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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