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

Hi Greg, Greg Landrum writes: > One thing that may help is this (somewhat older, but I believe still > accurate) post from Riccardo: > https://sourceforge.net/p/rdkit/mailman/message/30074971/ > > It's been a while since I looked at this (since I mainly use conda these

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

On Fri, Sep 15, 2017 at 1:37 PM, Loris Bennett wrote: > > When I did > > make test > > some of the tests failed: > > 61% tests passed, 46 tests failed out of 117 > > but most of the failures seemed to have been caused by > > ImportError: No module named rdkit >

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

Perfect, thank you! On Fri, Sep 15, 2017 at 9:47 AM, Greg Landrum wrote: > > > On Fri, Sep 15, 2017 at 9:25 AM, Michał Nowotka wrote: >> >> Thanks Greg, very helpful! >> Can you tell me how should I modify my code to provide the list of >> bonds to be

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

Greg Landrum writes: > On Fri, Sep 15, 2017 at 1:37 PM, Loris Bennett > wrote: > > When I did > > make test > > some of the tests failed: > > 61% tests passed, 46 tests failed out of 117 > > but most of the failures seemed to have been

[Rdkit-discuss] How to highligh a structure but avoid intersecting edges at the same time?

Hi, Thanks for all the help with 'forcing' molecule highlighing. I have a different (hopefully the last) problem now. When I align a structure to the pattern and highlight it I'm getting the attached result. The substructure is correctly aligned and highlighted but the other part intersects with

Re: [Rdkit-discuss] How to highligh a structure but avoid intersecting edges at the same time?

At the moment there's not a solution to that problem that I'm aware of. The constraints imposed by the alignment to the pattern end up confusing the rest of the coordinate generation code. -greg On Fri, Sep 15, 2017 at 4:08 PM, Michał Nowotka wrote: > Hi, > > Thanks for all

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

Well, if you have python 2.7 and 3.5 already running ,you can use (mini)conda for the RDKit installation (conda is anaconda but instead of one huge package you can install the packages you want including RDKit) On Fri, Sep 15, 2017 at 9:12 AM, Loris Bennett wrote: >

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

Thanks Greg, very helpful! Can you tell me how should I modify my code to provide the list of bonds to be highlighted, so I get the image generated by DrawMolecules looking the same way as produced by DrawMolecule? On Thu, Sep 14, 2017 at 4:36 PM, Greg Landrum wrote: > Hi

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

One thing that may help is this (somewhat older, but I believe still accurate) post from Riccardo: https://sourceforge.net/p/rdkit/mailman/message/30074971/ It's been a while since I looked at this (since I mainly use conda these days), but I just did a quick experiment with: mkdir build

Re: [Rdkit-discuss] Fixed scale drawing

Hi again, I've managed to make it work. Please find the working code attached as a notebook. Unfortunately, it seam there is a small bug with SetScale: if the diff in min/max x or y in the minimum point and maximum point is zero or close to zero, then the molecules are broken. I've added a margin

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

Hi Greg, Greg Landrum writes: > 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

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

BTW, python 3.6 is out since last Christmas ;-) (and made it to sub-release .2) On Fri, Sep 15, 2017 at 8:36 AM, Greg Landrum wrote: > I'll provide a more detailed answer in a bit, but since you aren't using > the system python anyway, is there any chance that you

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

On Fri, Sep 15, 2017 at 9:25 AM, Michał Nowotka wrote: > Thanks Greg, very helpful! > Can you tell me how should I modify my code to provide the list of > bonds to be highlighted, so I get the image generated by DrawMolecules > looking the same way as produced by DrawMolecule?

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

I'll provide a more detailed answer in a bit, but since you aren't using the system python anyway, is there any chance that you could switch to anaconda python on your machines? Anaconda is a great python distribution for scientific applications and it makes many things (including system