bool OpAlign::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol)
return false;
map<string,string>::const_iterator itr;
// Is there an -s option?
if(pConv->IsFirstInput())
{
_pOpIsoM = NULL; //assume no -s option
itr = pmap->find("s");
if(itr!=pmap->end())
{
//There is an -s option; check it is ok
_pOpIsoM = static_cast<OpNewS*>(OBOp::FindType("s"));
_stext = itr->second; //get its parameter(s)
if(!_pOpIsoM || _stext.empty())
{
obErrorLog.ThrowError(__FUNCTION__,
"No parameter on -s option, or its OBOp version is not loaded", obError);
pConv->SetOneObjectOnly(); //to finish
return false;
}
}
}
// If the output format is a 2D depiction format, then we should align
// on the 2D coordinates and not the 3D coordinates (if present). This
//means we need to generate the 2D coordinates at this point.
if(pmol->GetDimension()==3 && (pConv->GetOutFormat()->Flags() & DEPICTION2D))
{
OBOp* pgen = OBOp::FindType("gen2D");
if(pgen)
pgen->Do(pmol);
}
// All molecules must have coordinates, so add them if 0D
// They may be added again later when gen2D or gen3D is called, but they will be the same.
// It would be better if this op was called after them, which would happen
// if its name was alphabetically after "gen" (and before "s").
if(pmol->GetDimension()==0)
{
//Will the coordinates be 2D or 3D?
itr = pmap->find("gen3D");
OBOp* pgen = (itr==pmap->end()) ? OBOp::FindType("gen2D") : OBOp::FindType("gen3D");
if(pgen)
pgen->Do(pmol);
}
//Do the alignment in 2D if the output format is svg, png etc. and there is no -xn option
if(pmol->GetDimension()==3 && pConv && !pConv->IsOption("n"))
{
OBFormat* pOutFormat = pConv->GetOutFormat();
if(pOutFormat->Flags() & DEPICTION2D)
{
OBOp* pgen = OBOp::FindType("gen2D");
if(pgen)
pgen->Do(pmol);
}
}
if(pConv->IsFirstInput() || _refMol.NumAtoms()==0)
{
_refvec.clear();
// Reference molecule is basically the first molecule
_refMol = *pmol;
if(!_pOpIsoM)
//no -s option. Use a molecule reference.
_align.SetRefMol(_refMol);
else
{
//If there is a -s option, reference molecule has only those atoms that are matched
//Call the -s option from here
bool ret = _pOpIsoM->Do(pmol, _stext.c_str(), pmap, pConv);
// Get the atoms that were matched
vector<int> ats = _pOpIsoM->GetMatchAtoms();
if(!ats.empty())
{
// Make a vector of the matching atom coordinates...
for(vector<int>::iterator iter=ats.begin(); iter!=ats.end(); ++iter)
_refvec.push_back((pmol->GetAtom(*iter))->GetVector());
// ...and use a vector reference
_align.SetRef(_refvec);
}
// Stop -s option being called normally, although it will still be called once
// in the DoOps loop already started for the current (first) molecule.
pConv->RemoveOption("s",OBConversion::GENOPTIONS);
if(!ret)
{
// the first molecule did not match the -s option so a reference molecule
// could not be made. Keep trying.
_refMol.Clear();
//obErrorLog.ThrowError(__FUNCTION__, "The first molecule did not match the -s option\n"
// "so the reference structure was not derived from it", obWarning, onceOnly);
return false; //not matched
}
}
}
//All molecules
if(pmol->GetDimension()!= _refMol.GetDimension())
{
stringstream ss;
ss << "The molecule" << pmol->GetTitle()
<< " does not have the same dimensions as the reference molecule "
<< _refMol.GetTitle() << " and is ignored.";
obErrorLog.ThrowError(__FUNCTION__, ss.str().c_str(), obError);
return false;
}
if(_pOpIsoM) //Using -s option
{
//Ignore mol if it does not pass -s option
if(!_pOpIsoM->Do(pmol, "", pmap, pConv)) // "" means will use existing parameters
return false;
// Get the atoms equivalent to those in ref molecule
vector<int> ats = _pOpIsoM->GetMatchAtoms();
// Make a vector of their coordinates and get the centroid
vector<vector3> vec;
vector3 centroid;
for(vector<int>::iterator iter=ats.begin(); iter!=ats.end(); ++iter) {
vector3 v = pmol->GetAtom(*iter)->GetVector();
centroid += v;
vec.push_back(v);
}
centroid /= vec.size();
// Do the alignment
_align.SetTarget(vec);
if(!_align.Align())
return false;
// Get the centroid of the reference atoms
vector3 ref_centroid;
for(vector<vector3>::iterator iter=_refvec.begin(); iter!=_refvec.end(); ++iter)
ref_centroid += *iter;
ref_centroid /= _refvec.size();
//subtract the centroid, rotate the target molecule, then add the centroid
matrix3x3 rotmatrix = _align.GetRotMatrix();
for (unsigned int i = 1; i <= pmol->NumAtoms(); ++i)
{
vector3 tmpvec = pmol->GetAtom(i)->GetVector();
tmpvec -= centroid;
tmpvec *= rotmatrix; //apply the rotation
tmpvec += ref_centroid;
pmol->GetAtom(i)->SetVector(tmpvec);
}
}
else //Not using -s option)
{
_align.SetTargetMol(*pmol);
if(!_align.Align())
return false;
_align.UpdateCoords(pmol);
}
//Save rmsd as a property
OBPairData* dp = new OBPairData;
dp->SetAttribute("rmsd");
double val = _align.GetRMSD();
if(val<1e-12)
val = 0.0;
dp->SetValue(toString(val));
dp->SetOrigin(local);
pmol->SetData(dp);
return true;
}
void CalcRMSD::Run()
{
OBAlign align;
unsigned int cutoff_passed = 0;
unsigned int N = 0;
OBMol rmol, tmol;
vector<double> rmsd;
const double binvals_arr[8] = {0.2, 0.5, 1.0, 1.5, 2.0, 3.0, 4.0, 100.0};
vector<double> binvals(binvals_arr, binvals_arr+8);
// For every test_conf there is a reference, but not v.v.
bool more_to_come = tconv.Read(&tmol);
while (more_to_come) {
N++;
string title = tmol.GetTitle();
// Get the corresponding reference
rconv.Read(&rmol);
while (rmol.GetTitle() != title) {
cout << "..Molecule " << N
<< "\n..title = " << rmol.GetTitle()
<< "\n..number of confs = 0\n";
N++;
rconv.Read(&rmol);
}
cout << "..Molecule " << N << "\n..title = " << rmol.GetTitle() << "\n";
align.SetRefMol(rmol);
rmsd.clear();
while (tmol.GetTitle() == title) {
align.SetTargetMol(tmol);
align.Align();
rmsd.push_back(align.GetRMSD());
more_to_come = tconv.Read(&tmol);
if (!more_to_come) break;
}
sort(rmsd.begin(), rmsd.end());
cout << "..number of confs = " << rmsd.size() << "\n";
cout << "..minimum rmsd = " << rmsd.at(0) << "\n";
int bin_idx = 0;
vector<int> bins(binvals.size());
for(vector<double>::iterator it=rmsd.begin(); it!=rmsd.end(); ++it) {
while (*it > binvals[bin_idx])
bin_idx++;
bins[bin_idx]++;
}
vector<int> cumbins(bins);
for(int i=1; i<8; ++i)
cumbins[i] += cumbins[i-1];
cout << "..confs less than cutoffs: ";
cout << binvals[0];
for (int i=1; i < binvals.size(); i++)
cout << " " << binvals[i];
cout << "\n";
cout << ".." << cumbins[0];
for (int i=1; i < cumbins.size(); i++)
cout << " " << cumbins[i];
cout << "\n";
cout << "..cutoff (" << rmsd_cutoff << ") passed = ";
if (rmsd.at(0) <= rmsd_cutoff) {
cout << " Yes\n";
cutoff_passed++;
}
else
cout << " No\n";
cout << "\n";
}
cout << "\n**Summary\n..number of molecules = " << N
<< "\n..less than cutoff(" << rmsd_cutoff << ") = " << cutoff_passed << "\n";
}