mapper.readTree(url); | ||
| } catch (IOException ex) { | ||
| Logger.getLogger(ContactMapFromSwissModel.class.getName()).log(Level.SEVERE, null, ex); | ||
| return Collections.emptyList(); | ||
| } | ||
|
|
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| JsonNode structuresNode = root.get("result").get("structures"); | ||
| Iterator<JsonNode> it = structuresNode.elements(); | ||
| while (it.hasNext()) { | ||
| JsonNode strucNode = it.next(); | ||
| Map<String, Object> map = mapper.convertValue(strucNode, Map.class); | ||
| ret.add(map); | ||
| } | ||
|
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| return ret; | ||
| } | ||
|
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| private ContactMap getContactMap(Map<Integer, Set<Integer>> pdbContactMap, | ||
| int start, int end, int proteinLength) { | ||
| ContactMap contactMap = new ContactMap(proteinLength); | ||
| contactMap.setProteinLeft(start); | ||
| contactMap.setProteinRight(end); | ||
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| boolean[][] matrix = contactMap.getContact(); | ||
|
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| for (Map.Entry<Integer, Set<Integer>> entryPdbContactMap : pdbContactMap.entrySet()) { | ||
| int pdbPos = entryPdbContactMap.getKey(); | ||
|
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| Set<Integer> pdbNeighbors = entryPdbContactMap.getValue(); | ||
| if (pdbNeighbors.isEmpty()) { | ||
| continue; | ||
| } | ||
|
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| for (Integer pdbNeighbor : pdbNeighbors) { | ||
| matrix[pdbPos][pdbNeighbor] = true; | ||
| matrix[pdbNeighbor][pdbPos] = true; | ||
| } | ||
| } | ||
|
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| return contactMap; | ||
| } | ||
|
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| private Map<Integer, Set<Integer>> getPdbContactMap(String strUrl, double distanceThreashold) { | ||
| Map<Integer, Set<Integer>> map = new HashMap<>(); | ||
| try { | ||
| PDBFileReader reader = new PDBFileReader(); | ||
| URL url = new URL(strUrl); | ||
| Structure structure = reader.getStructure(url.openStream()); | ||
| Chain chain = structure.getChainByIndex(0); | ||
| AtomContactSet contacts = StructureTools.getAtomsInContact(chain, distanceThreashold); | ||
|
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| Iterator<AtomContact> it = contacts.iterator(); | ||
| while (it.hasNext()) { | ||
| AtomContact atomContact = it.next(); | ||
| Pair<Atom> atoms = atomContact.getPair(); | ||
| Group group1 = atoms.getFirst().getGroup(); | ||
| Group group2 = atoms.getSecond().getGroup(); | ||
| if (!group1.hasAminoAtoms() || !group2.hasAminoAtoms() || group1==group2) { | ||
| continue; | ||
| } | ||
|
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| Integer res1 = group1.getResidueNumber().getSeqNum(); | ||
| Integer res2 = group2.getResidueNumber().getSeqNum(); | ||
|
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| Set<Integer> neighbors = map.get(res1); | ||
| if (neighbors == null) { | ||
| neighbors = new HashSet<>(); | ||
| map.put(res1, neighbors); | ||
| } | ||
|
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| neighbors.add(res2); | ||
|
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| // we don't add res1 to the neighbors of res2, so it's not a complete map | ||
| } | ||
| } catch (Exception e) { | ||
| e.printStackTrace(); | ||
| System.err.println("Unable to calculate contact map for "+strUrl); | ||
| } | ||
|
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| return map; | ||
| } | ||
|
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| private OneToOneMap<Integer, Integer> getPdbSeqResidueMapping(List<Alignment> alignments) { | ||
| Collections.sort(alignments, (Alignment align1, Alignment align2) -> { | ||
| int ret = align1.getEvalue().compareTo(align2.getEvalue()); // sort from small evalue to large evalue | ||
| if (ret == 0) { | ||
| ret = -align1.getIdentity().compareTo(align2.getIdentity()); | ||
| } | ||
| return ret; | ||
| }); | ||
|
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| OneToOneMap<Integer, Integer> map = new OneToOneMap<Integer, Integer>(); | ||
|
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| for (Alignment alignment : alignments) { | ||
| List<ResidueMapping> residueMapping = alignment.getResidueMapping(); | ||
|
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| for (ResidueMapping r : residueMapping) { | ||
| if (!r.getQueryAminoAcid().equals(r.getPdbAminoAcid())) { | ||
| continue; | ||
| } | ||
|
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| Integer iseq = r.getQueryPosition(); | ||
| Integer ipdb = r.getPdbPosition(); | ||
|
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| map.put(ipdb, iseq); | ||
| } | ||
| } | ||
| return map; | ||
| } | ||
| } |
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30 changes: 30 additions & 0 deletions
30
...spots/mutationhotspotsdetection/utils/structure/ProteinStructureContactMapCalculator.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| /* | ||
| * To change this license header, choose License Headers in Project Properties. | ||
| * To change this template file, choose Tools | Templates | ||
| * and open the template in the editor. | ||
| */ | ||
| package org.cbioportal.mutationhotspots.mutationhotspotsdetection.utils.structure; | ||
|
|
||
| import java.util.Map; | ||
| import org.cbioportal.mutationhotspots.mutationhotspotsdetection.ContactMap; | ||
| import org.cbioportal.mutationhotspots.mutationhotspotsdetection.MutatedProtein; | ||
| import org.cbioportal.mutationhotspots.mutationhotspotsdetection.MutatedProtein3D; | ||
|
|
||
| /** | ||
| * | ||
| * @author jgao | ||
| */ | ||
| public interface ProteinStructureContactMapCalculator { | ||
| static final ProteinStructureContactMapCalculator pdbCalculator = new ContactMapFromPDB(); | ||
| public static ProteinStructureContactMapCalculator getPDBCalculator() { | ||
| return pdbCalculator; | ||
| } | ||
|
|
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| static final ProteinStructureContactMapCalculator swissModelCalculator = new ContactMapFromSwissModel(); | ||
| public static ProteinStructureContactMapCalculator getSwissModelCalculator() { | ||
| return swissModelCalculator; | ||
| } | ||
|
|
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| Map<MutatedProtein3D, ContactMap> getContactMaps(MutatedProtein mutatedProtein, double identpThreshold, double distanceThresholdClosestAtoms); | ||
|
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| } |
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