/**
* Separates interaction maps and associates them with a chain name then calls
* DBManager.writeComplexContactToDB()
*
* @param pdbid PDB Identifier
* @return true if DBManager is succesfull
*/
public boolean writeChainComplexContactInfoToDB(String pdbid) {
String chainA;
String chainB;
Integer numHelixHelixInteractions;
Integer numHelixStrandInteractions;
Integer numHelixLoopInteractions;
Integer numStrandStrandInteractions;
Integer numStrandLoopInteractions;
Integer numLoopLoopInteractions;
Integer numAllInteractions;
Integer numDisulfides;
for (Map.Entry pair : this.chainNamesInEdge.entrySet()) {
Edge curEdge = (Edge) pair.getKey();
String[] chainPair = (String[]) pair.getValue();
chainA = chainPair[0];
chainB = chainPair[1];
// interactions with ligands are NOT yet written to the database!
numHelixHelixInteractions = this.numHelixHelixInteractionsMap.get(curEdge);
numHelixStrandInteractions = this.numHelixStrandInteractionsMap.get(curEdge);
numHelixLoopInteractions = this.numHelixCoilInteractionsMap.get(curEdge);
numStrandStrandInteractions = this.numStrandStrandInteractionsMap.get(curEdge);
numStrandLoopInteractions = this.numStrandCoilInteractionsMap.get(curEdge);
numLoopLoopInteractions = this.numCoilCoilInteractionsMap.get(curEdge);
numDisulfides = this.numDisulfidesMap.get(curEdge);
numAllInteractions = this.numAllInteractionsMap.get(curEdge);
Integer[] interactionNums = {
numHelixHelixInteractions,
numHelixStrandInteractions,
numHelixLoopInteractions,
numStrandStrandInteractions,
numStrandLoopInteractions,
numLoopLoopInteractions,
numDisulfides,
numAllInteractions
};
// make sure no entry is null or something shitty
for (int i = 0; i < interactionNums.length; i++) {
if (interactionNums[i] == null) {
interactionNums[i] = 0;
}
}
try {
DBManager.writeChainComplexContactToDB(pdbid, chainA, chainB, interactionNums);
// it.remove(); // avoids a ConcurrentModificationException
} catch (SQLException ex) {
Logger.getLogger(ComplexGraph.class.getName()).log(Level.SEVERE, null, ex);
return false;
}
}
return true;
}
public void writeSSEComplexContactInfoToDB(String pdbid) {
// DBManager.writeSSEComplexContactToDB()
String chainA;
String chainB;
Integer numHelixHelixInteractions;
Integer numHelixStrandInteractions;
Integer numHelixLoopInteractions;
Integer numSSInteractions;
Integer numStrandLoopInteractions;
Integer numLoopLoopInteractions;
Integer numAllInteractions;
Integer numDisulfides;
int countInsert = 0;
int countFail = 0;
Boolean retVal = false;
for (Map.Entry<List<Integer>, Integer> pair : this.numSSEContacts.entrySet()) {
List<Integer> curSSEs = (List<Integer>) pair.getKey();
chainA = this.numSSEContactChainNames.get(curSSEs).get(0);
chainB = this.numSSEContactChainNames.get(curSSEs).get(1);
Integer sse1_dssp_start = (Integer) curSSEs.get(0);
Integer sse2_dssp_start = (Integer) curSSEs.get(1);
Integer contactCount = (Integer) pair.getValue();
Boolean res = false;
// this action could result in an error due to the definition of a PTGL SSE
// e.g. the SSE is too short and is merged to another SSE or not defined in the DB
try {
res =
DBManager.writeSSEComplexContactToDB(
pdbid, chainA, chainB, sse1_dssp_start, sse2_dssp_start, contactCount);
// it.remove(); // avoids a ConcurrentModificationException
if (res) {
countInsert++;
retVal = true;
} else {
countFail++;
retVal = false;
}
} catch (SQLException ex) {
DP.getInstance()
.e(
"ComplexGraph",
"writeSSEComplexContactInfoToDB: SQL exception: '" + ex.getMessage() + "'.");
Logger.getLogger(ComplexGraph.class.getName()).log(Level.SEVERE, null, ex);
}
}
if (!Settings.getBoolean("plcc_B_silent")) {
System.out.println(
" SSE Contacts written to DB: "
+ countInsert
+ " inserted, "
+ countFail
+ " skipped (contact involved coils).");
}
}
