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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
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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