Re: [Rdkit-discuss] Dividing inputstream over threads
On 15/01/2019 09:53, Andreas Luttens wrote: Hi! I have developed a small script that calculates molecules properties for molecules that are stored in a SMILES file. The properties should be stored in an SQL database, which works fine, but I would like to speed up the process a bit. I was thinking of implementing some parallelization for the calculating of properties and storing into separate connections to my SQL database. I have done this before in Python with OpenEye and seems to be doing the trick. I would however want my code to useable by people who do not hold a license for OpenEye, which is why I try RDKit. I would like my code to be in C++ as well. In C++, you could use OpenMP and the parallel for pragma. I was wondering how I would tackle this problem. Does the RDKit have a similar functionality as an "oemolithread" to chunk up the incoming stream? I haven't found something like this when I first scrolled through documentation. If it is not implemented, how would I divide the work on incoming molecules over N threads? All help is very appreciated. Thanks in advance. Best regards, Andreas Luttens ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Dividing inputstream over threads
Hi! I have developed a small script that calculates molecules properties for molecules that are stored in a SMILES file. The properties should be stored in an SQL database, which works fine, but I would like to speed up the process a bit. I was thinking of implementing some parallelization for the calculating of properties and storing into separate connections to my SQL database. I have done this before in Python with OpenEye and seems to be doing the trick. I would however want my code to useable by people who do not hold a license for OpenEye, which is why I try RDKit. I would like my code to be in C++ as well. I was wondering how I would tackle this problem. Does the RDKit have a similar functionality as an "oemolithread" to chunk up the incoming stream? I haven't found something like this when I first scrolled through documentation. If it is not implemented, how would I divide the work on incoming molecules over N threads? All help is very appreciated. Thanks in advance. Best regards, Andreas Luttens ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Initialize RDKit Wrapper in Visual Basic
Thanks Greg. Starting from your suggestion, I was able to discover the source of the problem and have submitted a ticket to the issue tracker. A followup question: the reason I am looking to use RDKit in VB.NET is in order to call the 2D alignment function GenerateDepictionMatching2DStructure (perhaps AlignMolToTemplate2D might also work here). However, I'm not certain that either of these functions are exposed through the C# wrapper as I do not see them in the available functions in RDKFuncs.dll. Is there a definitive way to tell what subset of the RDKit is exposed in the RDKit2DotNet C# wrapper? Thank you. On Mon, Jan 14, 2019 at 7:39 AM Greg Landrum wrote: > > Hi, > > This is a tough one to help with since I don't know Visual Basic and don't > have a copy installed/available to play with > The .Net package does require some DLLs, but they are all included as part > of the nuget package (at least I see them when I download the package and > look at its contents): > [image: image.png] > > You might want to check to see if Visual Basic somehow isn't finding these. > > > > On Sat, Jan 12, 2019 at 7:24 AM Good Eats wrote: > >> Hi, >> I want to use RDKit within a Visual Basic program I have written. A bit >> of searching showed that a .NET wrapper for RDKit is available through the >> VisualBasic NuGet package manager. I was able to use NuGet to add the >> RDKit2DotNet package to my project. In the code I add the following and get >> a successful compile: >> >> Imports GraphMolWrap >> ... >> RDKit.Initialize()'Line 1 >> myMol = RDKFuncs.MolBlockToMol(myString) 'Line 2 >> >> However, when run, I get a "NullObject" runtime error at Line 1 with no >> other descriptive message. >> If I comment out Line 1 and run again, I get a "dll could not be loaded >> runtime error at line 2. Seems like I am missing a step somewhere. Am I >> supposed to download and register any other .dlls to use these wrappers? >> >> Thank you. >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Initialize RDKit Wrapper in Visual Basic
Hi, This is a tough one to help with since I don't know Visual Basic and don't have a copy installed/available to play with The .Net package does require some DLLs, but they are all included as part of the nuget package (at least I see them when I download the package and look at its contents): [image: image.png] You might want to check to see if Visual Basic somehow isn't finding these. On Sat, Jan 12, 2019 at 7:24 AM Good Eats wrote: > Hi, > I want to use RDKit within a Visual Basic program I have written. A bit of > searching showed that a .NET wrapper for RDKit is available through the > VisualBasic NuGet package manager. I was able to use NuGet to add the > RDKit2DotNet package to my project. In the code I add the following and get > a successful compile: > > Imports GraphMolWrap > ... > RDKit.Initialize()'Line 1 > myMol = RDKFuncs.MolBlockToMol(myString) 'Line 2 > > However, when run, I get a "NullObject" runtime error at Line 1 with no > other descriptive message. > If I comment out Line 1 and run again, I get a "dll could not be loaded > runtime error at line 2. Seems like I am missing a step somewhere. Am I > supposed to download and register any other .dlls to use these wrappers? > > Thank you. > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
