/** 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;
}
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);
}
