The best bet is *always* to e-mail the list. My suggestion if you're writing
code is to look at what read/write conformers do. :-)
% less src/ops/readconformers.cpp:
…
/*
To use with OBConversion::Read(), etc.
OBMol mol;
vector<OBBase*> vec;
while(pConv->Read(&mol))
vec.push_back(&mol);
OBOp* pOp = OBOp::FindType("readconformers");
if(!pOp)
pOp->ProcessVec(vec);
vec now contains one or more molecules with multiple conformers
*/
…
% less src/obmolecformat.cpp
…
if(pConv->IsOption("writeconformers", OBConversion::GENOPTIONS)) {
//The last conformer is written in the calling function
unsigned int c = 0;
for (; c < pmol->NumConformers()-1; ++c) {
pmol->SetConformer(c);
if(!pConv->GetOutFormat()->WriteMolecule(pmol, pConv))
break;
}
pmol->SetConformer(c);
}
...
Not very hard, and of course you could do something like this:
// Write all conformers in pmol to std::cout
pConv->AddOption("writeconformers",OBConversion::GENOPTIONS);
pConv->Write(pmol, &cout);
Hope that helps,
-Geoff
On May 15, 2013, at 12:50 AM, bm <b...@berkeley.edu> wrote:
> Hello:
>
> I am using OpenBabel to help me generate multiple conformers of one molecule,
> and then using them to calculate spatial fit with another molecule. However,
> I would like to save the conformers to a single file as I run my
> calculations, so that I have a record of the random conformers I have used.
> Is there a way to get OBConversion to read and write multiple conformers of a
> single molecule? I understand that one can do this using the obabel
> program's --readconformer and --writeconformers flags, but I would like to do
> all this in-code; i.e.
>
> // to save conformers
> OBMol *mol = generateConformers();
> mol->NumConformers() // returns value greater than 1
> obconversion->saveMoleculeAndAllConformersToFile();
>
> // later, when I want to revisit my generated conformers
> obconversion->openFile("file")
> obconversion->loadAllConformersInFileToMolecule(mol)
> mol->NumConformers() // returns value greater than 1
>
> I also tried using OpReadConformers to help me, but its churning out an
> incomplete type error on compile...
>
> Any help would be greatly appreciated!
> bm
>
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