Re: [Rdkit-discuss] problems with installation on conda with python 3.5 32-bit

2017-02-21 Thread Greg Landrum 
Michal,

This morning I did a win32 build of the RDKit with python 3.5 and pushed it
to anaconda. You should (hopefully) be able to do "conda install -c rdkit
rdkit" now and have things work. I will try python 2.7 tomorrow.

It turns out that this isn't much extra effort, so assuming this build
works I should be able to keep doing these.

-greg


On Mon, Feb 20, 2017 at 9:33 PM, Michal Krompiec 
wrote:

> Hi Greg,
> Thanks for your reply. Actually, >50% of my (prospective) users are stuck
> on 32-bit. It would be really nice to have a python3 build (even once a
> year) but I understand that the demand is low and waning. I guess the
> solution is to use python2.7 for the time being...
> Thanks and kind regards,
> Michal
>
> On Monday, 20 February 2017, Greg Landrum  wrote:
>
>> Hi Michal,
>>
>> We've only ever done python2.7 builds for win32 and we stopped doing
>> those with the 2016.03 release.
>> I will have to check, but I think I probably can start doing these again,
>> but I'm reluctant due to the amount of effort required.
>> How many users do you need to support who are stuck on 32bit machines?
>>
>> -greg
>>
>>
>> On Mon, Feb 20, 2017 at 2:18 PM, Michal Krompiec <
>> michal.kromp...@gmail.com> wrote:
>>
>>> Hello,
>>> I can't install rdkit on anaconda with 32-bit python3 on Windows 7.
>>>
>>> When I try "the usual", conda tries to install python2.7 into the
>>> environment:
>>>
>>> >conda create -c rdkit -n my-rdkit-env rdkit
>>> Fetching package metadata .
>>> Solving package specifications: .
>>> Package plan for installation in environment
>>> C:\Anaconda3_32\envs\my-rdkit-env:
>>> The following NEW packages will be INSTALLED:
>>> boost:  1.56.0-py27_3 rdkit
>>> bzip2:  1.0.6-vc9_3 [vc9]
>>> mkl:2017.0.1-0
>>> numpy:  1.11.3-py27_0
>>> pip:9.0.1-py27_1
>>> python: 2.7.13-0
>>> rdkit:  2016.03.1-np111py27_1 rdkit
>>> setuptools: 27.2.0-py27_1
>>> vs2008_runtime: 9.00.30729.5054-0
>>> wheel:  0.29.0-py27_0
>>> zlib:   1.2.8-vc9_3 [vc9]
>>>
>>> If I create an empty environment, load python 3.5 into it and try
>>> installing rdkit, I get an error:
>>>
>>> >conda create -n my-rdkit-env python=3.5
>>> Fetching package metadata ...
>>> Solving package specifications: .
>>> Package plan for installation in environment
>>> C:\Anaconda3_32\envs\my-rdkit-env:
>>> The following NEW packages will be INSTALLED:
>>> pip:9.0.1-py35_1
>>> python: 3.5.2-0
>>> setuptools: 27.2.0-py35_1
>>> vs2015_runtime: 14.0.25123-0
>>> wheel:  0.29.0-py35_0
>>> Proceed ([y]/n)?
>>> #
>>> # To activate this environment, use:
>>> # > activate my-rdkit-env
>>> #
>>> # To deactivate this environment, use:
>>> # > deactivate my-rdkit-env
>>> #
>>> # * for power-users using bash, you must source
>>> #
>>>
>>> >conda install --name my-rdkit-env -f --channel
>>> https://conda.anaconda.org/rdkit rdkit
>>> Fetching package metadata .
>>> Solving package specifications: .
>>>
>>> UnsatisfiableError: The following specifications were found to be in
>>> conflict:
>>>   - python 3.5*
>>>   - rdkit -> python 2.7*
>>> Use "conda info " to see the dependencies for each package.
>>>
>>>
>>> I managed to install rdkit without any problems on the same machine in
>>> 64-bit anaconda with python3.5, but I need a separate 32-bit build to
>>> support users with 32-bit machines. Any help will be appreciated.
>>>
>>> Thanks and best regards,
>>>
>>> Michal
>>>
>>>
>>> 
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>>>
>>>
>>
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Re: [Rdkit-discuss] Problems with installation on Windows

2017-02-21 Thread Greg Landrum 
Hi Ilenia

The distributions available on github at the moment are source only. I
stopped doing the windows binaries on github because we now provide conda
builds for windows (and keep those up to date). If there is significant
interest from the community, I can think about going back to doing windows
builds for at least the first patch release of each new RDKit release.

How many windows users are there out there who can't use Anaconda Python?
-greg





On Tue, Feb 21, 2017 at 3:26 PM, Ilenia Giangreco 
wrote:

> Hello!
>
>
>
> I’d like to upgrade to the latest version of RDKit but I’m having troubles
> installing it.
>
> I’ve downloaded the zip folder from here
> , extracted it, renamed to
> “RDKit” and copied into C:\
>
> My environment variables are:
>
>- RDBASE: C:\RDKit
>- PYTHONPATH: C:\RDKit
>- PATH C:\RDKit\lib
>
>
>
> However, if I try to import Chem I get the following error message.
>
>
>
> Any help would be appreciated.
>
>
>
> Many thanks,
>
> Ilenia
>
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> and a Registered Charity. Registered in England No. 2155347 Registered
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[Rdkit-discuss] Problems with installation on Windows

2017-02-21 Thread Ilenia Giangreco 
Hello!

I'd like to upgrade to the latest version of RDKit but I'm having troubles 
installing it.
I've downloaded the zip folder from 
here, extracted it, renamed to "RDKit" 
and copied into C:\
My environment variables are:

  *   RDBASE: C:\RDKit
  *   PYTHONPATH: C:\RDKit
  *   PATH C:\RDKit\lib

However, if I try to import Chem I get the following error message.
[cid:image003.jpg@01D28C4E.6F2E78E0]

Any help would be appreciated.

Many thanks,
Ilenia


LEGAL NOTICE
Unless expressly stated otherwise, information contained in this
message is confidential. If this message is not intended for you,
please inform postmas...@ccdc.cam.ac.uk and delete the message.
The Cambridge Crystallographic Data Centre is a company Limited
by Guarantee and a Registered Charity.
Registered in England No. 2155347 Registered Charity No. 800579
Registered office 12 Union Road, Cambridge CB2 1EZ.


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Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecule

2017-02-21 Thread Chris Swain 
Sorry if I’m a bit late to the discussion, this is the sort of thing I use 
Openbabel for

http://openbabel.org/wiki/Obfit 

Align all the molecules in "testmv.sdf" on a single molecule of "testref.sdf" 
by superimposing them on its N-methylpiperidyl portion (and outputting a new SD 
file to the standard output):

obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf



> 
>> 
>> Thank you for your useful hints. All the compounds that I want to align
>> are supposed to belong to the same analogue series so they should shave a
>> common substructure with substantial size.

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Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

2017-02-21 Thread Thomas Evangelidis 
Hi Greg,

Many thanks for the awesome post! I am still having trouble though to
select the right reference ligand for each query molecule. In particular I
have 9 crystal ligands, so these are the possible scenarios given one query
compound:

1) Measure the overall fingerprint similarity between the query and each
crystal ligands. Use as reference the crystal ligand with the highest
fingerprint similarity to the query.

2) Do the same but considering only the scaffolds of the query and the
crystal ligands.

3) Find the MCS between the query and each crystal ligand and use as
reference the crystal ligand with the biggest MCS (excluding hydrogens).

4) Like 3) but considering only the scaffolds of the query and the crystal
ligands.

If someone had experience the same problem and could recommend which way
works best or suggest any better way I would be very grateful.

Thomas





On 21 February 2017 at 07:35, Greg Landrum  wrote:

>
>
> On Mon, Feb 20, 2017 at 6:17 PM, Thomas Evangelidis 
> wrote:
>
>>
>> Thank you for your useful hints. All the compounds that I want to align
>> are supposed to belong to the same analogue series so they should shave a
>> common substructure with substantial size.
>>
>
> In that case, using an MCS based alignment should work reasonably well,
> particularly if you do the MCS of the entire series instead of doing it
> pairwise. The approach there would be to find the MCS and then use the
> RDKit's RMSD-based alignment (AllChem.AlignMol) where you provide the
> atomMap argument to specify the atom--atom mapping for alignment.
>
> Here's a short example of how to do that:
>
> # generate 3d structures (in case you don't have them already):
> mhs = [Chem.AddHs(x) for x in mols]
> [AllChem.EmbedMolecule(x,AllChem.ETKDG()) for x in mhs]
> mols = [Chem.RemoveHs(x) for x in mhs]
>
> # Find the MCS:
> from rdkit.Chem import rdFMCS
> mcs = rdFMCS.FindMCS(mols,threshold=0.8,completeRingsOnly=True,
> ringMatchesRingOnly=True)
>
> # align everything to the first molecule
> patt = Chem.MolFromSmarts(mcs.smartsString)
> refMol = mols[0]
> refMatch = refMol.GetSubstructMatch(patt)
> rmsVs = []
> for probeMol in mols[1:]:
> mv = probeMol.GetSubstructMatch(patt)
> rms = AllChem.AlignMol(probeMol,refMol,atomMap=list(zip(mv,refMatch)))
> rmsVs.append(rms)
>
>
> What I want to emulate is the "core restrained docking" with glide, where
>> you specify the common core of the query and the reference ligand using a
>> SMARTS pattern and then glide docks the query compound to the binding
>> pocket but takes care to overlay the core atoms of the query to the core
>> atoms of the reference compound. Since RDKit does not do docking, I just
>> generate 30 conformers of each query compound and select the best one by
>> measuring the RMSD between the core of the query and the core of the
>> reference after the alignment. Of course the conformations of the core
>> atoms between the query and the reference are never identical hence the bad
>> alignment. Is there any smarter way to emulate the "core restrained
>> docking" with RDKit?
>>
>
> The docking part is not doable in any straightforward way at the moment
> since it's hard to take information about the protein into account. There's
> an idea for a student summer project to solve this problem floating around,
> let's see if that gets funded and we find the right student.
>
> If the goal is to generate a set of conformations where cores are aligned
> with each other, this blog post may be interesting:
> http://rdkit.blogspot.ch/2013/12/using-allchemconstrainedembed.html
>
> -greg
>
>


-- 

==

Thomas Evangelidis

Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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