Re: [Rdkit-discuss] compiling error with C++ on maverick

Peter, Thanks. Do you mean -lLibA_static -lLibB_static -lLibC_static -lLibA_static -lLibB_static -lLibC_static ? So, by this way, we don't need to worry about the order of these three libraries. Best, Yingfeng On Wed, Mar 16, 2016 at 12:36 AM, Peter S. Shenkin wrote: >

Re: [Rdkit-discuss] compiling error with C++ on maverick

Well, it's inelegant. But as my post-doc advisor, Cy Levinthal, once said, "Elegance is for tailors". Cheers, -P. On Wed, Mar 16, 2016 at 10:38 AM, Yingfeng Wang wrote: > Peter, > > Thanks. This is a PERFECT general solution to all of this kind of > headaches! > > Best, >

Re: [Rdkit-discuss] molfileAlias

Too simple. Thanks, Jean-Marc Le 16/03/2016 19:34, Greg Landrum a écrit : On Wed, Mar 16, 2016 at 10:58 AM, Jean-Marc Nuzillard > wrote: thank you for this efficient answer. Just one question. How would have it

Re: [Rdkit-discuss] molfileAlias

Hi Jean-Marc, You use the molFileAlias property like this: #--- In [9]: m = Chem.MolFromSmiles('CCO') In [10]: m.GetAtomWithIdx(0).SetProp('molFileAlias','alias 0') In [11]: m.GetAtomWithIdx(2).SetProp('molFileAlias','the_oxygen') In [12]: print(Chem.MolToMolBlock(m))

Re: [Rdkit-discuss] Problems with building RDKit on Linux

On 18/03/2016 19:23, Mendez Giraldez, Raul wrote: > Yes, I think so Paul. my $LD_LIBRARY_PATH points towards the installed boost > (by conda) is : > >

Re: [Rdkit-discuss] Problems with building RDKit on Linux

On 17/03/2016 18:00, Mendez Giraldez, Raul wrote: > Hi everybody, > > I'm trying to build RDKit on Red Hat Enterprise Linux Server release > 5.11 and I get the following problem after trying to import rdkit libraries: > > > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > Type "help",

Re: [Rdkit-discuss] Molecular properties + pickling

This is not a bug nor a feature per se. You need to set the compounds as PropteryMOl Ie Ketone = [x for x in supplAlkylKetones if x is not None] for i in range(len(Ketone)): Ketone[i] = PropertyMol(Ketone[i]) From: Maciek Wójcikowski [mailto:mac...@wojcikowski.pl] Sent: Friday, March 18,

Re: [Rdkit-discuss] compiling error with C++ on maverick

Brian, I think this is a good idea. Basically, I want to address the following two situations: 1) A user wants to compile my C++ source code. I want to provide my source code and Makefile, and remind to install RDKit first (I don't think we need to mention boost, which is required by RDKit). 2)

Re: [Rdkit-discuss] Problems with building RDKit on Linux

Yes, I think so Paul. my $LD_LIBRARY_PATH points towards the installed boost (by conda) is : /nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/include/boost:/nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/lib BTW, one of the system administrators of our cluster

Re: [Rdkit-discuss] molfileAlias

Hi again, thank you for this efficient answer. Just one question. How would have it been possible for me to arrive at this answer without your help? Cheers, Jean-Marc Le 16/03/2016 17:25, Greg Landrum a écrit : Hi Jean-Marc, You use the molFileAlias property like this:

Re: [Rdkit-discuss] GetAvalonFP returns ValueError: Sanitization error: Can't kekulize mol

Hi Greg, Thanks for quick reply! I noticed that it works if it is constructed from SMILES, but the queries I usually have are more complex and are constructed from SMARTS especially because I also do some query adjustments (similar to what was discussed here

[Rdkit-discuss] Molecular properties + pickling

Hi all, Is it a bug or am I doing something wrong - the properties are not passed during pickling in python. Here comes the example: from rdkit import Chem import cPickle as pickle mol = Chem.MolFromSmiles('c1c1') mol.SetProp('aaa', '123') print list(mol.GetPropNames()) # ['aaa'] mol2 =

Re: [Rdkit-discuss] compiling error with C++ on maverick

One thing we could fairly easily set up is a "companion" CMakeLists.txt for a sample C++ project that builds a test project against a built distribution. It could prove useful as a basis for building C++ extensions. Basically we would hedge our bets and just link against everything :) Cheers,