Hi,
I am following the documentation for postgres / rdkit. I have a table with
valid molfiles as confirmed from is_valid_ctab(). I am then trying to
insert into a table 'mols' using mol_from_ctab(molfile::cstring,true).
However, the coordinates are not preserved. Is there something I am missing?
Dear Paolo,
Thank you again for your code. Sorry for bothering you again. It works
all fine for monoterpenes but not for diterpenes, sesquiterpenes nor
triterpenes.
pattern: C~C~C(~C)~C
mol1: CC(=O)O[C@H]1CC[C@]2([C@H](C1(C)C)CC=C([C@@H]2CC/C(=C/C(=O)O)/C)C)C
=> ((17, 18, 19, 20, 23), (16,
Hi Paolo,
Thank you. You spoonfed me!
Nicolas
> On 5 May 2020, at 17:25, Paolo Tosco wrote:
>
> Hi Nicolas,
>
> quick and dirty solution: strip it with a regex, e.g.
>
> sed 's|^\(> <.*>\) *([0-9]*)|\1|'
>
> HTH,
> p.
>
> On 05/05/2020 16:35, Nicolas Bosc wrote:
>> Hi RDKit users,
>>
>>
Out of curiousity, which software are you using that can't read those index
values?
On Wed, May 6, 2020 at 11:25 AM Nicolas Bosc wrote:
> Hi Paolo,
>
> Thank you. You spoonfed me!
>
> Nicolas
>
> On 5 May 2020, at 17:25, Paolo Tosco wrote:
>
> Hi Nicolas,
>
> quick and dirty solution: strip it
It’s for an old internal tool that we are updating. It has apparently some
strict parsing rules at the moment.
> On 6 May 2020, at 10:37, Greg Landrum wrote:
>
> Out of curiousity, which software are you using that can't read those index
> values?
>
> On Wed, May 6, 2020 at 11:25 AM Nicolas
Dear all,
from:
m = Chem.MolFromSmiles("C(=O)OC")
[print(repr(x.GetHybridization())) for x in m.GetAtoms() if
x.GetSymbol() == 'O']
I obtained:
rdkit.Chem.rdchem.HybridizationType.SP2
rdkit.Chem.rdchem.HybridizationType.SP2
which is confusing because in methyl formiate, one of the two
Hi Greg, yes that mostly makes sense and is a great help.
What's not clear is the usage of mergeMethod as this does not seem to be
specifiable in CombineFeatMaps(), but you say that that method uses it
when calling MergeFeatPoints(). Why isn't it in the signature of the former?
Tim
On
We're deep in the underdocumented space now. Sorry about that.
Here's an attempt to provide some at least sense of what these things mean.
This is going from (old) memory and a quick skim of the code... hopefully I
don't make any egregious errors.
mergeMetric is the metric used to determine
On Wed, May 6, 2020 at 6:15 PM Tim Dudgeon wrote:
> What's not clear is the usage of mergeMethod as this does not seem to be
> specifiable in CombineFeatMaps(), but you say that that method uses it when
> calling MergeFeatPoints(). Why isn't it in the signature of the former?
>
> Because
I'm trying to use the FeatureMaps functionality in RDKit (described here
http://rdkit.blogspot.com/2017/11/using-feature-maps.html) and have a
question on the parameters for CombineFeatMaps.
See here:
10 matches
Mail list logo
