bool OBDepict::AddAtomLabels(AtomLabelType type)
{
d->painter->SetPenColor(OBColor("red"));
d->painter->SetFillColor(OBColor("red"));
d->painter->SetFontSize((int)(GetFontSize() * 0.8));// smaller text
OBAtomIterator i;
for (OBAtom *atom = d->mol->BeginAtom(i); atom; atom = d->mol->NextAtom(i)) {
vector3 pos(atom->GetVector());
std::stringstream ss;
switch (type) {
case AtomId:
ss << atom->GetId();
d->painter->DrawText(pos.x(), pos.y(), ss.str());
break;
case AtomSymmetryClass:
ss << GetAtomSymClass(atom);
d->painter->DrawText(pos.x(), pos.y(), ss.str());
break;
case AtomIndex:
ss << atom->GetIdx();
d->painter->DrawText(pos.x(), pos.y(), ss.str());
break;
default:
break;
}
}
return true;
}
int GetLabelAlignment(OBAtom *atom)
{
// compute the sum of the bond vectors, this gives
vector3 direction(VZero);
OBBondIterator i;
for (OBAtom *nbr = atom->BeginNbrAtom(i); nbr; nbr = atom->NextNbrAtom(i))
direction += atom->GetVector() - nbr->GetVector();
const double bias = -0.1; //towards left-alignment, which is more natural
int alignment = 0;
if (direction.y() < 0.0) {
if (direction.x() < bias)
alignment = BottomRight;
else
alignment = BottomLeft;
} else if (direction.x() > 0.0) {
if (direction.x() < bias)
alignment = TopRight;
else
alignment = TopLeft;
} else {
if (direction.x() < bias)
alignment = CenterRight;
else
alignment = CenterLeft;
}
return alignment;
}
bool BoxFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
//margin hardwired in new framework. Also was in old fileformat
double margin=1.0;
char buffer[BUFF_SIZE];
vector3 vcenter,vmin,vmax,vmid,vdim;
OBAtom *atom;
vector<OBAtom*>::iterator i;
vmax.Set(-10E10,-10E10,-10E10);
vmin.Set( 10E10, 10E10, 10E10);
for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
{
vcenter += atom->GetVector();
if (atom->x() < vmin.x())
vmin.SetX(atom->x());
if (atom->y() < vmin.y())
vmin.SetY(atom->y());
if (atom->z() < vmin.z())
vmin.SetZ(atom->z());
if (atom->x() > vmax.x())
vmax.SetX(atom->x());
if (atom->y() > vmax.y())
vmax.SetY(atom->y());
if (atom->z() > vmax.z())
vmax.SetZ(atom->z());
}
vcenter /= (double)mol.NumAtoms();
vector3 vmarg(margin,margin,margin);
vmin -= vmarg;
vmax += vmarg;
vdim = vmax - vmin;
vmid = vmin+vmax;
vmid /= 2.0;
ofs << "HEADER CORNERS OF BOX" << endl;
snprintf(buffer, BUFF_SIZE, "REMARK CENTER (X Y Z) %10.3f %10.3f %10.3f",
vmid.x(),vmid.y(),vmid.z());
ofs << buffer << endl;
snprintf(buffer, BUFF_SIZE, "REMARK DIMENSIONS (X Y Z) %10.3f %10.3f %10.3f",
vdim.x(),vdim.y(),vdim.z());
ofs << buffer << endl;
vdim /= 2.0;
vector3 vtmp;
int j;
for (j = 1; j <= 8; j++)
{
switch(j)
{
case 1:
vtmp = vmid-vdim;
break;
case 2:
vtmp.SetX(vmid.x()+vdim.x());
break;
case 3:
vtmp.SetZ(vmid.z()+vdim.z());
break;
case 4:
vtmp.SetX(vmid.x()-vdim.x());
break;
case 5:
vtmp = vmid-vdim;
vtmp.SetY(vmid.y()+vdim.y());
break;
case 6:
vtmp = vmid+vdim;
vtmp.SetZ(vmid.z()-vdim.z());
break;
case 7:
vtmp = vmid+vdim;
break;
case 8:
vtmp.SetX(vmid.x()-vdim.x());
break;
}
snprintf(buffer, BUFF_SIZE, "ATOM %d DUA BOX 1 %8.3f%8.3f%8.3f",
j,vtmp.x(),vtmp.y(),vtmp.z());
ofs << buffer << endl;
}
ofs << "CONECT 1 2 4 5" << endl;
ofs << "CONECT 2 1 3 6" << endl;
ofs << "CONECT 3 2 4 7" << endl;
ofs << "CONECT 4 1 3 8" << endl;
ofs << "CONECT 5 1 6 8" << endl;
ofs << "CONECT 6 2 5 7" << endl;
ofs << "CONECT 7 3 6 8" << endl;
ofs << "CONECT 8 4 5 7" << endl;
return(true);
}
//! \return whether partial charges were successfully assigned to this molecule
bool EQEqCharges::ComputeCharges(OBMol &mol)
{
int i, j, a, c, N = mol.NumAtoms();
double cellVolume;
VectorXf chi(N), J(N), b(N), x(N);
MatrixXf J_ij(N, N), A(N, N);
OBUnitCell *obuc;
matrix3x3 unitcell, fourier;
vector3 dx;
int numNeighbors[3];
OBAtom *atom;
// If parameters have not yet been loaded, do that
if (!_paramFileLoaded)
{
if (ParseParamFile())
{
_paramFileLoaded = true;
} else
{
return false;
}
}
// Calculate atomic properties based around their ionic charge
for (i = 0; i < N; i++)
{
atom = mol.GetAtom(i + 1);
a = atom->GetAtomicNum();
c = _chargeCenter[a];
// Fail if ionization data is missing for any atom in the molecule
if (_ionizations[a][c + 1] == -1 || _ionizations[a][c] == -1 || a > TABLE_OF_ELEMENTS_SIZE)
{
obErrorLog.ThrowError(__FUNCTION__, "Insufficient ionization data for atoms in the given molecule. Update `data/eqeqIonizations.txt` with missing information and re-run this function.", obError);
return false;
}
J(i) = _ionizations[a][c + 1] - _ionizations[a][c];
chi(i) = 0.5 * (_ionizations[a][c + 1] + _ionizations[a][c]) - (a == 1? 0 : c * J(i));
}
// If a unit cell is defined, use the periodic Ewald calculation
if (mol.HasData(OBGenericDataType::UnitCell))
{
// Get unit cell and calculate its Fourier transform + volume
obuc = (OBUnitCell *) mol.GetData(OBGenericDataType::UnitCell);
unitcell = obuc->GetCellMatrix();
fourier = (2 * PI * unitcell.inverse()).transpose();
cellVolume = obuc->GetCellVolume();
// Get the number of radial unit cells to use in x, y, and z
numNeighbors[0] = int(ceil(minCellLength / (2.0 * (obuc->GetA())))) - 1;
numNeighbors[1] = int(ceil(minCellLength / (2.0 * (obuc->GetB())))) - 1;
numNeighbors[2] = int(ceil(minCellLength / (2.0 * (obuc->GetC())))) - 1;
for (i = 0; i < N; i++)
{
atom = mol.GetAtom(i + 1);
for (j = 0; j < N; j++)
{
dx = atom->GetVector() - (mol.GetAtom(j + 1))->GetVector();
J_ij(i, j) = GetPeriodicEwaldJij(J(i), J(j), dx, (i == j), unitcell, fourier, cellVolume, numNeighbors);
}
}
// If no unit cell, use the simplified nonperiodic calculation
} else
{
for (i = 0; i < N; i++)
{
atom = mol.GetAtom(i + 1);
for (j = 0; j < N; j++)
{
J_ij(i, j) = GetNonperiodicJij(J(i), J(j), atom->GetDistance(j + 1), (i == j));
}
return false;
}
}
// Formulate problem as A x = b, where x is the calculated partial charges
// First equation is a simple overall balance: sum(Q) = 0
A.row(0) = VectorXf::Ones(N);
b(0) = 0;
// Remaining equations are based off of the fact that, at equilibrium, the
// energy of the system changes equally for a change in any charge:
// dE/dQ_1 = dE/dQ_2 = ... = dE/dQ_N
A.block(1, 0, N - 1, N) = J_ij.block(0, 0, N - 1, N) - J_ij.block(1, 0, N - 1, N);
b.tail(N - 1) = chi.tail(N - 1) - chi.head(N - 1);
// The solution is a list of charges in the system
x = A.colPivHouseholderQr().solve(b);
// Now we are done calculating, pass all this back to OpenBabel molecule
mol.SetPartialChargesPerceived();
OBPairData *dp = new OBPairData;
dp->SetAttribute("PartialCharges");
dp->SetValue("EQEq");
dp->SetOrigin(perceived);
mol.SetData(dp);
m_partialCharges.clear();
m_partialCharges.reserve(N);
m_formalCharges.clear();
m_formalCharges.reserve(N);
for (i = 0; i < N; i ++)
{
atom = mol.GetAtom(i + 1);
atom->SetPartialCharge(x(i));
m_partialCharges.push_back(x(i));
m_formalCharges.push_back(atom->GetFormalCharge());
}
obErrorLog.ThrowError(__FUNCTION__, "EQEq charges successfully assigned.", obInfo);
return true;
}
//! Calculate the signed volume for an atom. If the atom has a valence of 3
//! the coordinates of an attached hydrogen are calculated
//! Puts attached Hydrogen last at the moment, like mol V3000 format.
//! If ReZero=false (the default is true) always make pseudo z coords and leave them in mol
double CalcSignedVolume(OBMol &mol,OBAtom *atm, bool ReZeroZ)
{
vector3 tmp_crd;
vector<unsigned int> nbr_atms;
vector<vector3> nbr_crds;
bool use_central_atom = false,is2D=false;
// double hbrad = etab.CorrectedBondRad(1,0);
if (!ReZeroZ || !mol.Has3D()) //give pseudo Z coords if mol is 2D
{
vector3 v,vz(0.0,0.0,1.0);
is2D = true;
OBAtom *nbr;
OBBond *bond;
vector<OBBond*>::iterator i;
for (bond = atm->BeginBond(i);bond;bond = atm->NextBond(i))
{
nbr = bond->GetEndAtom();
if (nbr != atm)
{
v = nbr->GetVector();
if (bond->IsWedge())
v += vz;
else
if (bond->IsHash())
v -= vz;
nbr->SetVector(v);
}
else
{
nbr = bond->GetBeginAtom();
v = nbr->GetVector();
if (bond->IsWedge())
v -= vz;
else
if (bond->IsHash())
v += vz;
nbr->SetVector(v);
}
}
}
if (atm->GetHvyValence() < 3)
{
stringstream errorMsg;
errorMsg << "Cannot calculate a signed volume for an atom with a heavy atom valence of " << atm->GetHvyValence() << endl;
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obInfo);
return(0.0);
}
// Create a vector with the coordinates of the neighbor atoms
// Also make a vector with Atom IDs
OBAtom *nbr;
vector<OBBond*>::iterator bint;
for (nbr = atm->BeginNbrAtom(bint);nbr;nbr = atm->NextNbrAtom(bint))
{
nbr_atms.push_back(nbr->GetIdx());
}
// sort the neighbor atoms to insure a consistent ordering
sort(nbr_atms.begin(),nbr_atms.end());
for (unsigned int i = 0; i < nbr_atms.size(); ++i)
{
OBAtom *tmp_atm = mol.GetAtom(nbr_atms[i]);
nbr_crds.push_back(tmp_atm->GetVector());
}
/*
// If we have three heavy atoms we need to calculate the position of the fourth
if (atm->GetHvyValence() == 3)
{
double bondlen = hbrad+etab.CorrectedBondRad(atm->GetAtomicNum(),atm->GetHyb());
atm->GetNewBondVector(tmp_crd,bondlen);
nbr_crds.push_back(tmp_crd);
}
*/
for(unsigned int j=0;j < nbr_crds.size();++j) // Checks for a neighbour having 0 co-ords (added hydrogen etc)
{
// are the coordinates zero to 6 or more significant figures
if (nbr_crds[j].IsApprox(VZero, 1.0e-6) && use_central_atom==false)
use_central_atom=true;
else if (nbr_crds[j].IsApprox(VZero, 1.0e-6))
{
obErrorLog.ThrowError(__FUNCTION__, "More than 2 neighbours have 0 co-ords when attempting 3D chiral calculation", obInfo);
}
}
// If we have three heavy atoms we can use the chiral center atom itself for the fourth
// will always give same sign (for tetrahedron), magnitude will be smaller.
if(nbr_atms.size()==3 || use_central_atom==true)
{
nbr_crds.push_back(atm->GetVector());
nbr_atms.push_back(mol.NumAtoms()+1); // meed to add largest number on end to work
}
OBChiralData* cd=(OBChiralData*)atm->GetData(OBGenericDataType::ChiralData); //Set the output atom4refs to the ones used
if(cd==NULL)
{
cd = new OBChiralData;
cd->SetOrigin(perceived);
atm->SetData(cd);
}
cd->SetAtom4Refs(nbr_atms,calcvolume);
//re-zero psuedo-coords
if (is2D && ReZeroZ)
{
vector3 v;
OBAtom *atom;
vector<OBAtom*>::iterator k;
for (atom = mol.BeginAtom(k);atom;atom = mol.NextAtom(k))
{
v = atom->GetVector();
v.SetZ(0.0);
atom->SetVector(v);
}
}
return(signed_volume(nbr_crds[0],nbr_crds[1],nbr_crds[2],nbr_crds[3]));
}