Hi Eric,
some time ago, I wrote a method to append one molecule to another. You might be
able to adapt that method by creating an empty molecule and adding the atoms and
bonds you want to it. At the beginning, I had the same problems with bonds and
atom types not being correct but it's working now, at least printing out the
internal file format shows perfect agreement.
I did not manage to copy the bonds directly as you try right now. This is
probably because the bond directly points to the atoms (i.e., the data
structure) it connects, but since you're creating new atoms (new instances of
the type OBAtom) you'd be re-creating an already existing bond instead of
creating a new bond between those newly created atoms which messes up the
bond-order and the likes since the atoms the bond points to are not part of your
new molecule.
Here's the source after changing some bits to better fit your use case (not
tested directly but should work, please excuse typos):
void OBMol::AppendMolecule(const OBMol &source)
{
OBMol &src = (OBMol &)source;
vector<OBAtom*>::iterator i;
vector<OBBond*>::iterator j;
OBAtom *atom, *a;
OBBond *bond;
unsigned int at_count=1;
unsigned int begin_atom_idx, end_atom_idx, order, flags;
_vatom.reserve(src.NumAtoms());
_atomIds.reserve(src.NumAtoms());
_vbond.reserve(src.NumBonds());
_bondIds.reserve(src.NumBonds());
for (atom = src.BeginAtom(i);atom;atom = src.NextAtom(i))
{
AddAtom(*atom,true);
a=GetAtom(at_count);
a->Duplicate(atom);
++at_count;
}
for (bond = src.BeginBond(j);bond;bond = src.NextBond(j))
{
begin_atom_idx=bond->GetBeginAtomIdx();
end_atom_idx=bond->GetEndAtomIdx();
order=bond->GetBondOrder();
flags=bond->GetFlags();
AddBond(begin_atom_idx, end_atom_idx, order, flags, -1);
}
}
Again, you'd be using this by creating an empty molecule and adding all the
atoms and bond in the residue to your empty molecule by calling the above method
(or some variant of it). The important bit probably is the lower for-loop that
copies the bonds over by using each atom's Idx, the proper bond-order and flags.
You probably have to adjust the each atom's Idx properly since the original Idx
might not be the same as in your new molecule.
Hope this helps,
Torsten
PS: Sorry if it's the wrong name, I was a bit confused by your saying "Eric" in
combination with your email address.
> Dear all,
>
> I want to create a new OBMol object for the ligand within a protein-ligand
> complex.
> The atoms can be copied successfully, but I have some trouble with the
> bonds.
>
> Since the residue name (ATP for example), residue number and chain id of
> the ligand are known, I iterate all the atoms of the complex and insert the
> selected ones into a new OBMol.
>
> Codes:
> - - -
> void CopySelected(OBMol& new_mol, OBMol select_from, char selected_chain,
> string selected_resn, unsigned int selected_res_num)
> {
> OBAtom *atom;
> OBResidue *res;
>
> FOR_ATOMS_OF_MOL(atom, select_from) {
> res = atom->GetResidue(true);
>
> string resn = res->GetName();
> int res_num = res->GetNum();
> char chain = res->GetChain();
>
> if ((resn == selected_resn)
> && (res_num == selected_res_num)
> && (chain == selected_chain)) {
>
> bool is_success = new_mol.InsertAtom((*atom));
>
> for (auto bond_itr = atom->BeginBonds();
> bond_itr != atom->EndBonds();
> bond_itr++) {
> new_mol.AddBond(*(*bond_itr));
> }
> }
> }
> }
> - - -
>
> However, when the new molecule is written into sdf or mol2 format, some of
> the bonds are missing; the atom types are incorrect in mol2 file.
>
> Is there any established method to create a new molecule from part of the
> existing one while maintaining *all *the information? How can I improve my
> function here?
>
> Thanks!
>
>
> Eric
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