Skip empty features #140

NicoRenaud · 2020-04-06T09:31:25Z

handles missing CA/CB atoms in residue based features

used the center of the residue for ResidueDensity and BSA
Skip them for PSSM

Ignore Mac .DS_Store file

Added bug report tempalte

Update issue templates

Added feature request issue template

set export to False

Align

Development

Bumps [freesasa](https://github.com/mittinatten/freesasa) from 2.0.3.post7 to 2.0.5. - [Release notes](https://github.com/mittinatten/freesasa/releases) - [Changelog](https://github.com/mittinatten/freesasa/blob/master/CHANGELOG.md) - [Commits](https://github.com/mittinatten/freesasa/commits) Signed-off-by: dependabot-preview[bot] <support@dependabot.com>

Bump freesasa from 2.0.3.post7 to 2.0.5

Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. - [Release notes](https://github.com/pytorch/pytorch/releases) - [Commits](pytorch/pytorch@v0.1.1...v1.4.0) Signed-off-by: dependabot-preview[bot] <support@dependabot.com>

Realign hdf5

coveralls · 2020-04-06T09:38:07Z

Pull Request Test Coverage Report for Build 784

115 of 168 (68.45%) changed or added relevant lines in 9 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+2.7%) to 76.343%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
deeprank/features/BSA.py	3	4	75.0%
deeprank/features/ResidueDensity.py	3	5	60.0%
deeprank/features/FeatureClass.py	20	26	76.92%
deeprank/generate/DataGenerator.py	79	94	84.04%
deeprank/utils/cal_hitrate_successrate.py	3	32	9.38%

Totals
Change from base Build 689:	2.7%
Covered Lines:	1578
Relevant Lines:	2067

💛 - Coveralls

LilySnow · 2020-04-06T09:57:40Z

Shall we use residue center for all residues instead of for residues with missing atoms?

NicoRenaud · 2020-04-06T12:29:27Z

it was at the center first but then we decided to move to CB ...

Test realign

…to skip_empty_features fix test of the realign

NicoRenaud · 2020-04-06T13:04:05Z

I suggest we leave the features like that for now, This PR should fix the issue but we have then different default for different features when the PDB is faulty ...

CunliangGeng · 2020-04-07T08:09:12Z

deeprank/features/FullPSSM.py

@@ -212,6 +212,14 @@ def get_feature_value(self, cutoff=5.5):
                f"{self.mol_name}: The following interface residues have "
                f" no pssm value:\n {ctc_res_wo_pssm}"
            )
+        elif len(pssm_res_set.difference(ctc_res_set)) > 0:


The pssm_res_set contains pssm for all residues, and ctc_res_set consider only interface residues, so this condition should always be True.
Also pssm_res_wo_ctc = pssm_res_set.difference(ctc_res_set) misstreats the non-interface residues as residues with missing atoms.

The issue is that some of the res are missing in xyz_dict therefore leading to a keyError on line 229. I think we should create a get_residue_centers either in DeepRank or pdb2sql. There we could specify to get either CB, or CA if CB is missing or take the mean of the residue xyz if CA and CB are missing. The only issue is the we would have to loop over the residue and it will be a bit slow for large complexes ....

I think we need a data preprocess step in DeepRank to avoid these problems. We can could add a PDB validator in pdb2sql.

that's a good idea ... but I wouldn't know how to do it

I've introduced a get_residue_center in FetureClass I think we can live with that for now ....

Thanks, the get_residue_center looks good.

deeprank/features/BSA.py

deeprank/features/ResidueDensity.py

deeprank/features/FeatureClass.py

test/test_generate.py

CunliangGeng

Thanks, the changes look good.

LilySnow and others added 30 commits May 7, 2019 16:36

Update README.md

e251f8d

Update .gitignore

b8cb334

Ignore Mac .DS_Store file

Update issue templates

7df93d1

Added bug report tempalte

Merge pull request #124 from DeepRank/CunliangGeng-patch-1

caf5de5

Update issue templates

Update issue templates

476ad17

Added feature request issue template

change to _close() for pdb2sql

08d8d82

install align branch of pdb2sql

488377e

choose chains in interface align

f4e7b89

remove possible - in molname

19a43bc

export optional in DataGenerator

34c7979

fixed data augmentation

970e17d

Update generate_dataset.py

684ce11

set export to False

call Rscript from plot_utils.py instead of r2py

4ff7834

change install for new pdb2sql

5c33022

syntax

6c77a0a

align in doc

fd01c21

added test

31a6110

fix typo

7504da7

fix code reviews

5f68419

doc for itnerface alignement

5a90e9c

Merge pull request #130 from DeepRank/align

0711263

Align

Merge branch 'master' into development

954a271

Merge pull request #131 from DeepRank/development

97ea093

Development

versioning

7d7f5fc

fixed setup

4a19926

add doi

22fdb4f

Merge pull request #132 from DeepRank/dependabot/pip/freesasa-2.0.5

61728d3

Bump freesasa from 2.0.3.post7 to 2.0.5

remove torch version restriction

106d80f

NicoRenaud and others added 7 commits April 3, 2020 15:59

removed NaivePSSM

f2d572b

docstring of realign

4485712

removed mapped features

8bbf37d

Merge pull request #137 from DeepRank/realign_hdf5

eb7d6b5

Realign hdf5

add ploting R code to util

1e61cda

do not crash when missing CA/CB atoms

7e10e3f

fixed error message

d278b9d

NicoRenaud added 4 commits April 6, 2020 14:36

fixed test generate

0810416

Merge pull request #141 from DeepRank/test_realign

373ccda

Test realign

Merge branch 'development' of https://github.com/DeepRank/deeprank in…

e3e50a7

…to skip_empty_features fix test of the realign

fix tet generate

79d4c15

NicoRenaud requested review from CunliangGeng and LilySnow April 6, 2020 13:04

DarioMarzella force-pushed the development branch from 373ccda to f2021cb Compare April 6, 2020 15:13

CunliangGeng reviewed Apr 7, 2020

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CunliangGeng reviewed Apr 7, 2020

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NicoRenaud added 2 commits April 10, 2020 14:51

intoduced get_residue_center

1564d11

clean up

ffc29f4

CunliangGeng reviewed Apr 10, 2020

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CunliangGeng reviewed Apr 10, 2020

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test/test_generate.py Show resolved Hide resolved

fix import and uncomment tests

1c35cb7

NicoRenaud requested a review from CunliangGeng April 10, 2020 14:01

CunliangGeng approved these changes Apr 10, 2020

View reviewed changes

NicoRenaud merged commit 08fe153 into development Apr 10, 2020

NicoRenaud deleted the skip_empty_features branch October 23, 2020 14:42

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Skip empty features #140

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Skip empty features #140

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coveralls commented Apr 6, 2020 • edited Loading

Pull Request Test Coverage Report for Build 784

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