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/**********************************************************************
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
#include "mol.h"
using namespace std;
namespace OpenBabel {
bool ReadSDFile(istream &ifs,OBMol &mol,char *title) {
int i,natoms,nbonds;
char buffer[BUFF_SIZE];
char *comment = NULL;
string r1,r2;
if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
mol.SetTitle(buffer);
if (!ifs.getline(buffer,BUFF_SIZE)) return(false); //creator
if (!ifs.getline(buffer,BUFF_SIZE)) return(false); //comment
if (strlen(buffer) > 0) {
comment = new char [strlen(buffer)+1];
strcpy(comment,buffer);
}
if (!ifs.getline(buffer,BUFF_SIZE)) return(false); //atoms and bonds
r1 = buffer;
natoms = atoi((r1.substr(0,3)).c_str());
nbonds = atoi((r1.substr(3,3)).c_str());
mol.BeginModify();
mol.ReserveAtoms(natoms);
float x,y,z;
char type[5];
Vector v;
OBAtom atom;
int charge;
for (i = 0;i < natoms;i++) {
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
if (sscanf(buffer,"%f %f %f %s %*d %d",&x,&y,&z,type,&charge) != 5)
return(false);
v.SetX(x);v.SetY(y);v.SetZ(z);
atom.SetVector(v);
atom.SetAtomicNum(etab.GetAtomicNum(type));
atom.SetType(type);
switch (charge) {
case 0: break;
case 3: atom.SetFormalCharge(1); break;
case 2: atom.SetFormalCharge(2); break;
case 1: atom.SetFormalCharge(3); break;
case 5: atom.SetFormalCharge(-1); break;
case 6: atom.SetFormalCharge(-2); break;
case 7: atom.SetFormalCharge(-3); break;
}
if (!mol.AddAtom(atom))
return(false);
atom.Clear();
}
int start,end,order,flag,stereo;
for (i = 0;i < nbonds;i++) {
flag = 0;
if (!ifs.getline(buffer,BUFF_SIZE))
return(false);
r1 = buffer;
start = atoi((r1.substr(0,3)).c_str());
end = atoi((r1.substr(3,3)).c_str());
order = atoi((r1.substr(6,3)).c_str());
order = (order == 4) ? 5 : order;
if (r1.size() >= 12) { //handle wedge/hash data
stereo = atoi((r1.substr(9,3)).c_str());
if (stereo) {
if (stereo == 1) flag |= OB_WEDGE_BOND;
if (stereo == 6) flag |= OB_HASH_BOND;
}
}
if (!mol.AddBond(start,end,order,flag)) return(false);
}
mol.EndModify();
if (comment)
{
OBCommentData *cd = new OBCommentData;
mol.SetData(cd);
}
while (ifs.getline(buffer,BUFF_SIZE)) {
// RWT 4/7/2001
// added to get properties
if (strstr(buffer,"<")) {
string buff(buffer);
size_t lt=buff.find("<")+1;
size_t rt = buff.find_last_of(">");
string attr = buff.substr(lt,rt-lt);
ifs.getline(buffer,BUFF_SIZE);
OBPairData *dp = new OBPairData;
dp->SetAttribute(attr);
dp->SetValue(buffer);
mol.SetData(dp);
}
// end RWT
if (!strncmp(buffer,"$$$$",4)) break;
}
return(true);
}
bool WriteSDFile(ostream &ofs,OBMol &mol,char *dimension) {
char buff[BUFF_SIZE];
ofs << mol.GetTitle() << endl;
sprintf(buff," -ISIS- %s",dimension);
ofs << buff << endl;
if (mol.HasData(obCommentData))
{
OBCommentData *cd = (OBCommentData*)mol.GetData(obCommentData);
ofs << cd->GetData() << endl;
}
else
ofs << endl;
sprintf(buff,"%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d",
mol.NumAtoms(),mol.NumBonds(),0,0,0,0,0,0,0,0,0);
ofs << buff << endl;
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
int charge;
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) {
switch (atom->GetFormalCharge()) {
case 1: charge = 3; break;
case 2: charge = 2; break;
case 3: charge = 1; break;
case -1: charge = 5; break;
case -2: charge = 6; break;
case -3: charge = 7; break;
default:
charge=0; break;
}
sprintf(buff,"%10.4f%10.4f%10.4f %-3s%2d%3d%3d%3d%3d",
atom->GetX(),
atom->GetY(),
atom->GetZ(),
(etab.GetSymbol(atom->GetAtomicNum())),
0,charge,0,0,0);
ofs << buff << endl;
}
//so the bonds come out sorted
OBAtom *nbr;
OBBond *bond;
vector<OBEdgeBase*>::iterator j;
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
if (atom->GetIdx() < nbr->GetIdx()) {
bond = (OBBond*) *j;
sprintf(buff,"%3d%3d%3d%3d%3d%3d",
bond->GetBeginAtomIdx(),
bond->GetEndAtomIdx(),
(bond->GetBO() == 5) ? 4 : bond->GetBO(),
0/*bond->GetFlag()*/,0,0);
ofs << buff << endl;
}
ofs << "M END" << endl;
// RWT 4/7/2001
// now output properties if they exist
// MTS 4/17/2001
// changed to use new OBGenericData class
vector<OBGenericData*>::iterator k;
vector<OBGenericData*> vdata = mol.GetData();
for (k = vdata.begin();k != vdata.end();k++)
if ((*k)->GetDataType() == obPairData)
{
ofs << "> <" << (*k)->GetAttribute() << ">" << endl;
ofs << ((OBPairData*)(*k))->GetValue() << endl << endl;
}
// end RWT
ofs << "$$$$" << endl;
return(true);
}
}
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