Good point. It seems the algorithm uses bonds and not atoms, so radius 3
means include the next three bonds. Maybe Greg can comment here.
Best,
Peter
On Mon, Mar 27, 2017 at 10:39 AM Pavel Polishchuk <pavel_polishc...@ukr.net>
wrote:
> Thank you!
> That was a bug in my expectations. :)
>
> BTW, as I see from test examples for the 0 atom in CC1CC1 an environment
> with radius 3 exists. Thus, radius should be interpreted as a number of
> bonds from the rooted atom, not a number of atoms. I did not expect this as
> well.
>
>
> Pavel.
>
> On 03/27/2017 04:22 PM, Peter Gedeck wrote:
>
> I checked the unit tests for this function and this is expected
> behaviour.
>
> Best
>
> Peter
>
> void test2() {
> std::cout << "-----------------------\n Test2: Atom Environments"
> << std::endl;
> {
> std::string smiles = "CC1CC1";
> RWMol *mol = SmilesToMol(smiles);
> TEST_ASSERT(mol);
>
> PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 1, 0);
> TEST_ASSERT(pth.size() == 1);
> TEST_ASSERT(pth[0] == 0);
>
> pth = findAtomEnvironmentOfRadiusN(*mol, 2, 0);
> TEST_ASSERT(pth.size() == 3);
> TEST_ASSERT(pth[0] == 0);
>
> pth = findAtomEnvironmentOfRadiusN(*mol, 3, 0);
> TEST_ASSERT(pth.size() == 4);
> TEST_ASSERT(pth[0] == 0);
>
> pth = findAtomEnvironmentOfRadiusN(*mol, 4, 0);
> *TEST_ASSERT(pth.size() == 0);*
>
> pth = findAtomEnvironmentOfRadiusN(*mol, 1, 1);
> TEST_ASSERT(pth.size() == 3);
>
> pth = findAtomEnvironmentOfRadiusN(*mol, 2, 1);
> TEST_ASSERT(pth.size() == 4);
>
> pth = findAtomEnvironmentOfRadiusN(*mol, 3, 1);
> *TEST_ASSERT(pth.size() == 0);*
>
> delete mol;
> }
>
>
> On Mon, Mar 27, 2017 at 10:00 AM Pavel Polishchuk <
> pavel_polishc...@ukr.net> wrote:
>
> I guessed why it occurred. I'm interested is it expected behavior?
> So, if a radius is greater than the number of available bonds in all
> directions from the rooted atom the function will return empty list as it
> considers that such environment does not exist. Is this a correct
> expectation?
>
>
> Pavel.
>
>
> On 03/27/2017 03:53 PM, Peter Gedeck wrote:
>
> Hello,
>
> The atom numbers start with 0. From the middle atom, there are no
> environments with radius 2. You will get a result if you use the first (=0)
> or the last (=2) atom. Try this:
>
> m = Chem.MolFromSmiles("NCO")
> i = Chem.FindAtomEnvironmentOfRadiusN(m, 1, 0)
> Chem.MolToSmiles(Chem.PathToSubmol(m, i))
> i = Chem.FindAtomEnvironmentOfRadiusN(m, 2, 0)
> Chem.MolToSmiles(Chem.PathToSubmol(m, i))
> i = Chem.FindAtomEnvironmentOfRadiusN(m, 3, 0)
> Chem.MolToSmiles(Chem.PathToSubmol(m, i))
>
> and you will get:
>
> 'CN'
> 'NCO'
> ''
>
> Is this more intuitive to you?
>
> Best,
>
> Peter
>
>
> On Mon, Mar 27, 2017 at 9:35 AM Pavel Polishchuk <pavel_polishc...@ukr.net>
> wrote:
>
> Dear RDKitters,
>
> I found the issue with FindAtomEnvironmentOfRadiusN but this can be a
> feature. However, I did not findthis information in help and did not
> expect such behavior.
> If I apply FindAtomEnvironmentOfRadiusN function to a small molecule
> and specify the radius greater than the size of the molecule the
> function returns empty list of bond indices (and empty mol).
>
> m = Chem.MolFromSmiles("NCO")
>
> i = Chem.FindAtomEnvironmentOfRadiusN(m, 1, 1)
> Chem.MolToSmiles(Chem.PathToSubmol(m, i))
>
> returns "NCO"
>
> i = Chem.FindAtomEnvironmentOfRadiusN(m, 2, 1)
> Chem.MolToSmiles(Chem.PathToSubmol(m, i))
>
> returns ""
>
> In the latter case I expected the same output "NCO". Were my
> expectations mistaken?
>
> Kind regards,
> Pavel.
>
>
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