Improve unit cell detection for charmm trajectory (dcd) files #1064
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of steps is updated as well.
what format the unit cell values are in, try to detect automatically.
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Version 6.23.0.
Charmm trajectories can contain unit cell information as the symmetric shape matrix (charmm versions >= 22), an alternative form of the shape matrix that NAMD/VMD write, or X-aligned unit cell parameters (X Y Z alpha beta gamma), which was written by charmm versions < 22. Previously cpptraj used the version number in the charmm trajectory file to determine how the box was stored. This PR adds some heuristics to try to figure out what kind of unit cell is present no matter what the version number says, which should be more robust. Updates the manual.
This PR also improves the robustness of reading CHARMM restart files.