Re: [Rdkit-discuss] conda build errors on Windows 10

[Bob Funchess]

Hi Greg,



A tutorial would be greatly appreciated.



Kind Regards,

Bob



*From:* Greg Landrum [mailto:greg.land...@gmail.com]
*Sent:* Friday, May 12, 2017 4:54 AM
*To:* Bob Funchess 
*Cc:* RDKit Discuss 
*Subject:* Re: [Rdkit-discuss] conda build errors on Windows 10



Hi Bob,



On Thu, May 11, 2017 at 10:31 PM, Bob Funchess 
wrote:



I’m curious as to whether anyone is able to get RDKit to build on Windows
10 with Visual Studio 2015; I’ve been trying off and on to get this to work
for some time now with no discernable success.



Yeah, I was able to do so both while doing the conda builds and during the
testing phase (where I do the build manually).



PS My ultimate goal is to build the RDKit DLL and the C# wrappers and
that’s all I fundamentally care about; Java, Python, Postgres et al. are
irrelevant to me except insofar as they help me get the C# wrappers… the
Python version would be NICE (for testing), but I don’t actually NEED it.
If anyone has actually successfully built RDKFuncs.DLL and RDKit2DotNet.DLL
using the current version of RDKit, I would greatly appreciate any pointers.



Yeah, for this I think you really don't need/want to be using the conda
stuff.



How about this: I'll put together a short tutorial/walk-through on doing a
build of the C# wrappers with VS2015 under Win10 and we can see if that
helps. I can try a first pass over the weekend.





-greg
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[Rdkit-discuss] Differences in chirality with BRICS fragmentation

[Stephen Pickett]

Hi

I have come across a difference in behaviour with the BRICS algorithms 
depending on how the molecule is fragmented when using non-canonical smiles 
input.
RDKIT 2015_03, Python 2.7.10

BRICSDecompose gives back the starting chirality

>>> smi='C1CCOC[C@H]1NC'
>>> mol=Chem.MolFromSmiles(smi)
>>> cansmi=Chem.MolToSmiles(mol,1)
>>> cansmi
'CN[C@H]1CCCOC1'
>>> frags=BRICS.BRICSDecompose(mol,returnMols=True)
>>> bm=list(BRICS.BRICSBuild(frags))
>>> [Chem.MolToSmiles(m,1) for m in bm]
['CN[C@H]1CCCOC1']

BreakBRICSBonds inverts the centre.
>>> frags=Chem.GetMolFrags(BRICS.BreakBRICSBonds(mol),asMols=True)
>>> bm=list(BRICS.BRICSBuild(frags))
>>> [Chem.MolToSmiles(m,1) for m in bm]
['CN[C@@H]1CCCOC1']

Starting from the canonical smiles works fine
>>> smi='CN[C@H]1CCCOC1'
>>> mol=Chem.MolFromSmiles(smi)
>>> frags=Chem.GetMolFrags(BRICS.BreakBRICSBonds(mol),asMols=True)
>>> bm=list(BRICS.BRICSBuild(frags))
>>> [Chem.MolToSmiles(m,1) for m in bm]
['CN[C@H]1CCCOC1']

The inversion happens in BreakBRICSBonds
>>> smi='C1CCOC[C@H]1NC'
>>> mol=Chem.MolFromSmiles(smi)
>>> Chem.MolToSmiles(BRICS.BreakBRICSBonds(mol),1)
'[15*][C@@H]1CCCOC1.[5*]NC'

Using the pre canonicalised SMILES is clearly the way to go, but thought that 
this might be indicative of an issue somewhere.

Regards

Stephen



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Re: [Rdkit-discuss] conda build errors on Windows 10

[Mike Mazanetz]

Hi Greg,

 

It would be great to have a tutorial/ walkthrough on the PostgreSQL :: RDKit 
implementation.  

Paolo supplied me with this in the past – awesome extremely helpful thanks, 
which worked up to a point…  I haven’t had time to revisit this.

 

Hope this is useful !

 

Best,

mike

 

 

Pre-requisites: install Python 3.5.2 in C:\Python35. Install CMake and make 
sure the CMake bin folder is in your PATH. Install Gohlke's numpy and Pillow 
into your Python 3.5.2. Install Eigen3 into C:\build. Install PostgreSQL.

1) Create a rdkit35.bat file which defines the following variables:

@echo off
set RDBASE=c:\build\rdkit
set PATH=C:\Python35;C:\Program Files\Git\bin;C:\Program 
Files\Git\usr\bin;C:\Program Files\Java\jdk1.8.0_31\bin;%PATH%
set PATH=C:\boost\boost_1_62_0_py35\lib64-msvc-14.0;%RDBASE%\lib;%PATH%
set PYTHONPATH=%RDBASE%

The above assumes that you installed Python 3 in C:\Python35, that you have the 
Microsoft Git in C:\Program Files\Git, and Java in C:\Program 
Files\Java\jdk1.8.0_31, and that you are going to install boost in C:\boost, 
and rdkit in C:\build. Adjust paths as needed.

2) Open a CMD window, source the above bat file:

rdkit35.bat

Make sure that the Python version in your path (the one which starts issuing 
the python command) is the one you wish to build the boost-python library 
against.

3) Build Boost.

Create C:\64\boost_1_62_0_py35_build and C:\64\boost_1_62_0_py35_build\source.
Download zlib128.zip, bzip2-1.0.6.tar.gz and boost_1_62_0.7z, and put them into 
C:\64\boost_1_62_0_py35_build\source folder
Copy/paste the attached build.cmd (see below, I haven't attached it as most 
e-mail servers would strip it) into C:\64\boost_1_62_0_py35_build\build.cmd and 
make sure the following variables at the beginning of the file are correctly 
set and match your compiler version, your 7-Zip installation location, and your 
zlib, bz2lib and Boost versions:

set BOOST_TOOLSET=msvc-14.0
set BOOST_VERSION=1_62_0
set ZIP7=%PROGRAMFILES(X86)%\7-zip\7z.exe
:: The following are all optional; comment out if not needed.
set BZIP_VERSION=1.0.6
set ZLIB_FILE_VERSION=128
set ZLIB_VERSION=1.2.8

In the same CMD window that you opened above, cd to 
C:\64\boost_1_62_0_py35_build and run:

build.cmd

When the build is completed, copy 
C:\64\boost_1_62_0_py35_build\build\boost_1_62_0-x64\boost_1_59_0\stage\lib
to C:\boost\boost_1_62_0_py35. Rename lib to lib64-msvc-14.0 (or whatever MSVC 
version you used to build Boost).
Create a C:\boost\boost_1_62_0 directory and copy 
C:\64\boost_1_62_0_py35_build\build\boost_1_62_0-x64\boost_1_62_0\boost into 
C:\boost\boost_1_62_0.

4) Get the latest RDKit master from GitHub:

cd c:\build
git clone https://github.com/rdkit/rdkit.git

5) Build the RDKit:

cd c:\build\rdkit
mkdir build
cd build
cmake -DEIGEN3_INCLUDE_DIR=C:\build\include\eigen3 
-DPYTHON_LIBRARY=C:\Python35\libs\python35.lib 
-DPYTHON_INCLUDE_DIR=C:\Python35\include 
-DBOOST_LIBRARYDIR=C:\boost\boost_1_62_0_py35\lib64-msvc-14.0 
-DBOOST_ROOT=C:\boost\boost_1_62_0 -DRDK_BUILD_AVALON_SUPPORT=ON 
-DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program 
Files\PostgreSQL\9.5" -DRDK_BUILD_SWIG_WRAPPERS=ON 
-DRDK_BUILD_SWIG_JAVA_WRAPPER=ON -DSWIG_DIR=C:\msys64\usr\share\swig\3.0.7 
-DSWIG_EXECUTABLE=C:\msys64\usr\bin\swig.exe -G"Visual Studio 14 2015 Win64" ..
c:\Windows\Microsoft.NET\Framework\v4.0.30319\MSBuild.exe /m:4 
/p:Configuration=Release INSTALL.vcxproj

Follow the instructions in Code/PgSQL/rdkit/README to install the RDKit 
PostgreSQL cartridge DLL into your PostgreSQL installation.

I used the MSYS2 SWIG version packaged into MSYS2, but you can also get 
pre-built SWIG for Windows; change the above path accordingly.

If the above looks too scary, I'll provide you with my RDKit tree built against 
Boost 1.62, Python 3.5.1 (I think it should work also against Python 3.5.2) and 
PostgreSQL 9.5.

For Eigen 3:
- you won't need make.exe as you will use the native Microsoft toolchain to 
build Eigen3, you will only need cmake
- Install Visual Studio 2015 (14.0) Community Edition (Microsoft C and C++ 
compilers)
- Open a CMD window
- unzip the Eigen3 archive (I have just downloaded Eigen 3.3.1)
- cd to the eigen folder
- mkdir build
- cd build
- "C:\Program Files (x86)\Microsoft Visual Studio 
14.0\VC\bin\amd64\vcvars64.bat" (this will set the environment variables 
appropriate for the 64-bit version of the compiler)
- cmake -DCMAKE_INSTALL_PREFIX=C:\build .. (this will install Eigen 3 under 
C:\build\include\Eigen3; change the C:\build path if you wish to install Eigen3 
somewhere else)
- c:\Windows\Microsoft.NET\Framework\v4.0.30319\MSBuild.exe /m:4 
/p:Configuration=Release INSTALL.vcxproj (this will install Eigen3 headers into 
C:\build\include\Eigen3, or elsewhere depending on the CMAKE_INSTALL_PREFIX you 
chose.

For Boost 1.62:
- is Microsoft Visual Studio 14.0 Community Edition installed? If so, do the 
paths in build.cmd refer to the correct installation 

Re: [Rdkit-discuss] conda build errors on Windows 10

[Greg Landrum]

Hi Bob,

On Thu, May 11, 2017 at 10:31 PM, Bob Funchess 
wrote:

>
>
> I’m curious as to whether anyone is able to get RDKit to build on Windows
> 10 with Visual Studio 2015; I’ve been trying off and on to get this to work
> for some time now with no discernable success.
>
>
Yeah, I was able to do so both while doing the conda builds and during the
testing phase (where I do the build manually).


> PS My ultimate goal is to build the RDKit DLL and the C# wrappers and
> that’s all I fundamentally care about; Java, Python, Postgres et al. are
> irrelevant to me except insofar as they help me get the C# wrappers… the
> Python version would be NICE (for testing), but I don’t actually NEED it.
> If anyone has actually successfully built RDKFuncs.DLL and RDKit2DotNet.DLL
> using the current version of RDKit, I would greatly appreciate any pointers.
>

Yeah, for this I think you really don't need/want to be using the conda
stuff.

How about this: I'll put together a short tutorial/walk-through on doing a
build of the C# wrappers with VS2015 under Win10 and we can see if that
helps. I can try a first pass over the weekend.


-greg
--
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