Voronoi-based analyses of very large structures using tools in NucProt


I’m analyzing protein structures (specifically, I’m performing a Voronoi-based analysis) using the tools linked on the geometry page:


I’m using this on huge systems with more than 99,999 atoms. Is this possible?

I don’t think there’s any hard coded limitation in the number of atoms. Look at the read_pdb_file routine this source script:


This "mallocs" up space on demand so in theory if you have enough memory I think you can accommodate >100K atoms. However, the PDB format itself is an issue here. You can modify the PDB reading routines to a different format. Just modify the read_record routine in the same file. However, I don’t know if doing this in multiple "models" will work.