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scorecomplex commit for benchmark test
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@Woosub-Kim
Woosub-Kim committed Feb 22, 2024
1 parent 4f3bc39 commit 537c616
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Showing 2 changed files with 40 additions and 59 deletions.
5 changes: 3 additions & 2 deletions src/strucclustutils/createcomplexreport.h
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Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,9 @@ const double MAX_ASSIGNED_CHAIN_RATIO = 1.0;
const double TOO_SMALL_MEAN = 1.0;
const double TOO_SMALL_CV = 0.1;
const double FILTERED_OUT = 0.0;
const bool UNCLUSTERED = false;
const bool CLUSTERED = true;
//const bool UNCLUSTERED = false;
//const bool CLUSTERED = true;
const unsigned int INITIALIZED_LABEL = 0;
const unsigned int MIN_PTS = 2;
const float DEFAULT_EPS = 0.1;
const float LEARNING_RATE = 0.1;
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94 changes: 37 additions & 57 deletions src/strucclustutils/scorecomplex.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -275,22 +275,6 @@ bool compareChainToChainAlnByDbComplexId(const ChainToChainAln &first, const Cha
return false;
}

bool compareChainToChainAlnByClusterLabel(const ChainToChainAln &first, const ChainToChainAln &second) {
if (first.label < second.label)
return true;
if (first.label > second.label)
return false;
if (first.qChain.chainKey < second.qChain.chainKey)
return true;
if (first.qChain.chainKey > second.qChain.chainKey)
return false;
if (first.dbChain.chainKey < second.dbChain.chainKey)
return true;
if (first.dbChain.chainKey > second.dbChain.chainKey)
return false;
return false;
}

bool compareAssignment(const Assignment &first, const Assignment &second) {
if (first.qTmScore > second.qTmScore)
return true;
Expand All @@ -313,18 +297,17 @@ bool compareNeighborWithDist(const NeighborsWithDist &first, const NeighborsWith

class DBSCANCluster {
public:
DBSCANCluster(SearchResult &searchResult, double minCov) : searchResult(searchResult) {
DBSCANCluster(SearchResult &searchResult, std::set<cluster_t> &finalClusters, double minCov) : searchResult(searchResult), finalClusters(finalClusters) {
cLabel = 0;
minClusterSize = (unsigned int) ((double) searchResult.qChainKeys.size() * minCov);
idealClusterSize = std::min(searchResult.qChainKeys.size(), searchResult.dbChainKeys.size());
finalClusters.clear();
prevMaxClusterSize = 0;
maxDist = 0;
eps = DEFAULT_EPS;
learningRate = LEARNING_RATE;
}

unsigned int getAlnClusters() {
bool getAlnClusters() {
// rbh filter
filterAlnsByRBH();
fillDistMap();
Expand Down Expand Up @@ -352,11 +335,11 @@ class DBSCANCluster {
std::set<unsigned int> dbFoundChainKeys;
distMap_t distMap;
std::vector<cluster_t> currClusters;
std::set<cluster_t> finalClusters;
std::set<cluster_t> &finalClusters;
std::map<unsigned int, float> qBestBitScore;
std::map<unsigned int, float> dbBestBitScore;

unsigned int runDBSCAN() {
bool runDBSCAN() {
initializeAlnLabels();
if (eps >= maxDist)
return finishDBSCAN();
Expand Down Expand Up @@ -388,6 +371,8 @@ class DBSCANCluster {
neighbors.emplace_back(neighbor);
}
}
if (neighbors.size() > 3)
std::cout << std::endl;

if (neighbors.size() > idealClusterSize || checkChainRedundancy())
getNearestNeighbors(centerAlnIdx);
Expand Down Expand Up @@ -453,9 +438,9 @@ class DBSCANCluster {

void initializeAlnLabels() {
for (auto &aln : searchResult.alnVec) {
aln.label = UNCLUSTERED;
aln.label = INITIALIZED_LABEL;
}
cLabel = UNCLUSTERED;
cLabel = INITIALIZED_LABEL;
maxClusterSize = 0;
currClusters.clear();
}
Expand All @@ -476,14 +461,14 @@ class DBSCANCluster {

unsigned int checkClusteringNecessity() {
if (searchResult.alnVec.empty())
return UNCLUSTERED;
return false;
for (size_t alnIdx=0; alnIdx<searchResult.alnVec.size(); alnIdx++) {
neighbors.emplace_back(alnIdx);
}
if (checkChainRedundancy()) {
neighbors.clear();
if (searchResult.alnVec.size() < MULTIPLE_CHAINED_COMPLEX)
finishDBSCAN();
return finishDBSCAN();

return runDBSCAN();
}
Expand All @@ -492,26 +477,24 @@ class DBSCANCluster {
return finishDBSCAN();
}

unsigned int finishDBSCAN() {
bool finishDBSCAN() {
initializeAlnLabels();
if (prevMaxClusterSize < minClusterSize || finalClusters.empty()) return UNCLUSTERED;
cLabel = CLUSTERED;
for (auto &cluster: finalClusters) {
for (auto alnIdx: cluster) {
searchResult.alnVec[alnIdx].label = cLabel;
}
cLabel++;
}
SORT_SERIAL(searchResult.alnVec.begin(), searchResult.alnVec.end(), compareChainToChainAlnByClusterLabel);
return CLUSTERED;
neighbors.clear();
neighborsOfCurrNeighbor.clear();
neighborsWithDist.clear();
qFoundChainKeys.clear();
dbFoundChainKeys.clear();
distMap.clear();
return !finalClusters.empty() && prevMaxClusterSize >= minClusterSize;
}

void filterAlnsByRBH() {
unsigned int alnIdx = 0;
float bitScore;
unsigned int qKey;
unsigned int dbKey;

qBestBitScore.clear();
dbBestBitScore.clear();
for (auto qChainKey: searchResult.qChainKeys) {
qBestBitScore.insert({qChainKey, DEF_BIT_SCORE});
}
Expand All @@ -538,6 +521,8 @@ class DBSCANCluster {
}
searchResult.alnVec.erase(searchResult.alnVec.begin() + alnIdx);
}
qBestBitScore.clear();
dbBestBitScore.clear();
// return;
}

Expand Down Expand Up @@ -618,7 +603,6 @@ class ComplexScorer {
currAln = ChainToChainAln(qChain, dbChain, queryCaData, targetCaData, dbAlnResult, tmResult);
currAlns.emplace_back(currAln);
currAln.free();
// data = Util::skipLine(data);
} // while end
} // for end
// When alignments have no backtrace
Expand Down Expand Up @@ -664,28 +648,23 @@ class ComplexScorer {
maxResLen = std::max(searchResult.qChainKeys.size(), searchResult.dbChainKeys.size()) * maxChainLen;
tmAligner = new TMaligner(maxResLen, false, true, false);
}
unsigned int currLabel;
DBSCANCluster dbscanCluster = DBSCANCluster(searchResult, minAssignedChainsRatio);
currLabel = dbscanCluster.getAlnClusters();
if (currLabel == UNCLUSTERED) return;
finalClusters.clear();
DBSCANCluster dbscanCluster = DBSCANCluster(searchResult, finalClusters, minAssignedChainsRatio);
if (!dbscanCluster.getAlnClusters()) {
finalClusters.clear();
return;
}
assignment = Assignment(searchResult.qResidueLen, searchResult.dbResidueLen);
for (auto &currAln: searchResult.alnVec) {
if (currAln.label == UNCLUSTERED)
continue;

if (currAln.label != currLabel) {
assignment.getTmScore(*tmAligner);
assignment.updateResultToWriteLines();
assignments.emplace_back(assignment);
assignment.reset();
currLabel = currAln.label;
for (auto &cluster: finalClusters) {
for (auto alnIdx: cluster) {
assignment.appendChainToChainAln(searchResult.alnVec[alnIdx]);
}
assignment.appendChainToChainAln(currAln);
assignment.getTmScore(*tmAligner);
assignment.updateResultToWriteLines();
assignments.emplace_back(assignment);
assignment.reset();
}
assignment.getTmScore(*tmAligner);
assignment.updateResultToWriteLines();
assignments.emplace_back(assignment);
assignment.reset();
finalClusters.clear();
}

void free() {
Expand Down Expand Up @@ -714,6 +693,7 @@ class ComplexScorer {
std::vector<ChainToChainAln> currAlns;
Assignment assignment;
SearchResult paredSearchResult;
std::set<cluster_t> finalClusters;
bool hasBacktrace;

unsigned int getQueryResidueLength(std::vector<unsigned int> &qChainKeys) {
Expand Down

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