date:20160311

Re: [Rdkit-discuss] compiling error with C++ on maverick

2016-03-11 Thread Greg Landrum

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, 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)";
> InchiToInchiKey(curInchi);
> //cout << "Hello, World!" << endl;
> return 0;
> }
>
> with the following command,
>
> g++ -Wall -O2 -std=c++11 -I
> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/Code -I
> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/External -I
> /usr/local/Cellar/boost/1.60.0_1/include -o MYTEST main.cpp
>
> on my maverick Macbook. The RDKit has been installed at
>
> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/
>
> while boost is at
> /usr/local/Cellar/boost/1.60.0_1/
>
> The compiler information is
>
> g++ -v
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
> Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
> Target: x86_64-apple-darwin13.4.0
> Thread model: posix
>
> However, I got the following the error message.
>
> Undefined symbols for architecture x86_64:
>   "RDKit::InchiToInchiKey(std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&)",
> referenced from:
>   _main in main-dd8650.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
>
> I am very sure inchi.h and inchi.cpp are available at
> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/External/INCHI-API/
>
> and function
> std::string InchiToInchiKey(const std::string &inchi)
>
> is defined in inchi.cpp.
>
> Could you please give me some hints for solving this problem?
>
> Thanks.
>
> Yingfeng
>
>
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[Rdkit-discuss] compiling error with C++ on maverick

2016-03-11 Thread Yingfeng Wang

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)";
InchiToInchiKey(curInchi);
//cout << "Hello, World!" << endl;
return 0;
}

with the following command,

g++ -Wall -O2 -std=c++11 -I
/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/Code -I
/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/External -I
/usr/local/Cellar/boost/1.60.0_1/include -o MYTEST main.cpp

on my maverick Macbook. The RDKit has been installed at

/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/

while boost is at
/usr/local/Cellar/boost/1.60.0_1/

The compiler information is

g++ -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

However, I got the following the error message.

Undefined symbols for architecture x86_64:
  "RDKit::InchiToInchiKey(std::__1::basic_string, std::__1::allocator > const&)",
referenced from:
  _main in main-dd8650.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see
invocation)

I am very sure inchi.h and inchi.cpp are available at
/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/External/INCHI-API/

and function
std::string InchiToInchiKey(const std::string &inchi)

is defined in inchi.cpp.

Could you please give me some hints for solving this problem?

Thanks.

Yingfeng
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Re: [Rdkit-discuss] Stereochemistry question

2016-03-11 Thread Jean-Marc Nuzillard


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 the P=C bond,
contrarily to the compound that it was about in Greg's first message on 
this topic.


I also wanted to point out that chirality is not necessarily centered on 
an atom

but may be axial, like in allenes:
https://en.wikipedia.org/wiki/Axial_chirality

All the best,

Jean-Marc



Here i give to you some publications were can find a clear publication 
about cis/trans isomerism and the importance.


[1] Conformation isomerism and coupling constants of formylmethylene 
triphenylphosphorane (C6H5)3P=CH-CHO
Comptes Rendus des Seances de l'Academie des Sciences, Serie C: 
Sciences Chimiques (1970), 270, (21), 1747-9.


[2] Structural and conformational analysis of 
2-triphenylphosphoranylidene succinic acid derivatives by 1H, 13C 
and 31P one and two dimensional NMR spectroscopy and molecular modelling
Radu Bacaloglu,   Andrei Blaskó,   Clifford A. Bunton,   Giorgio 
Cerichelli,   Fernando Castaneda and   Enrique Rivera

J. Chem. Soc., Perkin Trans. 2, 1995, 965-972
DOI: 10.1039/P2995965


[3]  Favoured conformations of methyl isopropyl, ethyl isopropyl, 
methyl tert-butyl, and ethyl tert-butyl 
2-(triphenylphosphoranylidene)malonate


[4] Conformations of diester triphenylphosphonium ylides with an 
ylidic ester or keto and ester ylidic groups



Best regards
Marco










On 11 Mar 2016, at 10:12, Greg Landrum > wrote:



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 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 like O=P(/O)=C/C under normal circumstances?


It has a meaning to write that the configuration of the P=C bond
is Z or E.


If this is the case, I'd love to add some real examples to the test 
suite. Can you point me to some examples (or a paper/web page talking 
about the topic)?


-greg
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--
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CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/

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Re: [Rdkit-discuss] Pandas dataframe manipulation

2016-03-11 Thread Paul Czodrowski

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

Von: Maciek Wójcikowski [mailto:mac...@wojcikowski.pl]
Gesendet: Freitag, 11. März 2016 12:29
An: Paul Czodrowski 
Cc: rdkit 
Betreff: Re: [Rdkit-discuss] Pandas dataframe manipulation

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('>', '')})

http://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_csv.html


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-03-11 11:12 GMT+01:00 Paul Czodrowski 
mailto:paul.czodrow...@merckgroup.com>>:
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"]].applymap(np.isreal).all(1)]

I would like to get rid of this nasty ">2" entry in "row1" => This works 
perfect  given the snippet above.

However, when I read in a CSV file containing similar data (see the attached 
CSV) => The conversion does not work: all columns in the IC50 value are 
discarded and end up in yielding "NaN".

What is going wrong?


Thanks & Cheers,
Paul



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Re: [Rdkit-discuss] Pandas dataframe manipulation

2016-03-11 Thread Maciek Wójcikowski

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('>', '')})

http://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_csv.html


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-03-11 11:12 GMT+01:00 Paul Czodrowski :

> 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"]].applymap(np.isreal).all(1)]
>
>
>
> I would like to get rid of this nasty ">2" entry in "row1" => This works
> perfect  given the snippet above.
>
>
>
> However, when I read in a CSV file containing similar data (see the
> attached CSV) => The conversion does not work: all columns in the IC50
> value are discarded and end up in yielding "NaN".
>
>
>
> What is going wrong?
>
>
>
>
>
> Thanks & Cheers,
>
> Paul
>
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
> any other person. If you have received this transmission in error, please
> notify the sender immediately and delete the message and any attachment
> from your system. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not accept liability for any omissions or errors in this
> message which may arise as a result of E-Mail-transmission or for damages
> resulting from any unauthorized changes of the content of this message and
> any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not guarantee that this message is free of viruses and does
> not accept liability for any damages caused by any virus transmitted
> therewith.
>
>
>
> Click http://www.merckgroup.com/disclaimer to access the German, French,
> Spanish and Portuguese versions of this disclaimer.
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
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[Rdkit-discuss] Pandas dataframe manipulation

2016-03-11 Thread Paul Czodrowski

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"]].applymap(np.isreal).all(1)]

I would like to get rid of this nasty ">2" entry in "row1" => This works 
perfect  given the snippet above.

However, when I read in a CSV file containing similar data (see the attached 
CSV) => The conversion does not work: all columns in the IC50 value are 
discarded and end up in yielding "NaN".

What is going wrong?


Thanks & Cheers,
Paul



This message and any attachment are confidential and may be privileged or 
otherwise protected from disclosure. If you are not the intended recipient, you 
must not copy this message or attachment or disclose the contents to any other 
person. If you have received this transmission in error, please notify the 
sender immediately and delete the message and any attachment from your system. 
Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept 
liability for any omissions or errors in this message which may arise as a 
result of E-Mail-transmission or for damages resulting from any unauthorized 
changes of the content of this message and any attachment thereto. Merck KGaA, 
Darmstadt, Germany and any of its subsidiaries do not guarantee that this 
message is free of viruses and does not accept liability for any damages caused 
by any virus transmitted therewith.



Click http://www.merckgroup.com/disclaimer to access the German, French, 
Spanish and Portuguese versions of this disclaimer.


test_mw_r2.csv
Description: test_mw_r2.csv
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Re: [Rdkit-discuss] Stereochemistry question

2016-03-11 Thread Greg Landrum

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 at 10:38 AM, Giuseppe Marco Randazzo <
gmranda...@gmail.com> wrote:

> An example can be the case of this isomerism is given by
> triphenylphosphorane (Witting reagents).
>
> Here i give to you some publications were can find a clear publication
> about cis/trans isomerism and the importance.
>
> [1] Conformation isomerism and coupling constants of formylmethylene
> triphenylphosphorane (C6H5)3P=CH-CHO
> Comptes Rendus des Seances de l'Academie des Sciences, Serie C:
> Sciences Chimiques (1970), 270, (21), 1747-9.
>
> [2] Structural and conformational analysis of 2-triphenylphosphoranylidene
> succinic acid derivatives by 1H, 13C and 31P one and two dimensional NMR
> spectroscopy and molecular modelling
> Radu Bacaloglu,   Andrei Blaskó,   Clifford A. Bunton,   Giorgio
> Cerichelli,   Fernando Castaneda and   Enrique Rivera
> J. Chem. Soc., Perkin Trans. 2, 1995, 965-972
> DOI: 10.1039/P2995965
>
>
> [3]  Favoured conformations of methyl isopropyl, ethyl isopropyl,
> methyl tert-butyl, and ethyl tert-butyl
> 2-(triphenylphosphoranylidene)malonate
>
> [4] Conformations of diester triphenylphosphonium ylides with an ylidic
> ester or keto and ester ylidic groups
>
>
> Best regards
> Marco
>
>
>
>
>
>
>
> On 11 Mar 2016, at 10:12, Greg Landrum  wrote:
>
>
> 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 like O=P(/O)=C/C under normal circumstances?
>>
>>
>> It has a meaning to write that the configuration of the P=C bond is Z or
>> E.
>>
>
> If this is the case, I'd love to add some real examples to the test suite.
> Can you point me to some examples (or a paper/web page talking about the
> topic)?
>
> -greg
>
>
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>
>
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Re: [Rdkit-discuss] Stereochemistry question

2016-03-11 Thread Jean-Marc Nuzillard

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 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 like O=P(/O)=C/C under normal circumstances?


It has a meaning to write that the configuration of the P=C bond
is Z or E.


If this is the case, I'd love to add some real examples to the test 
suite. Can you point me to some examples (or a paper/web page talking 
about the topic)?


-greg



--
Jean-Marc Nuzillard
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/

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Re: [Rdkit-discuss] Stereochemistry question

2016-03-11 Thread Greg Landrum

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 like O=P(/O)=C/C under normal circumstances?
>
>
> It has a meaning to write that the configuration of the P=C bond is Z or
> E.
>

If this is the case, I'd love to add some real examples to the test suite.
Can you point me to some examples (or a paper/web page talking about the
topic)?

-greg
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Re: [Rdkit-discuss] Stereochemistry question

2016-03-11 Thread Jean-Marc Nuzillard


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 configuration of the P=C bond is Z or E.

All the best,

Jean-Marc



Here's a pubchem compound example that has the double bond crossed 
(possibly leading one to believe that it could have stereochemistry):

https://pubchem.ncbi.nlm.nih.gov/compound/56981965
Here's the corresponding substance record (which is how PubChem 
received the structure):

https://pubchem.ncbi.nlm.nih.gov/substance/135741697

Another example, this time without the crossed bond in the compound 
record:

https://pubchem.ncbi.nlm.nih.gov/compound/87396055






Best,
-greg







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Jean-Marc Nuzillard
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/

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Re: [Rdkit-discuss] Stereochemistry question

2016-03-11 Thread Giuseppe Marco Randazzo

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 important to describe this kind of isomerism. 

However about atropisomerism i’m a bit unconvinced to be added into a SMILES 
notation, because this kind of isomerism it depends on the conformation of the 
molecule and not in the configuration as in the case of the oxygen in Cis/Trans 
of the C=P group. 

Marco


> On 11 Mar 2016, at 09:48, Greg Landrum  wrote:
> 
> 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 that's for a different discussion
> 
> 
> On Fri, Mar 11, 2016 at 9:22 AM, Giuseppe Marco Randazzo 
> mailto:gmranda...@gmail.com>> wrote:
> 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 
> (MO), which says that when you make a bond between two atoms, orbitals need 
> to be  “in phase”, and aligned one along the other. MO use the linear 
> combination of atomic orbitals, which says that from N orbitals which are 
> combined, where generated N new orbitals:
> N/2 boding and N/2 antibonding.  These orbitals bonding and anti bonding, are 
> not chiral because the direction of these is given by the resolution of the 
> schroedinger equations so… and they have a well “defined” direction in the 3D 
> space (probability to find an electron in that space). So the concept of 
> phase between the orbitals which are combined is very important and can’t be 
> chiral because of the well defined direction in the 3D space. 
> 
> I’m available if you need something else.
> 
> Best regards
> Marco
> 
> 
>> On 11 Mar 2016, at 05:11, Greg Landrum > > wrote:
>> 
>> 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?
>> 
>> Here's a pubchem compound example that has the double bond crossed (possibly 
>> leading one to believe that it could have stereochemistry):
>> https://pubchem.ncbi.nlm.nih.gov/compound/56981965 
>> 
>> Here's the corresponding substance record (which is how PubChem received the 
>> structure):
>> https://pubchem.ncbi.nlm.nih.gov/substance/135741697 
>> 
>> 
>> Another example, this time without the crossed bond in the compound record:
>> https://pubchem.ncbi.nlm.nih.gov/compound/87396055 
>> 
>> 
>> Best,
>> -greg
>> 
>> 
>> 
>> 
>> 
>> --
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
>> Click to learn more.
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140___
>>  
>> 
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net 
>> 
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 
>> 
> 
> 

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Re: [Rdkit-discuss] Stereochemistry question

2016-03-11 Thread Greg Landrum

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 that's for a different discussion


On Fri, Mar 11, 2016 at 9:22 AM, Giuseppe Marco Randazzo <
gmranda...@gmail.com> wrote:

> 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 (MO), which says that when you make a bond between two atoms,
> orbitals need to be  “in phase”, and aligned one along the other. MO use
> the linear combination of atomic orbitals, which says that from N orbitals
> which are combined, where generated N new orbitals:
> N/2 boding and N/2 antibonding.  These orbitals bonding and anti bonding,
> are not chiral because the direction of these is given by the resolution of
> the schroedinger equations so… and they have a well “defined” direction in
> the 3D space (probability to find an electron in that space). So the
> concept of phase between the orbitals which are combined is very important
> and can’t be chiral because of the well defined direction in the 3D space.
>
> I’m available if you need something else.
>
> Best regards
> Marco
>
>
> On 11 Mar 2016, at 05:11, Greg Landrum  wrote:
>
> 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?
>
> Here's a pubchem compound example that has the double bond crossed
> (possibly leading one to believe that it could have stereochemistry):
> https://pubchem.ncbi.nlm.nih.gov/compound/56981965
> Here's the corresponding substance record (which is how PubChem received
> the structure):
> https://pubchem.ncbi.nlm.nih.gov/substance/135741697
>
> Another example, this time without the crossed bond in the compound record:
> https://pubchem.ncbi.nlm.nih.gov/compound/87396055
>
> Best,
> -greg
>
>
>
>
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
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Re: [Rdkit-discuss] Stereochemistry question

2016-03-11 Thread Giuseppe Marco Randazzo

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 
(MO), which says that when you make a bond between two atoms, orbitals need to 
be  “in phase”, and aligned one along the other. MO use the linear combination 
of atomic orbitals, which says that from N orbitals which are combined, where 
generated N new orbitals:
N/2 boding and N/2 antibonding.  These orbitals bonding and anti bonding, are 
not chiral because the direction of these is given by the resolution of the 
schroedinger equations so… and they have a well “defined” direction in the 3D 
space (probability to find an electron in that space). So the concept of phase 
between the orbitals which are combined is very important and can’t be chiral 
because of the well defined direction in the 3D space. 

I’m available if you need something else.

Best regards
Marco

> On 11 Mar 2016, at 05:11, Greg Landrum  wrote:
> 
> 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?
> 
> Here's a pubchem compound example that has the double bond crossed (possibly 
> leading one to believe that it could have stereochemistry):
> https://pubchem.ncbi.nlm.nih.gov/compound/56981965 
> 
> Here's the corresponding substance record (which is how PubChem received the 
> structure):
> https://pubchem.ncbi.nlm.nih.gov/substance/135741697 
> 
> 
> Another example, this time without the crossed bond in the compound record:
> https://pubchem.ncbi.nlm.nih.gov/compound/87396055 
> 
> 
> Best,
> -greg
> 
> 
> 
> 
> 
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

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