bool JaguarInputFormat::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];
OBAtom *atom;
ofs << mol.GetTitle() << endl << endl;
ofs << "&gen" << endl;
ofs << "&" << endl;
ofs << "&zmat" << endl;
for (i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE, " %s%d %12.7f %12.7f %12.7f",
etab.GetSymbol(atom->GetAtomicNum()), i,
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
ofs << "&" << endl;
return(true);
}
bool WriteXYZ(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
sprintf(buffer,"%d", mol.NumAtoms());
ofs << buffer << endl;
sprintf(buffer,"%s\tEnergy: %15.7f", mol.GetTitle(), mol.GetEnergy());
ofs << buffer << endl;
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"%3s%15.5f%15.5f%15.5f",
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
return(true);
}
bool PQSFormat::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];
OBAtom *atom;
ofs<<"TEXT="<<mol.GetTitle()<<endl;
ofs<<"GEOM=PQS"<<endl;
for (i=1; i<=mol.NumAtoms(); i++)
{
atom=mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE, "%s %10.6lf %10.6lf %10.6lf",
OBElements::GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs<<buffer<<endl;
}
return(true);
}
bool WriteViewMol(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
if (strlen(mol.GetTitle()) > 0)
ofs << "$title" << endl << mol.GetTitle() << endl;
ofs << "$coord 1.0" << endl;
OBAtom *atom;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"%22.14f%22.14f%22.14f %s",
atom->GetX(),
atom->GetY(),
atom->GetZ(),
etab.GetSymbol(atom->GetAtomicNum()));
ofs << buffer << endl;
}
ofs << "$end" << endl;
return(true);
}
bool TurbomoleFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
double UnitConv=AAU;
if(pConv->IsOption("a"))
UnitConv=1;
ofs << "$coord" <<endl;
char buffer[BUFF_SIZE];
OBAtom *atom;
vector<OBAtom*>::iterator i;
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
char symb[8];
strcpy(symb,OBElements::GetSymbol(atom->GetAtomicNum()));
snprintf(buffer, BUFF_SIZE, "%20.14f %20.14f %20.14f %s",
atom->GetX()/UnitConv,
atom->GetY()/UnitConv,
atom->GetZ()/UnitConv,
strlwr(symb) );
ofs << buffer << endl;
}
ofs << "$end" << endl;
return true;
}
bool WriteAlchemy(ostream &ofs,OBMol &mol)
{
unsigned int i;
char buffer[BUFF_SIZE];
char bond_string[10];
snprintf(buffer, BUFF_SIZE, "%5d ATOMS, %5d BONDS, 0 CHARGES",
mol.NumAtoms(),
mol.NumBonds());
ofs << buffer << endl;
ttab.SetFromType("INT"); ttab.SetToType("ALC");
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
ttab.Translate(str1,str);
snprintf(buffer, BUFF_SIZE, "%5d %-6s%8.4f %8.4f %8.4f 0.0000",
i,
(char*)str1.c_str(),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
OBBond *bond;
vector<OBEdgeBase*>::iterator j;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
switch(bond->GetBO())
{
case 1 : strcpy(bond_string,"SINGLE"); break;
case 2 : strcpy(bond_string,"DOUBLE"); break;
case 3 : strcpy(bond_string,"TRIPLE"); break;
case 5 : strcpy(bond_string,"AROMATIC"); break;
default : strcpy(bond_string,"SINGLE");
}
snprintf(buffer, BUFF_SIZE, "%5d %4d %4d %s",
bond->GetIdx()+1,
bond->GetBeginAtomIdx(),
bond->GetEndAtomIdx(),
bond_string);
ofs << buffer << endl;
}
return(true);
}
BoundingBox
NXOpenGLRenderingEngine::GetBoundingBox(OBMol *const molPtr)
{
BoundingBox bbox;
OBAtomIterator atomIter;
OBAtom *atomPtr = NULL;
for(atomPtr = molPtr->BeginAtom(atomIter);
atomPtr != NULL;
atomPtr = molPtr->NextAtom(atomIter))
{
Vector atomPos(real(atomPtr->GetX()),
real(atomPtr->GetY()),
real(atomPtr->GetZ()));
bbox += atomPos;
}
return bbox;
}
bool WriteHIN(ostream &ofs,OBMol &mol)
{
unsigned int i, file_num = 1;
string str,str1;
char buffer[BUFF_SIZE];
OBAtom *atom;
OBBond *bond;
vector<OBEdgeBase*>::iterator j;
char bond_char;
ofs << "mol " << file_num << " " << mol.GetTitle() << endl;;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
sprintf(buffer,"atom %d - %-3s ** - %8.5f %8.5f %8.5f %8.5f %d ",
i,
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetPartialCharge(),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atom->GetValence());
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
switch(bond->GetBO())
{
case 1 : bond_char = 's'; break;
case 2 : bond_char = 'd'; break;
case 3 : bond_char = 't'; break;
case 5 : bond_char = 'a'; break;
default: bond_char = 's'; break;
}
sprintf(buffer,"%d %c ", (bond->GetNbrAtom(atom))->GetIdx(), bond_char);
ofs << buffer;
}
ofs << endl;
}
ofs << "endmol " << file_num << endl;
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;
}
bool ZINDOFormat::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;
char buffer[BUFF_SIZE];
int orbitals, valenceE = 0;
vector<OBAtom*>::iterator i;
OBAtom *atom;
bool charged = false;
for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
{
switch (atom->GetAtomicNum())
{
case 1:
valenceE += 1;
break;
case 5:
case 13:
valenceE += 3;
break;
case 6:
case 14:
valenceE += 4;
break;
case 7:
case 15:
case 33:
valenceE += 5;
break;
case 8:
case 16:
case 34:
valenceE += 6;
break;
case 9:
case 17:
case 35:
valenceE += 7;
break;
default:
break;
}
}
orbitals = valenceE / 2;
if (charged)
{
orbitals = (valenceE / 2) - 1;
valenceE -= 1;
}
ofs << " $TITLEI" << endl;
ofs << endl;
ofs << " " << mol.GetTitle() << endl;
ofs << endl;
ofs << " $END" << endl;
ofs << endl;
ofs << " $CONTRL" << endl;
ofs << endl;
if (charged)
ofs << " SCFTYP ROHF RUNTYP CI ENTTYP COORD" << endl;
else
ofs << " SCFTYP RHF RUNTYP CI ENTTYP COORD" << endl;
ofs << " UNITS ANGS INTTYP 1 IAPX 3" << endl;
if (charged)
{
ofs << endl;
ofs << " NOP = 1 " << endl;
ofs << " NDT = 1 " << endl;
snprintf(buffer, BUFF_SIZE, " FOP(1) =% 4d% 10.6f",
valenceE - 1, 1.0);
ofs << buffer << endl;
}
snprintf(buffer, BUFF_SIZE, " NAT %4d NEL %4d MULT 1",
mol.NumAtoms(),
valenceE);
ofs << buffer << endl;
ofs << " IPRINT -1 ITMAX 100" << endl;
ofs << endl;
ofs << "! ***** BASIS SET AND C. I. SIZE INFORMATION ***** " << endl;
ofs << endl;
snprintf(buffer, BUFF_SIZE, " DYNAL(1) = 0%5d%5d 0 0 1200%5d",
mol.NumAtoms() - mol.NumHvyAtoms(),
mol.NumHvyAtoms(),
orbitals + 25);
ofs << buffer << endl;
ofs << endl;
ofs << " INTFA(1) = 1.000000 1.267000 0.680000 1.000000 1.000000 " << endl;
ofs << endl;
ofs << "! ***** OUTPUT FILE NAME ***** " << endl;
ofs << endl;
ofs << " ONAME = zindo " << endl;
ofs << endl;
ofs << " $END" << endl;
ofs << endl;
ofs << " $DATAIN " << endl;
ofs << endl;
for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
{
snprintf(buffer, BUFF_SIZE, "% 10.6f% 10.6f% 10.6f%5d",
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atom->GetAtomicNum());
ofs << buffer << endl;
}
ofs << endl;
ofs << " $END " << endl;
ofs << endl;
ofs << " $CIINPU" << endl;
ofs << endl;
ofs << "! ***** C. I. SPECIFICATION *****" << endl;
ofs << endl;
ofs << " 2 1 25 1 0 0 0 1 10 1 10" << endl;
ofs << " -60000.0 0.0000000" << endl;
ofs << endl;
if (charged)
snprintf(buffer, BUFF_SIZE, "%5d%5d%5d%5d", 1, orbitals, orbitals, orbitals + 1);
else
snprintf(buffer, BUFF_SIZE, "%5d%5d%5d", 1, orbitals, orbitals);
ofs << buffer << endl;
if (charged)
snprintf(buffer, BUFF_SIZE, "%5d%5d%5d%5d%5d",
21, (orbitals - 8), orbitals + 1, orbitals + 1, orbitals + 11);
else
snprintf(buffer, BUFF_SIZE, "%5d%5d%5d%5d%5d",
21, (orbitals - 9), orbitals, orbitals + 1, orbitals + 10);
ofs << buffer << endl;
ofs << endl;
ofs << " $END" << endl;
return(true);
}
bool TinkerFormat::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;
bool mmffTypes = pConv->IsOption("m",OBConversion::OUTOPTIONS) != NULL;
unsigned int i;
char buffer[BUFF_SIZE];
OBBond *bond;
vector<OBBond*>::iterator j;
// Before we try output of MMFF94 atom types, check if it works
OBForceField *ff = OpenBabel::OBForceField::FindForceField("MMFF94");
if (mmffTypes && ff && ff->Setup(mol))
mmffTypes = ff->GetAtomTypes(mol);
else
mmffTypes = false; // either the force field isn't available, or it doesn't work
if (!mmffTypes)
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM2 parameters\n",mol.NumAtoms(),mol.GetTitle());
else
snprintf(buffer, BUFF_SIZE, "%6d %-20s MMFF94 parameters\n",mol.NumAtoms(),mol.GetTitle());
ofs << buffer;
ttab.SetFromType("INT");
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
ttab.SetToType("MM2");
ttab.Translate(str1,str);
if (mmffTypes) {
// Override the MM2 typing
OBPairData *type = (OpenBabel::OBPairData*)atom->GetData("FFAtomType");
if (type)
str1 = type->GetValue().c_str();
}
snprintf(buffer, BUFF_SIZE, "%6d %2s %12.6f%12.6f%12.6f %5d",
i,
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atoi((char*)str1.c_str()));
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
snprintf(buffer, BUFF_SIZE, "%6d", (bond->GetNbrAtom(atom))->GetIdx());
ofs << buffer;
}
ofs << endl;
}
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 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 AlchemyFormat::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 bond_string[10];
snprintf(buffer, BUFF_SIZE, "%5d ATOMS, %5d BONDS, 0 CHARGES",
mol.NumAtoms(),
mol.NumBonds());
ofs << buffer << endl;
OBAtom *atom;
string str,str1;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
ttab.SetFromType("INT");
ttab.SetToType("ALC");
ttab.Translate(str1,str);
snprintf(buffer, BUFF_SIZE, "%5d %-6s%8.4f %8.4f %8.4f 0.0000",
i,
(char*)str1.c_str(),
atom->GetX(),
atom->GetY(),
atom->GetZ());
ofs << buffer << endl;
}
OBBond *bond;
vector<OBBond*>::iterator j;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
switch(bond->GetBO())
{
case 1 :
strcpy(bond_string,"SINGLE");
break;
case 2 :
strcpy(bond_string,"DOUBLE");
break;
case 3 :
strcpy(bond_string,"TRIPLE");
break;
case 5 :
strcpy(bond_string,"AROMATIC");
break;
default :
strcpy(bond_string,"SINGLE");
}
snprintf(buffer, BUFF_SIZE, "%5d %4d %4d %s",
bond->GetIdx()+1,
bond->GetBeginAtomIdx(),
bond->GetEndAtomIdx(),
bond_string);
ofs << buffer << endl;
}
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);
}
NXSGOpenGLNode*
NXOpenGLRenderingEngine::createOpenGLSceneGraph(OBMol *const molPtr)
{
assert(!molPtr->Empty());
#if 0 /// @todo Post-FNANO08 (Dna rendering)
/// @fixme r1.0.0 hacks
// -- begin hacks --
if(inDnaGroup && inDnaSegment) {
NXSGOpenGLNode *molSceneGraphNode =
createOpenGLDnaSegmentSceneGraph(molPtr);
if(molSceneGraphNode != NULL)
return molSceneGraphNode;
}
else if(inDnaGroup && inDnaStrand) {
NXSGOpenGLNode *molSceneGraphNode =
createOpenGLDnaStrandSceneGraph(molPtr);
if(molSceneGraphNode != NULL)
return molSceneGraphNode;
}
// -- end hacks --
#endif
Vector const canonicalZAxis(0.0, 0.0, 1.0);
OBAtomIterator atomIter;
// Find first atom that is not already rendered
// Necessary because bonds can bridge molecules and molecule-sets and in
// the case of the second to last molecules rendered, their first atoms
// may have been rendered while traversing the previous molecules.
OBAtom *firstAtomPtr = molPtr->BeginAtom(atomIter);
if(firstAtomPtr == (OBAtom*) NULL) {
string const source("Molecule scenegraph creation");
string const msg("empty molecule slipped past check");
SetResult(commandResult, NX_INTERNAL_ERROR, source + " - " + msg);
NX_DEBUG_FAIL;
return (NXSGOpenGLNode*) NULL;
}
while(firstAtomPtr != (OBAtom*) NULL && isRendered(firstAtomPtr))
firstAtomPtr = molPtr->NextAtom(atomIter);
if(firstAtomPtr == (OBAtom*) NULL) {
NXSGOpenGLNode *nullFirstAtomNode = new NXSGOpenGLNode;
SET_SCENEGRAPH_NAME(nullFirstAtomNode, "Null_first_atom");
return nullFirstAtomNode;
}
Vector const firstAtomPosition(firstAtomPtr->GetX(),
firstAtomPtr->GetY(),
firstAtomPtr->GetZ());
NXSGOpenGLTranslate *rootMoleculeNode = NULL;
try {
rootMoleculeNode =
new NXSGOpenGLTranslate(firstAtomPosition.x(),
firstAtomPosition.y(),
firstAtomPosition.z());
SET_SCENEGRAPH_NAME(rootMoleculeNode, "First_atom_position");
}
catch(...) {
if(rootMoleculeNode != NULL)
delete rootMoleculeNode;
rootMoleculeNode = NULL;
SetResult(commandResult,
NX_INTERNAL_ERROR,
"Error translating to first atom position");
NX_DEBUG_FAIL;
return NULL;
}
NXSGOpenGLNode *firstAtomNode =
createOpenGLSceneGraph(molPtr, firstAtomPtr, canonicalZAxis);
if(firstAtomNode != NULL &&
commandResult.getResult() == (int) NX_CMD_SUCCESS)
{
// submolecule scenegraph created completely and successfully
bool childAdded = rootMoleculeNode->addChild(firstAtomNode);
if(!childAdded) {
SetResult(commandResult, NX_INTERNAL_ERROR,
"Error adding child to first atom node");
NX_DEBUG_FAIL;
return rootMoleculeNode;
}
}
else {
NX_DEBUG_FAIL;
// either scenegraph could not be created or was created partially
// commandResult should hold the error
return rootMoleculeNode;
}
/// @todo POST-FNANO delete firstAtomNode upon failures?
// rest of the atoms
OBAtom *atomPtr = molPtr->NextAtom(atomIter);
for(; atomPtr != (OBAtom*) NULL;
atomPtr = molPtr->NextAtom(atomIter))
{
if(isRendered(atomPtr)) // atom already rendered
continue;
Vector const atomPosition(atomPtr->GetX(),
atomPtr->GetY(),
atomPtr->GetZ());
Vector const atomRelativePosition =
(atomPosition - firstAtomPosition);
// move scenegraph "cursor" to this atom
NXSGOpenGLTranslate *translateToAtomNode = NULL;
try {
translateToAtomNode =
new NXSGOpenGLTranslate(atomRelativePosition.x(),
atomRelativePosition.y(),
atomRelativePosition.z());
SET_SCENEGRAPH_NAME(translateToAtomNode,
"Translate_to_" + get_atom_scenegraph_name(atomPtr));
}
catch(...) {
if(translateToAtomNode != NULL)
delete translateToAtomNode;
SetResult(commandResult, NX_INTERNAL_ERROR,
"Error translating to atom");
NX_DEBUG_FAIL;
return rootMoleculeNode;
}
bool childAdded = rootMoleculeNode->addChild(translateToAtomNode);
if(!childAdded) {
SetResult(commandResult, NX_INTERNAL_ERROR,
"Error adding translate-to-atom node to molecule root");
NX_DEBUG_FAIL;
return rootMoleculeNode;
}
/// @todo POST-FNANO delete translateToAtomNode upon failure?
// render subscenegraph rooted at this atom
NXSGOpenGLNode *atomNode =
createOpenGLSceneGraph(molPtr, atomPtr, canonicalZAxis);
if(atomNode != NULL &&
commandResult.getResult() == (int) NX_CMD_SUCCESS)
{
bool childAdded = translateToAtomNode->addChild(atomNode);
if(!childAdded) {
SetResult(commandResult, NX_INTERNAL_ERROR,
"Error submolecule scenegraph as child of "
"translation");
NX_DEBUG_FAIL;
return rootMoleculeNode;
}
}
else {
NX_DEBUG_FAIL;
return rootMoleculeNode;
}
/// @todo POST-FNANO delete atomNode upon failures?
} // loop over atoms
return rootMoleculeNode;
}
bool HINFormat::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, file_num = 1;
string str,str1;
char buffer[BUFF_SIZE];
OBAtom *atom;
OBBond *bond;
vector<OBBond*>::iterator j;
char bond_char;
// make sure to escape titles in double quotes
// PR#1501694
ofs << "mol " << file_num << " \"" << mol.GetTitle() << "\"\n";
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
snprintf(buffer, BUFF_SIZE, "atom %d - %-3s ** - %8.5f %8.5f %8.5f %8.5f %d ",
i,
etab.GetSymbol(atom->GetAtomicNum()),
atom->GetPartialCharge(),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atom->GetValence());
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
switch(bond->GetBO())
{
case 1 :
bond_char = 's';
break;
case 2 :
bond_char = 'd';
break;
case 3 :
bond_char = 't';
break;
case 5 :
bond_char = 'a';
break;
default:
bond_char = 's';
break;
}
if (bond->IsAromatic())
bond_char = 'a';
snprintf(buffer,BUFF_SIZE, "%d %c ", (bond->GetNbrAtom(atom))->GetIdx(), bond_char);
ofs << buffer;
}
ofs << endl;
}
ofs << "endmol " << file_num << endl;
return(true);
}
bool TinkerFormat::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;
bool mm2Types = false;
bool mmffTypes = pConv->IsOption("m",OBConversion::OUTOPTIONS) != NULL;
bool mm3Types = pConv->IsOption("3",OBConversion::OUTOPTIONS) != NULL;
bool classTypes = pConv->IsOption("c", OBConversion::OUTOPTIONS) != NULL;
unsigned int i;
char buffer[BUFF_SIZE];
OBBond *bond;
vector<OBBond*>::iterator j;
// Before we try output of MMFF94 atom types, check if it works
OBForceField *ff = OpenBabel::OBForceField::FindForceField("MMFF94");
if (mmffTypes && ff && ff->Setup(mol))
mmffTypes = ff->GetAtomTypes(mol);
else
mmffTypes = false; // either the force field isn't available, or it doesn't work
if (!mmffTypes && !mm3Types && !classTypes) {
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM2 parameters\n",mol.NumAtoms(),mol.GetTitle());
mm2Types = true;
}
else if (mm3Types)
snprintf(buffer, BUFF_SIZE, "%6d %-20s MM3 parameters\n",mol.NumAtoms(),mol.GetTitle());
else if (classTypes)
snprintf(buffer, BUFF_SIZE, "%6d %-20s Custom parameters\n",mol.NumAtoms(),mol.GetTitle());
else
snprintf(buffer, BUFF_SIZE, "%6d %-20s MMFF94 parameters\n",mol.NumAtoms(),mol.GetTitle());
ofs << buffer;
ttab.SetFromType("INT");
OBAtom *atom;
string str,str1;
int atomType;
for(i = 1;i <= mol.NumAtoms(); i++)
{
atom = mol.GetAtom(i);
str = atom->GetType();
atomType = 0; // Something is very wrong if this doesn't get set below
if (mm2Types) {
ttab.SetToType("MM2");
ttab.Translate(str1,str);
atomType = atoi((char*)str1.c_str());
}
if (mmffTypes) {
// Override the MM2 typing
OBPairData *type = (OpenBabel::OBPairData*)atom->GetData("FFAtomType");
if (type) {
str1 = type->GetValue().c_str();
atomType = atoi((char*)str1.c_str());
}
}
if (mm3Types) {
// convert to integer for MM3 typing
atomType = SetMM3Type(atom);
}
if (classTypes) {
// Atom classes are set by the user, so use those
OBGenericData *data = atom->GetData("Atom Class");
if (data) {
OBPairInteger* acdata = dynamic_cast<OBPairInteger*>(data); // Could replace with C-style cast if willing to live dangerously
if (acdata) {
int ac = acdata->GetGenericValue();
if (ac >= 0)
atomType = ac;
}
}
}
snprintf(buffer, BUFF_SIZE, "%6d %2s %12.6f%12.6f%12.6f %5d",
i,
OBElements::GetSymbol(atom->GetAtomicNum()),
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atomType);
ofs << buffer;
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
{
snprintf(buffer, BUFF_SIZE, "%6d", (bond->GetNbrAtom(atom))->GetIdx());
ofs << buffer;
}
ofs << endl;
}
return(true);
}
bool MOL2Format::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;
bool ligandsOnly = pConv->IsOption("l", OBConversion::OUTOPTIONS)!=NULL;
//The old code follows....
string str,str1;
char buffer[BUFF_SIZE],label[BUFF_SIZE];
char rnum[BUFF_SIZE],rlabel[BUFF_SIZE];
ofs << "@<TRIPOS>MOLECULE" << endl;
str = mol.GetTitle();
if (str.empty())
ofs << "*****" << endl;
else
ofs << str << endl;
snprintf(buffer, BUFF_SIZE," %d %d 0 0 0", mol.NumAtoms(),mol.NumBonds());
ofs << buffer << endl;
ofs << "SMALL" << endl;
OBPairData *dp = (OBPairData*)mol.GetData("PartialCharges");
if (dp != NULL) {
// Tripos spec says:
// NO_CHARGES, DEL_RE, GASTEIGER, GAST_HUCK, HUCKEL, PULLMAN,
// GAUSS80_CHARGES, AMPAC_CHARGES, MULLIKEN_CHARGES, DICT_ CHARGES,
// MMFF94_CHARGES, USER_CHARGES
if (dp->GetValue() == "Mulliken")
ofs << "MULLIKEN_CHARGES" << endl;
else // should pick from the Tripos types
ofs << "GASTEIGER" << endl;
}
else { // No idea what these charges are... all our code sets "PartialCharges"
ofs << "GASTEIGER" << endl;
}
ofs << "Energy = " << mol.GetEnergy() << endl;
if (mol.HasData(OBGenericDataType::CommentData))
{
OBCommentData *cd = (OBCommentData*)mol.GetData(OBGenericDataType::CommentData);
ofs << cd->GetData();
}
ofs << endl;
ofs << "@<TRIPOS>ATOM" << endl;
OBAtom *atom;
OBResidue *res;
vector<OBAtom*>::iterator i;
vector<int> labelcount;
labelcount.resize( etab.GetNumberOfElements() );
ttab.SetFromType("INT");
ttab.SetToType("SYB");
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
//
// Use sequentially numbered atom names if no residues
//
snprintf(label,BUFF_SIZE, "%s%d",
etab.GetSymbol(atom->GetAtomicNum()),
++labelcount[atom->GetAtomicNum()]);
strcpy(rlabel,"<1>");
strcpy(rnum,"1");
str = atom->GetType();
ttab.Translate(str1,str);
//
// Use original atom names if there are residues
//
if (!ligandsOnly && (res = atom->GetResidue()) )
{
// use original atom names defined by residue
snprintf(label,BUFF_SIZE,"%s",(char*)res->GetAtomID(atom).c_str());
// make sure that residue name includes its number
snprintf(rlabel,BUFF_SIZE,"%s%d",res->GetName().c_str(), res->GetNum());
snprintf(rnum,BUFF_SIZE,"%d",res->GetNum());
}
snprintf(buffer,BUFF_SIZE,"%7d%1s%-6s%12.4f%10.4f%10.4f%1s%-5s%4s%1s %-8s%10.4f",
atom->GetIdx(),"",label,
atom->GetX(),atom->GetY(),atom->GetZ(),
"",str1.c_str(),
rnum,"",rlabel,
atom->GetPartialCharge());
ofs << buffer << endl;
}
ofs << "@<TRIPOS>BOND" << endl;
OBBond *bond;
vector<OBBond*>::iterator j;
OBSmartsPattern pat;
string s1, s2;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
{
s1 = bond->GetBeginAtom()->GetType();
s2 = bond->GetEndAtom()->GetType();
if (bond->IsAromatic() || s1 == "O.co2" || s2 == "O.co2")
strcpy(label,"ar");
else if (bond->IsAmide())
strcpy(label,"am");
else
snprintf(label,BUFF_SIZE,"%d",bond->GetBO());
snprintf(buffer, BUFF_SIZE,"%6d%6d%6d%3s%2s",
bond->GetIdx()+1,bond->GetBeginAtomIdx(),bond->GetEndAtomIdx(),
"",label);
ofs << buffer << endl;
}
// NO trailing blank line (PR#1868929).
// ofs << endl;
return(true);
}
bool BGFFormat::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;
vector<OBAtom*>::iterator i;
int max_val;
OBAtom *atom;
char buffer[BUFF_SIZE];
char elmnt_typ[8], dreid_typ[8], atm_sym[16], max_val_str[8];
mol.Kekulize();
ofs << "BIOGRF 200\n";
snprintf(buffer, BUFF_SIZE, "DESCRP %s\n",mol.GetTitle());
ofs << buffer;
snprintf(buffer, BUFF_SIZE, "REMARK BGF file created by Open Babel %s\n",BABEL_VERSION);
ofs << "FORCEFIELD DREIDING \n";
// write unit cell if available
if (mol.HasData(OBGenericDataType::UnitCell))
{
OBUnitCell *uc = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
// e.g. CRYSTX 49.30287 49.23010 25.45631 90.00008 89.99995 57.10041
snprintf(buffer, BUFF_SIZE,
"CRYSTX%12.5f%12.5f%12.5f%12.5f%12.5f%12.5f",
uc->GetA(), uc->GetB(), uc->GetC(),
uc->GetAlpha() , uc->GetBeta(), uc->GetGamma());
ofs << buffer << "\n";
}
ofs << "FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)\n";
ttab.SetFromType("INT");
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
strncpy(elmnt_typ,etab.GetSymbol(atom->GetAtomicNum()), 7); // make sure to null-terminate
elmnt_typ[sizeof(elmnt_typ) - 1] = '0';
ToUpper(elmnt_typ);
ttab.SetToType("DRE");
ttab.Translate(dreid_typ,atom->GetType());
ttab.SetToType("HAD");
ttab.Translate(max_val_str,atom->GetType());
max_val = atoi(max_val_str);
if (max_val == 0)
max_val = 1;
snprintf(atm_sym,16,"%s%d",elmnt_typ,atom->GetIdx());
snprintf(buffer,BUFF_SIZE,"%6s %5d %-5s %3s %1s %5s%10.5f%10.5f%10.5f %-5s%3d%2d %8.5f\n",
"HETATM",
atom->GetIdx(),
atm_sym,
"RES",
"A",
"444",
atom->GetX(),
atom->GetY(),
atom->GetZ(),
dreid_typ,
max_val,
0,
atom->GetPartialCharge());
ofs << buffer;
}
ofs<< "FORMAT CONECT (a6,12i6)\n\n";
OBAtom *nbr;
vector<OBBond*>::iterator j;
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
if (atom->GetValence())
{
snprintf(buffer,BUFF_SIZE,"CONECT%6d",atom->GetIdx());
ofs << buffer;
for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
{
snprintf(buffer,BUFF_SIZE,"%6d",nbr->GetIdx());
ofs << buffer;
}
ofs << endl;
snprintf(buffer,BUFF_SIZE,"ORDER %6d",atom->GetIdx());
ofs << buffer;
for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
{
snprintf(buffer,BUFF_SIZE,"%6d",(*j)->GetBO());
ofs << buffer;
}
ofs << endl;
}
ofs << "END" << endl;
return(true);
}