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()?
- Noel
On 19 March 2013 22:12, Noel O'Boyle <baoille...@gmail.com> wrote:
> I haven't looked into the details of your code (but I will if no-one
> else does), but regarding the relationship between different things,
> you may find the following notes I have made useful:
>
> In the Open Babel world, the "valence" methods of an atom refer to the
> number of bonds, rather than the sum of BOs (which is actual valence).
> In other words, they (a) are misnamed, and (b) our _impval should not
> be the underlying key data structure.
>
> GetValence() -> Num explicit bonds
> GetImplicitValence() -> Num explicit bonds plus num implicit bonds
> (i.e. total number of bonds) (_impval property on OBAtom)
> GetHvyAtomValence() -> Num explicit bonds to non-H atoms
>
> To find the number of implicit Hs, GetImplicitValence() - GetValence()
>
> BOSum() -> The sum of the BOs of explicit bonds (otherwise known as
> ExplicitValence)
>
> To find the actual valence: BOSum() + GetImplicitHydrogenCount()
>
> - Noel
>
> On 19 March 2013 19:08, Craig James <cja...@emolecules.com> wrote:
>> Below is a test program, highly stripped down, that illustrates a problem I
>> can't figure out. The idea is to find ions that are neutral and show them
>> with a charge (don't worry about the chemistry behind this; this is highly
>> stripped down from the real code and just illustrates the inconsistency).
>> When I run it, I get this:
>>
>> [BH3+3]
>> [Li+]
>> [Na+]
>> [K+]
>> [Be+2]
>> [Mg+2]
>> [Ca+2]
>> [AlH3+3]
>> [SiH4+4]
>> [Fe+2]
>>
>> Note that B, Si, and Fe don't lose their hydrogens, whereas all the others
>> do ... in spite of the fact that the program explicitely removes all H atoms
>> and resets the "valence perceived" flag.
>>
>> Digging through smilesformat.cpp, atom.cpp, the typer and so forth, I'm
>> completely baffled as to what's going on. (If anyone ever had time to
>> document the relationship and "synonym-ness" between bond order, number of
>> bonds, valence, implicit valence, charge, hydrogen count, and spin
>> multiplicity, that would sure be helpful!)
>>
>> I compiled this on Linux using:
>>
>> g++ -g -I/usr/local/openbabel/include/openbabel-2.0 -D_GNU_SOURCE \
>> -L/usr/local/openbabel/lib -lopenbabel -ldl -o foo foo.cpp
>>
>> 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_smiles[] = {"[BH3]", "[LiH]", "[NaH]", "[KH]", "[BeH]",
>> "[MgH2]", "[CaH2]", "[AlH3]", "[SiH4]", "[FeH2]"};
>> #define NSMILES (sizeof(test_smiles) / sizeof(string))
>>
>> static void remove_explicit_hydrogen(OBMol *pmol)
>> {
>> OBAtom *atom;
>> vector<OBNodeBase*> delete_h;
>> vector<OBNodeBase*>::iterator ai;
>>
>> for (atom = pmol->BeginAtom(ai); atom; atom = pmol->NextAtom(ai)) {
>> if (atom->GetAtomicNum() == 1)
>> delete_h.push_back(atom);
>> }
>> for (ai = delete_h.begin(); ai != delete_h.end(); ai++)
>> pmol->DeleteHydrogen((OBAtom*)*ai);
>> }
>>
>> int main(int argc,char **argv)
>> {
>> OBMol *pmol = new OBMol;
>> OBConversion conv(&cin, &cout);
>> conv.SetInAndOutFormats("smi", "smi");
>>
>> for (int i = 0; i < NSMILES; i++) {
>> pmol->Clear();
>> pmol->SetTitle("");
>> conv.ReadString(pmol, test_smiles[i]);
>>
>> if (pmol->Empty()) {
>> cerr << "Couldn't read SMILES: '" << test_smiles[i] << "'\n";
>> continue;
>> }
>> pmol->BeginModify();
>> remove_explicit_hydrogen(pmol);
>> OBAtom *a = pmol->GetAtom(1);
>>
>> int anum = a->GetAtomicNum();
>> int pos_charge = 0;
>> switch (anum) {
>> case 3: case 11: case 19: pos_charge = 1; break; // +1 - Li, Na, K
>> case 4: case 12: case 20: pos_charge = 2; break; // +2 - Be, Mg, Ca
>> case 26: pos_charge = 2; break; // +2 - Fe
>> case 5: case 13: pos_charge = 3; break; // +3 - B, Al
>> case 14: pos_charge = 4; break; // +4 - Si
>> }
>> a->SetFormalCharge(pos_charge);
>> pmol->UnsetImplicitValencePerceived();
>> atomtyper.AssignImplicitValence(*pmol);
>> pmol->EndModify();
>>
>> conv.Write(pmol);
>> }
>> }
>>
>>
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