Merge pull request #1391 from haddocking/1385-implement-adaptative-efficiency-submission-algorithm-for-modegrid

add adaptative job concatenation to `mode=grid`

Author: rvhonorato

.gitignore

@@ -159,3 +159,5 @@ docs/haddock.modules.base_cns_module.rst
 docs/setup.rst
 docs/clients/*rst
 log
+end-to-end_tests/ab-grid
+end-to-end_tests/prot-grid

end-to-end_tests/ab-grid.toml

@@ -0,0 +1,36 @@
+run_dir = "ab-grid"
+mode = "grid"
+ncores = 24
+molecules = [
+  "../examples/docking-antibody-antigen/data/4G6K_fv.pdb",
+  "../examples/docking-antibody-antigen/data/4I1B-matched.pdb",
+]
+[topoaa]
+[rigidbody]
+tolerance = 5
+ambig_fname = "../examples/docking-antibody-antigen/data/ambig.tbl"
+unambig_fname = "../examples/docking-antibody-antigen/data/unambig.tbl"
+sampling = 10000
+["caprieval.0"]
+reference_fname = "../examples/docking-antibody-antigen/data/4G6M-matched.pdb"
+[seletop]
+select = 500
+["caprieval.1"]
+reference_fname = "../examples/docking-antibody-antigen/data/4G6M-matched.pdb"
+[flexref]
+tolerance = 5
+ambig_fname = "../examples/docking-antibody-antigen/data/ambig.tbl"
+unambig_fname = "../examples/docking-antibody-antigen/data/unambig.tbl"
+["caprieval.2"]
+reference_fname = "../examples/docking-antibody-antigen/data/4G6M-matched.pdb"
+[emref]
+tolerance = 5
+ambig_fname = "../examples/docking-antibody-antigen/data/ambig.tbl"
+unambig_fname = "../examples/docking-antibody-antigen/data/unambig.tbl"
+["caprieval.3"]
+reference_fname = "../examples/docking-antibody-antigen/data/4G6M-matched.pdb"
+[clustfcc]
+[seletopclusts]
+top_models = 4
+["caprieval.4"]
+reference_fname = "../examples/docking-antibody-antigen/data/4G6M-matched.pdb"

end-to-end_tests/prot-grid.toml

@@ -0,0 +1,42 @@
+run_dir = "prot-grid"
+mode = "grid"
+molecules = [
+  "../examples/docking-protein-protein/data/e2aP_1F3G.pdb",
+  "../examples/docking-protein-protein/data/hpr_ensemble.pdb",
+]
+[topoaa]
+autohis = false
+[topoaa.mol1]
+nhisd = 0
+nhise = 1
+hise_1 = 75
+[topoaa.mol2]
+nhisd = 1
+hisd_1 = 76
+nhise = 1
+hise_1 = 15
+[rigidbody]
+tolerance = 5
+ambig_fname = "../examples/docking-protein-protein/data/e2a-hpr_air.tbl"
+sampling = 1000
+["caprieval.1"]
+reference_fname = "../examples/docking-protein-protein/data/e2a-hpr_1GGR.pdb"
+[seletop]
+select = 200
+["caprieval.2"]
+reference_fname = "../examples/docking-protein-protein/data/e2a-hpr_1GGR.pdb"
+[flexref]
+tolerance = 5
+ambig_fname = "../examples/docking-protein-protein/data/e2a-hpr_air.tbl"
+["caprieval.3"]
+reference_fname = "../examples/docking-protein-protein/data/e2a-hpr_1GGR.pdb"
+[emref]
+tolerance = 5
+ambig_fname = "../examples/docking-protein-protein/data/e2a-hpr_air.tbl"
+["caprieval.4"]
+reference_fname = "../examples/docking-protein-protein/data/e2a-hpr_1GGR.pdb"
+[clustfcc]
+[seletopclusts]
+top_models = 4
+["caprieval.5"]
+reference_fname = "../examples/docking-protein-protein/data/e2a-hpr_1GGR.pdb"