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1. Code checks: if min_hbonds==max_honds ==> loop is skipped.
2. if min_hbonds==max_honds == 0 ==> loop is skipped.
Change:
1. Assign rank as 0 if min_hbonds==max_honds == 0
2. Assign rank as 1 …
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Hi all,
I'd like to use an `RMSDForce` (ordinarily wrapped in a `CustomCVForce`) and subsequently change the reference positions. On examination, I appear to not see any force from the `RMSDForce` b…
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- [ ] calculate a measure of fit between the simulated incidence curve and the "observed" data.
- [ ] display said measure in the app (must update when sliders are moved)
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The output from `procrustesData` is calculated incorrectly for `"ag_rmsd"`, `"sr_rmsd"` and `"total_rmsd"`. The rmsd should be the rmsd of the positions (i.e the mean of the procrustes distances), no…
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I was wondering if you could let me know the simulation accuracy of making it rain pipeline. It turns out that a system which i have simulated has very unexpected data.
I have used 5000 cycle ener…
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Hi there, so I'm not sure where exactly to put this - and it might be my fault - but I am having problems with some protein comparisons.
I have taken the protein 1L14 from PDB, taken the sequence a…
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Dear professor:
I used autodock-vina 1.2.3 to dock my ligand and protein. However, the docking result confused me. The following is the docking result table. The lowest affinity value is -181 and th…
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CD-94 updated
2 years ago
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**Describe the bug**
In a case where the model and the reference file cannot be easily aligned, StructureSimilarity.compute_lrmsd_fast() and StructureSimilarity.comp
ute_lrmsd_fast() provide diffe…
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Code if this will be implemented in the future.
Where P is (N, natoms, 3) and Q is (M, natoms, 3).
```
C = np.dot(np.transpose(P, [0,2,1]), Q.T)
V, S, W = np.linalg.svd(np.transpose(C, [0,3,1,…