Build Error in Moldina C++ Version – Boost, Timer, and Split Module Issues

[Shakeel1679]

Dear Moldina Development Team,

I hope this message finds you well.

I have been attempting to compile the Moldina C++ repository from GitHub (https://github.com/It4innovations/moldina-multiple-ligand-molecular-docking-over-autodock-vina), but encountered several issues that may affect reproducibility on modern Linux systems (Ubuntu 22.04+, Boost ≥1.74).

Here is a summary of the issues encountered during the build process:

1. Incorrect Compiler Reference (ansi):
   The makefile_common file uses ansi as the compiler, which is not available on Linux systems. Replacing it with g++ resolved that step.

2. Missing File in split.cpp:
   The split.cpp file attempts to include file.h, which does not exist in the repository. This caused the build to fail when attempting to compile vina_split. I commented out the compilation lines related to split.o and vina_split as they are not essential to building the main moldina binary.

3. Boost Timer Deprecation:
   Compilation of parallel_mc.cpp fails with the error:
   atal error: boost/timer.hpp: No such file or directory

cpp
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The header appears to be deprecated in recent Boost versions. Replacing:

#include <boost/timer.hpp>
with:

cpp
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#include <boost/timer/timer.hpp>
resolves this issue.

Potential Improvements:

It may be worth updating the makefile_common with conditionally defined compiler variables and switching to cmake for portability.

A fallback check for Boost header compatibility would also help support systems running Boost ≥ 1.74.

I’m happy to share my corrected makefile_common and build instructions if needed.

Thank you for maintaining this useful tool — it’s a valuable addition to the structure-based drug design community. Looking forward to your guidance or confirmation if these changes are acceptable for a pull request.

Best regards,
Dr. Hoosdally Shakeel
Medicinal Chemist | Computational Oncology
[email protected]