From 095930689403fc263a948dd2704f48025af49201 Mon Sep 17 00:00:00 2001 From: "Rodrigo V. Honorato" Date: Fri, 23 Aug 2024 13:32:26 +0200 Subject: [PATCH 1/4] update `test_extract_data_from_capri_class` --- tests/test_module_caprieval.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/tests/test_module_caprieval.py b/tests/test_module_caprieval.py index 7179bb1b8..8e82477e4 100644 --- a/tests/test_module_caprieval.py +++ b/tests/test_module_caprieval.py @@ -992,6 +992,10 @@ def test_extract_data_from_capri_class(mocker): random_model = PDBFile( file_name=str(uuid.uuid4()), score=42, unw_energies={"energy": random_energy} ) + + random_clt_id = random.randint(0, 100) + random_clt_rank = random.randint(0, 100) + random_clt_model_rank = random.randint(0, 100) random_md5 = str(uuid.uuid4()) random_score = random.random() random_irmsd = random.random() @@ -1001,6 +1005,9 @@ def test_extract_data_from_capri_class(mocker): random_dockq = random.random() c.model = random_model + c.model.clt_id = random_clt_id + c.model.clt_rank = random_clt_rank + c.model.clt_model_rank = random_clt_model_rank c.md5 = random_md5 c.score = random_score c.irmsd = random_irmsd @@ -1024,3 +1031,6 @@ def test_extract_data_from_capri_class(mocker): assert observed_data[1]["ilrmsd"] == random_ilrmsd assert observed_data[1]["dockq"] == random_dockq assert observed_data[1]["energy"] == random_energy + assert observed_data[1]["cluster_id"] == random_clt_id + assert observed_data[1]["cluster_ranking"] == random_clt_rank + assert observed_data[1]["model-cluster_ranking"] == random_clt_model_rank From 63b72b31303e733815b67e2683ab8ad7e0717f57 Mon Sep 17 00:00:00 2001 From: "Rodrigo V. Honorato" Date: Fri, 23 Aug 2024 13:33:46 +0200 Subject: [PATCH 2/4] propagate `clt_id`, `clt_rank` and `clt_model_rank` --- src/haddock/modules/analysis/caprieval/capri.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/src/haddock/modules/analysis/caprieval/capri.py b/src/haddock/modules/analysis/caprieval/capri.py index 2414a6ab4..2d75e5ba4 100644 --- a/src/haddock/modules/analysis/caprieval/capri.py +++ b/src/haddock/modules/analysis/caprieval/capri.py @@ -224,6 +224,9 @@ def __init__( self.identificator = identificator self.core_model_idx = identificator self.less_io = less_io + self.cluster_id = None + self.cluster_ranking = None + self.model_cluster_ranking = None def calc_irmsd(self, cutoff: float = 5.0) -> None: """Calculate the I-RMSD. @@ -942,9 +945,11 @@ def extract_data_from_capri_class( "lrmsd": c.lrmsd, "ilrmsd": c.ilrmsd, "dockq": c.dockq, - "cluster_id": None, - "cluster_ranking": None, - "model-cluster_ranking": None, + "cluster_id": c.model.clt_id if c.model.clt_id else None, + "cluster_ranking": c.model.clt_rank if c.model.clt_rank else None, + "model-cluster_ranking": ( + c.model.clt_model_rank if c.model.clt_model_rank else None + ), } if c.model.unw_energies is not None: data[i].update(c.model.unw_energies) From c2bc47d2a03f38e4114fc232ceb4e001ed49f5d4 Mon Sep 17 00:00:00 2001 From: "Rodrigo V. Honorato" Date: Fri, 23 Aug 2024 13:39:56 +0200 Subject: [PATCH 3/4] add deprecation notice --- src/haddock/modules/analysis/caprieval/__init__.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/haddock/modules/analysis/caprieval/__init__.py b/src/haddock/modules/analysis/caprieval/__init__.py index 52947df76..b408d0177 100644 --- a/src/haddock/modules/analysis/caprieval/__init__.py +++ b/src/haddock/modules/analysis/caprieval/__init__.py @@ -144,6 +144,10 @@ def _run(self) -> None: ) else: + self.log( + msg="DEPRECATION NOTICE: This execution mode (less_io=False) will no longer be supported in the next version.", + level="warning", + ) jobs = merge_data(jobs) # Each job created one .tsv, unify them: From b281def514143bc5a23eb73b5632950815320da4 Mon Sep 17 00:00:00 2001 From: "Rodrigo V. Honorato" Date: Fri, 23 Aug 2024 13:40:11 +0200 Subject: [PATCH 4/4] cleaning --- src/haddock/modules/analysis/caprieval/capri.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/haddock/modules/analysis/caprieval/capri.py b/src/haddock/modules/analysis/caprieval/capri.py index 2d75e5ba4..2d29584ba 100644 --- a/src/haddock/modules/analysis/caprieval/capri.py +++ b/src/haddock/modules/analysis/caprieval/capri.py @@ -224,9 +224,6 @@ def __init__( self.identificator = identificator self.core_model_idx = identificator self.less_io = less_io - self.cluster_id = None - self.cluster_ranking = None - self.model_cluster_ranking = None def calc_irmsd(self, cutoff: float = 5.0) -> None: """Calculate the I-RMSD.