void BLAPDBImpl::write2PDB() {
string proteinName;
int subjectStart;
string subject;
int subjectEnd;
int queryStart;
string query;
int queryEnd;
int length;
for (int i = 0; i < blaPDBResultVector.size(); i++) {
proteinName = blaPDBResultVector[i].getProteinName();
queryStart = blaPDBResultVector[i].getQueryStart();
query = blaPDBResultVector[i].getQuery();
queryEnd = blaPDBResultVector[i].getQueryEnd();
subjectStart = blaPDBResultVector[i].getSubjectStart();
subject = blaPDBResultVector[i].getSubject();
subjectEnd = blaPDBResultVector[i].getSubjectEnd();
int queryHeadMore = queryStart - 1;
int queryTailMore = proteinSeqLength - queryEnd;
vector<float> Xs = blaPDBResultVector[i].getXCoords();
vector<float> Ys = blaPDBResultVector[i].getYCoords();
vector<float> Zs = blaPDBResultVector[i].getZCoords();
vector<char> templateSeq = blaPDBResultVector[i].getTemplateSeq();
length = blaPDBResultVector[i].getLength();
int subjectHeadMore = subjectStart - 1;
int subjectTailMore = length - subjectEnd;
int headMore = 0;
if (queryHeadMore > subjectHeadMore) {
headMore = subjectHeadMore;
} else {
headMore = queryHeadMore;
}
int tailMore = 0;
if (queryTailMore > subjectTailMore) {
tailMore = subjectTailMore;
} else {
tailMore = queryTailMore;
}
string protein3DCorrdsFilename(outputFileLocation);
protein3DCorrdsFilename += "/";
protein3DCorrdsFilename += rootName;
protein3DCorrdsFilename += "/BLAPDB/pdbFiles/";
protein3DCorrdsFilename += proteinName;
protein3DCorrdsFilename += "_";
protein3DCorrdsFilename += subject;
protein3DCorrdsFilename += ".pdb";
ofstream pdbFile((char*) protein3DCorrdsFilename.c_str(), ios::out);
while (headMore > 0) {
if (Xs[subjectStart - headMore - 1] != 10000
&& Ys[subjectStart - headMore - 1] != 10000
&& Zs[subjectStart - headMore - 1] != 10000) {
pdbFile << "ATOM "; //record name
pdbFile << right << setw(5) << subjectStart - headMore; // atom serial number
pdbFile << " CA "; //atom name
pdbFile << setw(3)
<< convertResidueName(
originalProteinSeq[queryStart - headMore - 1]);
//pdbFile<<templateSeq[subjectStart - headMore];//for debug
pdbFile << right << setw(6) << subjectStart - headMore; // atom serial number
pdbFile << " ";
pdbFile << right << setw(8.3)
<< Xs[subjectStart - headMore - 1];
pdbFile << right << setw(8.3)
<< Ys[subjectStart - headMore - 1];
pdbFile << right << setw(8.3)
<< Zs[subjectStart - headMore - 1];
pdbFile << " 1.00 0.00\n";
}
headMore--;
}
int queryPos = 1;
int subjectPos = 1;
for (int j = 0; j < subject.size(); j++) {
if (subject[j] == '-' || query[j] != '-') {
queryPos++;
continue;
//outJsonFile << "\"" << subject[j] << "\":\""
// << "10000,10000,10000\"\n";
} else if (subject[j] != '-' || query[j] == '-') {
subjectPos++;
continue;
} else if (subject[j] == '-' || query[j] == '-') {
continue;
} else {
if (Xs[subjectStart + subjectPos - 2] != 10000
&& Ys[subjectStart + subjectPos - 2] != 10000
&& Zs[subjectStart + subjectPos - 2] != 10000) {
pdbFile << "ATOM "; //record name
pdbFile << right << setw(5)
<< subjectStart + subjectPos - 1; // atom serial number
pdbFile << " CA "; //atom name
pdbFile << setw(3) << convertResidueName(query[j]);
//pdbFile<<query[ j - 1]; //for dubug
pdbFile << right << setw(6)
<< subjectStart + subjectPos - 1; // atom serial number
pdbFile << " ";
pdbFile << right << setw(8.3)
<< Xs[subjectStart + subjectPos - 2];
pdbFile << right << setw(8.3)
<< Ys[subjectStart + subjectPos - 2];
pdbFile << right << setw(8.3)
<< Zs[subjectStart + subjectPos - 2];
pdbFile << " 1.00 0.00\n";
}
subjectPos++;
queryPos++;
}
}
//cout<<"Tailmore"<<tailMore<<endl;;
if (tailMore > 0) {
for (int k = 0; k < tailMore; k++) {
if (Xs[subjectEnd + k] != 10000 && Ys[subjectEnd + k] != 10000
&& Zs[subjectEnd + k] != 10000) {
pdbFile << "ATOM "; //record name
pdbFile << right << setw(5) << subjectEnd + k; // atom serial number
pdbFile << " CA "; //atom name
pdbFile << setw(3)
<< convertResidueName(
originalProteinSeq[queryEnd + k]);
pdbFile << right << setw(6) << subjectEnd + k; // atom serial number
pdbFile << " ";
pdbFile << right << setw(8.3) << Xs[subjectEnd + k];
pdbFile << right << setw(8.3) << Ys[subjectEnd + k];
pdbFile << right << setw(8.3) << Zs[subjectEnd + k];
pdbFile << " 1.00 0.00\n";
}
}
}
pdbFile << "TER\n";
pdbFile.close();
}
}
// --------------------------------------------------------
// ---------- ReloadDB ------------------------------------
// --------------------------------------------------------
void MIViewBrowser::ReloadDB()
{
int i;
wxString msg;
/* before anything, clear the tree control */
treeFileList->DeleteAllItems();
/* read in the database file */
wxString line;
wxString patient, study, series, filename;
wxString date,time, dob;
wxDateTime studyDateTime;
int numLines;
wxTextFile pdbFile("browsedb.txt");
pdbFile.Open();
rootID = treeFileList->AddRoot("Root");
wxTreeItemId curPatientID, curStudyID, curSeriesID, curFileID;
/* loop through, line by line */
numLines = (int)pdbFile.GetLineCount();
/* setup the progress dialog */
wxProgressDialog progDlg(wxT("Loading Database..."), wxT(" "), numLines, this, wxPD_SMOOTH | wxPD_ELAPSED_TIME | wxPD_CAN_ABORT);
for (i=0;i<numLines;i++) {
if (!progDlg.Update(i,msg.Format("Reading entry %d of %d",i,numLines)))
break;
line = pdbFile[i];
if (line[0] != '\t') { /* its a new patient/DOB item */
/* add a node to the root, set current patient node ID */
patient = line.Trim(true).Trim(false);
dob = patient.AfterFirst('&');
dob = ParseDate(dob);
patient = patient.BeforeFirst('&');
patient.Replace("^",",");
patient += " (DOB: " + dob + ")";
curPatientID = treeFileList->AppendItem(rootID,patient,0);
treeFileList->SetItemBackgroundColour(curPatientID,wxColour(200,200,200));
treeFileList->SetItemBold(curPatientID);
}
if ((line[0] == '\t') && (line[1] != '\t')) {
/* add a new studyDate node, set current studyDate node ID */
study = line.Trim(true).Trim(false);
date = study.BeforeFirst('&');
time = study.AfterFirst('&');
study = ParseDateAndTime(date,time);
curStudyID = treeFileList->AppendItem(curPatientID,study,1);
treeFileList->SetItemBackgroundColour(curStudyID,wxColour(225,225,225));
}
if ((line[0] == '\t') && (line[1] == '\t') && (line[2] != '\t')) {
/* add a new seriesNumber node, set current seriesNumber node ID */
series = line.Trim(true).Trim(false);
curSeriesID = treeFileList->AppendItem(curStudyID,series,2);
}
if ((line[0] == '\t') && (line[1] == '\t') && (line[2] == '\t')) {
/* add a new filename node */
filename = line.Trim(true).Trim(false);
curFileID = treeFileList->AppendItem(curSeriesID,filename);
}
::wxSafeYield();
}
ExpandAllPatients();
}
