Hello, I have been working in a format for openbabel. I can compile, install and run the plugin. The format is http://www.lpmd.cl/index.php/documentation/the-lpmd-format
My problem is that the plugin run fine, for one molecule, but for multiple
molecules, this doesn't work fine ... or at least I think so. I build my
plugins based on the xyzformat.cpp and the exampleformat.cpp.
For example I have a xyz file with two configs :
$ cat test.xyz
2
AA
Si 0 0 0
Si 5 0 0
2
BB
Si 0 0 1
Si 0 5 0
So I can convert the xyz to a pdb using :
$ obabel -ixyz test.xyz -opdb -Otest.pdb
2 molecules converted
But when I run with my format (example attached here) :
$ obabel -ilpmd multiconfig.lpmd -opdb -Omulticonfig.pdb
1 molecule converted
jperaltac@baco:~/Projects/lpmd/06/lpmd/examples/lpmd-format$
However the mentioned above, I can do this :
$obabel multiconfig.lpmd -Otest*.pdb
5 molecules converted
5 files output. The first is test1.pdb
So, I don't understand why I can't convert directly in one single file. The
ReadMolecule method is :
bool LpmdFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if(pmol==NULL) return false;
N=0;
std::istream &ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
if(!ifs) return false;
//read the header only once.
if(file_line==0)
{
if ( ! ReadHeader( ifs, mol ) ) return false;
}
std::stringstream ErrMsg;
//Read the cell vectors.
double ax=0.0e0,ay=0.0e0,az=0.0e0;
double bx=0.0e0,by=0.0e0,bz=0.0e0;
double cx=0.0e0,cy=0.0e0,cz=0.0e0;
//Reading the number of atoms.
ifs.getline(buffer,BUFF_SIZE);
file_line++;
tokenize(tokens, buffer, " ");
if(tokens.size()!=1)
{
obErrorLog.ThrowError(__FUNCTION__,"The number of atoms line was not
correctly readed",obError);
}
from_string<int>(N, tokens.at(0), std::dec);
tokens.clear();
ifs.getline(buffer,BUFF_SIZE);
file_line++;
tokenize(tokens, buffer, " ");
line=buffer;
from_string<double>(ax, tokens.at(0), std::dec);
from_string<double>(ay, tokens.at(1), std::dec);
from_string<double>(az, tokens.at(2), std::dec);
from_string<double>(bx, tokens.at(3), std::dec);
from_string<double>(by, tokens.at(4), std::dec);
from_string<double>(bz, tokens.at(5), std::dec);
from_string<double>(cx, tokens.at(6), std::dec);
from_string<double>(cy, tokens.at(7), std::dec);
from_string<double>(cz, tokens.at(8), std::dec);
vector3 vx = vector3(ax,ay,az);
vector3 vy = vector3(bx,by,bz);
vector3 vz = vector3(cx,cy,cz);
// Add the Unit Cell to the molecule
OBUnitCell * unitcell = new OBUnitCell();
unitcell->SetData( vx, vy, vz );
mol.BeginModify();
mol.SetData( unitcell );
/** Parse the input stream and use the OpenBabel API to populate the OBMol
**/
for(int i=0 ; i<N ; ++i)
{
OBAtom *atom = mol.NewAtom();
ifs.getline(buffer,BUFF_SIZE);
file_line++;
line = buffer;
tokenize(tokens, buffer, " ");
if(int(headers.size()-1)!=tokens.size())
{
ErrMsg << "There was a problem reading an atomic configuration, "
<< "the line # " << file_line << " doesn't have the number "
<< "of columns indicated in the HDR (second line). ";
obErrorLog.ThrowError(__FUNCTION__, ErrMsg.str(), obError);
}
double X=0.0,Y=0.0,Z=0.0;
std::string symbol = "Xx";
for(int i=1 ; i < headers.size() ; ++i) //the first element is HDR
{
//Basic information position and atomic symbol.
if(headers.at(i).compare("X")==0) from_string<double>(X, tokens.at(i-1),
std::dec);
if(headers.at(i).compare("Y")==0) from_string<double>(Y, tokens.at(i-1),
std::dec);
if(headers.at(i).compare("Z")==0) from_string<double>(Z, tokens.at(i-1),
std::dec);
if(headers.at(i).compare("SYM")==0) symbol = tokens.at(i-1);
}
atom->SetVector(X,Y,Z);
int atomicNum = etab.GetAtomicNum(symbol.c_str());
atom->SetAtomicNum(atomicNum);
}
if (!pConv->IsOption("b",OBConversion::INOPTIONS))
mol.ConnectTheDots();
if (!pConv->IsOption("s",OBConversion::INOPTIONS) &&
!pConv->IsOption("b",OBConversion::INOPTIONS))
mol.PerceiveBondOrders();
mol.EndModify();
return true;
}
What could be the problem?
On the other hand, when I feel confident with the plugin, I have to submit
using subversion, or I'll need to e-mail this to someone?
Any help is welcome.
Best Regards
Joaquin Peralta
--
Joaquín Peralta C.
Postdoctoral Research Associate
Materials Science and Engineering
Iowa State University
3326 Hoover Hall
Ames, IA 50011
Phone Lab: 515-294-9547
http://www.lpmd.cl/jperalta
http://www.gnm.cl
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multiconfig.lpmd
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