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It appears that #1712 was reverted, requiring values to be true and false despite the truevalue/falsevalue of the controlling boolean param. The logic that controls if a variable should be included i…
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Sequences: 69
IDs ([Virus name list](https://raw.githubusercontent.com/alanrice/RSV_lineage_proposal/main/A.D.1.4X/virusNameList.txt)): EPI_ISL_19116647, EPI_ISL_19001955, EPI_ISL_19001958, EPI_ISL…
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A careful reviewer has come up with this (I'll cite my correspondence with him below).
This is related to #992 and #1041.
To summarize:
The goal here would be to find an interface which allow to writ…
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[GROMACS tutorial](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html )
[GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design](https://doi.org/10.1021/acs.jcim.2c0004…
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Hi,
PDBFixer is not finding the missing residues in 3sy7.pdb as retrieved from the
OPM database, while it did work for the 3sy7.pdb taken from the RCSB database.
The SEQRES section is identical …
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I tried to run the snpfilter.sh to obtain the vcf file for uncovering the allele-specific copy number alternations in the tumor samples. I prepared tumor bam file, common dbSNP vcf file, and hg38.fa, …
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The package has turned out quite clean with nice abstractions. The ideas from earlier versions have been distilled to an elegant set of types and functions, with some new additions.
The elephant in t…
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Hello,
I am working with the AminoAcid class (deeprankcore/models/amino_acid.py) because the Residue class (deeprankcore/models/structure.py) requires it, and running into an issue. The common 20 a…
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In the following line of code, it seems that the index of the atom in each residue that is to be used for distogram prediction is also being used as the representative (i.e., token) center atom of eac…