So the desired output is 1,2,3,4,5 instead of 3,3,3,4,5?
If so, isn't SetImplicitValence what you are looking for?
>>> mol = pybel.readstring("smi", "[AlH3]").OBMol
>>> mol.DeleteHydrogens()
True
>>> print pybel.Molecule(mol).write("smi")
[AlH3]
>>> print mol.GetAtom(1).GetImplicitValence() # 3
3
>>> mol.GetAtom(1).SetImplicitValence(2)
>>> print pybel.Molecule(mol).write("smi")
[AlH2]
In your example, you were using Begin/EndModify. Unfortunately,
EndModify() unsets ImplicitValencePerceived so that the atom typer is
called again next time a "valence" is requested:
>>> mol.BeginModify()
>>> mol.EndModify()
>>> print pybel.Molecule(mol).write("smi")
[AlH3]
...but never fear, we can override this by adding a
mol.SetImplicitValencePerceived() immediately after the EndModify().
The [AlH2] is then retained.
- Noel
On 20 March 2013 18:20, Craig James <cja...@emolecules.com> wrote:
> Hi Noel,
>
>
>
> On Tue, Mar 19, 2013 at 3:16 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
>>
>> I believe that the key value is the _impval property on an OBAtom,
>> which is assigned by the atomtyper. Can you ask your program to print
>> out the values after the EndModify() using atom->GetImplicitValence()?
>
>
> It looks like your analysis is spot on. Here is output of the program (not
> the original one, this is much simpler, see below):
>
> molecule starts with 4 atoms.
> delete H, idx = 4
> delete H, idx = 3
> delete H, idx = 2
> molecule now has 1 atoms.
> [AlH3]
> add H, idx = 2, molecule now has 2 atoms, _impval = 3
> [AlH3]
> add H, idx = 3, molecule now has 3 atoms, _impval = 3
> [AlH3]
> add H, idx = 4, molecule now has 4 atoms, _impval = 3
> [AlH3]
> add H, idx = 5, molecule now has 5 atoms, _impval = 4
> [AlH4]
> add H, idx = 6, molecule now has 6 atoms, _impval = 5
> [AlH5]
>
> What's the solution? I can't find any method on the atom or bond object
> that will force it to reset its _impval.
>
> Thanks,
> Craig
>
> #include <sstream>
>
> #include <openbabel/babelconfig.h>
> #include <openbabel/mol.h>
> #include <openbabel/obconversion.h>
>
> using namespace std;
> using namespace OpenBabel;
>
> static string test_mol
> (
> "\n"
> " OpenBabel03191316172D\n"
> "\n"
> " 4 3 0 0 0 0 0 0 0 0999 V2000\n"
> " 0.0000 0.0000 0.0000 Al 0 0 0 0 0 0 0 0 0 0 0 0\n"
> " 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
> " 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
> " 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
> " 1 2 1 0 0 0 0\n"
> " 1 3 1 0 0 0 0\n"
> " 1 4 1 0 0 0 0\n"
> "M END\n"
> "$$$$\n"
> );
>
> int main(int argc,char **argv)
> {
> OBAtom *atom;
> vector<OBAtom*> delete_h;
> vector<OBAtom*>::iterator ai;
>
> OBMol *pmol = new OBMol;
> OBConversion conv(&cin, &cout);
> conv.SetInAndOutFormats("sdf", "smi");
>
> pmol->Clear();
> conv.ReadString(pmol, test_mol);
> pmol->BeginModify();
>
> cout << "molecule starts with " << pmol->NumAtoms() << " atoms.\n";
> for (atom = pmol->BeginAtom(ai); atom; atom = pmol->NextAtom(ai)) {
> if (atom->GetAtomicNum() == 1)
> delete_h.push_back(atom);
> }
> for (ai = delete_h.end() - 1; ai >= delete_h.begin(); ai--) {
> atom = *ai;
> cout << "delete H, idx = " << atom->GetIdx() << "\n";
> pmol->DeleteAtom(atom);
> }
> cout << "molecule now has " << pmol->NumAtoms() << " atoms.\n";
> pmol->EndModify();
> conv.Write(pmol);
>
> for (int i = 2; i <= 6; i++) {
> pmol->BeginModify();
> atom = pmol->NewAtom(i);
> atom->SetAtomicNum(1);
> pmol->AddBond(1, i, 1);
> pmol->EndModify();
> cout << "add H, idx = " << i <<", molecule now has "
> << pmol->NumAtoms() << " atoms, _impval = "
> << pmol->GetAtom(1)->GetImplicitValence() << "\n";
> conv.Write(pmol);
> }
> }
>
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
