Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
Thanks Greg, Will this give the SHORTEST distance? Regards, Evgueni 2008/8/18 Greg Landrum greg.land...@gmail.com On Mon, Aug 18, 2008 at 12:42 PM, Evgueni Kolossov ekolos...@gmail.com 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 ekolos...@gmail.com 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] Calculation of atomic descriptors, Code snippet
2008/8/17 Evgueni Kolossov ekolos...@gmail.com
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.
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; iminRingSize; i++)
{
RDKit::Atom * pAtom = mol.getAtomWithIdx(ringIt[i]) ;
..
}
but this is not working.
Regards,
Evgueni
2008/8/15 Greg Landrum greg.land...@gmail.com
Dear Evgueni,
this is a general interest answer, so I'm directing it to the mailing
list.
On Fri, Aug 15, 2008 at 11:56 AM, Evgueni Kolossov
ekolos...@btinternet.com wrote:
I need to understand a little bit more about RingInfo.
For a given atom I got:
- the number of rings atom involved (pRingInfo-numAtomRings(Atom_Idx))
- the size of the smallest ring atom involved
(pRingInfo-minAtomRingSize(Atom_Idx))
correct.
Now I need to iterate through the atoms in the smallest ring with my
atom. I
can get atoms using pRingInfo-atomRings() but how I know this will give
me
the list of atoms in the smallest ring and in the ring where is my atom?
sample code, not actually tested, should give the idea:
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
}
}
}
}
What if my atom is a member of more than one ring?
The above code should work in that case as well.
-greg
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--
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
Dear Evgueni,
2008/8/17 Evgueni Kolossov ekolos...@gmail.com
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; iminRingSize; 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
Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
Dear Evgueni,
this is a general interest answer, so I'm directing it to the mailing list.
On Fri, Aug 15, 2008 at 11:56 AM, Evgueni Kolossov
ekolos...@btinternet.com wrote:
I need to understand a little bit more about RingInfo.
For a given atom I got:
- the number of rings atom involved (pRingInfo-numAtomRings(Atom_Idx))
- the size of the smallest ring atom involved
(pRingInfo-minAtomRingSize(Atom_Idx))
correct.
Now I need to iterate through the atoms in the smallest ring with my atom. I
can get atoms using pRingInfo-atomRings() but how I know this will give me
the list of atoms in the smallest ring and in the ring where is my atom?
sample code, not actually tested, should give the idea:
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
}
}
}
}
What if my atom is a member of more than one ring?
The above code should work in that case as well.
-greg
