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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