void OBChargeModel::FillChargeVectors(OBMol &mol)
{
OBAtom *atom;
vector<OBAtom*>::iterator itr;
m_partialCharges.clear();
m_partialCharges.reserve(mol.NumAtoms());
m_formalCharges.clear();
m_formalCharges.reserve(mol.NumAtoms());
for (atom = mol.BeginAtom(itr);atom;atom = mol.NextAtom(itr))
{
m_partialCharges.push_back(atom->GetPartialCharge());
m_formalCharges.push_back((double)(atom->GetFormalCharge()));
}
}
bool PDBFormat::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;
unsigned int i;
char buffer[BUFF_SIZE];
char type_name[10], padded_name[10];
char the_res[10];
char the_chain = ' ';
const char *element_name;
int res_num;
bool het=true;
int model_num = 0;
if (!pConv->IsLast() || pConv->GetOutputIndex() > 1)
{ // More than one molecule record
model_num = pConv->GetOutputIndex(); // MODEL 1-based index
snprintf(buffer, BUFF_SIZE, "MODEL %8d", model_num);
ofs << buffer << endl;
}
// write back all fields (REMARKS, HELIX, SHEET, SITE, ...)
bool compndWritten = false;
bool authorWritten = false;
std::vector<OBGenericData*> pairData = mol.GetAllData(OBGenericDataType::PairData);
for (std::vector<OBGenericData*>::iterator data = pairData.begin(); data != pairData.end(); ++data) {
OBPairData *pd = static_cast<OBPairData*>(*data);
string attr = pd->GetAttribute();
// filter to make sure we are writing pdb fields only
if (attr != "HEADER" && attr != "OBSLTE" && attr != "TITLE" && attr != "SPLIT" &&
attr != "CAVEAT" && attr != "COMPND" && attr != "SOURCE" && attr != "KEYWDS" &&
attr != "EXPDTA" && attr != "NUMMDL" && attr != "MDLTYP" && attr != "AUTHOR" &&
attr != "REVDAT" && attr != "SPRSDE" && attr != "JRNL" && attr != "REMARK" &&
attr != "DBREF" && attr != "DBREF1" && attr != "DBREF2" && attr != "SEQADV" &&
attr != "SEQRES" && attr != "MODRES" && attr != "HET" && attr != "HETNAM" &&
attr != "HETSYN" && attr != "FORMUL" && attr != "HELIX" && attr != "SHEET" &&
attr != "SSBOND" && attr != "LINK" && attr != "CISPEP" && attr != "SITE" &&
attr != "ORIGX1" && attr != "ORIGX2" && attr != "ORIGX3" && attr != "SCALE1" &&
attr != "SCALE2" && attr != "SCALE3" && attr != "MATRIX1" && attr != "MATRIX2" &&
attr != "MATRIX3" && attr != "MODEL")
continue;
if (attr == "COMPND")
compndWritten = true;
if (attr == "AUTHOR")
authorWritten = true;
// compute spacing needed. HELIX, SITE, HET, ... are trimmed when reading
int nSpacing = 6 - attr.size();
for (int i = 0; i < nSpacing; ++i)
attr += " ";
std::string lines = pd->GetValue();
string::size_type last = 0;
string::size_type pos = lines.find('\n');
while (last != string::npos) {
string line = lines.substr(last, pos - last);
if (pos == string::npos)
last = string::npos;
else
last = pos + 1;
pos = lines.find('\n', last);
ofs << attr << line << endl;
}
}
if (!compndWritten) {
if (strlen(mol.GetTitle()) > 0)
snprintf(buffer, BUFF_SIZE, "COMPND %s ",mol.GetTitle());
else
snprintf(buffer, BUFF_SIZE, "COMPND UNNAMED");
ofs << buffer << endl;
}
if (!authorWritten) {
snprintf(buffer, BUFF_SIZE, "AUTHOR GENERATED BY OPEN BABEL %s",BABEL_VERSION);
ofs << buffer << endl;
}
// Write CRYST1 record, containing unit cell parameters, space group
// and Z value (supposed to be 1)
if (pmol->HasData(OBGenericDataType::UnitCell))
{
OBUnitCell *pUC = (OBUnitCell*)pmol->GetData(OBGenericDataType::UnitCell);
if(pUC->GetSpaceGroup()){
string tmpHM=pUC->GetSpaceGroup()->GetHMName();
// Do we have an extended HM symbol, with origin choice as ":1" or ":2" ? If so, remove it.
size_t n=tmpHM.find(":");
if(n!=string::npos) tmpHM=tmpHM.substr(0,n);
snprintf(buffer, BUFF_SIZE,
"CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s 1",
pUC->GetA(), pUC->GetB(), pUC->GetC(),
pUC->GetAlpha(), pUC->GetBeta(), pUC->GetGamma(),
tmpHM.c_str());
}
else
snprintf(buffer, BUFF_SIZE,
"CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s 1",
pUC->GetA(), pUC->GetB(), pUC->GetC(),
pUC->GetAlpha(), pUC->GetBeta(), pUC->GetGamma(),
"P1");
ofs << buffer << endl;
}
// before we write any records, we should check to see if any coord < -1000
// which will cause errors in the formatting
double minX, minY, minZ;
minX = minY = minZ = -999.0f;
FOR_ATOMS_OF_MOL(a, mol)
{
if (a->GetX() < minX)
minX = a->GetX();
if (a->GetY() < minY)
minY = a->GetY();
if (a->GetZ() < minZ)
minZ = a->GetZ();
}
vector3 transV = VZero;
if (minX < -999.0)
transV.SetX(-1.0*minX - 900.0);
if (minY < -999.0)
transV.SetY(-1.0*minY - 900.0);
if (minZ < -999.0)
transV.SetZ(-1.0*minZ - 900.0);
// if minX, minY, or minZ was never changed, shift will be 0.0f
// otherwise, move enough so that smallest coord is > -999.0f
mol.Translate(transV);
OBAtom *atom;
OBResidue *res;
for (i = 1; i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
strncpy(type_name, etab.GetSymbol(atom->GetAtomicNum()), sizeof(type_name));
type_name[sizeof(type_name) - 1] = '\0';
//two char. elements are on position 13 and 14 one char. start at 14
if (strlen(type_name) > 1)
type_name[1] = toupper(type_name[1]);
else
{
char tmp[10];
strncpy(tmp, type_name, 9); // make sure to null-terminate tmp
snprintf(type_name, sizeof(type_name), " %-3s", tmp);
}
if ( (res = atom->GetResidue()) != 0 )
{
het = res->IsHetAtom(atom);
snprintf(the_res,4,"%s",(char*)res->GetName().c_str());
the_res[4] = '\0';
snprintf(type_name,5,"%s",(char*)res->GetAtomID(atom).c_str());
the_chain = res->GetChain();
//two char. elements are on position 13 and 14 one char. start at 14
if (strlen(etab.GetSymbol(atom->GetAtomicNum())) == 1)
{
if (strlen(type_name) < 4)
{
char tmp[10];
strncpy(tmp, type_name, 9); // make sure to null-terminate tmp
snprintf(padded_name, sizeof(padded_name), " %-3s", tmp);
strncpy(type_name,padded_name,4);
type_name[4] = '\0';
}
else
{
/*
type_name[4] = type_name[3];
type_name[3] = type_name[2];
type_name[2] = type_name[1];
type_name[1] = type_name[0];
type_name[0] = type_name[4];
*/
type_name[4] = '\0';
}
}
res_num = res->GetNum();
}
else
{
strcpy(the_res,"UNK");
the_res[3] = '\0';
snprintf(padded_name,sizeof(padded_name), "%s",type_name);
strncpy(type_name,padded_name,4);
type_name[4] = '\0';
res_num = 1;
}
element_name = etab.GetSymbol(atom->GetAtomicNum());
int charge = atom->GetFormalCharge();
char scharge[3] = { ' ', ' ', '\0' };
if(0 != charge)
{
snprintf(scharge, 3, "%+d", charge);
char tmp = scharge[1];
scharge[1] = scharge[0];
scharge[0] = tmp;
}
snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d %8.3f%8.3f%8.3f 1.00 0.00 %2s%2s\n",
het?"HETATM":"ATOM ",
i,
type_name,
the_res,
the_chain,
res_num,
atom->GetX(),
atom->GetY(),
atom->GetZ(),
element_name,
scharge);
ofs << buffer;
}
OBAtom *nbr;
vector<OBBond*>::iterator k;
for (i = 1; i <= mol.NumAtoms(); i ++)
{
atom = mol.GetAtom(i);
if (atom->GetValence() == 0)
continue; // no need to write a CONECT record -- no bonds
snprintf(buffer, BUFF_SIZE, "CONECT%5d", i);
ofs << buffer;
// Write out up to 4 real bonds per line PR#1711154
int currentValence = 0;
for (nbr = atom->BeginNbrAtom(k);nbr;nbr = atom->NextNbrAtom(k))
{
snprintf(buffer, BUFF_SIZE, "%5d", nbr->GetIdx());
ofs << buffer;
if (++currentValence % 4 == 0) {
// Add the trailing space to finish this record
ofs << " \n";
// write the start of a new CONECT record
snprintf(buffer, BUFF_SIZE, "CONECT%5d", i);
ofs << buffer;
}
}
// Add trailing spaces
int remainingValence = atom->GetValence() % 4;
for (int count = 0; count < (4 - remainingValence); count++) {
snprintf(buffer, BUFF_SIZE, " ");
ofs << buffer;
}
ofs << " \n";
}
snprintf(buffer, BUFF_SIZE, "MASTER 0 0 0 0 0 0 0 0 ");
ofs << buffer;
snprintf(buffer, BUFF_SIZE, "%4d 0 %4d 0\n",mol.NumAtoms(),mol.NumAtoms());
ofs << buffer;
ofs << "END\n";
if (model_num) {
ofs << "ENDMDL" << endl;
}
return(true);
}
bool OBChemTsfm::Apply(OBMol &mol)
{
if (!_bgn.Match(mol))
return(false);
mol.BeginModify();
vector<vector<int> > mlist = _bgn.GetUMapList();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::OBChemTransform", obAuditMsg);
if (!_vchrg.empty()) //modify charges
{
vector<vector<int> >::iterator i;
vector<pair<int,int> >::iterator j;
for (i = mlist.begin();i != mlist.end();++i)
for (j = _vchrg.begin();j != _vchrg.end();++j)
if (j->first < (signed)i->size()) { //goof proofing
OBAtom *atom = mol.GetAtom((*i)[j->first]);
int old_charge = atom->GetFormalCharge();
atom->SetFormalCharge(j->second);
int new_hcount = atom->GetImplicitHCount() + (j->second - old_charge);
if (new_hcount < 0)
new_hcount = 0;
atom->SetImplicitHCount(new_hcount);
}
}
if (!_vbond.empty()) //modify bond orders
{
OBBond *bond;
vector<vector<int> >::iterator i;
vector<pair<pair<int,int>,int> >::iterator j;
for (i = mlist.begin();i != mlist.end();++i)
for (j = _vbond.begin();j != _vbond.end();++j)
{
bond = mol.GetBond((*i)[j->first.first],(*i)[j->first.second]);
if (!bond)
{
obErrorLog.ThrowError(__FUNCTION__, "unable to find bond", obDebug);
continue;
}
unsigned int old_bond_order = bond->GetBondOrder();
bond->SetBondOrder(j->second);
for (int k = 0; k < 2; ++k) {
OBAtom* atom = k == 0 ? bond->GetBeginAtom() : bond->GetEndAtom();
int new_hcount = atom->GetImplicitHCount() - (j->second - old_bond_order);
if (new_hcount < 0)
new_hcount = 0;
atom->SetImplicitHCount(new_hcount);
}
}
}
if (!_vadel.empty() || !_vele.empty()) //delete atoms and change elements
{
vector<int>::iterator j;
vector<vector<int> >::iterator i;
if (!_vele.empty())
{
vector<pair<int,int> >::iterator k;
for (i = mlist.begin();i != mlist.end();++i)
for (k = _vele.begin();k != _vele.end();++k)
mol.GetAtom((*i)[k->first])->SetAtomicNum(k->second);
}
//make sure same atom isn't deleted twice
vector<bool> vda;
vector<OBAtom*> vdel;
vda.resize(mol.NumAtoms()+1,false);
for (i = mlist.begin();i != mlist.end();++i)
for (j = _vadel.begin();j != _vadel.end();++j)
if (!vda[(*i)[*j]])
{
vda[(*i)[*j]] = true;
vdel.push_back(mol.GetAtom((*i)[*j]));
}
vector<OBAtom*>::iterator k;
for (k = vdel.begin();k != vdel.end();++k)
mol.DeleteAtom((OBAtom*)*k);
}
mol.EndModify();
return(true);
}
bool ChemDrawXMLFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
static const xmlChar C_MOLECULE[] = "fragment";
static const xmlChar C_CDXML[] = "CDXML";
static const xmlChar C_BONDLENGTH[] = "BondLength";
static const xmlChar C_PAGE[] = "page";
static const xmlChar C_ATOM[] = "n";
static const xmlChar C_BOND[] = "b";
static const xmlChar C_ID[] = "id";
static const xmlChar C_CHARGE[] = "Charge";
static const xmlChar C_COORDS[] = "p";
static const xmlChar C_ELEMENT[] = "Element";
static const xmlChar C_ORDER[] = "Order";
static const xmlChar C_BEGIN[] = "B";
static const xmlChar C_END[] = "E";
static const xmlChar C_DISPLAY[] = "Display";
_pxmlConv = XMLConversion::GetDerived(pConv,false);
if(!_pxmlConv)
return false;
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
OBMol &mol = *pmol;
OBBond *pbond;
vector<OBBond*>::iterator j;
if(_pxmlConv->GetOutputIndex() == 1)
{
xmlTextWriterStartDocument(writer(), NULL, NULL, NULL);
xmlTextWriterWriteDTD(writer(), BAD_CAST "CDXML", NULL, BAD_CAST "http://www.camsoft.com/xml/cdxml.dtd", NULL);
xmlTextWriterStartElement(writer(), C_CDXML);
xmlTextWriterWriteFormatAttribute(writer(), C_BONDLENGTH , "30");
xmlTextWriterStartElement(writer(), C_PAGE); // put everything on one page
// now guess the average bond size for the first molecule and scale to 30.
_scale = 0.;
if (mol.NumBonds())
{
for (pbond = mol.BeginBond(j); pbond; pbond = mol.NextBond(j))
_scale += pbond->GetLength();
_scale /= mol.NumBonds();
}
else
_scale = 1.; // FIXME: what happens if the molecule has no bond?
_scale = 30. / _scale;
_offset = 0;
}
xmlTextWriterStartElement(writer(), C_MOLECULE);
OBAtom *patom;
vector<OBAtom*>::iterator i;
int n;
for (patom = mol.BeginAtom(i); patom; patom = mol.NextAtom(i))
{
xmlTextWriterStartElement(writer(), C_ATOM);
xmlTextWriterWriteFormatAttribute(writer(), C_ID , "%d", patom->GetIdx() + _offset);
xmlTextWriterWriteFormatAttribute(writer(), C_COORDS , "%f %f", patom->GetX() * _scale, patom->GetY() * _scale);
n = patom->GetAtomicNum();
if (n != 6)
{
xmlTextWriterWriteFormatAttribute(writer(), C_ELEMENT , "%d", n);
}
n = patom->GetFormalCharge();
if (n != 0)
{
xmlTextWriterWriteFormatAttribute(writer(), C_CHARGE , "%d", n);
}
xmlTextWriterEndElement(writer());
}
for (pbond = mol.BeginBond(j); pbond; pbond = mol.NextBond(j))
{
xmlTextWriterStartElement(writer(), C_BOND);
patom = pbond->GetBeginAtom();
xmlTextWriterWriteFormatAttribute(writer(), C_BEGIN , "%d", patom->GetIdx() + _offset);
patom = pbond->GetEndAtom();
xmlTextWriterWriteFormatAttribute(writer(), C_END , "%d", patom->GetIdx() + _offset);
n = pbond->GetBO();
if (n != 1)
{
xmlTextWriterWriteFormatAttribute(writer(), C_ORDER , "%d", n);
}
if (pbond->IsHash())
xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgeBegin");
else if (pbond->IsWedge())
xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgedHashEnd");
xmlTextWriterEndElement(writer());
}
_offset += mol.NumAtoms ();
xmlTextWriterEndElement(writer());//molecule
//TODO: Writing property block
if(_pxmlConv->IsLast())
{
xmlTextWriterEndDocument(writer()); // page
xmlTextWriterEndDocument(writer()); //document
OutputToStream();
}
return true;
}
bool OBDepict::DrawMolecule(OBMol *mol)
{
if (!d->painter)
return false;
d->mol = mol;
double width=0.0, height=0.0;
OBAtom *atom;
OBBondIterator j;
OBAtomIterator i;
if(mol->NumAtoms()>0) {
// scale bond lengths
double bondLengthSum = 0.0;
for (OBBond *bond = mol->BeginBond(j); bond; bond = mol->NextBond(j))
bondLengthSum += bond->GetLength();
const double averageBondLength = bondLengthSum / mol->NumBonds();
const double f = mol->NumBonds() ? d->bondLength / averageBondLength : 1.0;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
atom->SetVector(atom->GetX() * f, atom->GetY() * f, 0.0);
// find min/max values
double min_x, max_x;
double min_y, max_y;
atom = mol->BeginAtom(i);
min_x = max_x = atom->GetX();
min_y = max_y = atom->GetY();
for (atom = mol->NextAtom(i); atom; atom = mol->NextAtom(i)) {
min_x = std::min(min_x, atom->GetX());
max_x = std::max(max_x, atom->GetX());
min_y = std::min(min_y, atom->GetY());
max_y = std::max(max_y, atom->GetY());
}
const double margin = 40.0;
// translate all atoms so the bottom-left atom is at margin,margin
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
atom->SetVector(atom->GetX() - min_x + margin, atom->GetY() - min_y + margin, 0.0);
width = max_x - min_x + 2*margin;
height = max_y - min_y + 2*margin;
//d->painter->SetPenWidth(d->penWidth);
//d->painter->SetPenColor(d->pen));
//d->painter->SetFillColor(OBColor("black"));
}
d->painter->NewCanvas(width, height);
// draw bonds
if(d->options & genWedgeHash)
d->SetWedgeAndHash(mol);
for (OBBond *bond = mol->BeginBond(j); bond; bond = mol->NextBond(j)) {
OBAtom *begin = bond->GetBeginAtom();
OBAtom *end = bond->GetEndAtom();
if((d->options & internalColor) && bond->HasData("color"))
d->painter->SetPenColor(OBColor(bond->GetData("color")->GetValue()));
else
d->painter->SetPenColor(d->bondColor);
if (bond->IsWedge()) {
d->DrawWedge(begin, end);
} else if (bond->IsHash()) {
d->DrawHash(begin, end);
} else if (!bond->IsInRing()) {
d->DrawSimpleBond(begin, end, bond->GetBO());
}
}
// draw ring bonds
std::vector<OBRing*> rings(mol->GetSSSR());
OBBitVec drawnBonds;
for (std::vector<OBRing*>::iterator k = rings.begin(); k != rings.end(); ++k) {
OBRing *ring = *k;
std::vector<int> indexes = ring->_path;
vector3 center(VZero);
for (std::vector<int>::iterator l = indexes.begin(); l != indexes.end(); ++l) {
center += mol->GetAtom(*l)->GetVector();
}
center /= indexes.size();
for (unsigned int l = 0; l < indexes.size(); ++l) {
OBAtom *begin = mol->GetAtom(indexes[l]);
OBAtom *end;
if (l+1 < indexes.size())
end = mol->GetAtom(indexes[l+1]);
else
end = mol->GetAtom(indexes[0]);
OBBond *ringBond = mol->GetBond(begin, end);
if (drawnBonds.BitIsSet(ringBond->GetId()))
continue;
if((d->options & internalColor) && ringBond->HasData("color"))
d->painter->SetPenColor(OBColor(ringBond->GetData("color")->GetValue()));
else
d->painter->SetPenColor(d->bondColor);
d->DrawRingBond(begin, end, center, ringBond->GetBO());
drawnBonds.SetBitOn(ringBond->GetId());
}
}
// draw atom labels
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i)) {
double x = atom->GetX();
double y = atom->GetY();
int alignment = GetLabelAlignment(atom);
bool rightAligned = false;
switch (alignment) {
case TopRight:
case CenterRight:
case BottomRight:
rightAligned = true;
default:
break;
}
if((d->options & internalColor) && atom->HasData("color"))
d->painter->SetPenColor(OBColor(atom->GetData("color")->GetValue()));
else if(d->options & bwAtoms)
d->painter->SetPenColor(d->bondColor);
else
d->painter->SetPenColor(OBColor(etab.GetRGB(atom->GetAtomicNum())));
//charge and radical
int charge = atom->GetFormalCharge();
int spin = atom->GetSpinMultiplicity();
if(charge || spin) {
OBFontMetrics metrics = d->painter->GetFontMetrics("N");
double yoffset = d->HasLabel(atom) ? 0.4 * metrics.height : 0.0;
switch (GetLabelAlignment(atom)) {
case TopCenter:
case TopRight:
case TopLeft:
case CenterLeft:
case CenterRight:
yoffset = - 1.2 * metrics.height;
}
stringstream ss;
if(charge) {
if(abs(charge)!=1)
ss << abs(charge);
ss << (charge>0 ? "+" : "-") ;
}
if(spin) {
ss << (spin==2 ? "." : "..");
yoffset += 0.5 * metrics.height;
}
if(spin || charge<0)
d->painter->SetFontSize(2 * metrics.fontSize);
d->painter->DrawText(x-0.4*metrics.width, y-yoffset, ss.str());
d->painter->SetFontSize(metrics.fontSize);//restore
}
if (atom->IsCarbon()) {
if(!(d->options & drawAllC))
{
if (atom->GetValence() > 1)
continue;
if ((atom->GetValence() == 1) && !(d->options & drawTermC))//!d->drawTerminalC)
continue;
}
}
stringstream ss;
AliasData* ad = NULL;
if(d->aliasMode && atom->HasData(AliasDataType))
ad = static_cast<AliasData*>(atom->GetData(AliasDataType));
//For unexpanded aliases use appropriate form of alias instead of element symbol, Hs, etc
if(ad && !ad->IsExpanded())
{
ss <<ad->GetAlias(rightAligned);
OBColor aliasColor = !ad->GetColor().empty() ? ad->GetColor() : d->bondColor;
d->painter->SetPenColor(aliasColor);
}
else {
const char* atomSymbol;
if(atom->IsHydrogen() && atom->GetIsotope()>1)
atomSymbol = atom->GetIsotope()==2 ? "D" : "T";
else
atomSymbol = etab.GetSymbol(atom->GetAtomicNum());
unsigned int hCount = atom->ImplicitHydrogenCount();
// rightAligned:
// false CH3
// true H3C
if (hCount && rightAligned)
ss << "H";
if ((hCount > 1) && rightAligned)
ss << hCount;
ss << atomSymbol;
if (hCount && !rightAligned)
ss << "H";
if ((hCount > 1) && !rightAligned)
ss << hCount;
}
d->DrawAtomLabel(ss.str(), alignment, vector3(x, y, 0.0));
}
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;
}
bool PDBFormat::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;
unsigned int i;
char buffer[BUFF_SIZE];
char type_name[10], padded_name[10];
char the_res[10];
char the_chain = ' ';
const char *element_name;
int res_num;
bool het=true;
int model_num = 0;
if (!pConv->IsLast() || pConv->GetOutputIndex() > 1)
{ // More than one molecule record
model_num = pConv->GetOutputIndex(); // MODEL 1-based index
snprintf(buffer, BUFF_SIZE, "MODEL %8d", model_num);
ofs << buffer << endl;
}
if (strlen(mol.GetTitle()) > 0)
snprintf(buffer, BUFF_SIZE, "COMPND %s ",mol.GetTitle());
else
snprintf(buffer, BUFF_SIZE, "COMPND UNNAMED");
ofs << buffer << endl;
snprintf(buffer, BUFF_SIZE, "AUTHOR GENERATED BY OPEN BABEL %s",BABEL_VERSION);
ofs << buffer << endl;
// Write CRYST1 record, containing unit cell parameters, space group
// and Z value (supposed to be 1)
if (pmol->HasData(OBGenericDataType::UnitCell))
{
OBUnitCell *pUC = (OBUnitCell*)pmol->GetData(OBGenericDataType::UnitCell);
snprintf(buffer, BUFF_SIZE,
"CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s 1",
pUC->GetA(), pUC->GetB(), pUC->GetC(),
pUC->GetAlpha(), pUC->GetBeta(), pUC->GetGamma(),
pUC->GetSpaceGroup() ?
pUC->GetSpaceGroup()->GetHMName().c_str() : "P1");
ofs << buffer << endl;
}
// before we write any records, we should check to see if any coord < -1000
// which will cause errors in the formatting
double minX, minY, minZ;
minX = minY = minZ = -999.0f;
FOR_ATOMS_OF_MOL(a, mol)
{
if (a->GetX() < minX)
minX = a->GetX();
if (a->GetY() < minY)
minY = a->GetY();
if (a->GetZ() < minZ)
minZ = a->GetZ();
}
vector3 transV = VZero;
if (minX < -999.0)
transV.SetX(-1.0*minX - 900.0);
if (minY < -999.0)
transV.SetY(-1.0*minY - 900.0);
if (minZ < -999.0)
transV.SetZ(-1.0*minZ - 900.0);
// if minX, minY, or minZ was never changed, shift will be 0.0f
// otherwise, move enough so that smallest coord is > -999.0f
mol.Translate(transV);
OBAtom *atom;
OBResidue *res;
for (i = 1; i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
strncpy(type_name, etab.GetSymbol(atom->GetAtomicNum()), sizeof(type_name));
type_name[sizeof(type_name) - 1] = '\0';
//two char. elements are on position 13 and 14 one char. start at 14
if (strlen(type_name) > 1)
type_name[1] = toupper(type_name[1]);
else
{
char tmp[10];
strncpy(tmp, type_name, 10);
snprintf(type_name, sizeof(type_name), " %-3s", tmp);
}
if ( (res = atom->GetResidue()) != 0 )
{
het = res->IsHetAtom(atom);
snprintf(the_res,4,"%s",(char*)res->GetName().c_str());
snprintf(type_name,5,"%s",(char*)res->GetAtomID(atom).c_str());
the_chain = res->GetChain();
//two char. elements are on position 13 and 14 one char. start at 14
if (strlen(etab.GetSymbol(atom->GetAtomicNum())) == 1)
{
if (strlen(type_name) < 4)
{
char tmp[16];
strncpy(tmp, type_name, 16);
snprintf(padded_name, sizeof(padded_name), " %-3s", tmp);
strncpy(type_name,padded_name,4);
type_name[4] = '\0';
}
else
{
/*
type_name[4] = type_name[3];
type_name[3] = type_name[2];
type_name[2] = type_name[1];
type_name[1] = type_name[0];
type_name[0] = type_name[4];
*/
type_name[4] = '\0';
}
}
res_num = res->GetNum();
}
else
{
strcpy(the_res,"UNK");
snprintf(padded_name,sizeof(padded_name), "%s",type_name);
strncpy(type_name,padded_name,4);
type_name[4] = '\0';
res_num = 1;
}
element_name = etab.GetSymbol(atom->GetAtomicNum());
int charge = atom->GetFormalCharge();
char scharge[3] = { ' ', ' ', '\0' };
if(0 != charge)
{
snprintf(scharge, 3, "%+d", charge);
char tmp = scharge[1];
scharge[1] = scharge[0];
scharge[0] = tmp;
}
snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d %8.3f%8.3f%8.3f 1.00 0.00 %2s%2s\n",
het?"HETATM":"ATOM ",
i,
type_name,
the_res,
the_chain,
res_num,
atom->GetX(),
atom->GetY(),
atom->GetZ(),
element_name,
scharge);
ofs << buffer;
}
OBAtom *nbr;
vector<OBBond*>::iterator k;
for (i = 1; i <= mol.NumAtoms(); i ++)
{
atom = mol.GetAtom(i);
if (atom->GetValence() == 0)
continue; // no need to write a CONECT record -- no bonds
snprintf(buffer, BUFF_SIZE, "CONECT%5d", i);
ofs << buffer;
// Write out up to 4 real bonds per line PR#1711154
unsigned int currentValence = 0;
for (nbr = atom->BeginNbrAtom(k);nbr;nbr = atom->NextNbrAtom(k))
{
unsigned int order = mol.GetBond(atom, nbr)->GetBondOrder();
unsigned int it_order = 0;
for( it_order = 0; it_order < order; it_order++ )
{
if (0 != currentValence && 0 == currentValence % 4)
{
// Add the trailing space to finish this record
ofs << " \n";
// write the start of a new CONECT record
snprintf(buffer, BUFF_SIZE, "CONECT%5d", i);
ofs << buffer;
}
currentValence++;
snprintf(buffer, BUFF_SIZE, "%5d", nbr->GetIdx());
ofs << buffer;
}
}
// Add trailing spaces
unsigned int remainingValence = currentValence % 4;
if( 0 < remainingValence )
{
for (int count = 0; count < (4 - remainingValence); count++)
{
snprintf(buffer, BUFF_SIZE, " ");
ofs << buffer;
}
}
ofs << " \n";
}
snprintf(buffer, BUFF_SIZE, "MASTER 0 0 0 0 0 0 0 0 ");
ofs << buffer;
snprintf(buffer, BUFF_SIZE, "%4d 0 %4d 0\n",mol.NumAtoms(),mol.NumAtoms());
ofs << buffer;
ofs << "END\n";
if (model_num) {
ofs << "ENDMDL" << endl;
}
return(true);
}