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src/formats/pqrformat.cpp: Add write support (copied from pdbformat) and
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add atom radii.
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@timvdm
timvdm committed Jan 20, 2009
1 parent 0f6eaa7 commit 06628fb
Showing 1 changed file with 183 additions and 3 deletions.
186 changes: 183 additions & 3 deletions src/formats/pqrformat.cpp
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Expand Up @@ -51,9 +51,9 @@ namespace OpenBabel
//*** This section identical for most OBMol conversions ***
////////////////////////////////////////////////////
/// The "API" interface functions
virtual int SkipObjects(int n, OBConversion* pConv);
virtual int SkipObjects(int n, OBConversion* pConv);
virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv);
// virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);
virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv);

};
//***
Expand All @@ -68,7 +68,7 @@ namespace OpenBabel
double ParseAtomCharge(char *, OBMol &);
double ParseAtomRadius(char *, OBMol &);
/////////////////////////////////////////////////////////////////
int PQRFormat::SkipObjects(int n, OBConversion* pConv)
int PQRFormat::SkipObjects(int n, OBConversion* pConv)
{
if (n == 0)
++ n;
Expand Down Expand Up @@ -211,4 +211,184 @@ namespace OpenBabel
return 0.0;
}

bool PQRFormat::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;

// 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] = '\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());
//snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d %8.3f%8.3f%8.3f 1.00 0.00 %2s \n",
snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d %8.3f%8.3f%8.3f %11.8f%8.3f %2s \n",
het?"HETATM":"ATOM ",
i,
type_name,
the_res,
the_chain,
res_num,
atom->GetX(),
atom->GetY(),
atom->GetZ(),
atom->GetPartialCharge(),
etab.GetVdwRad(atom->GetAtomicNum()),
element_name);
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);
}


} //namespace OpenBabel

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