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Friday, 21 February 2020

Working around segmentation faults of pyrosetta: threads & processes

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Rosetta often does not die gracefully. Pyrosetta is the same. If the starting template is not great segmentation faults will result in the...
Wednesday, 12 February 2020

Guess bond order in Rdkit by number of bound atoms

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Some compChem/Biochem programs do not care about bond order and strip them, which is rather frustrating. Ligands in random PDB files witho...
1 comment:
Sunday, 15 December 2019

What-if: Biosynthesis of deazaguanine

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7-deazaguanine is an analogue of guanine that has a carbon instead of a nitrogen. This molecule that is not made in nature, but many subst...
2 comments:
Saturday, 30 November 2019

Convert Python docstrings to GitHub markdown readmes

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This is suited for very small projects were read-the-docs is way overkill, however for most project that will be more suited — see how-to po...
Thursday, 7 November 2019

Go away glycerol!!

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Due to the nature of crystallisation additives are often found in PDB structures. These are generally unwelcome, especially if you want to e...
Monday, 21 October 2019

RDKit for Rosetta: PLP ligand space as an example

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Docking requires a molecule to dock. Preparing a ligand is often tricky, especially if the ligand is complicated, such as PLP. PLP is an in...
2 comments:

Toasty CSS with BS4

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In Bootstrap 4 you can have appear small alert-like rectangles, called toasts. However, getting these to work like notifications on top of...