-
If MolSysMT is going to be used as support to build workflows, an auxiliary library to cite everything that was used along that workflow has to be included. If this library does not exist already, we …
-
What would be the best way to encode the list of hydrogen bonds found in a trajectory?
- A dictionary of lists (with frame indices where the bond was formed)
- A sparse tensor (3d with the library…
-
MolSysMT has to give a name to proteins, small molecules, and entities. These names can be extracted from an mmtf file, but what happens with other forms? We probably need to implement in Sabueso the …
-
There are faster libraries than Pandas. The concept of having the topology and the bonds as DataFrames is useful since we can, at any time, try other libraries such as [Vaex, PySpark, Dask, ..., which…
-
MolSysMT should be ready to understand the query sentence: 'all in groups of components in molecule_index==0'.
With the output as a list of lists of lists of atoms:
output[ii][jj][kk] = index of…
-
While we are documenting MolSysMT, we have come up with a solution to offer NGLView views interactively. @Daniel-Ibarrola, it would be great if you could do the same for the documentation of OpenPharm…
-
The following sequence of commands throws an error:
```python
import molsysmt as msm
mol_system_2 = msm.convert("1TCD", "molsysmt.MolSys")
mol_system_2 = msm.remove_solvent(mol_system_2, water=T…
-
MolSysMT should have its own file parsers. If not for every file format, at least for trajectory files -including pdbs-.
-
@kwrvf, Let's open this task for you to learn how projects work in GitHub.
Please, accept the admin rights for this project (did you receive it already by email?).
Once you have admin rights, please …
-
In my opinion, the only important functionality left to implement before publishing this is something to work with trajectories. We could probably discuss here how this tool could be shaped.
I would …