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Build a pdb molecule. problem to provide the atoms name

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Build a pdb molecule. problem to provide the atoms name

ivan.petit

Hi,


I’m trying to write a pdb file by using OBMol, OBAtom,... class in c++.

I only have a problem to define the name of the atoms. I need to choice myself there names.


For this I use SetType of OBAtom :


OBAtom *Atom;

Atom→SetType(NewName[i]); // NewName[i] is a string


The command Atom→GetType() works well and return the good name but nothing is written in the pdb file at the place of atom name ( column 3 ). Thus I think that SetType is not the attribute used to put the name of the atom in the pdb format.

How does work the attribution of the atom name in the pdb format? What should I do to provide the name of the atom and write well the column 3 of the pdb file ?


Greetings, Ivan


OBMol mol;

OBFormat *format;

OBConversion conv;

conv.SetOutFormat("pdb");

mol.BeginModify()

for (int i=0;i<ResiduIndex.size();i++)

{

item=i;

if ( std::find(atom.begin(), atom.end(), item) != atom.end() )

{

}

else

{

OBAtom *Atom;

OBResidue *Residu;

Residu=mol.NewResidue();

Atom=mol.NewAtom();

atom.push_back(i);

countAtom++;

countResidu++;

Atom->SetResidue(Residu);

Atom->SetType(NewName[i]);

Residu->SetName(AtomInResidu[i]);

Residu->SetNum(countResidu);

Atom->SetVector(coord[stepInitial][i][0],coord[stepInitial][i][1],coord[stepInitial][i][2]);

cout << Atom->GetIdx() << " " << Atom->GetType() << " " << Residu->GetName() << " " << Residu->GetIdx() << " " << Atom->GetVector() << endl ;

}

mol.EndModify();

conv.Write(&mol,&monFlux);


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Re: Build a pdb molecule. problem to provide the atoms name

David Hall
Residue->SetAtomId(atom, string)




-David

On Nov 18, 2016, at 8:27 AM, ivan petit <[hidden email]> wrote:

Hi,


I’m trying to write a pdb file by using OBMol, OBAtom,... class in c++.

I only have a problem to define the name of the atoms. I need to choice myself there names.


For this I use SetType of OBAtom :


OBAtom *Atom;

Atom→SetType(NewName[i]); // NewName[i] is a string


The command Atom→GetType() works well and return the good name but nothing is written in the pdb file at the place of atom name ( column 3 ). Thus I think that SetType is not the attribute used to put the name of the atom in the pdb format.

How does work the attribution of the atom name in the pdb format? What should I do to provide the name of the atom and write well the column 3 of the pdb file ?


Greetings, Ivan


OBMol mol;

OBFormat *format;

OBConversion conv;

conv.SetOutFormat("pdb");

mol.BeginModify()

for (int i=0;i<ResiduIndex.size();i++)

{

item=i;

if ( std::find(atom.begin(), atom.end(), item) != atom.end() )

{

}

else

{

OBAtom *Atom;

OBResidue *Residu;

Residu=mol.NewResidue();

Atom=mol.NewAtom();

atom.push_back(i);

countAtom++;

countResidu++;

Atom->SetResidue(Residu);

Atom->SetType(NewName[i]);

Residu->SetName(AtomInResidu[i]);

Residu->SetNum(countResidu);

Atom->SetVector(coord[stepInitial][i][0],coord[stepInitial][i][1],coord[stepInitial][i][2]);

cout << Atom->GetIdx() << " " << Atom->GetType() << " " << Residu->GetName() << " " << Residu->GetIdx() << " " << Atom->GetVector() << endl ;

}

mol.EndModify();

conv.Write(&mol,&monFlux);

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