Re: [Rdkit-discuss] RDKit compilation from source question

2021-04-28 Thread Guilherme Duarte Ramos Matos
Hi Paolo, You hit the nail right on the head: I defined the _GLIBCXX_USE_CXX11_ABI=0 macro and RDKit compiled and linked normally. I still need to figure out what exactly happened (I compiled Boost in my project space because I do not have admin privileges to update the precompiled version SBU

Re: [Rdkit-discuss] RDKit compilation from source question

2021-04-28 Thread Paolo Tosco
Hi Guilherme, it looks like it might be this: https://github.com/rdkit/rdkit/issues/2013#issuecomment-553563418 This can happen if you are using pre-compiled Boost libraries that were compiled with a different compiler from the one you are using for RDKit. To check if that's the case, compare

[Rdkit-discuss] RDKit compilation from source question

2021-04-28 Thread Guilherme Duarte Ramos Matos
Dear RDKit community, I use the RDKit C++ libraries (version 2019_09_1) in one of my projects and I have a linking problem that I am having a hard time troubleshooting. When I try to compile and link using the CMake command below * cmake .. -DRDK_INSTALL_INTREE=OFF \ *

[Rdkit-discuss] FW: Problems when aligning the moment of inertia with the principal axes

2021-04-28 Thread Pablo Ramos
I just solve it, Just in case someone also needs it. You can compute the inertia tensor after aligning with the principal axes with CanonicalizeConformer(). This tensor is now therefore diagonal, and the symbol of the ii components tell you the direction they are pointing out. Just rotate in

[Rdkit-discuss] Problems when aligning the moment of inertia with the principal axes

2021-04-28 Thread Pablo Ramos
Dear community, There is the function CanonicalizeConformer() that allows you to align molecules based in the moment of inertia. I want to use it to align molecules that are exactly the same, but whose atom indices are different. rdkit.Chem.rdMolAlign module contains functions that take