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Use znjson
instead of znframe
#481
Conversation
Radii for np.nan values |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #481 +/- ##
==========================================
+ Coverage 49.45% 52.89% +3.44%
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Files 26 28 +2
Lines 2010 2142 +132
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+ Hits 994 1133 +139
+ Misses 1016 1009 -7 ☔ View full report in Codecov by Sentry. |
…nto 201-use-znjson
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I think use_bonds
should be a flag in the CLI. Having control via python would also be nice.
This PR replace the use of the
znframe
package with a definition on how to convert / readase.Atoms
from json strings through the use of znjson.vis
is now optional by settingvis.bonds_calculator=None
.covalent_radii
fromase
Old ideas
Thereby I also looked into making computing the bonds optional.
Bonds computation can be expensive, thus loading the trajectory and visualizing it first and adding the bonds afterwards would be my prioritized way of doing things. We could use two celery workers for this:
Where do we want to define if bonds should be computed? E.b.
ZnDraw(bonds=True)
? Via the CLI?Further this PR now uses
covalent_radii
from ase. VdW are too large, evencovalent
look a bit weird compared to what we had before.znjson.loads
inf
data file reading