Yingfeng,
you have forgotten to link against the rdkit libraries. If you are using
the InChI code, you need to link against: RDInchiLib, InChi, GraphMol, and
RDGeneral. There may be a few others as well.
-greg
On Sat, Mar 12, 2016 at 5:13 AM, Yingfeng Wang wrote:
> After installing RDKit,
After installing RDKit, I try to compile the following code in main.cpp,
#include
#include
using namespace RDKit;
using namespace std;
int main(int argc, const char * argv[]) {
string curInchi =
"InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)";
InchiToIn
Le 11/03/2016 10:38, Giuseppe Marco Randazzo a écrit :
An example can be the case of this isomerism is given by
triphenylphosphorane (Witting reagents).
Wittig reagents with their three identical phenyl groups on the
phosphorus atom
do not present any intriguing configuration problem around t
Maciek, thanks for the note via private message!
To all of you: Here comes the solution to just skip entries inside a column
that contain a combination of float and “>” :
pd.read_csv('test_mw_r2.csv', sep=';', converters={'r2': lambda x: np.NaN if x
and x[0] == '>' else x}).dropna(axis=0)
Paul
Hi Paul,
I would suggest:
- assigning dtype of dataframe/column to str/np.object
- cleaning up the IC50s
- casting to float/int as dataframe.astype()
Or alternatively you could use "converters" argument:
pd.read_csv('filename.csv', converters={'ic50_colname': lambda x:
x.replace('>', ''
Dear RDKitter & Pandas-Dataframes heavy users,
please find below a question concerning the conversion of pandas dataframes:
df = pd.DataFrame({"item": ["a", "b", "c", "d", "e"], "row1": [1,2,3,">2",5],
"row2":[0.1,0.2,0.3,0.4,0.5],"row3":["ab","cd","ed","gh","ij"]})
df_new = df[df[["row1"]].apply
I think these are all different. The substructure in question here is
R1O/P(=O)=C/R2
I think I managed to convince myself that stereochemistry here is
reasonable by rewriting the structure as:
R1O/[P+]([O-])=C/R2
but I would still certainly like some real examples.
-greg
On Fri, Mar 11, 2016 a
I do not have the feeling that the handling of a C=P bond should be
different of the one of a C=C bond.
Jean-Marc
Le 11/03/2016 10:12, Greg Landrum a écrit :
On Fri, Mar 11, 2016 at 10:05 AM, Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Le 11/03/2016 05:11, Greg Lan
On Fri, Mar 11, 2016 at 10:05 AM, Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:
>
> Le 11/03/2016 05:11, Greg Landrum a écrit :
>
>
> Here's a question for the chemists in the group: do we need to be
> concerned about representing the stereochemistry of the P=C bond in
> substructures l
Dear all,
Le 11/03/2016 05:11, Greg Landrum a écrit :
Dear all,
Here's a question for the chemists in the group: do we need to be
concerned about representing the stereochemistry of the P=C bond in
substructures like O=P(/O)=C/C under normal circumstances?
It has a meaning to write that the
ahhh :-) now i understand. Ok it’s an other point of question so…
if the oxygen bonded to the Phosphor of the group C=P is in Cis or Trans. Yes,
describe this feature make sense.
The bond C=P is blocked, so the oxygen is not free to be rotated along the bond
C=P.
Finally, i think is importan
Hi Marco,
Sorry I wasn't clear in the original question. I was asking about the
cis/trans stereochemistry of the C=P bond. I agree that it's not generally
useful to think of bonds as being chiral.[1]
-greg
[1] There's an argument to be made here about the best way to represent
atropisomers, but t
Dear Greg,
as i know from organic/inorganic and physical chemistry courses a
stereochemistry like that is unreal and i think it’s a bug of the pubchem
depiction generator.
Atoms can be chiral.
Bonds are not chiral.
Why bonds are not chiral? The answer is given by the molecular orbital theory
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