[Rdkit-discuss] How to get more CPU utilization for RDkit calculations

[James T. Metz via Rdkit-discuss]

RDkit Discussion Group,


I am running the RDkit diverse max min picker code on my WINDOWS 7
64 bit 4 dual core I7 computer.  I have tested the code on a small set of 
compounds
and the results are OK.


I am now running diverse subset picking on an SDF containing about 40k 
compounds.  The CPU usage across all 8 CPUs is about 14 - 15 %.  Are there
any flags or parameters that can be set in the PYTHON or RDkit code to get
more CPU utilization?  Thank you.


Jim Metz

Metz Research LLC




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[Rdkit-discuss] (no subject)

[Phuong Chau]

Hello,

I am writing most of my code on Java but I need to use the fingerprint
function from RDkit. Is there a way to run fingerprint function on Java?
Thank you so much for your help!

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Re: [Rdkit-discuss] PDBBlock file

[Phuong Chau]

Hi,

I am using the 2015.03.1 version. How do I update to the newest version? I
used the same command line as it mentioned in this website:
https://github.com/rdkit/rdkit/releases

sudo apt-get install python-rdkit librdkit1 rdkit-data



On Fri, Jul 6, 2018 at 10:47 AM, Greg Landrum 
wrote:

> How old is the version of the RDKit that you are using?
> If you are using the most recent version, AllChem.EmbedMolecule() will use
> the correct parameters by default.
>
> -greg
>
>
> On Fri, Jul 6, 2018 at 6:28 PM Phuong Chau  wrote:
>
>> I tried the code: AllChem.EmbedMolecule(x, params = AllChem.ETKDGv2())
>>
>> but it shows me the error:
>> AttributeError: 'module' object has no attribute 'ETKDGv2'
>>
>> How do I fix this problem? I imported rdkit.Chem and AllChem.
>>
>>
>> On Fri, Jul 6, 2018 at 10:03 AM, Sereina 
>> wrote:
>>
>>> The default conformer generator in RDKit is plain distance geometry,
>>> which is known to not be able to provide perfectly flat aromatic rings.
>>> You can use the ETKDG conformer generator instead:
>>>
>>> AllChem.EmbedMolecule(mol, params=AllChem.ETKDGv2())
>>>
>>> Best,
>>> Sereina
>>>
>>>
>>> On 6 Jul 2018, at 17:54, Phuong Chau  wrote:
>>>
>>> Follow up question regarding to PDB file:
>>>
>>> Thank you for your help. I was able to create the non-zero coordinates
>>> of the chemical. However, when I tried to view it on VMD, the chemical that
>>> I used is c1c1 (benzene). The ring itself (and the atoms coming off it,
>>> which are mostly hydrogens) should all be in-plane but the pdb file shows
>>> that it is slightly puckered. Would anyone explain this for me? How can I
>>> make it be in-plane ?
>>>
>>> Here is a screenshot of the molecule.
>>> 
>>> ​
>>>
>>> On Fri, Jul 6, 2018 at 6:21 AM, Dmitri Maziuk via Rdkit-discuss <
>>> rdkit-discuss@lists.sourceforge.net> wrote:
>>>
 On 7/5/2018 1:39 PM, Paolo Tosco wrote:

 As the PDB format includes no stereochemistry, no coordinates are
> needed, and by default they are zero, as the molecule does not have a
> conformation yet.
>

 Hmm. One could argue that PDB format *is* 3D coordinates, so a block
 with all zeroes is quite pointless. And of course counter-intuitive.

 Dima



 
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>>>
>>>
>>>
>>> --
>>> Phuong Chau
>>> Smith College '20
>>> Engineering Major
>>> 
>>> --
>>> 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
>>>
>>>
>>>
>>
>>
>> --
>> Phuong Chau
>> Smith College '20
>> Engineering Major
>> 
>> --
>> 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
>>
>


-- 
Phuong Chau
Smith College '20
Engineering Major
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Re: [Rdkit-discuss] PDBBlock file

[Greg Landrum]

How old is the version of the RDKit that you are using?
If you are using the most recent version, AllChem.EmbedMolecule() will use
the correct parameters by default.

-greg


On Fri, Jul 6, 2018 at 6:28 PM Phuong Chau  wrote:

> I tried the code: AllChem.EmbedMolecule(x, params = AllChem.ETKDGv2())
>
> but it shows me the error:
> AttributeError: 'module' object has no attribute 'ETKDGv2'
>
> How do I fix this problem? I imported rdkit.Chem and AllChem.
>
>
> On Fri, Jul 6, 2018 at 10:03 AM, Sereina 
> wrote:
>
>> The default conformer generator in RDKit is plain distance geometry,
>> which is known to not be able to provide perfectly flat aromatic rings.
>> You can use the ETKDG conformer generator instead:
>>
>> AllChem.EmbedMolecule(mol, params=AllChem.ETKDGv2())
>>
>> Best,
>> Sereina
>>
>>
>> On 6 Jul 2018, at 17:54, Phuong Chau  wrote:
>>
>> Follow up question regarding to PDB file:
>>
>> Thank you for your help. I was able to create the non-zero coordinates of
>> the chemical. However, when I tried to view it on VMD, the chemical that I
>> used is c1c1 (benzene). The ring itself (and the atoms coming off it,
>> which are mostly hydrogens) should all be in-plane but the pdb file shows
>> that it is slightly puckered. Would anyone explain this for me? How can I
>> make it be in-plane ?
>>
>> Here is a screenshot of the molecule.
>> 
>> ​
>>
>> On Fri, Jul 6, 2018 at 6:21 AM, Dmitri Maziuk via Rdkit-discuss <
>> rdkit-discuss@lists.sourceforge.net> wrote:
>>
>>> On 7/5/2018 1:39 PM, Paolo Tosco wrote:
>>>
>>> As the PDB format includes no stereochemistry, no coordinates are
 needed, and by default they are zero, as the molecule does not have a
 conformation yet.

>>>
>>> Hmm. One could argue that PDB format *is* 3D coordinates, so a block
>>> with all zeroes is quite pointless. And of course counter-intuitive.
>>>
>>> Dima
>>>
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>
>>
>>
>> --
>> Phuong Chau
>> Smith College '20
>> Engineering Major
>>
>> --
>> 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
>>
>>
>>
>
>
> --
> Phuong Chau
> Smith College '20
> Engineering Major
>
> --
> 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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>
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Re: [Rdkit-discuss] PDBBlock file

[Phuong Chau]

I tried the code: AllChem.EmbedMolecule(x, params = AllChem.ETKDGv2())

but it shows me the error:
AttributeError: 'module' object has no attribute 'ETKDGv2'

How do I fix this problem? I imported rdkit.Chem and AllChem.


On Fri, Jul 6, 2018 at 10:03 AM, Sereina  wrote:

> The default conformer generator in RDKit is plain distance geometry, which
> is known to not be able to provide perfectly flat aromatic rings.
> You can use the ETKDG conformer generator instead:
>
> AllChem.EmbedMolecule(mol, params=AllChem.ETKDGv2())
>
> Best,
> Sereina
>
>
> On 6 Jul 2018, at 17:54, Phuong Chau  wrote:
>
> Follow up question regarding to PDB file:
>
> Thank you for your help. I was able to create the non-zero coordinates of
> the chemical. However, when I tried to view it on VMD, the chemical that I
> used is c1c1 (benzene). The ring itself (and the atoms coming off it,
> which are mostly hydrogens) should all be in-plane but the pdb file shows
> that it is slightly puckered. Would anyone explain this for me? How can I
> make it be in-plane ?
>
> Here is a screenshot of the molecule.
> 
> ​
>
> On Fri, Jul 6, 2018 at 6:21 AM, Dmitri Maziuk via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
>> On 7/5/2018 1:39 PM, Paolo Tosco wrote:
>>
>> As the PDB format includes no stereochemistry, no coordinates are needed,
>>> and by default they are zero, as the molecule does not have a conformation
>>> yet.
>>>
>>
>> Hmm. One could argue that PDB format *is* 3D coordinates, so a block with
>> all zeroes is quite pointless. And of course counter-intuitive.
>>
>> Dima
>>
>>
>>
>> 
>> --
>> 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
>>
>
>
>
> --
> Phuong Chau
> Smith College '20
> Engineering Major
> 
> --
> 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
>
>
>


-- 
Phuong Chau
Smith College '20
Engineering Major
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Re: [Rdkit-discuss] PDBBlock file

[Sereina]

The default conformer generator in RDKit is plain distance geometry, which is 
known to not be able to provide perfectly flat aromatic rings.
You can use the ETKDG conformer generator instead:

AllChem.EmbedMolecule(mol, params=AllChem.ETKDGv2())

Best,
Sereina


> On 6 Jul 2018, at 17:54, Phuong Chau  wrote:
> 
> Follow up question regarding to PDB file:
> 
> Thank you for your help. I was able to create the non-zero coordinates of the 
> chemical. However, when I tried to view it on VMD, the chemical that I used 
> is c1c1 (benzene). The ring itself (and the atoms coming off it, which 
> are mostly hydrogens) should all be in-plane but the pdb file shows that it 
> is slightly puckered. Would anyone explain this for me? How can I make it be 
> in-plane ?
> 
> Here is a screenshot of the molecule.
> 
> ​
> 
> On Fri, Jul 6, 2018 at 6:21 AM, Dmitri Maziuk via Rdkit-discuss 
>  > wrote:
> On 7/5/2018 1:39 PM, Paolo Tosco wrote:
> 
> As the PDB format includes no stereochemistry, no coordinates are needed, and 
> by default they are zero, as the molecule does not have a conformation yet.
> 
> Hmm. One could argue that PDB format *is* 3D coordinates, so a block with all 
> zeroes is quite pointless. And of course counter-intuitive.
> 
> Dima
> 
> 
> 
> --
> 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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> Rdkit-discuss@lists.sourceforge.net 
> 
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 
> 
> 
> 
> 
> -- 
> Phuong Chau 
> Smith College '20
> Engineering Major 
> --
> 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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Re: [Rdkit-discuss] PDBBlock file

[Dmitri Maziuk via Rdkit-discuss]

On 7/5/2018 1:39 PM, Paolo Tosco wrote:

As the PDB format includes no stereochemistry, no coordinates are 
needed, and by default they are zero, as the molecule does not have a 
conformation yet.


Hmm. One could argue that PDB format *is* 3D coordinates, so a block 
with all zeroes is quite pointless. And of course counter-intuitive.


Dima


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