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Table 3 Average Scoria execution times for various file I/O tasks, running in three different Python environments

From: Scoria: a Python module for manipulating 3D molecular data

Action

Python with NumPy/SciPy

Python without dependencies

PyPy (incompatible with dependencies)

Save PDB

0.0055 ± 0.0010

0.0085 ± 0.0016

0.0036 ± 0.0043

Load PDB (without calculating bonds by distance)

0.0104 ± 0.0010

0.0643 ± 0.0028

0.0198 ± 0.0163

Save PYM

0.0024 ± 0.0013

N/A

N/A

Load PYM

0.0008 ± 0.0004

N/A

N/A

  1. Saving and loading PYM files requires NumPy and so could only be tested in environments with that module installed (“N/A” otherwise)