Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-19 Thread Stiefl, Nikolaus 
Then I guess Greg’s solution is the better suited one since you don’t have to 
specify a list of isotopes (assuming that your input compounds will not have 
things like 12C specified). Minor modification:

In [23]: q = rdqueries.IsotopeGreaterQueryAtom(1)

In [24]: atomNums = [1,6,7,8,15,16]

In [25]: [x.GetIdx() for x in 
Chem.MolFromSmiles('CCC[13CH3]').GetAtomsMatchingQuery(q) if x.GetAtomicNum() 
in atomNums]
Out[25]: [3]

In [26]: [x.GetIdx() for x in 
Chem.MolFromSmiles('CCC[19F]').GetAtomsMatchingQuery(q) if x.GetAtomicNum() in 
atomNums]
Out[26]: []





From: Milinda Samaraweera <milindaatw...@gmail.com>
Date: Wednesday 18 January 2017 at 23:01
To: Bob Funchess <bfunch...@kelaroo.com>
Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>, Greg Landrum 
<greg.land...@gmail.com>
Subject: Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

Hi Bob,
I am trying to filter out any compound that does not have the most stable 
isotopic form;  (anything other than: 12C,1H,14N,16O, 31P, 32S) or to contain 
only MonoIsotopic compounds.
Thanks,
Milinda
​
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Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Milinda Samaraweera 
Yes, most common should be the correct term.

Thanks,
Milinda

On Wed, Jan 18, 2017 at 5:49 PM, Peter S. Shenkin  wrote:

> You say "most stable", but I think you mean "most common." 2H is as stable
> as 1H, but less common.
>
> -P.
>
> On Wed, Jan 18, 2017 at 5:01 PM, Milinda Samaraweera <
> milindaatw...@gmail.com> wrote:
>
>> Hi Bob,
>>
>> I am trying to filter out any compound that does not have the most stable
>> isotopic form;  (anything other than: 12C,1H,14N,16O, 31P, 32S) or to
>> contain only MonoIsotopic compounds.
>>
>> Thanks,
>> Milinda
>> ​
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>


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University of Connecticut
69 North Eagleville road
Storrs, CT, 06269
milindaatw...@gmail.com
860-617-8046
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Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Peter S. Shenkin 
You say "most stable", but I think you mean "most common." 2H is as stable
as 1H, but less common.

-P.

On Wed, Jan 18, 2017 at 5:01 PM, Milinda Samaraweera <
milindaatw...@gmail.com> wrote:

> Hi Bob,
>
> I am trying to filter out any compound that does not have the most stable
> isotopic form;  (anything other than: 12C,1H,14N,16O, 31P, 32S) or to
> contain only MonoIsotopic compounds.
>
> Thanks,
> Milinda
> ​
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Milinda Samaraweera 
Hi Bob,

I am trying to filter out any compound that does not have the most stable
isotopic form;  (anything other than: 12C,1H,14N,16O, 31P, 32S) or to
contain only MonoIsotopic compounds.

Thanks,
Milinda
​
--
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Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Bob Funchess 
Hi Milinda,



As an aside, most of the isotopes you listed are stable.  The only nuclides
in the list that are actually unstable are 14C, 3H, 24P and 46P.



If your goal is to exclude isotopically enriched structures rather than
radioactive ones, it might be better to just look for ANY isotopic
specification, rather than for a specific list.



Kind Regards,

Bob



--

Bob Funchess, Ph.D.Kelaroo,
Inc

Director of Software Support & Development
www.kelaroo.com

bfunch...@kelaroo.com (858)
259-7561 x3







*From:* Milinda Samaraweera [mailto:milindaatw...@gmail.com]
*Sent:* Wednesday, January 18, 2017 11:48 AM
*To:* Greg Landrum <greg.land...@gmail.com>
*Cc:* RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
*Subject:* Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit



Greg,

I am looking to remove entries that contain un-stable isotopes of elements
CHNOPS (e.g. heavy_isotopes =['13C', '14C', '2H', '3H', '15N', '24P',
'46P', '33S', '34S', '36S'] ). Is there a way to modify the above code to
achieve that?

Thanks,

Milinda





On Wed, Jan 18, 2017 at 11:16 AM, Greg Landrum <greg.land...@gmail.com>
wrote:

Hi Milinda,



Here's an approach that finds all the atoms that have an isotope specified:



In [1]: from rdkit import Chem



In [2]: from rdkit.Chem import rdqueries



In [3]: q = rdqueries.IsotopeGreaterQueryAtom(1)



In [7]: list(x.GetIdx() for x in
Chem.MolFromSmiles('CC[13CH3]').GetAtomsMatchingQuery(q))

Out[7]: [2]



In [8]: list(x.GetIdx() for x in
Chem.MolFromSmiles('[12CH3]CC[13CH3]').GetAtomsMatchingQuery(q))

Out[8]: [0, 3]



Does that do what you want it to do?



-greg







On Wed, Jan 18, 2017 at 3:56 PM, Milinda Samaraweera <
milindaatw...@gmail.com> wrote:

Dear Experts,

I am trying to figure out a way to exclude entries which contain heavy
atoms (13C, 2H, 3H, etc), from a SD file (which has close to two thousand
entries) and write an updated file with the remaining entries.

I do understand how to read/write SD files using rdkit.

What I do understand is how to detect entries with heavy isotopes: Is there
an efficient and correct way of achieving this using rdkit?



thanks,

-- 

Milinda Samaraweera



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-- 

Milinda Samaraweera, Ph.D.

Postdoctoral Fellow, Department of Pharmacy

University of Connecticut

69 North Eagleville road

Storrs, CT, 06269

milindaatw...@gmail.com
860-617-8046
--
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Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Stiefl, Nikolaus 
Hi
Maybe this is much less efficient but I guess if you need it for specific 
isotopes then you could try using a smarts pattern and check for that?

In [20]: q = Chem.MolFromSmarts("[13C,14C,2H,3H,15N,24P,46P,33S,34S,36S]")

In [21]: m = Chem.MolFromSmiles('CC[15NH2]')

In [22]: m.HasSubstructMatch(q)
Out[22]: True


So you could loop over your molecules and then remove the ones that match the 
smarts.
Ciao
Nik


From: Milinda Samaraweera <milindaatw...@gmail.com>
Date: Wednesday 18 January 2017 at 20:47
To: Greg Landrum <greg.land...@gmail.com>
Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

Greg,
I am looking to remove entries that contain un-stable isotopes of elements 
CHNOPS (e.g. heavy_isotopes =['13C', '14C', '2H', '3H', '15N', '24P', '46P', 
'33S', '34S', '36S'] ). Is there a way to modify the above code to achieve that?
Thanks,
Milinda


On Wed, Jan 18, 2017 at 11:16 AM, Greg Landrum 
<greg.land...@gmail.com<mailto:greg.land...@gmail.com>> wrote:
Hi Milinda,

Here's an approach that finds all the atoms that have an isotope specified:

In [1]: from rdkit import Chem

In [2]: from rdkit.Chem import rdqueries

In [3]: q = rdqueries.IsotopeGreaterQueryAtom(1)

In [7]: list(x.GetIdx() for x in 
Chem.MolFromSmiles('CC[13CH3]').GetAtomsMatchingQuery(q))
Out[7]: [2]

In [8]: list(x.GetIdx() for x in 
Chem.MolFromSmiles('[12CH3]CC[13CH3]').GetAtomsMatchingQuery(q))
Out[8]: [0, 3]

Does that do what you want it to do?

-greg



On Wed, Jan 18, 2017 at 3:56 PM, Milinda Samaraweera 
<milindaatw...@gmail.com<mailto:milindaatw...@gmail.com>> wrote:
Dear Experts,
I am trying to figure out a way to exclude entries which contain heavy atoms 
(13C, 2H, 3H, etc), from a SD file (which has close to two thousand entries) 
and write an updated file with the remaining entries.

I do understand how to read/write SD files using rdkit.

What I do understand is how to detect entries with heavy isotopes: Is there an 
efficient and correct way of achieving this using rdkit?

thanks,
--
Milinda Samaraweera

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
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--
Milinda Samaraweera, Ph.D.
Postdoctoral Fellow, Department of Pharmacy
University of Connecticut
69 North Eagleville road
Storrs, CT, 06269
milindaatw...@gmail.com<mailto:milindaatw...@gmail.com>
860-617-8046
--
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Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Milinda Samaraweera 
Nik,

That works too...

Thanks
Milinda

On Wed, Jan 18, 2017 at 3:08 PM, Stiefl, Nikolaus <
nikolaus.sti...@novartis.com> wrote:

> Hi
>
> Maybe this is much less efficient but I guess if you need it for specific
> isotopes then you could try using a smarts pattern and check for that?
>
>
>
> In [*20*]: q = Chem.MolFromSmarts("[13C,14C,2H,3H,15N,24P,46P,33S,34S,36S]
> ")
>
>
>
> In [*21*]: m = Chem.MolFromSmiles('CC[15NH2]')
>
>
>
> In [*22*]: m.HasSubstructMatch(q)
>
> Out[*22*]: True
>
>
>
>
>
> So you could loop over your molecules and then remove the ones that match
> the smarts.
>
> Ciao
>
> Nik
>
>
>
>
>
> *From: *Milinda Samaraweera <milindaatw...@gmail.com>
> *Date: *Wednesday 18 January 2017 at 20:47
> *To: *Greg Landrum <greg.land...@gmail.com>
> *Cc: *RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
> *Subject: *Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit
>
>
>
> Greg,
>
> I am looking to remove entries that contain un-stable isotopes of elements
> CHNOPS (e.g. heavy_isotopes =['13C', '14C', '2H', '3H', '15N', '24P',
> '46P', '33S', '34S', '36S'] ). Is there a way to modify the above code to
> achieve that?
>
> Thanks,
>
> Milinda
>
>
>
>
>
> On Wed, Jan 18, 2017 at 11:16 AM, Greg Landrum <greg.land...@gmail.com>
> wrote:
>
> Hi Milinda,
>
>
>
> Here's an approach that finds all the atoms that have an isotope specified:
>
>
>
> In [1]: from rdkit import Chem
>
>
>
> In [2]: from rdkit.Chem import rdqueries
>
>
>
> In [3]: q = rdqueries.IsotopeGreaterQueryAtom(1)
>
>
>
> In [7]: list(x.GetIdx() for x in Chem.MolFromSmiles('CC[13CH3]'
> ).GetAtomsMatchingQuery(q))
>
> Out[7]: [2]
>
>
>
> In [8]: list(x.GetIdx() for x in Chem.MolFromSmiles('[12CH3]CC[13CH3]').
> GetAtomsMatchingQuery(q))
>
> Out[8]: [0, 3]
>
>
>
> Does that do what you want it to do?
>
>
>
> -greg
>
>
>
>
>
>
>
> On Wed, Jan 18, 2017 at 3:56 PM, Milinda Samaraweera <
> milindaatw...@gmail.com> wrote:
>
> Dear Experts,
>
> I am trying to figure out a way to exclude entries which contain heavy
> atoms (13C, 2H, 3H, etc), from a SD file (which has close to two thousand
> entries) and write an updated file with the remaining entries.
>
> I do understand how to read/write SD files using rdkit.
>
> What I do understand is how to detect entries with heavy isotopes: Is
> there an efficient and correct way of achieving this using rdkit?
>
>
>
> thanks,
>
> --
>
> Milinda Samaraweera
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
>
>
>
> --
>
> Milinda Samaraweera, Ph.D.
>
> Postdoctoral Fellow, Department of Pharmacy
>
> University of Connecticut
>
> 69 North Eagleville road
>
> Storrs, CT, 06269
>
> milindaatw...@gmail.com
> 860-617-8046 <(860)%20617-8046>
>



-- 
Milinda Samaraweera, Ph.D.
Postdoctoral Fellow, Department of Pharmacy
University of Connecticut
69 North Eagleville road
Storrs, CT, 06269
milindaatw...@gmail.com
860-617-8046
--
Check out the vibrant tech community on one of the world's most
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Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Milinda Samaraweera 
Greg,

I am looking to remove entries that contain un-stable isotopes of elements
CHNOPS (e.g. heavy_isotopes =['13C', '14C', '2H', '3H', '15N', '24P',
'46P', '33S', '34S', '36S'] ). Is there a way to modify the above code to
achieve that?

Thanks,
Milinda



On Wed, Jan 18, 2017 at 11:16 AM, Greg Landrum 
wrote:

> Hi Milinda,
>
> Here's an approach that finds all the atoms that have an isotope specified:
>
> In [1]: from rdkit import Chem
>
> In [2]: from rdkit.Chem import rdqueries
>
> In [3]: q = rdqueries.IsotopeGreaterQueryAtom(1)
>
> In [7]: list(x.GetIdx() for x in Chem.MolFromSmiles('CC[13CH3]'
> ).GetAtomsMatchingQuery(q))
> Out[7]: [2]
>
> In [8]: list(x.GetIdx() for x in Chem.MolFromSmiles('[12CH3]CC[13CH3]').
> GetAtomsMatchingQuery(q))
> Out[8]: [0, 3]
>
> Does that do what you want it to do?
>
> -greg
>
>
>
> On Wed, Jan 18, 2017 at 3:56 PM, Milinda Samaraweera <
> milindaatw...@gmail.com> wrote:
>
>> Dear Experts,
>>
>> I am trying to figure out a way to exclude entries which contain heavy
>> atoms (13C, 2H, 3H, etc), from a SD file (which has close to two thousand
>> entries) and write an updated file with the remaining entries.
>>
>> I do understand how to read/write SD files using rdkit.
>>
>> What I do understand is how to detect entries with heavy isotopes: Is
>> there an efficient and correct way of achieving this using rdkit?
>>
>> thanks,
>> --
>> Milinda Samaraweera
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>


-- 
Milinda Samaraweera, Ph.D.
Postdoctoral Fellow, Department of Pharmacy
University of Connecticut
69 North Eagleville road
Storrs, CT, 06269
milindaatw...@gmail.com
860-617-8046
--
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Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Greg Landrum 
Hi Milinda,

Here's an approach that finds all the atoms that have an isotope specified:

In [1]: from rdkit import Chem

In [2]: from rdkit.Chem import rdqueries

In [3]: q = rdqueries.IsotopeGreaterQueryAtom(1)

In [7]: list(x.GetIdx() for x in
Chem.MolFromSmiles('CC[13CH3]').GetAtomsMatchingQuery(q))
Out[7]: [2]

In [8]: list(x.GetIdx() for x in
Chem.MolFromSmiles('[12CH3]CC[13CH3]').GetAtomsMatchingQuery(q))
Out[8]: [0, 3]

Does that do what you want it to do?

-greg



On Wed, Jan 18, 2017 at 3:56 PM, Milinda Samaraweera <
milindaatw...@gmail.com> wrote:

> Dear Experts,
>
> I am trying to figure out a way to exclude entries which contain heavy
> atoms (13C, 2H, 3H, etc), from a SD file (which has close to two thousand
> entries) and write an updated file with the remaining entries.
>
> I do understand how to read/write SD files using rdkit.
>
> What I do understand is how to detect entries with heavy isotopes: Is
> there an efficient and correct way of achieving this using rdkit?
>
> thanks,
> --
> Milinda Samaraweera
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
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Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Peter S. Shenkin 
How about a regex filter on the all-atom SMILES?

-P.

On Wed, Jan 18, 2017 at 9:56 AM, Milinda Samaraweera <
milindaatw...@gmail.com> wrote:

> Dear Experts,
>
> I am trying to figure out a way to exclude entries which contain heavy
> atoms (13C, 2H, 3H, etc), from a SD file (which has close to two thousand
> entries) and write an updated file with the remaining entries.
>
> I do understand how to read/write SD files using rdkit.
>
> What I do understand is how to detect entries with heavy isotopes: Is
> there an efficient and correct way of achieving this using rdkit?
>
> thanks,
> --
> Milinda Samaraweera
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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[Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Milinda Samaraweera 
Dear Experts,

I am trying to figure out a way to exclude entries which contain heavy
atoms (13C, 2H, 3H, etc), from a SD file (which has close to two thousand
entries) and write an updated file with the remaining entries.

I do understand how to read/write SD files using rdkit.

What I do understand is how to detect entries with heavy isotopes: Is there
an efficient and correct way of achieving this using rdkit?

thanks,
-- 
Milinda Samaraweera
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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