bool WriteGromos96(ostream &ofs,OBMol &mol,double fac)
{
char type_name[10];
char res_name[10],padded_name[10];
char buffer[BUFF_SIZE];
int res_num;
sprintf(buffer,"#GENERATED BY OPEN BABEL %s",BABEL_VERSION);
ofs << buffer << endl;
/* GROMOS wants a TITLE block, so let's write one*/
sprintf(buffer,"TITLE\n%s\nEND",mol.GetTitle());
ofs << buffer << endl;
ofs << "POSITION" << endl;
OBAtom *atom;
OBResidue *res;
vector<OBNodeBase*>::iterator i;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if (res = atom->GetResidue())
{
strcpy(res_name,(char*)res->GetName().c_str());
strcpy(type_name,(char*)res->GetAtomID(atom).c_str());
res_num = res->GetNum();
}
else
{
strcpy(type_name,etab.GetSymbol(atom->GetAtomicNum()));
strcpy(res_name,"UNK");
sprintf(padded_name,"%2s",type_name);
strcpy(type_name,padded_name);
res_num = 1;
}
sprintf(buffer,"%5d %5s %5s %6d %15.5f %15.5f %15.5f",
res_num,res_name,type_name,atom->GetIdx(),
atom->x()*fac,atom->y()*fac,atom->z()*fac);
ofs << buffer << endl;
if (!(atom->GetIdx()%10))
{
sprintf(buffer,"# %d",atom->GetIdx());
ofs << buffer << endl;
}
}
ofs << "END" << endl;
return(true);
}
void CSRFormat::WriteCSRCoords(ostream &ofs,OBMol &mol)
{
int the_size,jconf;
double x,y,z,energy;
char title[100];
char *tag;
the_size = sizeof(int) + sizeof(double) + (80 * sizeof(char));
jconf = 1;
energy = -2.584565;
snprintf(title, 80, "%s:%d",mol.GetTitle(),MolCount);
tag = PadString(title,80);
WriteSize(the_size,ofs);
ofs.write((char*)&jconf,sizeof(int));
ofs.write((char*)&energy,sizeof(double));
ofs.write(tag,80*sizeof(char));
WriteSize(the_size,ofs);
WriteSize(mol.NumAtoms()*sizeof(double),ofs);
OBAtom *atom;
vector<OBAtom*>::iterator i;
for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
{
x = atom->x();
ofs.write((char*)&x,sizeof(double));
}
WriteSize(mol.NumAtoms()*sizeof(double),ofs);
WriteSize(mol.NumAtoms()*sizeof(double),ofs);
for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
{
y = atom->y();
ofs.write((char*)&y,sizeof(double));
}
WriteSize(mol.NumAtoms()*sizeof(double),ofs);
WriteSize(mol.NumAtoms()*sizeof(double),ofs);
for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
{
z = atom->z();
ofs.write((char*)&z,sizeof(double));
}
WriteSize(mol.NumAtoms()*sizeof(double),ofs);
delete [] tag;
}
bool CacaoFormat::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;
OBAtom *atom;
char buffer[BUFF_SIZE];
vector<OBAtom*>::iterator i;
snprintf(buffer, BUFF_SIZE, "%s\n",mol.GetTitle());
ofs << buffer;
snprintf(buffer, BUFF_SIZE, "%3d DIST 0 0 0\n",mol.NumAtoms());
ofs << buffer;
if (!mol.HasData(OBGenericDataType::UnitCell))
ofs << "CELL 1.,1.,1.,90.,90.,90.\n";
else
{
OBUnitCell *uc = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
snprintf(buffer, BUFF_SIZE, "CELL %f,%f,%f,%f,%f,%f\n",
uc->GetA(), uc->GetB(), uc->GetC(),
uc->GetAlpha(), uc->GetBeta(), uc->GetGamma());
ofs << buffer;
}
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
snprintf(buffer,BUFF_SIZE,"%2s %7.4f, %7.4f, %7.4f\n",
etab.GetSymbol(atom->GetAtomicNum()),
atom->x(),
atom->y(),
atom->z());
ofs << buffer;
}
return(true);
}
bool WriteFeat(ostream &ofs,OBMol &mol)
{
char buffer[BUFF_SIZE];
ofs << mol.NumAtoms() << endl;
ofs << mol.GetTitle() << endl;
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
sprintf(buffer,"%-3s %8.5f %8.5f %8.5f ",
etab.GetSymbol(atom->GetAtomicNum()),
atom->x(),
atom->y(),
atom->z());
ofs << buffer << endl;
}
return(true);
}
//copy data needed to write out pmol from obmol
void PMolCreator::copyFrom(OBMol& mol, bool deleteH)
{
static OBIsotopeTable isotable;
name = mol.GetTitle();
//first construct atoms
int typeindex[256]; //position in atoms vector of an atom type, indexed by atomic number
int tmpatomindex[mol.NumAtoms()]; //position within the atom type vector
memset(typeindex, -1, sizeof(typeindex));
memset(tmpatomindex, -1, sizeof(tmpatomindex));
for (OBAtomIterator aitr = mol.BeginAtoms(); aitr != mol.EndAtoms(); ++aitr)
{
OBAtom *atom = *aitr;
unsigned int idx = atom->GetIdx();
unsigned anum = atom->GetAtomicNum();
assert(anum < 256);
if(deleteH && anum == 1)
continue;
int pos = typeindex[anum];
if (pos < 0) // no vector for this type yet
{
pos = typeindex[anum] = atoms.size();
atoms.push_back(AtomGroup(anum));
}
tmpatomindex[idx] = atoms[pos].coords.size();
atoms[pos].coords.push_back(FloatCoord(atom->x(), atom->y(), atom->z()));
}
//create mapping to actual atom index
numAtoms = 0;
BOOST_FOREACH(AtomGroup& ag, atoms)
{ ag.startIndex = numAtoms;
numAtoms += ag.coords.size();
}
bool GROMOS96Format::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 fac = pConv->IsOption("n") ? 0.1 : 1.0; //new framework
char type_name[16];
char res_name[16];
char buffer[BUFF_SIZE];
string res_num;
snprintf(buffer, BUFF_SIZE, "#GENERATED BY OPEN BABEL %s\n",BABEL_VERSION);
ofs << buffer;
/* GROMOS wants a TITLE block, so let's write one*/
ofs << "TITLE\n" << mol.GetTitle() << "\nEND\n";
ofs << "POSITION\n";
OBAtom *atom;
OBResidue *res;
vector<OBAtom*>::iterator i;
for(atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if ( (res = atom->GetResidue()) )
{
// 16 = sizeof(res_name) and sizeof(type_name)
strncpy(res_name,(char*)res->GetName().c_str(), 16);
res_name[15] = '\0';
strncpy(type_name,(char*)res->GetAtomID(atom).c_str(), 16);
type_name[15] = '\0';
res_num = res->GetNumString();
}
else
{
strncpy(type_name,OBElements::GetSymbol(atom->GetAtomicNum()), 16);
strcpy(res_name,"UNK");
res_num = "1";
}
snprintf(buffer, BUFF_SIZE, "%5s %5s %5s %6d %15.5f %15.5f %15.5f\n",
res_num.c_str(),res_name,type_name,atom->GetIdx(),
atom->x()*fac,atom->y()*fac,atom->z()*fac);
ofs << buffer;
if (!(atom->GetIdx()%10))
{
snprintf(buffer, BUFF_SIZE, "# %d\n",atom->GetIdx());
ofs << buffer;
}
}
ofs << "END\n";
return(true);
}
bool BoxFormat::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;
//margin hardwired in new framework. Also was in old fileformat
double margin=1.0;
char buffer[BUFF_SIZE];
vector3 vcenter,vmin,vmax,vmid,vdim;
OBAtom *atom;
vector<OBAtom*>::iterator i;
vmax.Set(-10E10,-10E10,-10E10);
vmin.Set( 10E10, 10E10, 10E10);
for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
{
vcenter += atom->GetVector();
if (atom->x() < vmin.x())
vmin.SetX(atom->x());
if (atom->y() < vmin.y())
vmin.SetY(atom->y());
if (atom->z() < vmin.z())
vmin.SetZ(atom->z());
if (atom->x() > vmax.x())
vmax.SetX(atom->x());
if (atom->y() > vmax.y())
vmax.SetY(atom->y());
if (atom->z() > vmax.z())
vmax.SetZ(atom->z());
}
vcenter /= (double)mol.NumAtoms();
vector3 vmarg(margin,margin,margin);
vmin -= vmarg;
vmax += vmarg;
vdim = vmax - vmin;
vmid = vmin+vmax;
vmid /= 2.0;
ofs << "HEADER CORNERS OF BOX" << endl;
snprintf(buffer, BUFF_SIZE, "REMARK CENTER (X Y Z) %10.3f %10.3f %10.3f",
vmid.x(),vmid.y(),vmid.z());
ofs << buffer << endl;
snprintf(buffer, BUFF_SIZE, "REMARK DIMENSIONS (X Y Z) %10.3f %10.3f %10.3f",
vdim.x(),vdim.y(),vdim.z());
ofs << buffer << endl;
vdim /= 2.0;
vector3 vtmp;
int j;
for (j = 1; j <= 8; j++)
{
switch(j)
{
case 1:
vtmp = vmid-vdim;
break;
case 2:
vtmp.SetX(vmid.x()+vdim.x());
break;
case 3:
vtmp.SetZ(vmid.z()+vdim.z());
break;
case 4:
vtmp.SetX(vmid.x()-vdim.x());
break;
case 5:
vtmp = vmid-vdim;
vtmp.SetY(vmid.y()+vdim.y());
break;
case 6:
vtmp = vmid+vdim;
vtmp.SetZ(vmid.z()-vdim.z());
break;
case 7:
vtmp = vmid+vdim;
break;
case 8:
vtmp.SetX(vmid.x()-vdim.x());
break;
}
snprintf(buffer, BUFF_SIZE, "ATOM %d DUA BOX 1 %8.3f%8.3f%8.3f",
j,vtmp.x(),vtmp.y(),vtmp.z());
ofs << buffer << endl;
}
ofs << "CONECT 1 2 4 5" << endl;
ofs << "CONECT 2 1 3 6" << endl;
ofs << "CONECT 3 2 4 7" << endl;
ofs << "CONECT 4 1 3 8" << endl;
ofs << "CONECT 5 1 6 8" << endl;
ofs << "CONECT 6 2 5 7" << endl;
ofs << "CONECT 7 3 6 8" << endl;
ofs << "CONECT 8 4 5 7" << endl;
return(true);
}
int main(int argc,char *argv[])
{
// turn off slow sync with C-style output (we don't use it anyway).
std::ios::sync_with_stdio(false);
OBConversion conv;
OBFormat *inFormat, *canFormat;
OBMol mol;
ifstream ifs;
vector<OBMol> fragments;
unsigned int fragmentCount = 0; // track how many in library -- give a running count
map<string, int> index; // index of cansmi
string currentCAN;
unsigned int size;
OBAtom *atom;
OBBond *bond;
bool nonRingAtoms, nonRingBonds;
char buffer[BUFF_SIZE];
canFormat = conv.FindFormat("can");
conv.SetOutFormat(canFormat);
if (argc < 2)
{
cout << "Usage: obfragment <file>" << endl;
return(-1);
}
for (int i = 1; i < argc; i++) {
cerr << " Reading file " << argv[i] << endl;
inFormat = conv.FormatFromExt(argv[i]);
if(inFormat==NULL || !conv.SetInFormat(inFormat))
{
cerr << " Cannot read file format for " << argv[i] << endl;
continue; // try next file
}
ifs.open(argv[i]);
if (!ifs)
{
cerr << "Cannot read input file: " << argv[i] << endl;
continue;
}
while(ifs.peek() != EOF && ifs.good())
{
conv.Read(&mol, &ifs);
if (!mol.Has3D()) continue; // invalid coordinates!
mol.DeleteHydrogens(); // remove these before we do anything else
do {
nonRingAtoms = false;
size = mol.NumAtoms();
for (unsigned int i = 1; i <= size; ++i)
{
atom = mol.GetAtom(i);
if (!atom->IsInRing()) {
mol.DeleteAtom(atom);
nonRingAtoms = true;
break; // don't know how many atoms there are
}
// Previously, we changed atoms to carbon here.
// Now we perform this alchemy in terms of string-rewriting
// once the canonical SMILES is generated
}
} while (nonRingAtoms);
if (mol.NumAtoms() < 3)
continue;
if (mol.NumBonds() == 0)
continue;
do {
nonRingBonds = false;
size = mol.NumBonds();
for (unsigned int i = 0; i < size; ++i)
{
bond = mol.GetBond(i);
if (!bond->IsInRing()) {
mol.DeleteBond(bond);
nonRingBonds = true;
break; // don't know how many bonds there are
}
}
} while (nonRingBonds);
fragments = mol.Separate();
for (unsigned int i = 0; i < fragments.size(); ++i)
{
if (fragments[i].NumAtoms() < 3) // too small to care
continue;
currentCAN = conv.WriteString(&fragments[i], true);
currentCAN = RewriteSMILES(currentCAN); // change elements to "a/A" for compression
if (index.find(currentCAN) != index.end()) { // already got this
index[currentCAN] += 1; // add to the count for bookkeeping
continue;
}
index[currentCAN] = 1; // don't ever write this ring fragment again
// OK, now retrieve the canonical ordering for the fragment
vector<string> canonical_order;
if (fragments[i].HasData("Canonical Atom Order")) {
OBPairData *data = (OBPairData*)fragments[i].GetData("Canonical Atom Order");
tokenize(canonical_order, data->GetValue().c_str());
}
// Write out an XYZ-style file with the CANSMI as the title
cout << fragments[i].NumAtoms() << '\n';
cout << currentCAN << '\n'; // endl causes a flush
vector<string>::iterator can_iter;
unsigned int order;
OBAtom *atom;
fragments[i].Center();
fragments[i].ToInertialFrame();
for (unsigned int index = 0; index < canonical_order.size();
++index) {
order = atoi(canonical_order[index].c_str());
atom = fragments[i].GetAtom(order);
snprintf(buffer, BUFF_SIZE, "C%8.3f%8.3f%8.3f\n",
atom->x(), atom->y(), atom->z());
cout << buffer;
}
}
fragments.clear();
if (index.size() > fragmentCount) {
fragmentCount = index.size();
cerr << " Fragments: " << fragmentCount << endl;
}
} // while reading molecules (in this file)
ifs.close();
ifs.clear();
} // while reading files
// loop through the map and output frequencies
map<string, int>::const_iterator indexItr;
for (indexItr = index.begin(); indexItr != index.end(); ++indexItr) {
cerr << (*indexItr).second << " INDEX " << (*indexItr).first << "\n";
}
return(0);
}
//computes a set of solitary grid points that represent the interaction between
//this ligand and the provided receptor in some way
void OBAMolecule::computeInteractionGridPoints(OBAMolecule& receptor,
MGrid& grid, double interactionDist,
double maxClusterDist,
unsigned minClusterPoints, double interactionPointRadius)
{
grid.clear();
//first construct a bounding box for the ligand while assembling a
//vector of atomic coordinates
BoundingBox ligandBox;
vector<AtomPoint> points;
points.reserve(mol.NumAtoms());
for (OBAtomIterator aitr = mol.BeginAtoms(); aitr != mol.EndAtoms(); ++aitr)
{
OBAtom* atom = *aitr;
points.push_back(AtomPoint(atom->x(), atom->y(), atom->z()));
ligandBox.update(atom->x(), atom->y(), atom->z());
}
ligandBox.extend(interactionDist);
//then identify all coordinates that are interacting
double idistSq = interactionDist * interactionDist;
OBMol& rmol = receptor.getMol();
for (OBAtomIterator aitr = rmol.BeginAtoms(); aitr != rmol.EndAtoms();
++aitr)
{
OBAtom* a = *aitr;
if (ligandBox.contains(a->x(), a->y(), a->z()))
{
for (unsigned i = 0, n = points.size(); i < n; i++)
{
if (points[i].distSq(a->x(), a->y(), a->z()) <= idistSq)
{
points[i].interactingCnt++;
}
}
}
}
//prune out non-interacting poitns
vector<AtomPoint> tmp;
tmp.reserve(points.size());
for (unsigned i = 0, n = points.size(); i < n; i++)
{
if (points[i].interactingCnt > 0)
tmp.push_back(points[i]);
}
points.swap(tmp);
tmp.clear();
//cluster these coordinates
vector<vector<unsigned> > clusters;
clusterPoints(points, maxClusterDist, clusters);
//make the cluster centers the interaction grid points
for (unsigned i = 0, n = clusters.size(); i < n; i++)
{
double xtot = 0, ytot = 0, ztot = 0;
unsigned npts = clusters[i].size();
if (npts >= minClusterPoints)
{
for (unsigned j = 0; j < npts; j++)
{
xtot += points[clusters[i][j]].x;
ytot += points[clusters[i][j]].y;
ztot += points[clusters[i][j]].z;
}
double xave = xtot / (double) npts;
double yave = ytot / (double) npts;
double zave = ztot / (double) npts;
grid.setPoint(xave, yave, zave);
if(interactionPointRadius > 0)
{
grid.markXYZSphere(xave,yave,zave,interactionPointRadius);
}
}
}
}