-
Related to #31
I have made an implementation here but if we use a common function to do this that will improve confidence that we're using the same metrics across tasks:
https://github.com/chod…
-
* MD DaVis version: 0.4.0
* Python version: Python 3.10.6
* Operating System: Ubuntu 22.04
### Description
Trying to make the .h5 file (HDF) on command line for the tutorial example 2VH7.
T…
-
Greetings. I want to calculate the free energy & enthalpy changes for the binding of a series of 1+ small molecule guests, to a neutral macrocyclic host, in water. I've performed a set of calculation…
ghost updated
2 years ago
-
Here is an example of the PDBDEV_00000018:
```python
with open('PDBDEV_00000018.cif') as fh:
mmcif,= ihm.reader.read(fh, model_class=ihm.model.Model)
print('num_models:', mmcif.ensembles[0].…
-
Using the `--use-reflections` option with the `calculate_rmsd` script affects the computed rmsd, but it doesn't seem to affect the output structure when `-p` is used too:
```
$ cat a.xyz
8
C …
-
Hi, I've been trying to use python binding of vina. And here is my question: when I run docking in parallel, is there any way to hide only the docking output message.
-
For HEMNME-3D, it has to be done after the change of angles and shifts to be like the ground truth.
The RMSD is a good idea if the number of modes used in the alignment and synthesis is not the same.…
-
Thanks for your promising contribution! I have a small question when reading the code. I found out that when using `read_mol` method, you remove the hydrogen atom and `mol` object is used for the late…
-
I am getting the following error message using your code example:
```
ERROR: DomainError with 1.2266298878305306:
acos(x) not defined for |x| > 1
Stacktrace:
[1] acos_domain_error(x::Float64)…
-
I'm getting very large RMSD's between unbound/bound receptor chains for a few targets.
Upon further inspection, it almost appears that the bound and unbound chains have
I'm not sure, but e.g. 6…