PS: I found that if you want to use the non-strict version, you can do this:
from rdkit.Chem import rdMolDescriptors
rdMolDescriptors.CalcNumRotatableBonds(mol, 0)
(where 0 means NonStrict, 1 means Strict, and -1 means Default.)
I tested this with a molecule containing t-butyl and got different results
for strict and non-strict, as expected, and the default was the same as
strict.
On Tue, Oct 15, 2019 at 1:57 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> This is from lipinski.cpp:
>
> if (strict == NonStrict) {
> std::string pattern = "[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]";
> pattern_flyweight m(pattern);
> return m.get().countMatches(mol);
> }
> else if (strict==Strict) {
> std::string strict_pattern =
>
> "[!$(*#*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])("
>
> "[CH3])[CH3])&!$([CD3](=[N,O,S])-!@[#7,O,S!D1])&!$([#7,O,S!D1]-!@[CD3]="
>
> "[N,O,S])&!$([CD3](=[N+])-!@[#7!D1])&!$([#7!D1]-!@[CD3]=[N+])]-!@[!$(*#"
>
> "*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])([CH3])"
> "[CH3])]";
> pattern_flyweight m(strict_pattern);
> return m.get().countMatches(mol);
> } else {
>
> I suspect that it's taking the "Strict" brach, where the SMARTS pattern is
> more complex and actually has a rule that excludes tert-butyl (the
> "&!$(C([CH3])([CH3])[CH3])]" at the end).
>
> Ivan
>
>
> On Tue, Oct 15, 2019 at 1:06 PM Geoffrey Hutchison <
> geoff.hutchi...@gmail.com> wrote:
>
>> I'm using a script in RDKit to grab a bunch of descriptors for QSAR / ML.
>> I have a particular question about the # of rotatable bonds:
>>
>> Consider:
>>
>> from rdkit import Chem
>> from rdkit.Chem import Descriptors
>> example = Chem.MolFromSmiles("CN(C(=O)OC(C)(C)C)C(=S)NC(=O)OC(C)(C)C")
>> Descriptors.NumRotatableBonds(example)
>> 0
>>
>> example2 = Chem.MolFromSmiles("CC(C)(C)CCC(C)(C)C")
>> Descriptors.NumRotatableBonds(example2)
>> 1
>>
>>
>> Can someone explain why a terminal butyl isn't a rotatable bond? Based on
>> mailing list questions, I thought NumRotatableBonds was supposed to return
>> matches for the SMARTS "[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]" (e.g. what's
>> defined in the Lipinski code).
>>
>> Thanks,
>> -Geoff
>>
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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