Skip to content

Commit

Permalink
scorecomplex complex alignment redundancy solved
Browse files Browse the repository at this point in the history
  • Loading branch information
@Woosub-Kim
Woosub-Kim committed Feb 27, 2024
1 parent d725f0e commit e77b643
Show file tree
Hide file tree
Showing 2 changed files with 27 additions and 47 deletions.
1 change: 1 addition & 0 deletions src/strucclustutils/createcomplexreport.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ const float TM_SCORE_MARGIN = 0.7;
const float DEF_TM_SCORE = -1.0;
const int UNINITIALIZED = 0;
const unsigned int MULTIPLE_CHAINED_COMPLEX = 2;
const unsigned int SIZE_OF_SUPERPOSITION_VECTOR = 12;
typedef std::pair<std::string, std::string> compNameChainName_t;
typedef std::map<unsigned int, unsigned int> chainKeyToComplexId_t;
typedef std::map<unsigned int, std::vector<unsigned int>> complexIdToChainKeys_t;
Expand Down
73 changes: 26 additions & 47 deletions src/strucclustutils/scorecomplex.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ struct ChainToChainAln {
}
}
char buffer[4096];
label = 0;
label = INITIALIZED_LABEL;
superposition[0] = tmResult.u[0][0];
superposition[1] = tmResult.u[0][1];
superposition[2] = tmResult.u[0][2];
Expand All @@ -80,13 +80,13 @@ struct ChainToChainAln {
unsigned int matches;
unsigned int alnLength;
resultToWrite_t resultToWrite;
double superposition[12];
double superposition[SIZE_OF_SUPERPOSITION_VECTOR];
unsigned int label;
float tmScore;

float getDistance(const ChainToChainAln &o) {
float dist = 0;
for (size_t i=0; i<12; i++) {
for (size_t i=0; i<SIZE_OF_SUPERPOSITION_VECTOR; i++) {
dist += std::pow(superposition[i] - o.superposition[i], 2);
}
dist = std::sqrt(dist);
Expand Down Expand Up @@ -120,62 +120,41 @@ struct SearchResult {
dbResidueLen = residueLen;
}

void filterAlnVec(double minAlignedQueryChainRatio) {
void standardize() {
if (dbResidueLen == 0)
alnVec.clear();

if (alnVec.empty() || minAlignedQueryChainRatio==0)
return;

ChainToChainAln &firstAln = alnVec[0];
unsigned int minAlignedQueryChainNum = qChainKeys.size() * minAlignedQueryChainRatio;
unsigned int qChainCount = 1;
unsigned int qPrevChainKey = firstAln.qChain.chainKey;

for (auto &aln : alnVec) {
if (aln.qChain.chainKey == qPrevChainKey)
continue;

qPrevChainKey = aln.qChain.chainKey;
if (++qChainCount >= minAlignedQueryChainNum)
return;
}
alnVec.clear();
}

void standardize() {
if (alnVec.empty())
return;

double length = alnVec.size();
double mean[12] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
double var[12] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
double sd[12] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
double cv[12] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
double mean[SIZE_OF_SUPERPOSITION_VECTOR] = {};
double var[SIZE_OF_SUPERPOSITION_VECTOR] = {};
double sd[SIZE_OF_SUPERPOSITION_VECTOR] = {};
double cv[SIZE_OF_SUPERPOSITION_VECTOR] = {};

for (auto &aln: alnVec) {
for (size_t i = 0; i < 12; i++ ) {
for (size_t i = 0; i < SIZE_OF_SUPERPOSITION_VECTOR; i++ ) {
mean[i] += aln.superposition[i] / length;
}
}

for (auto &aln: alnVec) {
for (size_t i = 0; i < 12; i++ ) {
for (size_t i = 0; i < SIZE_OF_SUPERPOSITION_VECTOR; i++ ) {
var[i] += std::pow(aln.superposition[i] - mean[i], 2) / length;
}
}

for (size_t i=0; i<12; i++) {
for (size_t i=0; i<SIZE_OF_SUPERPOSITION_VECTOR; i++) {
sd[i] = std::sqrt(var[i]);
cv[i] = (abs(mean[i]) > TOO_SMALL_MEAN) ? sd[i]/std::abs(mean[i]) : sd[i];
}

for (auto &aln: alnVec) {
for (size_t i = 0; i < 12; i++ ) {
for (size_t i = 0; i < SIZE_OF_SUPERPOSITION_VECTOR; i++ ) {
aln.superposition[i] = cv[i] < TOO_SMALL_CV ? FILTERED_OUT : (aln.superposition[i] - mean[i]) / sd[i];
}
}
// return;
}
};

Expand Down Expand Up @@ -397,7 +376,7 @@ class DBSCANCluster {
finalClusters.clear();
prevMaxClusterSize = maxClusterSize;
}

SORT_SERIAL(currClusters.begin(), currClusters.end());
finalClusters.insert(currClusters.begin(), currClusters.end());
eps += learningRate;
return runDBSCAN();
Expand Down Expand Up @@ -430,7 +409,6 @@ class DBSCANCluster {

neighborVec.emplace_back(neighborIdx);
}
// return;
}

void initializeAlnLabels() {
Expand Down Expand Up @@ -479,6 +457,8 @@ class DBSCANCluster {
neighbors.clear();
neighborsOfCurrNeighbor.clear();
neighborsWithDist.clear();
qBestTmScore.clear();
dbBestTmScore.clear();
qFoundChainKeys.clear();
dbFoundChainKeys.clear();
distMap.clear();
Expand All @@ -493,6 +473,8 @@ class DBSCANCluster {
unsigned int dbKey;
qBestTmScore.clear();
dbBestTmScore.clear();
qFoundChainKeys.clear();
dbFoundChainKeys.clear();
for (auto qChainKey: searchResult.qChainKeys) {
qBestTmScore.insert({qChainKey, DEF_TM_SCORE});
}
Expand All @@ -510,15 +492,17 @@ class DBSCANCluster {
qKey = searchResult.alnVec[alnIdx].qChain.chainKey;
dbKey = searchResult.alnVec[alnIdx].dbChain.chainKey;
tmScore = searchResult.alnVec[alnIdx].tmScore;
if (tmScore >= std::max(qBestTmScore[qKey], dbBestTmScore[dbKey]) * TM_SCORE_MARGIN) {
alnIdx ++;
if (tmScore < std::max(qBestTmScore[qKey], dbBestTmScore[dbKey]) * TM_SCORE_MARGIN) {
searchResult.alnVec.erase(searchResult.alnVec.begin() + alnIdx);
continue;
}
searchResult.alnVec.erase(searchResult.alnVec.begin() + alnIdx);
qFoundChainKeys.insert(qKey);
dbFoundChainKeys.insert(dbKey);
alnIdx ++;
}
qBestTmScore.clear();
dbBestTmScore.clear();
// return;

if (qFoundChainKeys.size() < minClusterSize || dbFoundChainKeys.size() < minClusterSize)
searchResult.alnVec.clear();
}

void getNearestNeighbors(unsigned int centerIdx) {
Expand All @@ -529,20 +513,17 @@ class DBSCANCluster {
for (auto neighborIdx: neighbors) {
if (neighborIdx == centerIdx)
continue;
neighborsWithDist.emplace_back(neighborIdx, neighborIdx < centerIdx ? distMap[{neighborIdx, centerIdx}] : distMap[{centerIdx, neighborIdx}]);
neighborsWithDist.emplace_back(neighborIdx, distMap[{std::min(centerIdx, neighborIdx), std::max(centerIdx, neighborIdx)}]);
}
SORT_SERIAL(neighborsWithDist.begin(), neighborsWithDist.end(), compareNeighborWithDist);
neighbors.clear();
for (auto neighborWithDist : neighborsWithDist) {
if (!qFoundChainKeys.insert(searchResult.alnVec[neighborWithDist.neighbor].qChain.chainKey).second)
break;

if (!dbFoundChainKeys.insert(searchResult.alnVec[neighborWithDist.neighbor].dbChain.chainKey).second)
break;

neighbors.emplace_back(neighborWithDist.neighbor);
}
// return;
}
};

Expand Down Expand Up @@ -614,7 +595,6 @@ class ComplexScorer {
paredSearchResult.alnVec.emplace_back(aln);
continue;
}
paredSearchResult.filterAlnVec(minAssignedChainsRatio);
paredSearchResult.standardize();
if (!paredSearchResult.alnVec.empty())
searchResults.emplace_back(paredSearchResult);
Expand All @@ -627,7 +607,6 @@ class ComplexScorer {
paredSearchResult.alnVec.emplace_back(aln);
}
currAlns.clear();
paredSearchResult.filterAlnVec(minAssignedChainsRatio);
paredSearchResult.standardize();
if (!paredSearchResult.alnVec.empty() && currDbChainKeys.size() >= MULTIPLE_CHAINED_COMPLEX)
searchResults.emplace_back(paredSearchResult);
Expand Down

0 comments on commit e77b643

Please sign in to comment.