Update configs

maabuu · Aug 13, 2024 · 63d784a · 63d784a
1 parent 88e7f4f
commit 63d784a
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Showing 4 changed files with 49 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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: