Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
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
> Dear Evgueni,
>
> > 2008/8/17 Evgueni Kolossov
> >>
> >> 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 >> {
> >> 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)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
[Rdkit-discuss] Fwd: Calculation of atomic descriptors, Code snippet
-- Forwarded message --
From: Evgueni Kolossov
Date: 2008/8/18
Subject: Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
To: Greg Landrum
Greg,
Another question: getAllRotatableBonds(RDKit::ROMol &mol) - will this take
in account hydrogens or not?
> Regards,
> Evgueni
>
> 2008/8/17 Greg Landrum
>
> Dear Evgueni,
>>
>> > 2008/8/17 Evgueni Kolossov
>> >>
>> >> 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> >> {
>> >> 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)
> ekolos...@gmail.com
> Tel. +44(0)1628 627168
> Mob. +44(0)7812070446
>
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
On Mon, Aug 18, 2008 at 12:42 PM, Evgueni Kolossov wrote: > 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 I'm not clear what you're looking for. double *dm = MolOps::getDistanceMat(mol); // distance between atom 3 and 7: dm[3*mol.getNumAtoms()+7]; -greg
Re: [Rdkit-discuss] Fwd: Calculation of atomic descriptors, Code snippet
On Mon, Aug 18, 2008 at 2:55 PM, Evgueni Kolossov wrote: > > Another question: getAllRotatableBonds(RDKit::ROMol &mol) - will this take > in account hydrogens or not? I think you're talking about the function that's in : .../Code/GraphMol/Depictor/DepictUtils.h That looks for bonds that are rotatable as far as the depictor is concerned, which probably isn't interesting to you. I would otherwise define rotatable bonds using a SMARTS pattern. This is the one used in the python descriptor calculator: [!$(*#*)&!D1]-&!...@[!$(*#*)&!D1] (heh, taken out of context SMARTS really can look like line noise!) There's already sample code connected with this in the Getting Started cpp. -greg
Re: [Rdkit-discuss] Fwd: Calculation of atomic descriptors, Code snippet
Ok, I understood - there is no function to get the number of non-terminal rotatable bonds... Another question - is there function to calculate the longest chain of non-hydrogen atoms? Regards, Evgueni 2008/8/18 Greg Landrum > On Mon, Aug 18, 2008 at 2:55 PM, Evgueni Kolossov > wrote: > > > > Another question: getAllRotatableBonds(RDKit::ROMol &mol) - will this > take > > in account hydrogens or not? > > I think you're talking about the function that's in : > .../Code/GraphMol/Depictor/DepictUtils.h > That looks for bonds that are rotatable as far as the depictor is > concerned, which probably isn't interesting to you. > > I would otherwise define rotatable bonds using a SMARTS pattern. This > is the one used in the python descriptor calculator: > > [!$(*#*)&!D1]-&!...@[!$(*#*)&!D1] > > (heh, taken out of context SMARTS really can look like line noise!) > > There's already sample code connected with this in the Getting Started cpp. > > -greg > -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
Thanks Greg, Will this give the SHORTEST distance? Regards, Evgueni 2008/8/18 Greg Landrum > On Mon, Aug 18, 2008 at 12:42 PM, Evgueni Kolossov > wrote: > > 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 > > I'm not clear what you're looking for. > > double *dm = MolOps::getDistanceMat(mol); > // distance between atom 3 and 7: > dm[3*mol.getNumAtoms()+7]; > > -greg > -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
On Mon, Aug 18, 2008 at 8:15 PM, Evgueni Kolossov wrote: > Thanks Greg, > > Will this give the SHORTEST distance? Yes. As the header file says, it uses the all-pairs shortest paths algorithm. -greg
Re: [Rdkit-discuss] Fwd: Calculation of atomic descriptors, Code snippet
On Mon, Aug 18, 2008 at 8:12 PM, Evgueni Kolossov wrote: > Ok, > I understood - there is no function to get the number of non-terminal > rotatable bonds... Correct, you have to do that with SMARTS. > Another question - is there function to calculate the longest chain of > non-hydrogen atoms? Nope. that would have to be done by hand. Or by assuming that it's going to be less than a particular value (say 10) and using SMARTS queries for that as well. -greg
