/** module initialization */
bool TopparManager::load()
{
SysConfig *pconf = SysConfig::getInstance();
SysConfig::Section *psec = pconf->getSection("toppar");
bool bOK = false;
if (psec!=NULL) {
SysConfig::const_iterator iter = psec->begin();
iter=psec->findName(iter, "toppar_file");
for (; iter!=psec->end(); iter=psec->findName(++iter, "toppar_file")) {
SysConfig::Section *pchild = *iter;
LString val = pchild->getStringData();
if (val.isEmpty()) continue;;
int cpos = val.indexOf(':');
if (cpos<0) continue;
LString type = val.substr(0, cpos);
LString fnam = val.substr(cpos+1);
fnam = pconf->convPathName(fnam);
/*if (!fnam.startsWith(MB_PATH_SEPARATOR)) {
LString config_dir = pconf->get("config_dir");
fnam = config_dir + MB_PATH_SEPARATOR + fnam;
}*/
if (readPrmTop(fnam, type))
bOK = true;
}
}
if (!bOK) {
//
// read from default directory with default type/filename
//
LString type("cns");
LString fnam;
for ( ;; ) {
fnam = "queptl.prm";
if (!readPrmTop(fnam, type))
break;
fnam = "queptl.top";
if (!readPrmTop(fnam, type))
break;
fnam = "queptl.lin";
if (!readPrmTop(fnam, type))
break;
return true;
}
LOG_DPRINTLN("Toppar> warning: no mol topology/parameter files is loaded.");
}
// m_pTopoDB->dump();
return true;
}
void clConsole::DisplayMessage( const LString& Message, const LConsoleMessageType MSGType ) const
{
if ( Env )
{
Env->SendSync( L_EVENT_CONSOLELOG, LEventArgs( &Message ), false );
}
FTimeVisible = MESSAGE_VISIBILITY_TIME;
LVector4 Color;
switch ( MSGType )
{
case CMSG_ENGINEMESSAGE:
Color = LC_LinderdaumConsoleEM;
break;
case CMSG_ERRORMESSAGE:
Color = LC_LinderdaumConsoleERR;
break;
case CMSG_INFOTIP:
Color = LC_LinderdaumConsoleIT;
break;
default:
FATAL_MSG( "Unknown message type" );
}
LString Msg = Message;
LMutex Lock( &FMessagesHistoryMutex );
while ( true )
{
size_t Separation = Msg.find( "\n" );
if ( Separation == LString::npos )
{
break;
}
LString NewMsg = Msg.substr( 0, Separation );
FMessagesHistory.push_back( sConsoleMessage( NewMsg, Color ) );
if ( FMessagesHistory.size() > MAX_HISTORY_SIZE )
{
FMessagesHistory.pop_front();
}
Msg = Msg.substr( Separation + 1, Message.length() - 1 );
}
FMessagesHistory.push_back( sConsoleMessage( Msg, Color ) );
}
void clLocalizer::SetLocale( const LString& LocaleName )
{
guard( "%s", LocaleName.c_str() );
ClearLocalization();
FLocaleName = LocaleName;
const LString FileName( FLocalePath + "/Localizer-" + LocaleName + ".txt" );
if ( Env->FileSystem->FileExists( FileName ) )
{
Env->Logger->LogP( L_NOTICE, "Reading locale from %s", FileName.c_str() );
iIStream* Stream = Env->FileSystem->CreateFileReader( FileName );
while ( !Stream->Eof() )
{
LString Line = Stream->ReadLine();
size_t SepPos = Line.find( "~" );
FATAL( SepPos == Line.npos, "Invalid locale translation file format: missing ~" );
LString Text( Line.substr( 0, SepPos ) );
LString Translation( Line.substr( SepPos + 1, Line.length() - SepPos - 1 ) );
FTranslations[ Text ] = Translation;
}
delete( Stream );
}
else
{
Env->Logger->LogP( L_NOTICE, "Locale %s not found", FileName.c_str() );
}
this->SendAsync( L_EVENT_LOCALE_CHANGED, LEventArgs(), false );
unguard();
}
void getRec(int pos, int unit, LString &ret)
{
int beg = pos*unit;
if (beg>=m_line.length() ||
beg<0) {
MB_THROW(qlib::FileFormatException, "");
return;
}
ret = m_line.substr(beg, unit);
}
LString PDBFileWriter::formatAtomName(MolAtomPtr pAtom)
{
LString atomnam = pAtom->getName();
char cConfID = pAtom->getConfID();
int elem = pAtom->getElement();
if (cConfID=='\0')
cConfID = ' ';
// invalid name case
if (atomnam.length()>=4||
elem==ElemSym::XX) {
return LString::format("%4s%c", atomnam.c_str(), cConfID);
}
LString elenam = ElemSym::symID2Str(elem);
elenam = elenam.toUpperCase();
int elepos = atomnam.indexOf(elenam);
if (elepos<0) {
return LString::format("%4s%c", atomnam.c_str(), cConfID);
}
LString atommod;
// if (atomnam.equals(elenam)) {
// // atom name==elem name
// shead += LString::format(" %2s ", elenam.c_str());
// break;
// }
elepos += elenam.length();
atommod = atomnam.substr(elepos);
elenam = atomnam.substr(0, elepos);
if (atommod.length()<=2) {
return LString::format("%2s%-2s%c",
elenam.c_str(), atommod.c_str(), cConfID);
}
return LString::format("%4s%c", atomnam.c_str(), cConfID);
}
//------------------------------------------------------------------------------
int LArguments::parse(int argc, char* argv[]) {
LString opt;
int find;
int ret;
for(int num = 1; num < argc; num++) {
opt = LString(argv[num]);
if(opt.find("--") == 0) {
if((find = opt.find("=")) != (int)string::npos) {
if((ret = parseInternalOptionWithParamater(opt.substr(0, find), opt.substr(find + 1))) != L_OK) {
return ret;
}
}
else {
if((ret = parseInternalOption(opt)) != L_OK) {
return ret;
}
}
}
else if(opt.find("-") == 0) {
if((find = opt.find("=")) != (int)string::npos) {
if((ret = parseInternalOptionWithParamater(opt.substr(0, find), opt.substr(find + 1))) != L_OK) {
return ret;
}
}
else {
if((ret = parseInternalOption(opt)) != L_OK) {
return ret;
}
}
}
else {
if((ret = parseInternalArgument(opt)) != L_OK) {
return ret;
}
}
}
return L_OK;
}
LString readStr(int start, int end) {
if (m_recbuf.isEmpty()) return LString();
start --; end --;
if (end >= m_recbuf.length())
end = m_recbuf.length()-1;
if (start<0)
start = 0;
if (start>end)
start = end;
return m_recbuf.substr(start, end-start+1);
}
int getInt(int pos, int unit)
{
int ret;
int beg = pos*unit;
if (beg>=m_line.length() ||
beg<0) {
MB_THROW(qlib::FileFormatException, "");
return -1;
}
LString s = m_line.substr(beg, unit);
if (!s.toInt(&ret)) {
MB_THROW(qlib::FileFormatException, "");
return -1;
}
return ret;
}
// write PDB file to stream
bool PDBFileWriter::write(qlib::OutStream &outs)
{
m_pMol = getTarget<MolCoord>();
if (m_pMol==NULL) {
LOG_DPRINTLN("PDBWriter> MolCoord is not attached !!");
return false;
}
// check extension record handlers
PDBFileReader::HndlrTab &htab = PDBFileReader::m_htab;
bool bUseHndlr = htab.size()>0;
MolCoord *pMol = m_pMol;
qlib::PrintStream prs(outs);
//
// write header
//
//LString sbuf = pqsys->getVersion();
//prs.formatln("REMARK PDB File Generated by CueMol (ver %s)", sbuf.c_str());
prs.formatln("REMARK PDB File Generated by CueMol2");
//
// write SSBOND record
//
writeSSBonds(prs);
//
// write LINK record
//
writeLinks(prs);
writeSecstr(prs);
//
// write extension records (CRYST1)
//
if (bUseHndlr) {
LString sbuf;
PDBFileReader::HndlrTab::const_iterator iter = htab.begin();
for (; iter!=htab.end(); ++iter) {
PDBFileReader::RecordHandler *ph = iter->second;
if (ph!=NULL && ph->write(sbuf, pMol)) {
prs.println(sbuf);
}
}
}
//
// write body (ATOM/ANISOU records)
//
int nserial = 1;
// Sort chain names by ASCII order
// take care of '_' (empty) chain
std::list<LString> chnames;
{
MolCoord::ChainIter iter = pMol->begin();
bool bHasEmptyChain = false;
for (; iter!=pMol->end(); ++iter) {
MolChainPtr pChn = iter->second;
LString chnam = (pChn->getName().c_str());
if (chnam.equals("_")) {
bHasEmptyChain = true;
continue;
}
chnames.push_back(chnam);
}
chnames.sort();
if (bHasEmptyChain)
chnames.push_back("_");
}
std::list<LString>::const_iterator cniter = chnames.begin();
for (; cniter!=chnames.end(); ++cniter) {
LString chnam = *cniter;
MolChainPtr pChn = pMol->getChain(chnam);
// format chain name
char cch = convChainName(chnam);
LString resnam;
MolChain::ResidCursor2 riter = pChn->begin2();
// int nlastres = 0;
for (; riter!=pChn->end2(); ++riter) {
//MolResiduePtr pRes = *riter;
MolResiduePtr pRes = riter->second;
if (pRes.isnull()) continue;
ResidIndex rindex = pRes->getIndex();
resnam = pRes->getName();
// format residue name
// resnam = resnam.toUpperCase();
resnam = resnam.substr(0,3);
// sort atom by AID
std::list<int> atmlist;
{
MolResidue::AtomCursor aiter = pRes->atomBegin();
for (; aiter!=pRes->atomEnd(); ++aiter) {
atmlist.push_back(aiter->second);
}
atmlist.sort();
}
std::list<int>::const_iterator iter = atmlist.begin();
for (; iter!=atmlist.end(); ++iter) {
int aid = *iter;
MolAtomPtr pAtm = pMol->getAtom(aid);
if (pAtm.isnull())
continue;
if (!m_pSel.isnull()) {
if (!m_pSel->isSelected(pAtm))
continue; // skip nonselected atom
}
writeAtomLine(nserial, rindex, resnam,
cch, pAtm, prs);
nserial++;
}
// nlastres = rindex.first;
}
// print TER record
/*prs.formatln("TER "
"%5d"
" "
"%3s "
"%1s"
"%4d"
" ",
nserial, resnam.c_str(), chnam.c_str(), nlastres);*/
prs.println("TER");
nserial ++;
}
//prs.println("END ");
prs.println("END");
return true;
}
void PDBFileWriter::writeSecstr(qlib::PrintStream &prs)
{
MolResiduePtr pRes1;
int nhx = 1;
MolCoordPtr pMol(m_pMol);
ResidIterator riter(pMol); //(MolCoordPtr(m_pMol));
// Write HELIX records
for (riter.first(); riter.hasMore(); riter.next()) {
LString sec;
LString pfx;
MolResiduePtr pRes = riter.get();
pRes->getPropStr("secondary2", sec);
// MB_DPRINTLN("%s%d => %s", pRes->getChainName().c_str(), pRes->getIndex().first, sec.c_str());
if (sec.length()>=2)
pfx= sec.substr(1,1);
if (!(sec.startsWith("H")||sec.startsWith("G")||sec.startsWith("I")))
continue;
if (pfx.equals("s"))
pRes1 = pRes;
else if (pfx.equals("e")) {
LString resn1 = pRes1->getName().substr(0,3);
LString chn1 = pRes1->getChainName().substr(0,1);
ResidIndex resix1 = pRes1->getIndex();
char ins1 = resix1.second;
if (ins1=='\0') ins1 = ' ';
LString resn2 = pRes->getName().substr(0,3);
LString chn2 = pRes->getChainName().substr(0,1);
ResidIndex resix2 = pRes->getIndex();
char ins2 = resix2.second;
if (ins2=='\0') ins2 = ' ';
prs.print("HELIX ");
// helix seqno
prs.format(" %3d", nhx);
// helix ID
prs.format(" %3d", nhx);
// start resname
prs.format(" %3s", resn1.c_str());
prs.format(" %1s", chn1.c_str());
prs.format(" %4d", resix1.first);
prs.format("%c", ins1);
// end resname
prs.format(" %3s", resn2.c_str());
prs.format(" %1s", chn2.c_str());
prs.format(" %4d", resix2.first);
prs.format("%c", ins2);
// typeof helix
int ntype = 1;
if (sec.startsWith("G"))
ntype = 5;
else if (sec.startsWith("I"))
ntype = 3;
prs.format("%2d", ntype);
prs.println("");
++nhx;
}
}
// Write SHEET records
int nsh = 1;
for (riter.first(); riter.hasMore(); riter.next()) {
LString sec;
LString pfx;
MolResiduePtr pRes = riter.get();
pRes->getPropStr("secondary2", sec);
// MB_DPRINTLN("%s%d => %s", pRes->getChainName().c_str(), pRes->getIndex().first, sec.c_str());
if (sec.length()>=2)
pfx= sec.substr(1,1);
if (!(sec.startsWith("E")))
continue;
if (pfx.equals("s"))
pRes1 = pRes;
else if (pfx.equals("e")) {
LString resn1 = pRes1->getName().substr(0,3);
LString chn1 = pRes1->getChainName().substr(0,1);
ResidIndex resix1 = pRes1->getIndex();
char ins1 = resix1.second;
if (ins1=='\0') ins1 = ' ';
LString resn2 = pRes->getName().substr(0,3);
LString chn2 = pRes->getChainName().substr(0,1);
ResidIndex resix2 = pRes->getIndex();
char ins2 = resix2.second;
if (ins2=='\0') ins2 = ' ';
prs.print("SHEET ");
// helix seqno
prs.format(" %3d", nsh);
// helix ID
prs.format(" %3d", nsh);
// num of strands
prs.print(" 1");
// start resname
prs.format(" %3s", resn1.c_str());
prs.format(" %1s", chn1.c_str());
prs.format("%4d", resix1.first);
prs.format("%c", ins1);
// end resname
prs.format(" %3s", resn2.c_str());
prs.format(" %1s", chn2.c_str());
prs.format("%4d", resix2.first);
prs.format("%c", ins2);
// direction
prs.print(" 0");
prs.println("");
++nsh;
}
} // for
}
void clConsole::SendCommand( const LString& CMDName )
{
guard( "%s", CMDName.c_str() );
FSendCommandResult.assign( "" );
if ( CMDName.size() == 0 )
{
return;
}
bool IsScript = ( LStr::GetUpper( LStr::GetToken( CMDName, 1 ) ) == "RS" );
// split command
size_t CommandsSeparator = FindCommandsSeparator( CMDName );
LString ThisCMDString = CMDName;
LString RestCMDString( "" );
if ( !IsScript )
{
if ( CommandsSeparator )
{
ThisCMDString = CMDName.substr( 0, CommandsSeparator );
RestCMDString = CMDName.substr( CommandsSeparator,
CMDName.length() - CommandsSeparator );
if ( RestCMDString.length() > 0 )
{
LStr::pop_front( &RestCMDString );
}
}
}
// extract command name and parameters
LString ThisCMDName = LStr::GetToken( ThisCMDString, 1 );
LString ThisCMDParam = ThisCMDString.substr( ThisCMDName.length(),
ThisCMDString.length() - ThisCMDName.length() );
if ( ThisCMDParam.length() > 0 )
{
LStr::pop_front( &ThisCMDParam );
}
LStr::ToUpper( &ThisCMDName );
if ( IsScript )
{
// execute script and return
ExecuteStatement( ThisCMDParam );
return;
}
if ( ThisCMDName.find( "WAIT" ) == 0 )
{
// Leave the rest of the command until the next frame
if ( CommandsSeparator )
{
QueryCommand( RestCMDString );
}
return;
}
else
{
clCommandsList::const_iterator i = FCommandsList.find( ThisCMDName );
if ( i != FCommandsList.end() )
{
( i->second ).Exec( clFileSystem::ReplaceEnvVars( ThisCMDParam ) );
}
else
{
clAliasesList::const_iterator j = FAliasesList.find( ThisCMDName );
if ( j != FAliasesList.end() )
{
QueryCommand( j->second );
}
else
{
DisplayError( "Unknown command: " + ThisCMDName );
}
}
}
if ( CommandsSeparator )
{
SendCommand( RestCMDString );
}
unguard();
}
