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);
}
}
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