Re: [Rdkit-discuss] SDMolSupplier, next()
Dear Jean-Marc,
in Python 3 you need to use next(suppl) or suppl.__next__().
Cheers,
p.
On 10/15/19 21:34, Jean-Marc Nuzillard wrote:
Dear all,
The code:
from rdkit import Chem
sdfnamein = "simple.sdf"
suppl = Chem.SDMolSupplier(sdfnamein)
m = suppl.next()
print(m.GetNumAtoms())
prints:
Traceback (most recent call last):
File "demo.py", line 4, in
m = suppl.next()
AttributeError: 'SDMolSupplier' object has no attribute 'next'
even though the code in
http://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.SDMolSupplier,
at paragraph "Lazy evaluation 2" indicates:
>>> suppl = SDMolSupplier('in.sdf')
>>> mol1 = suppl.next()
I run rdkit 2018.09.1.0 from Anaconda in Windows 10.
for mol in suppl:
mol.GetNumAtoms()
works fine.
Best,
Jean-Marc
--
Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry, CNRS UMR 7312
Faculté des Sciences Exactes et Naturelles, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax : 33 3 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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[Rdkit-discuss] SDMolSupplier, next()
Dear all,
The code:
from rdkit import Chem
sdfnamein = "simple.sdf"
suppl = Chem.SDMolSupplier(sdfnamein)
m = suppl.next()
print(m.GetNumAtoms())
prints:
Traceback (most recent call last):
File "demo.py", line 4, in
m = suppl.next()
AttributeError: 'SDMolSupplier' object has no attribute 'next'
even though the code in
http://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.SDMolSupplier,
at paragraph "Lazy evaluation 2" indicates:
suppl = SDMolSupplier('in.sdf')
mol1 = suppl.next()
I run rdkit 2018.09.1.0 from Anaconda in Windows 10.
for mol in suppl:
mol.GetNumAtoms()
works fine.
Best,
Jean-Marc
--
Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry, CNRS UMR 7312
Faculté des Sciences Exactes et Naturelles, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax : 33 3 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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Re: [Rdkit-discuss] RDKit Num Rotors descriptors?
> 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. Excellent, thanks! -Geoff ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit Num Rotors descriptors?
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]-&!@[!$(*#*)&!D1]" (e.g. what's
> defined in the Lipinski code).
>
> Thanks,
> -Geoff
>
>
>
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Re: [Rdkit-discuss] RDKit Num Rotors descriptors?
PS: I found that if you want to use the non-strict version, you can do this:
from rdkit.Chem import rdMolDescriptors
rdMolDescriptors.CalcNumRotatableBonds(mol, 0)
(where 0 means NonStrict, 1 means Strict, and -1 means Default.)
I tested this with a molecule containing t-butyl and got different results
for strict and non-strict, as expected, and the default was the same as
strict.
On Tue, Oct 15, 2019 at 1:57 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> This is from lipinski.cpp:
>
> if (strict == NonStrict) {
> std::string pattern = "[!$(*#*)&!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
>>
>>
>>
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>>
>
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[Rdkit-discuss] RDKit Num Rotors descriptors?
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
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