polyply_1.0
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marrink-lab
Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
For some edge cases the exclusions are incorrectly expanded. I'm investigating
Except if you explicitly target python < 3.6, you may not need the OrderedDict anymore. Starting with python 3.6, dictionaries are insertion ordered, from python 3.7 it is not considered...
- Effectively the molecules take up as much space as the meta-molecules. - analyzing the actual memory consumption of attributes is close to impossible
I suggest passing the file handle as argument, rahter than the filepath. That way reading e.g. compressed files or network streams becomes possible rather than painful _Originally posted by @pckroon...
There is one logic fault with regard to chirality in the current package. If the chiral atoms are all in one residue currently we build only one template. But if...
Currently because each molecule in a system is represented by one graph memory consumption for large systems is huge and system sizes are limited to 3 million particles. This can...
I think now the programs does all operations on float64(s), but would be more memory efficient to switch to use 32 if the accuracy permits it.
One rate limiting operation is whenever a processor has to loop over the complete molecule list and pick molecules based on certain conditions like are they solvents, are they build....
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Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates