Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet

[Evgueni K. <eko...@gm...>]

Thanks Greg - this is works.
Another question:
Can you please provide an example of use MolOps::getDistanceMat with the
samples how to extract distance data from this matrix

Regards,
Evgueni

2008/8/17 Greg Landrum <gre...@gm...>

> Dear Evgueni,
>
> > 2008/8/17 Evgueni Kolossov <eko...@gm...>
> >>
> >> Thanks Greg,
> >>
> >> But this is not enough:
> >>
> >> unsigned int minRingSize=ringInfo->
> >>>
> >>> minAtomRingSize(atomIdx);
> >>> for(VECT_INT_VECT_CI ringIt=ringInfo->atomRings().begin();
> >>>    ringIt!=ringInfo->atomRings().end();++ringIt){
> >>>  if(ringIt->size()==minRingSize){
> >>>    if(std::find(ringIt->begin(),ringIt->end(),atomIdx)!=ringIt->end()){
> >>>      // our atom is in this ring; do something
> >>>    }
> >>>  }
> >>>  }
> >>> }
> >>
> >> In this case we got an iterator (ringIt) which is itself a vector (if I
> am
> >> right) of Ring atoms.
>
> It's a vector of ring atom indices. You can use these to get the
> corresponding atoms from the molecule.
>
> >> So to do something with atoms  inside this ring we need somehow iterate
> >> through the atoms...
> >> Can you show how to do this?
> >> I have tried to do it this way:
> >> for (unsighed int i=0; i<minRingSize; i++)
> >> {
> >>     RDKit::Atom * pAtom = mol.getAtomWithIdx(ringIt[i]) ;
> >>     ..........
> >> }
> >> but this is not working.
>
> Here's a sample that is actually tested. It's now part of the getting
> started in C++ sample code. We loop over all atom rings, then grab
> each atom in the 5-rings and test to see if it's aromatic.
> I think this, combined with the earlier stuff I posted, should get you
> started:
>
> ---------------
>  mol=SmilesToMol("C1CC2=C(C1)C1=C(NC3=C1C=CC=C3)C=C2");
>  ringInfo = mol->getRingInfo();
>  atomRings=ringInfo->atomRings();
>
>  unsigned int nMatchingAtoms=0;
>  for(VECT_INT_VECT_CI ringIt=atomRings.begin();
>      ringIt!=atomRings.end();++ringIt){
>    if(ringIt->size()!=5){
>      continue;
>    }
>    bool isAromatic=true;
>    for(INT_VECT_CI atomIt=ringIt->begin();
>        atomIt!=ringIt->end();++atomIt){
>      if(!mol->getAtomWithIdx(*atomIt)->getIsAromatic()){
>        isAromatic=false;
>        break;
>      }
>    }
>    if(isAromatic){
>      nMatchingAtoms+=5;
>    }
>  }
>  TEST_ASSERT(nMatchingAtoms==5);
> ---------------
>
> Best Regards,
> -greg
>



-- 
Dr. Evgueni Kolossov (PhD)
eko...@gm...
Tel. +44(0)1628 627168
Mob. +44(0)7812070446