Hi everyone,
As some one asked today about the Multiple conformations in one molecule, I
thought I would give it a crack, I've managed to get the conformations in to
one molecule (with what looks like a memory leak, that I can't seem to shift)
but I can't seem to write them back out again, I think the issue is with
conformer ids however I can't find any neat way of returning the conformer ids.
I has a look through the source and couldn't find too much, I had a check to
see if I could store them in the function, but the ids seem to be the same, so
I'm a little confused. Source is below...
With regards to the memory leak, this is poor programming not an RDKit issue,
anyone know why I can't seem to delete the ROMol mol? The compiler throws up an
error when I do. Is this even a memory leak or is the memory being sucked up by
the conformations, because it seems like a lot.
It was nice to meet you all and hear some excellent talks.
#include <iostream>
#include <string>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/Conformer.h>
using namespace std;
using namespace RDKit;
ROMol *SDConfSupplier(string);
int main(int argc, char *argv []){
ROMol *mol;
mol= SDConfSupplier(argv[1]); //takes first argument as the input file
SDWriter writer("out.txt");
cout << mol->getNumConformers() << endl;
for(int i=0; i<mol->getNumConformers(); ++i){
writer.write(*mol,i);
}
return 0;
}
ROMol* SDConfSupplier(string filename){
SDMolSupplier suppl(filename);
ROMol *res=0;
res = suppl.next();
while(!suppl.atEnd()){
ROMol *mol;
unsigned short resNumAtoms=res->getNumAtoms(), confNumAtoms=0;
try{
mol= suppl.next();
confNumAtoms = mol->getNumAtoms();
if(confNumAtoms!= resNumAtoms){
cerr << "Number of atoms in conformer incorrect\n";
exit(0);
}
Conformer *conf = &(mol->getConformer(0));
res->addConformer(conf, true);
delete conf;
} catch(...){
continue;
}
//delete mol;
}
return res;
}
Best,
Nick
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
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