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sasascore module #862

Merged
merged 57 commits into from
Oct 16, 2024
Merged

sasascore module #862

merged 57 commits into from
Oct 16, 2024

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mgiulini
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@mgiulini mgiulini commented Apr 16, 2024

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Closes #861 by creating a sasascore module, which allows to score PDB files against existing accessibility information.

As an example, if some glycosylation sites on chain A (say residues 40 and 50) are known to be preserved upon complex formation, a penalty can be added if they are buried in the resulting model. At the same time, if some residues are known to be buried in the complex, we can impose a penalty if they are accessible.

An example application of the module:

[sasascore]
resdic_accessible_A = [40,50]
residic_buried_B = [22,23,24]

This will create a sasascore.tsv file, analogous to the other scoring tsv files.

structure       original_name   md5     score
cluster_1_model_1.pdb   emref_1.pdb     None    2
cluster_1_model_2.pdb   emref_2.pdb     None    2
cluster_2_model_1.pdb   emref_4.pdb     None    5
cluster_3_model_1.pdb   emref_3.pdb     None    5
cluster_2_model_2.pdb   emref_5.pdb     None    5

Here the score is the number of times the input information has not be satisfied (the lower the better). A file named violations.tsv is also produced, with a detailed picture of the violations:

structure             bur_A acc_B
cluster_1_model_1.pdb 40 22
cluster_1_model_2.pdb 50 23 
cluster_2_model_1.pdb 40,50 22,23,24
cluster_3_model_1.pdb 40,50 22,23,24  
cluster_2_model_2.pdb 40,50 22,23,24

@mgiulini mgiulini self-assigned this Apr 16, 2024
@mgiulini mgiulini added enhancement Enhancing an existing feature of adding a new one community contributions from people outside the haddock team m|accscoring related to accessibility (a posteriori) scoring labels Apr 16, 2024
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@amjjbonvin amjjbonvin left a comment

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I would suggest to rename this module to sasascore

@mgiulini mgiulini changed the title Accscoring module sasascore module Apr 25, 2024
VGPReys
VGPReys previously approved these changes Oct 4, 2024
Co-authored-by: Victor Reys <132575181+VGPReys@users.noreply.github.com>
VGPReys
VGPReys previously approved these changes Oct 8, 2024
sverhoeven added a commit to i-VRESSE/workflow-builder that referenced this pull request Oct 9, 2024
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🚀

@rvhonorato rvhonorato merged commit e084a38 into main Oct 16, 2024
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@rvhonorato rvhonorato deleted the accscoring branch October 16, 2024 11:53
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accessibility based scoring
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