[Rdkit-discuss] molecular descriptors in C++

[Gonzalo Colmenarejo-Sanchez]

Hi,

I'm trying to calculate molecular descriptors in C++ with the RDKit. Does 
anyone have a code example that could help in this case?

Thanks a lot,

Gonzalo Colmenarejo

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Re: [Rdkit-discuss] molecular descriptors in C++

[Nicholas Firth]

Also to add to my previous email, when I started out with C++ RDKit I found it 
really useful to dig into the source code. Especially look through the code 
written to test the descriptors, more often than not you can adapt what Greg 
and co. have done already to do what you want.

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 nicholas.fi...@icr.ac.uk | 
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On 27 Aug 2013, at 15:05, Gonzalo Colmenarejo-Sanchez 
mailto:gonzalo.2.colmenar...@gsk.com>> wrote:

Hi,

I’m trying to calculate molecular descriptors in C++ with the RDKit. Does 
anyone have a code example that could help in this case?

Thanks a lot,

Gonzalo Colmenarejo

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Re: [Rdkit-discuss] molecular descriptors in C++

[Nicholas Firth]

Hi Gonzalo,

I shamelessly only have an example using PBF. Forgive the slightly dirty C++ 
coding, but you can get the idea of descriptor calculation.

using namespace std;
using namespace RDKit;

int main(int argc, char *argv[]){



string fileName = argv[1];
SDMolSupplier reader(fileName,false, false);
fileName = fileName.substr(0,fileName.size()-4);
fileName += "_Scored_PBF.sdf";
SDWriter *writer = new SDWriter(fileName);
while(!reader.atEnd()){
ROMol *m=reader.next();
//MolOps::removeHs(*m);
if(!m) continue;
double dpbf=PBFRD(*m);
m->setProp("PBF_Score", dpbf);
writer->write(*m);
delete m;
}
writer->flush();
writer->close();



return 0;
}



I hope that is helpful.

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 nicholas.fi...@icr.ac.uk | 
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On 27 Aug 2013, at 15:05, Gonzalo Colmenarejo-Sanchez 
mailto:gonzalo.2.colmenar...@gsk.com>> wrote:

Hi,

I’m trying to calculate molecular descriptors in C++ with the RDKit. Does 
anyone have a code example that could help in this case?

Thanks a lot,

Gonzalo Colmenarejo

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Re: [Rdkit-discuss] molecular descriptors in C++

[Greg Landrum]

Nick beat me to it (thanks Nick!)
I was going to send the suggestion that a good place to look is the testing
code:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Descriptors/test.cpp

-greg



On Tue, Aug 27, 2013 at 4:32 PM, Nicholas Firth wrote:

> Also to add to my previous email, when I started out with C++ RDKit I
> found it really useful to dig into the source code. Especially look through
> the code written to test the descriptors, more often than not you can adapt
> what Greg and co. have done already to do what you want.
>
>
> 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* nicholas.fi...@icr.ac.uk | *W* www.icr.ac.uk | *
> Twitter* @ICRnews 
>
> *Facebook* www.facebook.com/theinstituteofcancerresearch
>
> *Making the discoveries that defeat cancer*
>
>
> On 27 Aug 2013, at 15:05, Gonzalo Colmenarejo-Sanchez <
> gonzalo.2.colmenar...@gsk.com> wrote:
>
>  Hi,
> ** **
> I’m trying to calculate molecular descriptors in C++ with the RDKit. Does
> anyone have a code example that could help in this case?
>
> Thanks a lot,
>
> Gonzalo Colmenarejo
> ** **
>
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Re: [Rdkit-discuss] molecular descriptors in C++

[Gonzalo Colmenarejo-Sanchez]

Thanks to both for the fast and extremely helpful reply!

Gonzalo

From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 27 August 2013 16:39
To: rdkit-discuss@lists.sourceforge.net
Cc: Gonzalo Colmenarejo-Sanchez
Subject: Re: [Rdkit-discuss] molecular descriptors in C++

Nick beat me to it (thanks Nick!)
I was going to send the suggestion that a good place to look is the testing 
code:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Descriptors/test.cpp

-greg


On Tue, Aug 27, 2013 at 4:32 PM, Nicholas Firth 
mailto:nicholas.fi...@icr.ac.uk>> wrote:
Also to add to my previous email, when I started out with C++ RDKit I found it 
really useful to dig into the source code. Especially look through the code 
written to test the descriptors, more often than not you can adapt what Greg 
and co. have done already to do what you want.


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 nicholas.fi...@icr.ac.uk | 
W www.icr.ac.uk | Twitter 
@ICRnews
Facebook 
www.facebook.com/theinstituteofcancerresearch
Making the discoveries that defeat cancer

[cid:image001.gif@01CEA346.77BA4F60]

On 27 Aug 2013, at 15:05, Gonzalo Colmenarejo-Sanchez 
mailto:gonzalo.2.colmenar...@gsk.com>> wrote:

Hi,

I'm trying to calculate molecular descriptors in C++ with the RDKit. Does 
anyone have a code example that could help in this case?

Thanks a lot,

Gonzalo Colmenarejo

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[Rdkit-discuss] name generator

[Sergio Martinez Cuesta]

Hi,

is there any IUPAC name generator in RDKit?

e.g. for transforming "CC(C)O" into "propan-2-ol" ?

Many thanks
Sergio
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Re: [Rdkit-discuss] name generator

[Greg Landrum]

Dear Sergio,


On Tue, Aug 27, 2013 at 5:21 PM, Sergio Martinez Cuesta  wrote:

> is there any IUPAC name generator in RDKit?
>
> e.g. for transforming "CC(C)O" into "propan-2-ol" ?
>
>
There is not. In fact, I'm not aware of any open source structure->name
converters.

-greg
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Re: [Rdkit-discuss] name generator

[Sergio Martinez Cuesta]

thanks Greg,

indeed, I only found commercial software for it

http://www.chemaxon.com/marvin/help/applications/molconvert.html

cheers
Sergio


On 27 August 2013 16:45, Greg Landrum  wrote:

> Dear Sergio,
>
>
> On Tue, Aug 27, 2013 at 5:21 PM, Sergio Martinez Cuesta <
> sermar...@gmail.com> wrote:
>
>> is there any IUPAC name generator in RDKit?
>>
>> e.g. for transforming "CC(C)O" into "propan-2-ol" ?
>>
>>
> There is not. In fact, I'm not aware of any open source structure->name
> converters.
>
> -greg
>
>
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Re: [Rdkit-discuss] name generator

[Markus Hartenfeller]

Hi Sergio,

here is a solution that uses a free web service offered by the NIH.

It's independent of the rdkit but rather slow. Anyway, if you don't need 
to process too many molecules at a time or if time is not the critical 
factor maybe it could serve as an intermediate solution:



import urllib2

def smi_to_iupac(smi):

try:
url = 
'http://cactus.nci.nih.gov/chemical/structure/'+smi+'/iupac_name'


iupacName = urllib2.urlopen(url).read()
#print iupacName
return iupacName

except urllib2.HTTPError, e:
print "HTTP error: %d" % e.code
return None
except urllib2.URLError, e:
print "Network error: %s" % e.reason.args[1]
return None
except:
print "conversion failed for smiles "+ smi
return None

smiles = ["CC(O)C","CC(=O)O", "O=C2OCC(=C2\c1c1)\c3ccc(cc3)S(=O)(=O)C"]

for s in smiles:
print smi_to_iupac(s)


returns

Propan-2-ol
acetic acid
4-(4-methylsulfonylphenyl)-3-phenyl-5H-furan-2-one


By the way, this service offers conversions between many different 
molecule formats/identifiers. I have used it in the past for CAS number 
look-up.


Best,
Markus


On 08/27/2013 05:21 PM, Sergio Martinez Cuesta wrote:

Hi,

is there any IUPAC name generator in RDKit?

e.g. for transforming "CC(C)O" into "propan-2-ol" ?

Many thanks
Sergio


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Re: [Rdkit-discuss] name generator

[David Hall]

Not sure what software is behind it, but the NCI's Chemical Identifier Resolver 
may suit your needs.

For your example, the URL:

http://cactus.nci.nih.gov/chemical/structure/CC(C)O/iupac_name

returns Propan-2-ol

-David

On Aug 27, 2013, at 11:54 AM, Sergio Martinez Cuesta  
wrote:

> thanks Greg,
> 
> indeed, I only found commercial software for it
> 
> http://www.chemaxon.com/marvin/help/applications/molconvert.html
> 
> cheers
> Sergio
> 
> 
> On 27 August 2013 16:45, Greg Landrum  wrote:
>> Dear Sergio,
>> 
>> 
>> On Tue, Aug 27, 2013 at 5:21 PM, Sergio Martinez Cuesta 
>>  wrote:
>>> is there any IUPAC name generator in RDKit?
>>> 
>>> e.g. for transforming "CC(C)O" into "propan-2-ol" ?
>> 
>> There is not. In fact, I'm not aware of any open source structure->name 
>> converters.
>> 
>> -greg
> 
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Re: [Rdkit-discuss] name generator

[George Papadatos]

I think this is not an actual structure to name converter but a look-up service 
based on a a predefined dictionary. 
If this is true, then it won't return anything for any novel/unseen structures. 
Give it a try and let us know. 

George. 

Sent from my giPhone

On 27 Aug 2013, at 18:39, David Hall  wrote:

> Not sure what software is behind it, but the NCI's Chemical Identifier 
> Resolver may suit your needs.
> 
> For your example, the URL:
> 
> http://cactus.nci.nih.gov/chemical/structure/CC(C)O/iupac_name
> 
> returns Propan-2-ol
> 
> -David
> 
> On Aug 27, 2013, at 11:54 AM, Sergio Martinez Cuesta  
> wrote:
> 
>> thanks Greg,
>> 
>> indeed, I only found commercial software for it
>> 
>> http://www.chemaxon.com/marvin/help/applications/molconvert.html
>> 
>> cheers
>> Sergio
>> 
>> 
>> On 27 August 2013 16:45, Greg Landrum  wrote:
>>> Dear Sergio,
>>> 
>>> 
>>> On Tue, Aug 27, 2013 at 5:21 PM, Sergio Martinez Cuesta 
>>>  wrote:
 is there any IUPAC name generator in RDKit?
 
 e.g. for transforming "CC(C)O" into "propan-2-ol" ?
>>> 
>>> There is not. In fact, I'm not aware of any open source structure->name 
>>> converters.
>>> 
>>> -greg
>> 
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Re: [Rdkit-discuss] name generator

[Vladimir Chupakhin]

Hi,

did you tried http://opsin.ch.cam.ac.uk/ ?

Vladimir Chupakhin



On Tue, Aug 27, 2013 at 6:48 PM, Markus Hartenfeller <
markus.hartenfel...@molecularhealth.com> wrote:

>  Hi Sergio,
>
> here is a solution that uses a free web service offered by the NIH.
>
> It's independent of the rdkit but rather slow. Anyway, if you don't need
> to process too many molecules at a time or if time is not the critical
> factor maybe it could serve as an intermediate solution:
>
>
> import urllib2
>
> def smi_to_iupac(smi):
>
> try:
> url = '
> http://cactus.nci.nih.gov/chemical/structure/'+smi+'/iupac_name'
>
> iupacName = urllib2.urlopen(url).read()
> #print iupacName
> return iupacName
>
> except urllib2.HTTPError, e:
> print "HTTP error: %d" % e.code
> return None
> except urllib2.URLError, e:
> print "Network error: %s" % e.reason.args[1]
> return None
> except:
> print "conversion failed for smiles "+ smi
> return None
>
> smiles = ["CC(O)C","CC(=O)O", "O=C2OCC(=C2\c1c1)\c3ccc(cc3)S(=O)(=O)C"]
>
> for s in smiles:
> print smi_to_iupac(s)
>
>
> returns
>
> Propan-2-ol
> acetic acid
> 4-(4-methylsulfonylphenyl)-3-phenyl-5H-furan-2-one
>
>
> By the way, this service offers conversions between many different
> molecule formats/identifiers. I have used it in the past for CAS number
> look-up.
>
> Best,
> Markus
>
>
> On 08/27/2013 05:21 PM, Sergio Martinez Cuesta wrote:
>
>  Hi,
>
> is there any IUPAC name generator in RDKit?
>
> e.g. for transforming "CC(C)O" into "propan-2-ol" ?
>
> Many thanks
> Sergio
>
>
>
> --
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>
>
>
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Re: [Rdkit-discuss] name generator

[George Papadatos]

OPSIN wouldn't help very much here, as it deals with the inverse problem, i.e. 
name to structure. 

George. 


Sent from my giPhone

On 27 Aug 2013, at 19:40, Vladimir Chupakhin  wrote:

> Hi,
> 
> did you tried http://opsin.ch.cam.ac.uk/ ?
> 
> Vladimir Chupakhin
> 
> 
> 
> On Tue, Aug 27, 2013 at 6:48 PM, Markus Hartenfeller 
>  wrote:
>> Hi Sergio,
>> 
>> here is a solution that uses a free web service offered by the NIH. 
>> 
>> It's independent of the rdkit but rather slow. Anyway, if you don't need to 
>> process too many molecules at a time or if time is not the critical factor 
>> maybe it could serve as an intermediate solution:
>> 
>> 
>> import urllib2
>> 
>> def smi_to_iupac(smi):
>> 
>> try:
>> url = 
>> 'http://cactus.nci.nih.gov/chemical/structure/'+smi+'/iupac_name'
>> 
>> iupacName = urllib2.urlopen(url).read()
>> #print iupacName
>> return iupacName
>> 
>> except urllib2.HTTPError, e:
>> print "HTTP error: %d" % e.code
>> return None
>> except urllib2.URLError, e:
>> print "Network error: %s" % e.reason.args[1]
>> return None
>> except:
>> print "conversion failed for smiles "+ smi
>> return None
>> 
>> smiles = ["CC(O)C","CC(=O)O",   
>> "O=C2OCC(=C2\c1c1)\c3ccc(cc3)S(=O)(=O)C"]
>> 
>> for s in smiles:
>> print smi_to_iupac(s)
>> 
>> 
>> returns
>> Propan-2-ol
>> acetic acid
>> 4-(4-methylsulfonylphenyl)-3-phenyl-5H-furan-2-one
>> 
>> By the way, this service offers conversions between many different 
>> molecule formats/identifiers. I have used it in the past for CAS number 
>> look-up.
>> 
>> Best,
>> Markus
>> 
>> 
>> On 08/27/2013 05:21 PM, Sergio Martinez Cuesta wrote:
>>> 
>>> Hi,
>>> 
>>> is there any IUPAC name generator in RDKit?
>>> 
>>> e.g. for transforming "CC(C)O" into "propan-2-ol" ?
>>> 
>>> Many thanks
>>> Sergio
>>> 
>>> 
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Re: [Rdkit-discuss] name generator

[Markus Sitzmann]

Yes, in this direction (structure to name) the Resolver is only a database lookup, in the other direction (name to structure), it first uses OPSIN (Daniel Lowe's library)which can resolve correct IUPAC names generically, if OPSIN "fails" it does a database lookup, too.MarkusNot sure what software is behind it, but the NCI's Chemical Identifier Resolver may suit your needs.For your example, the URL:http://cactus.nci.nih.gov/chemical/structure/CC(C)O/iupac_namereturns Propan-2-ol-DavidOn Aug 27, 2013, at 11:54 AM, Sergio Martinez Cuesta  wrote:thanks Greg,--
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Re: [Rdkit-discuss] name generator

[Sergio Martinez Cuesta]

Oc(:[nH2]):[nH2] does not seem to be in the database

http://cactus.nci.nih.gov/chemical/structure/Oc(:[nH2]):[nH2]/iupac_name

molcovert does not generate a name either.




On 27 August 2013 18:54, Markus Sitzmann  wrote:

> **
> Yes, in this direction (structure to name) the Resolver is only a database
> lookup,
> in the other direction (name to structure), it first uses OPSIN (Daniel
> Lowe's library)
> which can resolve correct IUPAC names generically, if OPSIN "fails" it
> does a database
> lookup, too.
>
> Markus
>
>
> Not sure what software is behind it, but the NCI's Chemical Identifier
> Resolver may suit your needs.
>
> For your example, the URL:
>
> http://cactus.nci.nih.gov/chemical/structure/CC(C)O/iupac_name
>
> returns Propan-2-ol
>
> -David
>
> On Aug 27, 2013, at 11:54 AM, Sergio Martinez Cuesta 
> wrote:
>
> thanks Greg,
>
>
>
>
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Re: [Rdkit-discuss] name generator

[Greg Landrum]

On Tue, Aug 27, 2013 at 10:32 PM, Sergio Martinez Cuesta <
sermar...@gmail.com> wrote:

> Oc(:[nH2]):[nH2] does not seem to be in the database
>
> http://cactus.nci.nih.gov/chemical/structure/Oc(:[nH2]):[nH2]/iupac_name
>
> molcovert does not generate a name either.
>

That's not actually a stable molecule. it is, at best, a piece of a
molecule. OC(N)N works fine with the NCI lookup.
What molecule are you trying to name?

-greg
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