/// Convert aid to (persistent) string representation
LString MolCoord::toStrAID(int atomid) const
{
MolAtomPtr pAtom = getAtom(atomid);
if (pAtom.isnull()) return LString();
LString value = LString::format("%s.%s.%s",
pAtom->getChainName().c_str(),
pAtom->getResIndex().toString().c_str(),
pAtom->getName().c_str());
char conf_id = pAtom->getConfID();
if (conf_id)
value += ":" + LString(conf_id);
return value;
}
bool MolCoord::removeAtom(int atomid)
{
MolAtomPtr pAtom = getAtom(atomid);
if (pAtom.isnull() || pAtom->getParentUID()!=getUID())
return false;
m_atomPool.remove(atomid);
// invalidate ID
pAtom->setID(-1);
const LString &aname = pAtom->getName();
char cConfID = pAtom->getConfID();
ResidIndex nresid = pAtom->getResIndex();
const LString &cname = pAtom->getChainName();
MolChainPtr pCh = getChain(cname);
if (pCh.isnull())
return false;
MolResiduePtr pRes = getResidue(cname, nresid);
if (pRes.isnull())
return false;
// remove atom
if (!pRes->removeAtom(aname, cConfID))
return false;
if (pRes->getAtomSize()>0)
return true;
// purge the empty residue
if (!pCh->removeResidue(nresid))
return false;
// delete pRes;
if (pCh->getSize()>0)
return true;
// purge the empty chain
if (!removeChain(cname))
return false;
// delete pCh;
return true;
}
void MolArrayMap::setup(MolCoordPtr pRefMol)
{
m_data.erase(m_data.begin(), m_data.end());
int i = 0;
AtomIterator iter(pRefMol);
for (iter.first(); iter.hasMore(); iter.next(), ++i) {
MolAtomPtr pa = iter.get();
MolArrayMapElem a;
a.chain = pa->getChainName().c_str();
a.resid = pa->getResIndex().toInt();
a.atom = pa->getName().c_str();
a.pA = pa;
m_data.insert(data_t::value_type(a, -1));
//MB_DPRINTLN("fitref %s %d %s", a.chain.c_str(), a.resid, a.atom.c_str());
}
setupIndex();
}
int MolCoord::appendAtom(MolAtomPtr pAtom)
{
pAtom->setParentUID(getUID());
const LString &cname = pAtom->getChainName();
const LString &rname = pAtom->getResName();
const LString &aname = pAtom->getName();
ResidIndex nresid = pAtom->getResIndex();
if (cname.length()<=0 ||
aname.length()<=0) {
LString msg =
LString::format("MolCoord> ERROR: appending atom with invalid properties"
" (c:'%s' rn:'%s' ri:'%s' an:'%s')",
cname.c_str(), rname.c_str(), nresid.toString().c_str(),
aname.c_str());
MB_DPRINTLN(msg);
MB_THROW(qlib::IllegalArgumentException, msg);
return -1;
}
MolChainPtr pCh = getChain(cname);
if (pCh.isnull()) {
pCh = MolChainPtr(MB_NEW MolChain());
pCh->setParentUID(getUID());
pCh->setName(cname);
appendChain(pCh);
}
MolResiduePtr pRes = pCh->getResidue(nresid);
if (pRes.isnull()) {
pRes = MolResiduePtr(MB_NEW MolResidue());
pRes->setParentUID(getUID());
pRes->setIndex(nresid);
pRes->setName(rname);
// pRes->setChainName(cname);
pCh->appendResidue(pRes);
}
else {
const LString &pre_rname = pRes->getName();
if (!pre_rname.equals(rname)) {
MB_DPRINTLN("MolCoord> ERROR: appending an atom (%s %s%s %s) with inconsistent residue (%s)",
cname.c_str(), rname.c_str(),
nresid.toString().c_str(), aname.c_str(),
pre_rname.c_str());
// TO DO: throw exception (???)
// This is often the case, so is not an exception.
// return -1;
}
}
//
// Append to the atompool --> assign the atom ID
//
int atomid = m_atomPool.put(pAtom);
if (atomid<0) {
// This isn't fail in normal situation.
MB_THROW(qlib::RuntimeException, "append to the atompool failed");
return -1;
}
pAtom->setID(atomid);
// MolResidue::appendAtom() must be called after setID(),
// because MolResidue makes map from name to AID, which requires "AID".
if (!pRes->appendAtom(pAtom)) {
// This is often the case with malformed PDB files, so is not an exception.
MB_DPRINTLN("MolCoord> ERROR: appending duplicated atom (%s %s%s %s)",
cname.c_str(), rname.c_str(), nresid.toString().c_str(),
aname.c_str());
// Remove the mis-appended atom from the pool.
m_atomPool.remove(atomid);
return -1;
}
// Update the cached xform matrix if required
pAtom->resetXformMatrix();
if (!getXformMatrix().isIdent())
pAtom->setXformMatrix(getXformMatrix());
return atomid;
}
