bool ReadAlchemy(istream &ifs,OBMol &mol, const char *title)
{
int i;
int natoms,nbonds;
char buffer[BUFF_SIZE];
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%d %*s %d", &natoms, &nbonds);
if (!natoms) return(false);
mol.ReserveAtoms(natoms);
ttab.SetFromType("ALC");
string str;
double x,y,z;
OBAtom *atom;
vector<string> vs;
for (i = 1; i <= natoms; i ++)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
tokenize(vs,buffer);
if (vs.size() != 6) return(false);
atom = mol.NewAtom();
x = atof((char*)vs[2].c_str());
y = atof((char*)vs[3].c_str());
z = atof((char*)vs[4].c_str());
atom->SetVector(x,y,z); //set coordinates
//set atomic number
ttab.SetToType("ATN"); ttab.Translate(str,vs[1]);
atom->SetAtomicNum(atoi(str.c_str()));
//set type
ttab.SetToType("INT"); ttab.Translate(str,vs[1]);
atom->SetType(str);
}
char bobuf[100];
string bostr;
int bgn,end,order;
for (i = 0; i < nbonds; i++)
{
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
sscanf(buffer,"%*d%d%d%s",&bgn,&end,bobuf);
bostr = bobuf; order = 1;
if (bostr == "DOUBLE") order = 2;
else if (bostr == "TRIPLE") order = 3;
else if (bostr == "AROMATIC") order = 5;
mol.AddBond(bgn,end,order);
}
mol.SetTitle(title);
return(true);
}
void OBAtomTyper::AssignTypes(OBMol &mol)
{
if (!_init)
Init();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::AssignTypes", obAuditMsg);
mol.SetAtomTypesPerceived();
vector<vector<int> >::iterator j;
vector<pair<OBSmartsPattern*,string> >::iterator i;
for (i = _vexttyp.begin();i != _vexttyp.end();++i)
if (i->first->Match(mol))
{
_mlist = i->first->GetMapList();
for (j = _mlist.begin();j != _mlist.end();++j)
mol.GetAtom((*j)[0])->SetType(i->second);
}
// Special cases
vector<OBAtom*>::iterator a;
OBAtom* atom;
for (atom = mol.BeginAtom(a); atom; atom = mol.NextAtom(a)) {
// guanidinium. Fixes PR#1800964
if (strncasecmp(atom->GetType(),"C2", 2) == 0) {
int guanidineN = 0;
OBAtom *nbr;
vector<OBBond*>::iterator k;
for (nbr = atom->BeginNbrAtom(k);nbr;nbr = atom->NextNbrAtom(k)) {
if (strncasecmp(nbr->GetType(),"Npl", 3) == 0 ||
strncasecmp(nbr->GetType(),"N2", 2) == 0 ||
strncasecmp(nbr->GetType(),"Ng+", 3) == 0)
++guanidineN;
}
if (guanidineN == 3)
atom->SetType("C+");
} // end C2 carbon for guanidinium
} // end special cases
}
bool MOL2Format::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
istream &ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
//Old code follows...
bool foundAtomLine = false;
char buffer[BUFF_SIZE];
char *comment = NULL;
string str,str1;
vector<string> vstr;
int len;
mol.BeginModify();
for (;;)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
if (EQn(buffer,"@<TRIPOS>MOLECULE",17))
break;
}
int lcount;
int natoms,nbonds;
for (lcount=0;;lcount++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
if (EQn(buffer,"@<TRIPOS>ATOM",13))
{
foundAtomLine = true;
break;
}
if (lcount == 0)
{
tokenize(vstr,buffer);
if (!vstr.empty())
mol.SetTitle(buffer);
}
else if (lcount == 1)
sscanf(buffer,"%d%d",&natoms,&nbonds);
else if (lcount == 4) //energy
{
tokenize(vstr,buffer);
if (!vstr.empty() && vstr.size() == 3)
if (vstr[0] == "Energy")
mol.SetEnergy(atof(vstr[2].c_str()));
}
else if (lcount == 5) //comment
{
if ( buffer[0] )
{
len = (int) strlen(buffer)+1;
// TODO allow better multi-line comments
// which don't allow ill-formed data to consume memory
// Thanks to Andrew Dalke for the pointer
if (comment != NULL)
delete [] comment;
comment = new char [len];
memcpy(comment,buffer,len);
}
}
}
if (!foundAtomLine)
{
mol.EndModify();
mol.Clear();
obErrorLog.ThrowError(__FUNCTION__, "Unable to read Mol2 format file. No atoms found.", obWarning);
return(false);
}
mol.ReserveAtoms(natoms);
int i;
vector3 v;
OBAtom atom;
bool hasPartialCharges=false;
double x,y,z,pcharge;
char temp_type[BUFF_SIZE], resname[BUFF_SIZE], atmid[BUFF_SIZE];
int elemno, resnum = -1;
ttab.SetFromType("SYB");
for (i = 0;i < natoms;i++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
sscanf(buffer," %*s %1024s %lf %lf %lf %1024s %d %1024s %lf",
atmid, &x,&y,&z, temp_type, &resnum, resname, &pcharge);
atom.SetVector(x, y, z);
// Handle "CL" and "BR" and other mis-typed atoms
str = temp_type;
if (strncmp(temp_type, "CL", 2) == 0) {
str = "Cl";
} else if (strncmp(temp_type,"BR",2) == 0) {
str = "Br";
} else if (strncmp(temp_type,"S.o2", 4) == 02) {
str = "S.O2";
} else if (strncmp(temp_type,"S.o", 3) == 0) {
str = "S.O";
} else if (strncmp(temp_type,"SI", 2) == 0) {
str = "Si";
// The following cases are entries which are not in openbabel/data/types.txt
// and should probably be added there
} else if (strncmp(temp_type,"S.1", 3) == 0) {
str = "S.2"; // no idea what the best type might be here
} else if (strncmp(temp_type,"P.", 2) == 0) {
str = "P.3";
} else if (strncasecmp(temp_type,"Ti.", 3) == 0) { // e.g. Ti.th
str = "Ti";
} else if (strncasecmp(temp_type,"Ru.", 3) == 0) { // e.g. Ru.oh
str = "Ru";
}
ttab.SetToType("ATN");
ttab.Translate(str1,str);
elemno = atoi(str1.c_str());
ttab.SetToType("IDX");
// We might have missed some SI or FE type things above, so here's
// another check
if( !elemno && isupper(temp_type[1]) )
{
temp_type[1] = (char)tolower(temp_type[1]);
str = temp_type;
ttab.Translate(str1,str);
elemno = atoi(str1.c_str());
}
// One last check if there isn't a period in the type,
// it's a malformed atom type, but it may be the element symbol
// GaussView does this (PR#1739905)
if ( !elemno ) {
obErrorLog.ThrowError(__FUNCTION__, "This Mol2 file is non-standard. Cannot interpret atom types correctly, instead attempting to interpret as elements instead.", obWarning);
string::size_type dotPos = str.find('.');
if (dotPos == string::npos) {
elemno = etab.GetAtomicNum(str.c_str());
}
}
atom.SetAtomicNum(elemno);
ttab.SetToType("INT");
ttab.Translate(str1,str);
atom.SetType(str1);
atom.SetPartialCharge(pcharge);
if (!mol.AddAtom(atom))
return(false);
if (!IsNearZero(pcharge))
hasPartialCharges = true;
// Add residue information if it exists
if (resnum != -1 && resnum != 0 &&
strlen(resname) != 0 && strncmp(resname,"<1>", 3) != 0)
{
OBResidue *res = (mol.NumResidues() > 0) ?
mol.GetResidue(mol.NumResidues()-1) : NULL;
if (res == NULL || res->GetName() != resname ||
static_cast<int>(res->GetNum()) != resnum)
{
vector<OBResidue*>::iterator ri;
for (res = mol.BeginResidue(ri) ; res ; res = mol.NextResidue(ri))
if (res->GetName() == resname &&
static_cast<int>(res->GetNum())
== resnum)
break;
if (res == NULL)
{
res = mol.NewResidue();
res->SetName(resname);
res->SetNum(resnum);
}
}
OBAtom *atomPtr = mol.GetAtom(mol.NumAtoms());
res->AddAtom(atomPtr);
res->SetAtomID(atomPtr, atmid);
} // end adding residue info
}
for (;;)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
str = buffer;
if (!strncmp(buffer,"@<TRIPOS>BOND",13))
break;
}
int start,end,order;
for (i = 0; i < nbonds; i++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
sscanf(buffer,"%*d %d %d %1024s",&start,&end,temp_type);
str = temp_type;
order = 1;
if (str == "ar" || str == "AR" || str == "Ar")
order = 5;
else if (str == "AM" || str == "am" || str == "Am")
order = 1;
else
order = atoi(str.c_str());
mol.AddBond(start,end,order);
}
// update neighbour bonds information for each atom.
vector<OBAtom*>::iterator apos;
vector<OBBond*>::iterator bpos;
OBAtom* patom;
OBBond* pbond;
for (patom = mol.BeginAtom(apos); patom; patom = mol.NextAtom(apos))
{
patom->ClearBond();
for (pbond = mol.BeginBond(bpos); pbond; pbond = mol.NextBond(bpos))
{
if (patom == pbond->GetBeginAtom() || patom == pbond->GetEndAtom())
{
patom->AddBond(pbond);
}
}
}
// Suggestion by Liu Zhiguo 2008-01-26
// Mol2 files define atom types -- there is no need to re-perceive
mol.SetAtomTypesPerceived();
mol.EndModify();
//must add generic data after end modify - otherwise it will be blown away
if (comment)
{
OBCommentData *cd = new OBCommentData;
cd->SetData(comment);
cd->SetOrigin(fileformatInput);
mol.SetData(cd);
delete [] comment;
comment = NULL;
}
if (hasPartialCharges)
mol.SetPartialChargesPerceived();
// continue untill EOF or untill next molecule record
streampos pos;
for(;;)
{
pos = ifs.tellg();
if (!ifs.getline(buffer,BUFF_SIZE))
break;
if (EQn(buffer,"@<TRIPOS>MOLECULE",17))
break;
}
ifs.seekg(pos); // go back to the end of the molecule
return(true);
}
bool MacroModFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
istream &ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
const char* defaultTitle = pConv->GetTitle();
// Get Title
char buffer[BUFF_SIZE];
int natoms;
vector<vector<pair<int,int> > > connections;
if (ifs.getline(buffer,BUFF_SIZE))
{
vector<string> vs;
tokenize(vs,buffer," \n");
if ( !vs.empty() && vs.size() > 0)
sscanf(buffer,"%i%*s",&natoms);
if (natoms == 0)
return false;
if ( !vs.empty() && vs.size() > 1)
mol.SetTitle(vs[1]);
else
{
string s = defaultTitle;
mol.SetTitle(defaultTitle);
}
}
else
return(false);
mol.BeginModify();
mol.ReserveAtoms(natoms);
connections.resize(natoms+1);
/***********************************************************************/
// Get Type Bonds, BondOrder, X, Y, Z
double x,y,z;
vector3 v;
char temp_type[10];
int i,j;
double charge;
OBAtom atom;
ttab.SetFromType("MMD");
for (i = 1; i <= natoms; i++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
break;
int end[6], order[6];
sscanf(buffer,"%9s%d%d%d%d%d%d%d%d%d%d%d%d%lf%lf%lf",
temp_type,&end[0],&order[0],&end[1],&order[1],&end[2],&order[2],
&end[3], &order[3], &end[4], &order[4], &end[5], &order[5],
&x, &y, &z);
pair<int,int> tmp;
for ( j = 0 ; j <=5 ; j++ )
{
if ( end[j] > 0 && end[j] > i)
{
tmp.first = end[j];
tmp.second = order[j];
connections[i].push_back(tmp);
}
}
v.SetX(x);
v.SetY(y);
v.SetZ(z);
atom.SetVector(v);
string str = temp_type,str1;
ttab.SetToType("ATN");
ttab.Translate(str1,str);
atom.SetAtomicNum(atoi(str1.c_str()));
ttab.SetToType("INT");
ttab.Translate(str1,str);
atom.SetType(str1);
// stuff for optional fields
buffer[109]='\0';
sscanf(&buffer[101],"%lf", &charge);
atom.SetPartialCharge(charge);
mol.AddAtom(atom);
}
for (i = 1; i <= natoms; i++)
for (j = 0; j < (signed)connections[i].size(); j++)
mol.AddBond(i, connections[i][j].first, connections[i][j].second);
mol.EndModify();
OBBond *bond;
vector<OBBond*>::iterator bi;
for (bond = mol.BeginBond(bi);bond;bond = mol.NextBond(bi))
if (bond->GetBO() == 5 && !bond->IsInRing())
bond->SetBO(1);
if ( natoms != (signed)mol.NumAtoms() )
return(false);
// clean out remaining blank lines
while(ifs.peek() != EOF && ifs.good() &&
(ifs.peek() == '\n' || ifs.peek() == '\r'))
ifs.getline(buffer,BUFF_SIZE);
return(true);
}
bool BGFFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
istream &ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
mol.SetTitle( pConv->GetTitle()); //default title is the filename
mol.BeginModify();
char buffer[BUFF_SIZE];
char tmp[16],tmptyp[16];
vector<string> vs;
while (ifs.getline(buffer,BUFF_SIZE)) {
if (EQn(buffer,"CRYSTX",6)) {
// Parse unit cell
tokenize(vs,buffer," \n\t,");
if (vs.size() != 7)
continue; // something strange
double A, B, C, Alpha, Beta, Gamma;
A = atof(vs[1].c_str());
B = atof(vs[2].c_str());
C = atof(vs[3].c_str());
Alpha = atof(vs[4].c_str());
Beta = atof(vs[5].c_str());
Gamma = atof(vs[6].c_str());
OBUnitCell *uc = new OBUnitCell;
uc->SetOrigin(fileformatInput);
uc->SetData(A, B, C, Alpha, Beta, Gamma);
mol.SetData(uc);
} else if (EQn(buffer,"FORMAT",6))
break;
}
ttab.SetFromType("DRE");
ttab.SetToType("INT");
OBAtom *atom;
double x,y,z,chrg;
for (;;)
{
if (!ifs.getline(buffer,BUFF_SIZE))
break;
if (EQn(buffer,"FORMAT",6))
break;
sscanf(buffer,"%*s %*s %*s %*s %*s %*s %lf %lf %lf %15s %*s %*s %lf",
&x,&y,&z,
tmptyp,
&chrg);
atom = mol.NewAtom();
ttab.Translate(tmp,tmptyp);
atom->SetType(tmp);
CleanAtomType(tmptyp);
atom->SetAtomicNum(etab.GetAtomicNum(tmptyp));
atom->SetVector(x,y,z);
}
unsigned int i;
vector<int> vtmp;
vector<vector<int> > vcon;
vector<vector<int> > vord;
for (i = 0; i < mol.NumAtoms();i++)
{
vcon.push_back(vtmp);
vord.push_back(vtmp);
}
unsigned int bgn;
for (;;)
{
if (!ifs.getline(buffer,BUFF_SIZE) || EQn(buffer,"END",3))
break;
tokenize(vs,buffer);
if (vs.empty() || vs.size() < 3 || vs.size() > 10)
continue;
if (EQn(buffer,"CONECT",6))
{
bgn = atoi((char*)vs[1].c_str()) - 1;
if (bgn < 1 || bgn > mol.NumAtoms())
continue;
for (i = 2;i < vs.size();i++)
{
vcon[bgn].push_back(atoi((char*)vs[i].c_str()));
vord[bgn].push_back(1);
}
}
else
if (EQn(buffer,"ORDER",5))
{
bgn = atoi((char*)vs[1].c_str()) - 1;
if (bgn < 1 || bgn > mol.NumAtoms())
continue;
if (vs.size() > vord[bgn].size()+2)
continue;
for (i = 2;i < vs.size();i++)
vord[bgn][i-2] = atoi((char*)vs[i].c_str());
}
}
unsigned int j;
for (i = 1;i <= mol.NumAtoms();i++)
if (!vcon[i - 1].empty())
for (j = 0;j < vcon[i - 1].size();j++)
{
mol.AddBond(i,vcon[i - 1][j],vord[i - 1][j]);
}
//load up the next line after the END marker
ifs.getline(buffer,BUFF_SIZE);
mol.EndModify();
return(true);
}
bool AlchemyFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
istream &ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
const char* title = pConv->GetInFilename().c_str();
int i;
int natoms = 0, nbonds = 0;
char buffer[BUFF_SIZE];
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer," %d %*s %d", &natoms, &nbonds);
if (!natoms)
{
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer," %d %*s %d", &natoms, &nbonds);
if (!natoms)
return(false);
}
mol.ReserveAtoms(natoms);
mol.BeginModify();
ttab.SetFromType("ALC");
string str;
double x,y,z;
OBAtom *atom;
vector<string> vs;
for (i = 1; i <= natoms; i ++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
tokenize(vs,buffer);
if (vs.size() < 5)
return(false);
atom = mol.NewAtom();
x = atof((char*)vs[2].c_str());
y = atof((char*)vs[3].c_str());
z = atof((char*)vs[4].c_str());
atom->SetVector(x,y,z); //set coordinates
//set atomic number
ttab.SetToType("ATN");
ttab.Translate(str,vs[1]);
atom->SetAtomicNum(atoi(str.c_str()));
//set type
ttab.SetToType("INT");
ttab.Translate(str,vs[1]);
atom->SetType(str);
}
char bobuf[100];
string bostr;
int bgn,end,order;
for (i = 0; i < nbonds; i++)
{
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
sscanf(buffer," %*d%d%d%99s",&bgn,&end,bobuf);
bostr = bobuf;
order = 1;
if (bostr == "DOUBLE")
order = 2;
else if (bostr == "TRIPLE")
order = 3;
else if (bostr == "AROMATIC")
order = 5;
mol.AddBond(bgn,end,order);
}
// clean out remaining blank lines
while(ifs.peek() != EOF && ifs.good() &&
(ifs.peek() == '\n' || ifs.peek() == '\r'))
ifs.getline(buffer,BUFF_SIZE);
mol.EndModify();
mol.SetTitle(title);
return(true);
}
bool ReadXYZ(istream &ifs,OBMol &mol,const char *title)
{
char buffer[BUFF_SIZE];
// Read the first line, which should contain the number of atoms in
// the molecule.
if (!ifs.getline(buffer,BUFF_SIZE)) {
cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
<< " Could not read the first line, file error." << endl;
return(false);
}
unsigned int natoms; // [ejk] assumed natoms could not be -ve
if (sscanf(buffer,"%d", &natoms) == 0) {
cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
<< " Problems reading the first line. The first line must contain the number of atoms." << endl
<< " OpenBabel found the line '" << buffer << "'" << endl
<< " which could not be interpreted as a number." << endl;
return(false);
}
if (!natoms) {
cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
<< " Problems reading the first line. The first line must contain the number of atoms." << endl
<< " OpenBabel found the number '0' which obviously does not work." << endl;
return(false);
}
mol.ReserveAtoms(natoms);
// The next line contains a title string for the molecule. Use this
// as the title for the molecule if the line is not
// empty. Otherwise, use the title given by the calling function.
if (!ifs.getline(buffer,BUFF_SIZE)) {
cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
<< " Could not read the second line, file error." << endl;
return(false);
}
if (strlen(buffer) == 0)
mol.SetTitle(buffer);
else
mol.SetTitle(title);
// The next lines contain four items each, separated by white
// spaces: the atom type, and the coordinates of the atom
vector<string> vs;
for (unsigned int i = 1; i <= natoms; i ++) {
if (!ifs.getline(buffer,BUFF_SIZE)) {
cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
<< " Could not read line #" << i+2 << ", file error." << endl
<< " According to line one, there should be " << natoms << " atoms, and therefore " << natoms+2 << " lines in the file" << endl;
return(false);
}
tokenize(vs,buffer);
if (vs.size() != 4) {
cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
<< " Could not read line #" << i+2 << "." << endl
<< " OpenBabel found the line '" << buffer << "'" << endl
<< " According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
<< " However, OpenBabel found " << vs.size() << " items." << endl;
return(false);
}
// Atom Type: get the atomic number from the element table, using
// the first entry in the currently read line. If the entry makes
// sense, set the atomic number and leave the atomic type open
// (the type is then later faulted in when atom->GetType() is
// called). If the entry does not make sense to use, set the atom
// type manually, assuming that the author of the xyz-file had
// something "special" in mind.
OBAtom *atom = mol.NewAtom();
int atomicNum = etab.GetAtomicNum(vs[0].c_str());
atom->SetAtomicNum(etab.GetAtomicNum(vs[0].c_str())); //set atomic number, or '0' if the atom type is not recognized
if (atomicNum == 0)
atom->SetType(vs[0]);
// Read the atom coordinates
char *endptr;
double x = strtod((char*)vs[1].c_str(),&endptr);
if (endptr == (char*)vs[1].c_str()) {
cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
<< " Could not read line #" << i+2 << "." << endl
<< " OpenBabel found the line '" << buffer << "'" << endl
<< " According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
<< " Item #0: Atom Type, Items #1-#3 cartesian coordinates in Angstrom." << endl
<< " OpenBabel could not interpret item #1 as a number." << endl;
return(false);
}
double y = strtod((char*)vs[2].c_str(),&endptr);
if (endptr == (char*)vs[2].c_str()) {
cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
<< " Could not read line #" << i+2 << "." << endl
<< " OpenBabel found the line '" << buffer << "'" << endl
<< " According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
<< " Item #0: Atom Type, Items #1-#3 cartesian coordinates in Angstrom." << endl
<< " OpenBabel could not interpret item #2 as a number." << endl;
return(false);
}
double z = strtod((char*)vs[3].c_str(),&endptr);
if (endptr == (char*)vs[3].c_str()) {
cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
<< " Could not read line #" << i+2 << "." << endl
<< " OpenBabel found the line '" << buffer << "'" << endl
<< " According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
<< " Item #0: Atom Type, Items #1-#3 cartesian coordinates in Angstrom." << endl
<< " OpenBabel could not interpret item #3 as a number." << endl;
return(false);
}
atom->SetVector(x,y,z); //set coordinates
}
mol.ConnectTheDots();
mol.PerceiveBondOrders();
return(true);
}
bool CHEM3D1Format::ReadChem3d(istream &ifs,OBMol &mol,bool mmads,const char *type_key)
{
char buffer[BUFF_SIZE];
int natoms,i;
char tmp[16],tmp1[16];
char atomic_type[16];
double exponent = 0.0;
double divisor = 1.0;
double Alpha,Beta,Gamma,A,B,C;
bool has_fractional = false, has_divisor = false;
matrix3x3 m;
vector<string> vs;
ifs.getline(buffer,BUFF_SIZE);
tokenize(vs,buffer);
if (mmads)
{
if (vs.empty())
return(false);
natoms = atoi((char*)vs[0].c_str());
if (vs.size() == 2)
mol.SetTitle(vs[1]);
}
else
{
switch(vs.size())
{
case 7 :
sscanf(buffer,"%d%lf%lf%lf%lf%lf%lf",
&natoms,&Alpha,&Beta,&Gamma,&A,&B,&C);
m.FillOrth(Alpha,Beta,Gamma,A,B,C);
has_fractional = true;
break;
case 8 :
sscanf(buffer,"%d%lf%lf%lf%lf%lf%lf%lf",
&natoms,&Alpha,&Beta,&Gamma,&A,&B,&C,&exponent);
m.FillOrth(Alpha,Beta,Gamma,A,B,C);
has_fractional = true;
has_divisor = true;
break;
default :
sscanf(buffer,"%d",&natoms);
break;
}
}
if (!natoms)
return(false);
divisor = pow(10.0,exponent);
mol.ReserveAtoms(natoms);
ttab.SetToType("INT");
ttab.SetFromType(type_key);
OBAtom *atom;
double x,y,z;
vector3 v;
unsigned int k;
for (i = 1; i <= natoms; i++)
{
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%15s%*d%lf%lf%lf%15s",
atomic_type,
&x,
&y,
&z,
tmp);
v.Set(x,y,z);
if (has_fractional)
v *= m;
if (has_divisor)
v/= divisor;
tokenize(vs,buffer);
if (vs.empty())
return(false);
atom = mol.NewAtom();
ttab.Translate(tmp1,tmp);
atom->SetType(tmp1);
atom->SetVector(v);
atom->SetAtomicNum(etab.GetAtomicNum(atomic_type));
for (k = 6;k < vs.size(); k++)
mol.AddBond(atom->GetIdx(),atoi((char*)vs[k].c_str()),1);
}
// clean out remaining blank lines
while(ifs.peek() != EOF && ifs.good() &&
(ifs.peek() == '\n' || ifs.peek() == '\r'))
ifs.getline(buffer,BUFF_SIZE);
mol.PerceiveBondOrders();
return(true);
}
bool TurbomoleFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if(pmol==NULL)
return false;
//Define some references so we can use the old parameter names
istream &ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
double UnitConv=AAU;
if(pConv->IsOption("a", OBConversion::INOPTIONS))
UnitConv=1;
char buffer[BUFF_SIZE];
do
{
ifs.getline(buffer,BUFF_SIZE);
if (ifs.peek() == EOF || !ifs.good())
return false;
}
while(strncmp(buffer,"$coord",6));
mol.BeginModify();
OBAtom atom;
while(!(!ifs))
{
ifs.getline(buffer,BUFF_SIZE);
if(*buffer=='$')
break;
if(*buffer=='#')
continue;
float x,y,z;
char atomtype[8];
if(sscanf(buffer,"%f %f %f %7s",&x,&y,&z,atomtype)!=4)
return false;
atom.SetVector(x*UnitConv, y*UnitConv, z*UnitConv);
atom.SetAtomicNum(OBElements::GetAtomicNum(atomtype));
atom.SetType(atomtype);
if(!mol.AddAtom(atom))
return false;
atom.Clear();
}
while(!(!ifs) && strncmp(buffer,"$end",4))
ifs.getline(buffer,BUFF_SIZE);
if (!pConv->IsOption("b",OBConversion::INOPTIONS))
mol.ConnectTheDots();
if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
mol.PerceiveBondOrders();
// clean out remaining blank lines
std::streampos ipos;
do
{
ipos = ifs.tellg();
ifs.getline(buffer,BUFF_SIZE);
}
while(strlen(buffer) == 0 && !ifs.eof() );
ifs.seekg(ipos);
mol.EndModify();
return true;
}
