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I've run into issues with the docking procedure, using codes from [here](https://github.com/asapdiscovery/asapdiscovery/blob/main/examples/docking_and_scoring.ipynb).
I was docking a new ligand into …
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Hello, first of all, thank you very much for making such a valuable research publicly available. I have some questions regarding the application of molecular generation to new proteins:
I used the "s…
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when multiple small molecule inputs (B, C, D...) predicted with one protein molecule result clashes between small molecules. I assume that they don't consider interactions between small molecules... i…
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There is no documentation for the Molecule crates.
https://crates.io/crates/molecule
https://crates.io/crates/molecule-codegen
https://crates.io/crates/moleculec
Particularly for the first one…
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With the current setup in `openfe` every time a molecule gets loaded with user-set partial charges the user receives a warning `Partial charges have been provided, these will preferentially be used in…
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In the Build a Molecule simulations, the chemical formulas are shown incorrectly.
Here is an example from a similar language, Pashto, where they are shown correctly:
![Screenshot 2024-06-27 at 2 1…
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**Description:**
When a GiST index is present, exact searching with the @= operator is 3x slower than without the index and much slower than @> or Gather (cost=1000.00..222107.52 rows=1 width=62) …
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## Stencil Mobile
Stencil Mobile is an initiative to create a comprehensive design library for mobile that encapsulates various components, referred to as "molecules". Each molecule is a small, self-…
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Hi,
I am trying to build a coarse-grain system that has a lipid, sodium, and protein, but it seems martinize doesn't recognize lipid molecules (POPC/POPE) and sodium ions.
The command I used:
…
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Here's some notes that I have for the current implementation of the Molecule class:
1. I'm noticing some methods associated with the Molecule superclass that utilize `self.data` (see below), which…