Hi Hitesh
I use the PropertyMol object to save molecules with properties, setting a
property for a molecule is fairly simple,
m.SetProp(_Name,”mol_name)
for m in mol_lst:
pm = AllChem.PropertyMol(m)
pm.SetProp(_Name, name)
pm.SetProp(_Energy, None)
Hi there,
I am new to RDkti.
Is there a way to save custom property for each atoms and save that to any
file format and use it again?
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Hi Adam,
Sorry I forgot to mention that.
If you are building your own version of the RDKit, you will need to provide
the flag RDK_THREADSAFE_SSS=ON to cmake. You can do this when you first
call cmake or, if you have run it already, by runing ccmake in your build
directory, modifying the value of
Hi Josh,
Thanks for your quick reply. But, sorry, I want to set atom properties, not
molecule properties. Like,
atom = m.GetAtomWithIdx(5)
atom.SetProp('my_property', 'value_of_my_property')
I want to save this property associated with each atom.
Regards,
Hitesh Patel
On Fri, Jul 3, 2015 at
Hitesh,
It is certainly possible to set atom properties. I don't think any of the
output formats the rdkit can generate really support atom properties
though. What format did you envision writing and how would the atom
properties be encoded?
-greg
On Friday, July 3, 2015, Hitesh Patel
Hi Greg,
This is super feature, but are there any downsides? Why not to enable it by
default (provided the dependencies are met)?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-07-03 16:54 GMT+02:00 Greg Landrum greg.land...@gmail.com:
Hi Adam,
Sorry I
Hi Axel,
I was sure there was something in the core that did this but I can't seem to
find it now! I have a function that uses isotope labelled dummy atoms to attach
fragments if it's of any use? As with most the code I write, it doesn't have
the greatest error handling, or rational use of
Nicholas,
thanks a lot for the code, I will definitely look into it.
Kind regards,
Axel
On 03.07.2015 09:19, Nicholas Firth wrote:
Hi Axel,
I was sure there was something in the core that did this but I can't seem to
find it now! I have a function that uses isotope labelled dummy atoms to
Axel,
This is excellent. I may actually be able to get other people to use my work
now I can use a nice interface!
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E
Dear fellow RDKitters,
I use ReplaceCore and GetMolFrags to create a 2D SAR table:
tmp = Chem.ReplaceCore(mol, core_mol, labelByIndex=True)
frag_mols = list(Chem.GetMolFrags(tmp, asMols=True))
Is it also possible to do the reverse? Create a new molecule from the
core and two fragments?
I
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