unsigned int OBRing::GetRootAtom()
{
vector<int>::iterator i;
OBMol *mol = (OBMol*)GetParent();
//if (!IsAromatic())
// return 0;
if (Size() == 6)
for (i = _path.begin();i != _path.end();++i)
if (mol->GetAtom(*i)->GetAtomicNum() != OBElements::Carbon)
return (*i);
if (Size() == 5)
for (i = _path.begin();i != _path.end();++i) {
OBAtom *atom = mol->GetAtom(*i);
switch (atom->GetAtomicNum()) {
case OBElements::Sulfur:
if (atom->GetValence() == 2)
return (*i);
break;
case OBElements::Oxygen:
if (atom->GetValence() == 2)
return (*i);
break;
case OBElements::Nitrogen:
if (atom->BOSum() == atom->GetValence())
return (*i);
break;
}
}
return 0;
}
unsigned int OBRing::GetRootAtom()
{
vector<int>::iterator i;
OBMol *mol = (OBMol*)GetParent();
//if (!IsAromatic())
// return 0;
if (Size() == 6)
for (i = _path.begin();i != _path.end();++i)
if (!(mol->GetAtom(*i))->IsCarbon())
return (*i);
if (Size() == 5)
for (i = _path.begin();i != _path.end();++i) {
OBAtom *atom = mol->GetAtom(*i);
if (atom->IsSulfur() && (atom->GetValence() == 2))
return (*i);
if (atom->IsOxygen() && (atom->GetValence() == 2))
return (*i);
if (atom->IsNitrogen() && (atom->BOSum() == atom->GetValence()))
return (*i);
}
return 0;
}
void OBAtomTyper::AssignImplicitValence(OBMol &mol)
{
// FF Make sure that valence has not been perceived
if(mol.HasImplicitValencePerceived())
return;
if (!_init)
Init();
mol.SetImplicitValencePerceived();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::AssignImplicitValence", obAuditMsg);
// FF Ensure that the aromatic typer will not be called
int oldflags = mol.GetFlags(); // save the current state flags
mol.SetAromaticPerceived(); // and set the aromatic perceived flag on
OBAtom *atom;
vector<OBAtom*>::iterator k;
for (atom = mol.BeginAtom(k);atom;atom = mol.NextAtom(k))
atom->SetImplicitValence(atom->GetValence());
vector<vector<int> >::iterator j;
vector<pair<OBSmartsPattern*,int> >::iterator i;
for (i = _vimpval.begin();i != _vimpval.end();++i)
if (i->first->Match(mol))
{
_mlist = i->first->GetMapList();
for (j = _mlist.begin();j != _mlist.end();++j)
mol.GetAtom((*j)[0])->SetImplicitValence(i->second);
}
if (!mol.HasAromaticCorrected())
CorrectAromaticNitrogens(mol);
for (atom = mol.BeginAtom(k);atom;atom = mol.NextAtom(k))
{
if (atom->GetImplicitValence() < atom->GetValence())
atom->SetImplicitValence(atom->GetValence());
}
// FF Come back to the initial flags
mol.SetFlags(oldflags);
return;
}
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 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 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);
}
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 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 OBCisTransStereo::IsOnSameAtom(unsigned long id1, unsigned long id2) const
{
const OBMol *mol = GetMolecule();
if (!mol) {
obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : No valid molecule set", obError);
return false;
}
OBAtom *begin = mol->GetAtomById(m_cfg.begin);
if (!begin) {
obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : Begin reference id is not valid.", obError);
return false;
}
OBAtom *end = mol->GetAtomById(m_cfg.end);
if (!end) {
obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : End reference id is not valid.", obError);
return false;
}
OBAtom *a = mol->GetAtomById(id1);
OBAtom *b = mol->GetAtomById(id2);
if (a && b) {
// both on begin atom?
if (a->IsConnected(begin) && b->IsConnected(begin))
return true;
// both on end atom?
if (a->IsConnected(end) && b->IsConnected(end))
return true;
return false;
} else {
if (a) {
// b atom not found, could be a deleted hydrogen...
if (a->IsConnected(begin)) {
// a is connected to begin. if this is the atom missing a hydrogen, return false
if (begin->GetValence() == 2)
return true;
// check if the end atom really is missing an atom
if (end->GetValence() != 2) {
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : id2 is not valid and is not a missing hydrogen.", obError);
return false;
}
// inform user we are treating id2 as deleted hydrogen
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : Atom with id2 doesn't exist anymore, must be a (deleted) hydrogen.", obInfo);
} else if (a->IsConnected(end)) {
// a is connected to end. again, if this is the atom missing a hydrogen, return false
if (end->GetValence() == 2)
return true;
// check if the begin atom really is missing an atom
if (begin->GetValence() != 2) {
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : id2 is not valid and is not a missing hydrogen.", obError);
return true;
}
// inform user we are treating id2 as deleted hydrogen
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : Atom with id2 doesn't exist, must be a (deleted) hydrogen.", obInfo);
} else {
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : Atom with id1 isn't connected to the begin or end atom.", obError);
return true;
}
} else if (b) {
// a atom not found, could be a deleted hydrogen...
if (b->IsConnected(begin)) {
// b is connected to begin. if this is the atom missing a hydrogen, return false
if (begin->GetValence() == 2)
return true;
// check if the end atom really is missing an atom
if (end->GetValence() != 2) {
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : id1 is not valid and is not a missing hydrogen.", obError);
return true;
}
// inform user we are treating id1 as deleted hydrogen
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : Atom with id1 doesn't exist, must be a (deleted) hydrogen.", obInfo);
} else if (b->IsConnected(end)) {
// a is connected to end. again, if this is the atom missing a hydrogen, return false
if (end->GetValence() == 2)
return true;
// check if the begin atom really is missing an atom
if (begin->GetValence() != 2) {
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : id1 is not valid and is not a missing hydrogen.", obError);
return true;
}
// inform user we are treating id2 as deleted hydrogen
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : Atom with id1 doesn't exist, must be a (deleted) hydrogen.", obInfo);
} else {
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : Atom with id1 isn't connected to the begin or end atom.", obError);
return true;
}
} else {
OBAtom *c = 0, *d = 0;
// no a & b, check the remaining ids which will reveal same info
for (int i = 0; i < 4; ++i) {
if ((m_cfg.refs.at(i) == id1) || (m_cfg.refs.at(i) == id2))
continue;
if (!c) {
c = mol->GetAtomById(m_cfg.refs.at(i));
} else {
d = mol->GetAtomById(m_cfg.refs.at(i));
}
}
if (!c || !d) {
obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : invalid stereochemistry!", obError);
return true;
}
if ((begin->GetValence() != 2) || (end->GetValence() != 2)) {
obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : invalid stereochemistry!", obError);
return true;
}
obErrorLog.ThrowError(__FUNCTION__,
"OBCisTransStereo::IsOnSameAtom : Atoms with id1 & id2 don't exist, must be a (deleted) hydrogens.", obInfo);
return IsOnSameAtom(c->GetId(), d->GetId());
}
}
return false;
}
int SetMM3Type(OBAtom *atom)
{
OBAtom *b; // neighbor
OBBondIterator i, j;
int countNeighborO, countNeighborS, countNeighborN, countNeighborC;
countNeighborO = countNeighborS = countNeighborN = countNeighborC = 0;
// The MM2 typing isn't very good, so we do this ourselves for the most common atom types
switch (atom->GetAtomicNum()) {
case 1: // Hydrogen
b = atom->BeginNbrAtom(j);
if (b->IsCarboxylOxygen())
return 24;
if (b->GetAtomicNum() == OBElements::Sulfur)
return 44;
if (b->GetAtomicNum() == OBElements::Nitrogen) {
if (b->IsAmideNitrogen())
return 28;
if (b->GetValence() > 3)
return 48;// ammonium
return 23; // default amine/imine
}
if (b->GetAtomicNum() == OBElements::Carbon && b->GetHyb() == 1)
return 124; // acetylene
if (b->GetAtomicNum() == OBElements::Oxygen) {
if (b->HasAlphaBetaUnsat())
return 73; // includes non-enol/phenol, but has the right spirit
return 21; // default alcohol
}
return 5; // default H
break;
case 2: // Helium
return 51; break;
case 3: // Li
return 163; break;
case 5: // B
if (atom->GetValence() >= 4)
return 27; // tetrahedral
return 26; break;
case 6: // C
if (atom->IsInRingSize(3)) { // cyclopropane / cyclopropene
if (atom->GetHyb() == 3)
return 22;
if (atom->GetHyb() == 2) {
if (atom->CountFreeOxygens() == 1) // propanone
return 67;
return 38; // propane
}
}
if (atom->IsInRingSize(4)) { // cyclobutane or cyclobutene
if (atom->GetHyb() == 3)
return 56;
if (atom->GetHyb() == 2) {
if (atom->CountFreeOxygens() == 1) // butanone
return 58;
return 57; // regular cyclobutane
}
}
if (atom->CountBondsOfOrder(2) == 2) { // allene
if (atom->CountFreeOxygens() == 1) // ketene
return 106;
return 68;
}
if (atom->GetFormalCharge() == +1)
return 30;
if (atom->GetSpinMultiplicity() == 2)
return 29;
if (atom->GetHyb() == 3)
return 1;
else if (atom->GetHyb() == 2) {
if (atom->CountFreeOxygens() >= 1)
return 3;
return 2;
}
else if (atom->GetHyb() == 1)
return 4;
break;
case 7: // N
// TODO
if (atom->IsAmideNitrogen())
return 151;
if (atom->IsAromatic()) {
if (atom->GetFormalCharge() == 1)
return 111;
if (atom->IsInRingSize(5)) // pyrrole
return 40;
if (atom->IsInRingSize(6)) // pyridine
return 37;
}
if (atom->CountFreeOxygens() == 2) // nitro
return 46;
if (atom->GetHyb() == 3) {
if (atom->GetValence() > 3)
return 39; // ammonium
return 8;
}
else if (atom->GetHyb() == 2)
return 9;
else if (atom->GetHyb() == 1)
return 10;
break;
case 8: // O
//TODO
if (atom->IsPhosphateOxygen())
return 159;
if (atom->IsCarboxylOxygen())
return 75;
if (atom->IsInRingSize(3))
return 49; // epoxy
b = atom->BeginNbrAtom(j);
if (atom->HasBondOfOrder(2) && b->GetAtomicNum() == OBElements::Carbon) { // O=C
return 7;
}
if (atom->IsAromatic())
return 41; // furan
return 6;
break;
case 9: // F
return 11; break;
case 10: // Ne
return 52; break;
case 12: // Mg
return 59; break;
case 14: // Si
return 19; break;
case 15: // P
if (atom->CountFreeOxygens() > 0)
return 153; // phosphate
if (atom->BOSum() > 3)
return 60; // phosphorus V
return 25; break;
case 16: // S
if (atom->IsAromatic())
return 42; // thiophene
if (atom->GetFormalCharge() == 1)
return 16; // sulfonium
// look at the neighbors
for (b = atom->BeginNbrAtom(j); b; b = atom->NextNbrAtom(j))
{
switch (b->GetAtomicNum()) {
case 6:
if (b->GetHyb() == 2) // S=C
countNeighborC++; break;
case 7:
countNeighborN++; break;
case 8:
if (b->GetHvyValence() == 1)
countNeighborO++;
break;
case 16:
countNeighborS++; break;
default:
continue;
}
}
if (countNeighborO == 1)
return 17; // sulfoxide
if (countNeighborO >= 2) {
if (countNeighborN)
return 154; // sulfonamide
return 18; // sulfone or sulfate
}
if (countNeighborC)
return 74; // S=C
if (countNeighborS == 1)
return 104; // S-S disulfide
else if (countNeighborS > 1)
return 105;
return 15; break;
case 17: // Cl
return 12; break;
case 18: // Ar
return 153; break;
case 20: // Ca
return 125; break;
case 26: // Fe
if (atom->GetFormalCharge() == 2)
return 61;
return 62; break;
case 27: // Co
if (atom->GetFormalCharge() == 2)
return 65;
return 66; break;
case 28: // Ni
if (atom->GetFormalCharge() == 2)
return 63;
return 64; break;
case 32: // Ge
return 31; break;
case 34: // Se
return 34; break;
case 35: // Br
return 13; break;
case 36: // Kr
return 54; break;
case 38: // Sr
return 126; break;
case 50: // Sn
return 32; break;
case 52: // Te
return 35; break;
case 53: // I
return 14; break;
case 54: // Xe
return 55; break;
case 56: // Ba
return 127; break;
case 57:
return 128; break;
case 58:
return 129; break;
case 59:
return 130; break;
case 60:
return 131; break;
case 61:
return 132; break;
case 62:
return 133; break;
case 63:
return 134; break;
case 64:
return 135; break;
case 65:
return 136; break;
case 66:
return 137; break;
case 67:
return 138; break;
case 68:
return 139; break;
case 69:
return 140; break;
case 70:
return 141; break;
case 71:
return 142; break;
case 82: // Pb
return 33; break;
default:
break;
}
return 0;
}
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);
}
