From fb242a8bc28596c2f1c5ced6a4c1f4fe436b58bc Mon Sep 17 00:00:00 2001 From: sverhoeven Date: Fri, 6 Sep 2024 10:23:28 +0200 Subject: [PATCH 1/7] Set tolerance to 10 for topoaa and emscoring modules --- src/haddock/modules/scoring/emscoring/defaults.yaml | 2 +- src/haddock/modules/topology/topoaa/defaults.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/haddock/modules/scoring/emscoring/defaults.yaml b/src/haddock/modules/scoring/emscoring/defaults.yaml index bc54ef51b..ac9fadd67 100644 --- a/src/haddock/modules/scoring/emscoring/defaults.yaml +++ b/src/haddock/modules/scoring/emscoring/defaults.yaml @@ -277,7 +277,7 @@ nemsteps: group: 'sampling' explevel: expert tolerance: - default: 0 + default: 10 type: integer min: 0 max: 99 diff --git a/src/haddock/modules/topology/topoaa/defaults.yaml b/src/haddock/modules/topology/topoaa/defaults.yaml index 237089432..27275409c 100644 --- a/src/haddock/modules/topology/topoaa/defaults.yaml +++ b/src/haddock/modules/topology/topoaa/defaults.yaml @@ -85,7 +85,7 @@ set_bfactor: group: module explevel: expert tolerance: - default: 0 + default: 10 type: integer min: 0 max: 99 From 6ff6e3bc5f019b08db81308dde8e8a5b75a90a29 Mon Sep 17 00:00:00 2001 From: sverhoeven Date: Fri, 6 Sep 2024 10:33:41 +0200 Subject: [PATCH 2/7] Reset topoaa tolerance + set all *ref tolerance to 5 --- examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl | 1 - setup.py | 2 +- src/haddock/clis/cli_analyse.py | 1 + src/haddock/modules/refinement/emref/defaults.yaml | 2 +- src/haddock/modules/topology/topoaa/defaults.yaml | 2 +- 5 files changed, 4 insertions(+), 4 deletions(-) diff --git a/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl b/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl index 82b883e67..245d61426 100644 --- a/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl +++ b/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl @@ -133,7 +133,6 @@ assign ( resid 500 and segid B) ( resid 118 and segid A) ) 2.0 2.0 0.0 - ! HADDOCK AIR restraints for 3rd selection ! diff --git a/setup.py b/setup.py index 08ce8a5c2..d915b4fe0 100644 --- a/setup.py +++ b/setup.py @@ -68,7 +68,7 @@ def read(*names, **kwargs) -> str: 'Protein docking', 'Proteins', ], - python_requires='>=3.9, <3.10', + python_requires='>=3.9, <3.13', install_requires=[ # not added on purpose ], diff --git a/src/haddock/clis/cli_analyse.py b/src/haddock/clis/cli_analyse.py index c4230ba46..258d30bf8 100644 --- a/src/haddock/clis/cli_analyse.py +++ b/src/haddock/clis/cli_analyse.py @@ -615,6 +615,7 @@ def main( f"""Could not execute the analysis for step {step}. The following error occurred {e}""" ) + log.exception(e) if error: bad_folder_paths.append(target_path) else: diff --git a/src/haddock/modules/refinement/emref/defaults.yaml b/src/haddock/modules/refinement/emref/defaults.yaml index 720cd3325..8e00b8520 100644 --- a/src/haddock/modules/refinement/emref/defaults.yaml +++ b/src/haddock/modules/refinement/emref/defaults.yaml @@ -1391,7 +1391,7 @@ keepwater: group: 'sampling' explevel: guru tolerance: - default: 0 + default: 5 type: integer min: 0 max: 99 diff --git a/src/haddock/modules/topology/topoaa/defaults.yaml b/src/haddock/modules/topology/topoaa/defaults.yaml index 27275409c..237089432 100644 --- a/src/haddock/modules/topology/topoaa/defaults.yaml +++ b/src/haddock/modules/topology/topoaa/defaults.yaml @@ -85,7 +85,7 @@ set_bfactor: group: module explevel: expert tolerance: - default: 10 + default: 0 type: integer min: 0 max: 99 From 4e7f7d0d17a8a97ff1f227834b71ad1dab8cecd6 Mon Sep 17 00:00:00 2001 From: sverhoeven Date: Fri, 6 Sep 2024 10:41:17 +0200 Subject: [PATCH 3/7] Set rigidbody tol default to 5 --- src/haddock/modules/sampling/rigidbody/defaults.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/haddock/modules/sampling/rigidbody/defaults.yaml b/src/haddock/modules/sampling/rigidbody/defaults.yaml index c92d1a31d..1175f1a3a 100644 --- a/src/haddock/modules/sampling/rigidbody/defaults.yaml +++ b/src/haddock/modules/sampling/rigidbody/defaults.yaml @@ -900,7 +900,7 @@ inter_rigid: group: 'sampling' explevel: expert tolerance: - default: 0 + default: 5 type: integer min: 0 max: 99 From ad1196e0d892da792aa13c71da702453c4745865 Mon Sep 17 00:00:00 2001 From: sverhoeven Date: Fri, 6 Sep 2024 10:42:50 +0200 Subject: [PATCH 4/7] Set tolerance default to 5 in emref --- src/haddock/modules/refinement/emref/defaults.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/haddock/modules/refinement/emref/defaults.yaml b/src/haddock/modules/refinement/emref/defaults.yaml index 8e00b8520..f8f43c72c 100644 --- a/src/haddock/modules/refinement/emref/defaults.yaml +++ b/src/haddock/modules/refinement/emref/defaults.yaml @@ -1385,7 +1385,7 @@ iniseed: keepwater: default: false type: boolean - title: Write water molecules to output file + title: Write water molecules to output file` short: Write water molecules if present to the output file. long: Write water molecules if present to the output file. group: 'sampling' From 0a6d6449c9b53ac19c9bb71b502ade7f5ed0021d Mon Sep 17 00:00:00 2001 From: sverhoeven Date: Fri, 6 Sep 2024 10:46:41 +0200 Subject: [PATCH 5/7] Undo my local changes --- examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl | 2 +- setup.py | 2 +- src/haddock/clis/cli_analyse.py | 1 - src/haddock/modules/refinement/emref/defaults.yaml | 2 +- 4 files changed, 3 insertions(+), 4 deletions(-) diff --git a/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl b/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl index 245d61426..857140714 100644 --- a/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl +++ b/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl @@ -133,6 +133,7 @@ assign ( resid 500 and segid B) ( resid 118 and segid A) ) 2.0 2.0 0.0 + ! HADDOCK AIR restraints for 3rd selection ! @@ -145,4 +146,3 @@ assign ( resid 500 and segid B) ! HADDOCK AIR restraints for 6th selection ! - diff --git a/setup.py b/setup.py index d915b4fe0..08ce8a5c2 100644 --- a/setup.py +++ b/setup.py @@ -68,7 +68,7 @@ def read(*names, **kwargs) -> str: 'Protein docking', 'Proteins', ], - python_requires='>=3.9, <3.13', + python_requires='>=3.9, <3.10', install_requires=[ # not added on purpose ], diff --git a/src/haddock/clis/cli_analyse.py b/src/haddock/clis/cli_analyse.py index 258d30bf8..c4230ba46 100644 --- a/src/haddock/clis/cli_analyse.py +++ b/src/haddock/clis/cli_analyse.py @@ -615,7 +615,6 @@ def main( f"""Could not execute the analysis for step {step}. The following error occurred {e}""" ) - log.exception(e) if error: bad_folder_paths.append(target_path) else: diff --git a/src/haddock/modules/refinement/emref/defaults.yaml b/src/haddock/modules/refinement/emref/defaults.yaml index f8f43c72c..8e00b8520 100644 --- a/src/haddock/modules/refinement/emref/defaults.yaml +++ b/src/haddock/modules/refinement/emref/defaults.yaml @@ -1385,7 +1385,7 @@ iniseed: keepwater: default: false type: boolean - title: Write water molecules to output file` + title: Write water molecules to output file short: Write water molecules if present to the output file. long: Write water molecules if present to the output file. group: 'sampling' From 4f0e3d0386575765cf6e9851fe20f62ccb637f6f Mon Sep 17 00:00:00 2001 From: sverhoeven Date: Fri, 6 Sep 2024 10:48:58 +0200 Subject: [PATCH 6/7] Undo change to file that is not part of pr --- examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl | 1 + 1 file changed, 1 insertion(+) diff --git a/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl b/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl index 857140714..82b883e67 100644 --- a/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl +++ b/examples/docking-protein-ligand/data/ambig-active-rigidbody.tbl @@ -146,3 +146,4 @@ assign ( resid 500 and segid B) ! HADDOCK AIR restraints for 6th selection ! + From 72b145c931791193a14f0fa15c7c55d3ce743242 Mon Sep 17 00:00:00 2001 From: sverhoeven Date: Fri, 6 Sep 2024 10:52:09 +0200 Subject: [PATCH 7/7] Make tolerance default 5 everywhere execpt topoaa which stays at 0 --- src/haddock/modules/scoring/emscoring/defaults.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/haddock/modules/scoring/emscoring/defaults.yaml b/src/haddock/modules/scoring/emscoring/defaults.yaml index ac9fadd67..a4ac2e233 100644 --- a/src/haddock/modules/scoring/emscoring/defaults.yaml +++ b/src/haddock/modules/scoring/emscoring/defaults.yaml @@ -277,7 +277,7 @@ nemsteps: group: 'sampling' explevel: expert tolerance: - default: 10 + default: 5 type: integer min: 0 max: 99