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In Fingerprint.run_from_iterable(), it expects that the iterable yields a molecule. Sometimes we would like to iterate over different conformers of the same molecule, such that the pharmacophores can…
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Currently, in qFit, removing conformers below a certain density level is defined as:
if any voxel in the conformed has a density intensity =5 atoms lack support (or somewhere around there).
This s…
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```
Done generating conformers in AutoTST...
80 conformers found
Skipping unconverged shell 1
Skipping unconverged shell 22
Skipping unconverged shell 49
Traceback (most recent call last):
Fi…
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Hello,
The maximum force on any atom of each conformer is, on average, 0.03139 Hartree/Bohr, which is about 70-fold larger than Gaussian's convergence criterion at 0.00045 Hartree/Bohr. This was ca…
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**Describe the bug**
Hi All, I am having some problems with AutodE trying to calculate an energy profile of a reaction of a direct carboxylation with CO2. No matter what I do, the calculation exits w…
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In the case of running isicle.md.XTBWrapper() to optimize structures then passing this geom to isicle.mdXTBWrapper() to generate conformers, an uncaught error occurs.
- isicle.md.XTBWrapper.set_geo…
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The attached script allows for multiple substitutions of similar amino acid types, which increases speed and quality of conformers generated. The script also builds in chunks of 3, 4 or 5, which also …
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**Avogadro version: (please complete the following information from the About box):**
- Avogadrolibs: 1.99.0
- Qt: 5.15.2
**Desktop version: (please complete the following information):**
- O…
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Is there a way to speed up EmbedMultipleConfs function without sacrificing the quality of generated conformers? I am talking beyond increasing CPU count. Maybe doing it on GPUs?
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**Tool:**
CB Downloads polling logic
**Bug Description:**
Polling needs to become more sophisticated. The motivation behind this issue is we want speed, so we send many requests until we get the …