Re: [Rdkit-discuss] ImportError: No module named rdkit

On Thu, Sep 14, 2017 at 9:58 PM, Andrew Dalke wrote: > On Sep 14, 2017, at 19:26, Dimitri Maziuk wrote: > > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > > linux distros that will be officially with us until June 30,

Re: [Rdkit-discuss] Non-redundant database of molecules

I have try this command several times and doesn't fixed. Maybe because all the others commands, this works now. Thanks for the help -- Wandré Nunes de Pinho Veloso Professor Assistente - Unifei - Campus Avançado de Itabira-MG Doutorando em Bioinformática - Universidade Federal de Minas Gerais -

Re: [Rdkit-discuss] Non-redundant database of molecules

Hmm, your last command "conda install -c rdkit rdkit" should have been sufficient for the installation (after installing anaconda) On Thu, Sep 14, 2017 at 11:57 PM, Malitha Kabir wrote: > That's great to hear you got things running. That was basically due to the > path

Re: [Rdkit-discuss] Non-redundant database of molecules

That's great to hear you got things running. That was basically due to the path update. Have a great day! - malitha. On Sep 15, 2017 3:44 AM, "Wandré" wrote: > I don't know what I do, but now everything *is working fine.* > My last commands: > > Reinstall Anaconda2 > >

Re: [Rdkit-discuss] Non-redundant database of molecules

I don't know what I do, but now everything *is working fine.* My last commands: Reinstall Anaconda2 Trying to compile the RDKit - sudo tar xzvf RDKit_2016_03_1.tgz -C ~/anaconda2/ - vim ~/.bashrc (update the variables with the new path of rdkit) - . ~/.bashrc - cd ~/anaconda2/rdkit

Re: [Rdkit-discuss] Non-redundant database of molecules

I really can't do this right... I am thinking in reinstall Ubuntu and try again. Now the RDKit doesn't works. -- Wandré Nunes de Pinho Veloso Professor Assistente - Unifei - Campus Avançado de Itabira-MG Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG Pesquisador do

Re: [Rdkit-discuss] ImportError: No module named rdkit

On 09/14/2017 03:04 PM, Markus Sitzmann wrote: > Not on Centos 6 - Docker requires Centos 7 for the host system. You can't win... :( -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature

Re: [Rdkit-discuss] ImportError: No module named rdkit

Not on Centos 6 - Docker requires Centos 7 for the host system. On Thu, Sep 14, 2017 at 10:01 PM, Dimitri Maziuk wrote: > On 09/14/2017 02:58 PM, Andrew Dalke wrote: > > > If only Greg got as much money for long term RDKit support as Red Hat > > gets for long term RHEL

Re: [Rdkit-discuss] ImportError: No module named rdkit

On 09/14/2017 02:58 PM, Andrew Dalke wrote: > If only Greg got as much money for long term RDKit support as Red Hat > gets for long term RHEL support. :) Yep. But an rdkit docker container might be feasible. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison --

Re: [Rdkit-discuss] ImportError: No module named rdkit

On Sep 14, 2017, at 19:26, Dimitri Maziuk wrote: > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > linux distros that will be officially with us until June 30, 2024. If only Greg got as much money for long term RDKit support as Red Hat gets for

Re: [Rdkit-discuss] bad inchi or parsing problem?

Thanks to Curt, Markus, and John for helping me understand this. I knew that inchi had its limitations, but that didn't jump out at me here because there's no hydrogen migration between the different forms - not realizing these forms also qualify as tautomers. But So this is definitely a feature

Re: [Rdkit-discuss] ImportError: No module named rdkit

On Thu, Sep 14, 2017 at 9:07 PM, Dimitri Maziuk wrote: > > All great when it's one computer and that one's your own personal laptop. > > > # yum ls \*python27\* > > ... > > python27.x86_642.7.13-2.ius.el6 > @salt-2015.8 > >

Re: [Rdkit-discuss] ImportError: No module named rdkit

On Thu, Sep 14, 2017 at 7:26 PM, Dimitri Maziuk wrote: > On 09/14/2017 10:43 AM, Greg Landrum wrote: > > > Just to do some expectation management: python 2.6 is pretty ancient and > > there's no guarantee that all of the RDKit code will work with it. Python > > 2.7 is the

Re: [Rdkit-discuss] bad inchi or parsing problem?

On Thu, Sep 14, 2017 at 8:09 PM, Jason Biggs wrote: > Okay, all three of these smiles strings resolve to the same inchi, > > "O=[N+](C1=NC2=CC=CC=C2N=C1)[N-](=O)C1=NC2=CC=CC=C2N=C1" > "C1=CC=C2C(=C1)N=CC(=N2)N(=N(=O)C3=NC4=CC=CC=C4N=C3)=O" >

Re: [Rdkit-discuss] bad inchi or parsing problem?

On Thu, Sep 14, 2017 at 8:09 PM, Jason Biggs wrote: > Okay, all three of these smiles strings resolve to the same inchi, > > "O=[N+](C1=NC2=CC=CC=C2N=C1)[N-](=O)C1=NC2=CC=CC=C2N=C1" > "C1=CC=C2C(=C1)N=CC(=N2)N(=N(=O)C3=NC4=CC=CC=C4N=C3)=O" >

Re: [Rdkit-discuss] bad inchi or parsing problem?

On Thu, Sep 14, 2017 at 7:38 PM, John Mayfield wrote: > InChI is an identifier and not a representation, you should not read > InChIs... but we are beyond hope there so... > Wonderfully said - unfortunately one day they decided to make InChIs "readable" ... > The

Re: [Rdkit-discuss] bad inchi or parsing problem?

I'm not 100% sure about this particular case, but I suspect this is a limitation of InChI. For example, the InChI representation of zwitterionic phenylalanine (negative COO-, positive NH3+) and "neutral" phenylalanine (neutral COOH, neutral NH2) is exactly the same. This is by design. See

Re: [Rdkit-discuss] ImportError: No module named rdkit

On 09/14/2017 01:41 PM, Riccardo Vianello wrote: > True, but there shouldn't be any strong need for using the system python > for running application software. Python 2.7 (together with python 3) has > been available to RHEL6 subscribers since almost five years, as part of the > Red Hat Software

Re: [Rdkit-discuss] Fixed scale drawing

I've tried that, but ended up with molecules out of picture. I'll try again tomorrow and ping back here should I succeed. The real problem were two atom molecules, which have delta x or y = 0, such as C=0 or CN. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl

Re: [Rdkit-discuss] ImportError: No module named rdkit

On Thu, Sep 14, 2017 at 7:26 PM, Dimitri Maziuk wrote: > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > linux distros that will be officially with us until June 30, 2024. > True, but there shouldn't be any strong need for using the system

Re: [Rdkit-discuss] bad inchi or parsing problem?

Okay, all three of these smiles strings resolve to the same inchi, "O=[N+](C1=NC2=CC=CC=C2N=C1)[N-](=O)C1=NC2=CC=CC=C2N=C1" "C1=CC=C2C(=C1)N=CC(=N2)N(=N(=O)C3=NC4=CC=CC=C4N=C3)=O" "[O-][N+](c1cnc2c2n1)=[N+]([O-])c3cnc4c4n3" even though to me they seem like different structures due to the

Re: [Rdkit-discuss] Non-redundant database of molecules

Hi Wandré, Sorry to see you in trouble again. If you see the massages then # All requested packages already installed. # packages in environment at /home/wandre/anaconda2: # rdkit 2017.03.3 np111py27_1rdkit so your rdkit should be at /home/wandre/anaconda2/

Re: [Rdkit-discuss] Non-redundant database of molecules

Thanks Malitha, When I install Anaconda I said yes to all questions. When I trying to reinstall the RDKit, this message appears: wandre@wandreLinux:~/anaconda2$ conda install -c rdkit rdkit Fetching package metadata ... Solving package specifications: . # All requested packages already

Re: [Rdkit-discuss] bad inchi or parsing problem?

InChI is an identifier and not a representation, you should not read InChIs... but we are beyond hope there so... The InChI string is correct and is the same if you roundtrip your preferred one with charge separated bonds and the 5 valent one. All toolkits will use the InChI library to

Re: [Rdkit-discuss] ImportError: No module named rdkit

On 09/14/2017 10:43 AM, Greg Landrum wrote: > Just to do some expectation management: python 2.6 is pretty ancient and > there's no guarantee that all of the RDKit code will work with it. Python > 2.7 is the minimum version that we "officially" support. It's a very good > idea to update. Just

Re: [Rdkit-discuss] counting stereocenters

Hi Daniel, this is some oddity that happens with molecules constructed from InChIs. CalcNumAtomStereoCenters() returns sensible results if you call it on the molecules constructed from SMILES: In [24]: mol_list2 = [Chem.MolFromSmiles(Chem.MolToSmiles(mol,True)) for mol in mol_list] In [25]:

Re: [Rdkit-discuss] ImportError: No module named rdkit

Hi Loris, On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett wrote: > > I am trying to install RDKit on a university cluster running Linux from > source. The build seem to go OK and 'make install' copied the > directories > > lib > rdkit > > to the NFS share where

Re: [Rdkit-discuss] Using the new drawing code

Hi Michal, There are a couple of things in here. On Fri, Aug 25, 2017 at 11:42 AM, Michał Nowotka wrote: > Hi, > > I finally decided to try the new C++ drawing code and I found some > issues with it. I'll try to descibe my problems. > > First, lets start with a code that

Re: [Rdkit-discuss] Fixed scale drawing

Hi Maciek, You can do this by calling setScale() method on MolDraw2D(). There's not a decent python example around yet (would be something for the cookbook I suppose), but the C++ code isn't too complex and demonstrates how it works:

[Rdkit-discuss] counting stereocenters

Hi All, I have a list of compounds (InChi strings) that I need to filter. Basically I need to identify which molecules are missing stereo information. I came across the "CalcNumUnspecifiedAtomStereoCenters" which sounded exactly like what I needed, but unfortunately all it does it return 0s,

[Rdkit-discuss] ImportError: No module named rdkit

Hi, I am trying to install RDKit on a university cluster running Linux from source. The build seem to go OK and 'make install' copied the directories lib rdkit to the NFS share where the software should reside. I then do export RDBASE=/cm/shared/apps/rdkit/rdkit_2017_03_3 export

Re: [Rdkit-discuss] Non-redundant database of molecules

Hi Wandré, Good day! It's malitha. Considering your first question I would say, the path variable NOT set correctly. To avoid having gymnastic with linux system you may consider the following steps: 1. Install miniconda or andcona from https://conda.io/miniconda.html and command yes (y)

Re: [Rdkit-discuss] HasSubstructMatch doesn't work as expected

On Thu, Sep 14, 2017 at 12:05 PM, Michał Nowotka wrote: > Using > > params = AdjustQueryParameters() > params.makeAtomsGeneric = True > params.makeBondsGeneric = True > pattern = AdjustQueryProperties(pattern, params) > > Seems to solve my problem - I'm getting

Re: [Rdkit-discuss] is there an issue with my code or with GetNeighbors function ?

Dear Guillaume, I'm not sure what your code should do and what behavior you expect. I see that you do not change the value of t when you see a single bond. So maybe you just do not update this value and print and old one? Also, you iterate over bonds of atom's last neighbor (so for H you loop

Re: [Rdkit-discuss] Non-redundant database of molecules

So, 1) I run all the commands in tutorial of installation of RDKit in Conda ( https://github.com/rdkit/conda-rdkit), but, when I run python and try to import Chem ("from rdkit import Chem") appears an error message: Traceback (most recent call last): File "", line 1, in File

Re: [Rdkit-discuss] is there an issue with my code or with GetNeighbors function ?

Dear Marta, this function works now: from rdkit import Chem from rdkit.Chem.rdchem import BondType AROMATIC = BondType.AROMATIC SINGLE = BondType.SINGLE DOUBLE = BondType.DOUBLE TRIPLE = BondType.TRIPLE def atomtype(mol,atom): t=1 for linkatoms in atom.GetNeighbors():

Re: [Rdkit-discuss] HasSubstructMatch doesn't work as expected

Using params = AdjustQueryParameters() params.makeAtomsGeneric = True params.makeBondsGeneric = True pattern = AdjustQueryProperties(pattern, params) Seems to solve my problem - I'm getting a match now (but I haven't yet verified if the match is correct and I don't understand why

[Rdkit-discuss] is there an issue with my code or with GetNeighbors function ?

Dear all from rdkit import Chem from rdkit.Chem.rdchem import BondType AROMATIC = BondType.AROMATIC SINGLE = BondType.SINGLE DOUBLE = BondType.DOUBLE TRIPLE = BondType.TRIPLE suppl = Chem.SDMolSupplier('/Users/GVALMTGG/Downloads/neemp-sources/examples/set00.sdf',removeHs = False) i=0 for

[Rdkit-discuss] is there an issue with my code or with GetNeighbors function ?

? Dear all from rdkit import Chem from rdkit.Chem.rdchem import BondType AROMATIC = BondType.AROMATIC SINGLE = BondType.SINGLE DOUBLE = BondType.DOUBLE TRIPLE = BondType.TRIPLE suppl = Chem.SDMolSupplier('/Users/GVALMTGG/Downloads/neemp-sources/examples/set00.sdf',removeHs = False) i=0

[Rdkit-discuss] is there an issue with my code or with GetNeighbors function ?

Dear all from rdkit import Chem from rdkit.Chem.rdchem import BondType AROMATIC = BondType.AROMATIC SINGLE = BondType.SINGLE DOUBLE = BondType.DOUBLE TRIPLE = BondType.TRIPLE suppl = Chem.SDMolSupplier('/Users/GVALMTGG/Downloads/neemp-sources/examples/set00.sdf',removeHs = False) i=0

[Rdkit-discuss] Fixed scale drawing

Hi RDKitters! Quick question: is there a way to force drawing to output molecules on a grid image or separate in fixed scale (i.e. constant/matching bond length)? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl