Compiling smina on macosx m1 arm64?

[Kalen Josifovski]

Hi all,

I am an organic chemist and aspirational comoutational chemist trying to run through the teachopencadd course by the Volkamer lab. A part of the requirments I need to install smina to carry out some docking (see T015 · Protein ligand docking; https://github.com/volkamerlab/teachopencadd/tree/master/teachopencadd/talktorials/T015_protein_ligand_docking)
I followed the build instructions and got my first error (smina_error1.txt) after cmake ..
It seemed that cmake was unable to find certain boost dependencies. Attempting to point cmake to these dependencies led to the second error (smina_error2.txt) where it seems there seems to be compatibility issues between boost and std. The error quote 'error: friend declaration of 'unordered_map' does not match any declaration in namespace 'std' seems to come up repeatedly through the terminal output.

I am some experience in python but almost no experience in c. If anyone has any insight into this issue or could help in anyway, I would appreciat it greatly.

Many thanks, Kalen

[Kalen Josifovski]

Nvm, turns out the precompiled binaries were available through the downloads section the whole time. Got it working now.

[David Koes]

Looks like you didn't have openbabel3 installed (or at least it couldn't find it). Glad to hear the precompiled binaries still work.

[Kalen Josifovski]

Hi David,
Yes while I havent actually done any docking with it as I have yet to reach that module of the course; I can at least display the help message so Im assuming its working ok.

As for openbabel3, a cursory search of brew gives me this;

KalenJosifovski@Kalens-MBP ~/Smina $ brew list open-babel
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obabel
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obconformer
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obdistgen
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obenergy
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obfit
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obfitall
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obgen
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obgrep
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obminimize
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obmm
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obprobe
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obprop
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obrms
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obrotamer
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obrotate
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obspectrophore
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obsym
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obtautomer
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/obthermo
/opt/homebrew/Cellar/open-babel/3.1.1_2/bin/roundtrip
/opt/homebrew/Cellar/open-babel/3.1.1_2/include/openbabel3/ (90 files)
/opt/homebrew/Cellar/open-babel/3.1.1_2/lib/libopenbabel.7.0.0.dylib
/opt/homebrew/Cellar/open-babel/3.1.1_2/lib/cmake/ (4 files)
/opt/homebrew/Cellar/open-babel/3.1.1_2/lib/openbabel/ (127 files)
/opt/homebrew/Cellar/open-babel/3.1.1_2/lib/pkgconfig/openbabel-3.pc
/opt/homebrew/Cellar/open-babel/3.1.1_2/lib/python3.13/ (4 files)
/opt/homebrew/Cellar/open-babel/3.1.1_2/lib/ (2 other files)
/opt/homebrew/Cellar/open-babel/3.1.1_2/sbom.spdx.json
/opt/homebrew/Cellar/open-babel/3.1.1_2/share/man/ (20 files)
/opt/homebrew/Cellar/open-babel/3.1.1_2/share/openbabel/ (55 files)

Seems to be fine to me, so im still not sure what the issues was when it came to compiling the binaries. Maybe the wrong version of one of the required libraries?

[David Koes]

Doesn't look like brew installed the development (header) files.