From 63d784aaad6d34d3580aad375b546658b0ab3e0c Mon Sep 17 00:00:00 2001 From: maabuu <42468905+maabuu@users.noreply.github.com> Date: Tue, 13 Aug 2024 09:15:47 +0200 Subject: [PATCH] Update configs --- posebusters/config/dock.yml | 19 ++++++++++++++++++- posebusters/config/gen.yml | 4 +++- posebusters/config/mol.yml | 9 ++++++++- posebusters/config/redock.yml | 21 ++++++++++++++++++++- 4 files changed, 49 insertions(+), 4 deletions(-) diff --git a/posebusters/config/dock.yml b/posebusters/config/dock.yml index 1702071..2ec1752 100644 --- a/posebusters/config/dock.yml +++ b/posebusters/config/dock.yml @@ -8,22 +8,28 @@ modules: rename_outputs: mol_pred_loaded: "MOL_PRED loaded" mol_cond_loaded: "MOL_COND loaded" + - name: "Chemistry" function: rdkit_sanity chosen_binary_test_output: - passes_rdkit_sanity_checks rename_outputs: - passes_rdkit_sanity_checks: "RDKit sanitization" + passes_rdkit_sanity_checks: "Sanitization" + - name: "Chemistry" function: inchi_convertible chosen_binary_test_output: - inchi_convertible rename_outputs: inchi_convertible: "InChI convertible" + - name: "Chemistry" function: atoms_connected chosen_binary_test_output: - all_atoms_connected + rename_outputs: + all_atoms_connected: "All atoms connected" + - name: "Geometry" function: "distance_geometry" parameters: @@ -45,6 +51,7 @@ modules: bond_lengths_within_bounds: "Bond lengths" bond_angles_within_bounds: "Bond angles" no_internal_clash: "Internal steric clash" + - name: "Ring flatness" function: "flatness" parameters: @@ -59,6 +66,7 @@ modules: num_systems_passed: number_aromatic_rings_pass max_distance: aromatic_ring_maximum_distance_from_plane flatness_passes: "Aromatic ring flatness" + - name: "Double bond flatness" function: "flatness" parameters: @@ -72,6 +80,7 @@ modules: num_systems_passed: number_double_bonds_pass max_distance: double_bond_maximum_distance_from_plane flatness_passes: "Double bond flatness" + - name: "Energy ratio" function: energy_ratio parameters: @@ -81,6 +90,7 @@ modules: - energy_ratio_passes rename_outputs: energy_ratio_passes: "Internal energy" + - name: "Distance to protein" function: "intermolecular_distance" parameters: @@ -100,6 +110,7 @@ modules: not_too_far_away: "Protein-ligand maximum distance" no_clashes: "Minimum distance to protein" rename_suffix: "_protein" + - name: "Distance to organic cofactors" function: "intermolecular_distance" parameters: @@ -117,6 +128,7 @@ modules: rename_outputs: no_clashes: "Minimum distance to organic cofactors" rename_suffix: "_organic_cofactors" + - name: "Distance to inorganic cofactors" function: "intermolecular_distance" parameters: @@ -134,6 +146,7 @@ modules: rename_outputs: no_clashes: "Minimum distance to inorganic cofactors" rename_suffix: "_inorganic_cofactors" + - name: "Distance to waters" function: "intermolecular_distance" parameters: @@ -151,6 +164,7 @@ modules: rename_outputs: no_clashes: "Minimum distance to waters" rename_suffix: "_waters" + - name: "Volume overlap with protein" function: volume_overlap parameters: @@ -167,6 +181,7 @@ modules: volume_overlap: "volume_overlap_protein" no_volume_clash: "Volume overlap with protein" rename_suffix: "_protein" + - name: "Volume overlap with organic cofactors" function: volume_overlap parameters: @@ -183,6 +198,7 @@ modules: volume_overlap: "volume_overlap_organic_cofactors" no_volume_clash: "Volume overlap with organic cofactors" rename_suffix: "_organic_cofactors" + - name: "Volume overlap with inorganic cofactors" function: volume_overlap parameters: @@ -199,6 +215,7 @@ modules: volume_overlap: "volume_overlap_inorganic_cofactors" no_volume_clash: "Volume overlap with inorganic cofactors" rename_suffix: "_inorganic_cofactors" + - name: "Volume overlap with waters" function: volume_overlap parameters: diff --git a/posebusters/config/gen.yml b/posebusters/config/gen.yml index ff6ec65..efdf7fb 100644 --- a/posebusters/config/gen.yml +++ b/posebusters/config/gen.yml @@ -16,7 +16,7 @@ modules: chosen_binary_test_output: - passes_rdkit_sanity_checks rename_outputs: - passes_rdkit_sanity_checks: "RDKit sanitization" + passes_rdkit_sanity_checks: "Sanitization" - name: "Chemistry" function: inchi_convertible @@ -29,6 +29,8 @@ modules: function: atoms_connected chosen_binary_test_output: - all_atoms_connected + rename_outputs: + all_atoms_connected: "All atoms connected" - name: "Geometry" function: "distance_geometry" diff --git a/posebusters/config/mol.yml b/posebusters/config/mol.yml index 001481f..f81d205 100644 --- a/posebusters/config/mol.yml +++ b/posebusters/config/mol.yml @@ -6,24 +6,28 @@ modules: - mol_pred_loaded rename_outputs: mol_pred_loaded: "MOL_PRED loaded" + - name: "Chemistry" function: rdkit_sanity chosen_binary_test_output: - passes_rdkit_sanity_checks rename_outputs: - passes_rdkit_sanity_checks: "RDKit sanitization" + passes_rdkit_sanity_checks: "Sanitization" + - name: "Chemistry" function: inchi_convertible chosen_binary_test_output: - inchi_convertible rename_outputs: inchi_convertible: "InChI convertible" + - name: "Chemistry" function: atoms_connected chosen_binary_test_output: - all_atoms_connected rename_outputs: all_atoms_connected: "All atoms connected" + - name: "Geometry" function: "distance_geometry" parameters: @@ -45,6 +49,7 @@ modules: bond_lengths_within_bounds: "Bond lengths" bond_angles_within_bounds: "Bond angles" no_internal_clash: "Internal steric clash" + - name: "Ring flatness" function: "flatness" parameters: @@ -59,6 +64,7 @@ modules: num_systems_passed: number_aromatic_rings_pass max_distance: aromatic_ring_maximum_distance_from_plane flatness_passes: "Aromatic ring flatness" + - name: "Double bond flatness" function: "flatness" parameters: @@ -72,6 +78,7 @@ modules: num_systems_passed: number_double_bonds_pass max_distance: double_bond_maximum_distance_from_plane flatness_passes: "Double bond flatness" + - name: "Energy ratio" function: energy_ratio parameters: diff --git a/posebusters/config/redock.yml b/posebusters/config/redock.yml index a713ee5..008d463 100644 --- a/posebusters/config/redock.yml +++ b/posebusters/config/redock.yml @@ -10,22 +10,28 @@ modules: mol_pred_loaded: "MOL_PRED loaded" mol_true_loaded: "MOL_TRUE loaded" mol_cond_loaded: "MOL_COND loaded" + - name: "Chemistry" function: rdkit_sanity chosen_binary_test_output: - passes_rdkit_sanity_checks rename_outputs: - passes_rdkit_sanity_checks: "RDKit sanitization" + passes_rdkit_sanity_checks: "Sanitization" + - name: "Chemistry" function: inchi_convertible chosen_binary_test_output: - inchi_convertible rename_outputs: inchi_convertible: "InChI convertible" + - name: "Chemistry" function: atoms_connected chosen_binary_test_output: - all_atoms_connected + rename_outputs: + all_atoms_connected: "All atoms connected" + - name: "Chemistry" function: identity parameters: @@ -41,6 +47,7 @@ modules: stereo_dbond: "Double bond stereochemistry" stereo_tetrahedral: "Tetrahedral chirality" stereo: "Stereochemistry preserved" + - name: "Geometry" function: "distance_geometry" parameters: @@ -62,6 +69,7 @@ modules: bond_lengths_within_bounds: "Bond lengths" bond_angles_within_bounds: "Bond angles" no_internal_clash: "Internal steric clash" + - name: "Ring flatness" function: "flatness" parameters: @@ -76,6 +84,7 @@ modules: num_systems_passed: number_aromatic_rings_pass max_distance: aromatic_ring_maximum_distance_from_plane flatness_passes: "Aromatic ring flatness" + - name: "Double bond flatness" function: "flatness" parameters: @@ -89,6 +98,7 @@ modules: num_systems_passed: number_double_bonds_pass max_distance: double_bond_maximum_distance_from_plane flatness_passes: "Double bond flatness" + - name: "Energy ratio" function: energy_ratio parameters: @@ -98,6 +108,7 @@ modules: - energy_ratio_passes rename_outputs: energy_ratio_passes: "Internal energy" + - name: "Distance to protein" function: "intermolecular_distance" parameters: @@ -117,6 +128,7 @@ modules: not_too_far_away: "Protein-ligand maximum distance" no_clashes: "Minimum distance to protein" rename_suffix: "_protein" + - name: "Distance to organic cofactors" function: "intermolecular_distance" parameters: @@ -134,6 +146,7 @@ modules: rename_outputs: no_clashes: "Minimum distance to organic cofactors" rename_suffix: "_organic_cofactors" + - name: "Distance to inorganic cofactors" function: "intermolecular_distance" parameters: @@ -151,6 +164,7 @@ modules: rename_outputs: no_clashes: "Minimum distance to inorganic cofactors" rename_suffix: "_inorganic_cofactors" + - name: "Distance to waters" function: "intermolecular_distance" parameters: @@ -168,6 +182,7 @@ modules: rename_outputs: no_clashes: "Minimum distance to waters" rename_suffix: "_waters" + - name: "Volume overlap with protein" function: volume_overlap parameters: @@ -184,6 +199,7 @@ modules: volume_overlap: "volume_overlap_protein" no_volume_clash: "Volume overlap with protein" rename_suffix: "_protein" + - name: "Volume overlap with organic cofactors" function: volume_overlap parameters: @@ -200,6 +216,7 @@ modules: volume_overlap: "volume_overlap_organic_cofactors" no_volume_clash: "Volume overlap with organic cofactors" rename_suffix: "_organic_cofactors" + - name: "Volume overlap with inorganic cofactors" function: volume_overlap parameters: @@ -216,6 +233,7 @@ modules: volume_overlap: "volume_overlap_inorganic_cofactors" no_volume_clash: "Volume overlap with inorganic cofactors" rename_suffix: "_inorganic_cofactors" + - name: "Volume overlap with waters" function: volume_overlap parameters: @@ -232,6 +250,7 @@ modules: volume_overlap: "volume_overlap_waters" no_volume_clash: "Volume overlap with waters" rename_suffix: "_waters" + - name: "RMSD" function: rmsd parameters: