Re: [Rdkit-discuss] has multiple H count specifications

Hi, There are two problems here: The warning is telling you that you've included inconsistent information about the product in the product specification. It's a good idea to just use dummies or plain atoms in the products and not include extra info in the products unless you really intend to. For

Re: [Rdkit-discuss] running RunReactants with Reactants that have a plus one charge

Hi, The reactants that are part of your reaction definition are queries. If those queries include a charge they won't match molecules that don't have a charge. If you'd like the reactant patterns to match neutral molecules as well as charged ones, just remove the charge from the reaction

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

Dear All, Thanks Greg! Using your command compilation line (see bellow), It's the first time I can really test mutlithread rdkit on my mac. "cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG

Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

David, Yes, it is very clear. I am confident to use the version Igor suggested now. Thanks. Yingfeng On Mon, Apr 11, 2016 at 8:36 AM, David Hall wrote: > When I want to replicate one of RDKit’s python functions in C++, I go to > the source. RDKit has very readable

Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

When I want to replicate one of RDKit’s python functions in C++, I go to the source. RDKit has very readable wrappers that make this a surprisingly nice approach (many other pieces of software have pretty ugly wrappers, so this is a major compliment to RDKit). For this, I think the source is:

Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

lgor, Yes, this version looks good. But, I am wondering whether I can specify asMols. I specify asMols in the python version of my tool, so I want to do the same thing for getting the same result in my C++ code. Or could you help me to confirm that the version you mentioned actually has the same

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

Gianluca, This could be the issue fixed by this PR from Matt Swain: https://github.com/rdkit/rdkit/pull/856 -greg On Mon, Apr 11, 2016 at 12:32 PM, Gianluca Sforna wrote: > On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum > wrote: > > I have tagged a

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum wrote: > I have tagged a beta of the next RDKit release here: > https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1 Tried to rebuild the RPMs but got this right on cmake: -- Found INCHI: /usr/lib64/libinchi.so

[Rdkit-discuss] has multiple H count specifications

hi Greg, when I use the AllChem.ReactionFromSmarts and the RunReactants predict a reaction,just like below: input transformation - "[CH2,CH3:8][OH:9].[O:1]=[O:2]>>[OH:1][OH:2].[CH2,CH3:8](=[O:9]", input reactants- reactants1 = ['CO','CCO','CC(C)O','COC','c1c1O',] reactants2= ['O=O']

[Rdkit-discuss] running RunReactants with Reactants that have a plus one charge

Hi Greg, when I run the AllChem.RunReactants with rxn'patterns that the reactant have a plus one charge ,like this : ''' patterns = [ "[NH+:2]1[C:3][C:4][C:5][C@@H:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",