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## Expected behavior ##
When I pass in keywords that don't exist to analysis classes, it fails.
## Actual behavior ##
`**kwargs` in classes like RMSD get passed to AnalysisBase, whi…
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This issue is not related with deeprank code directly. It is to record a data error introduced when we use haddock to generate data.
Some i-RMSDs reported in XXX.stats do not seem to be correct. …
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This is because the ligand is glycine. The scorer doesn't distinguish between ligand and protein atoms in calculating all possible RMSDs.
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In the 14-17 benchmark, some reference structures (input/structures/14_17_res/rosetta/reference/ folder) have HETATMS:
1r6x
1ra0
1rdq
1s95
2aeb
2b0t
2bwr
2puh
3a3p
3a64
3b40
3cnq
3ea1
…
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For molecules with saturated ring systems (e.g. sugars) it can be useful to implement sampling of initial ring conformations, dock them separately and choose best output. This looks critically importa…
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The test code can be found in https://github.com/HanatoK/Intel_Compiler_2019_bug_test, which should use the same algorithm as Colvars. However, even if I use Eigen3 or `math_eigen_impl.h`, the calcula…
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Hello,
Does BARNABA have the ability to read modified residues. And can it calculate features of these residues like eRMSD, RMSD and gvectors? If yes, how?
Thank you,
Tia
ghost updated
4 years ago
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## Is your feature request related to a problem? ##
I often encounter landing on the old version of documentation when searching through Google.
For example, if I search for `mdanalysis rmsd` in…
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Hello, I am interested in utilizing your tool for docking structures that lack a native complex structure. Without a native structure, I am unable to use metrics like DockQ or RMSD. Could you please e…
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Currently we only analyze sequence identity distributions, RMSD distributions, and final energies from the implicit solvent MD refinement step.
More specific analysis has been included for Src and Ab…