Merge pull request #83 from openforcefield/perses-edges

Adding new directory structure for edges and preliminary edges
openforcefield · Jun 5, 2023 · a0b67b9 · a0b67b9
2 parents d338760 + d2f51ac
commit a0b67b9
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diff --git a/data/cdk2/00_data/edges.yml b/data/cdk2/00_data/edges.yml
diff --git a/data/cdk2/03_edges/01_perses_openfe.yml b/data/cdk2/03_edges/01_perses_openfe.yml
@@ -0,0 +1,85 @@
+mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True,
+  coordinate_tolerance=0.2), default non geometric scorer
+planner: openfe v0.5 minimal_spanning_graph
+edges:
+  edge_lig_22_lig_1oiy:
+    ligand_a: lig_22
+    ligand_b: lig_1oiy
+    atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10,
+      11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20,
+      21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30,
+      31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46,
+      47: 47, 48: 48}
+    score: '0.907'
+  edge_lig_20_lig_1oiy:
+    ligand_a: lig_20
+    ligand_b: lig_1oiy
+    atom mapping: {5: 33, 6: 35, 8: 41, 9: 42, 10: 43, 11: 44, 12: 30, 13: 28, 14: 29,
+      15: 27, 16: 26, 17: 4, 18: 5, 19: 6, 20: 8, 21: 7, 22: 9, 23: 10, 24: 23, 25: 24,
+      26: 25, 27: 20, 28: 21, 29: 22, 30: 17, 31: 19, 32: 18, 33: 14, 34: 16, 35: 15,
+      36: 11, 37: 12, 38: 13, 39: 3, 40: 2, 41: 1, 42: 0, 43: 47, 44: 48, 45: 46,
+      46: 45, 47: 31, 48: 32}
+    score: '0.907'
+  edge_lig_17_lig_1oiy:
+    ligand_a: lig_17
+    ligand_b: lig_1oiy
+    atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10,
+      11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20,
+      21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30,
+      31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 39: 31, 40: 32, 41: 45, 42: 46,
+      43: 47, 44: 48}
+    score: '0.954'
+  edge_lig_21_lig_1oiy:
+    ligand_a: lig_21
+    ligand_b: lig_1oiy
+    atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10,
+      11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20,
+      21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30,
+      31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46,
+      47: 47, 48: 48}
+    score: '0.907'
+  edge_lig_1oiu_lig_1h1r:
+    ligand_a: lig_1oiu
+    ligand_b: lig_1h1r
+    atom mapping: {0: 43, 1: 40, 2: 39, 3: 15, 4: 16, 5: 18, 6: 19, 7: 20, 8: 21,
+      9: 22, 10: 38, 11: 23, 12: 37, 13: 36, 14: 24, 15: 35, 16: 34, 17: 25, 18: 32,
+      19: 33, 20: 26, 21: 30, 22: 31, 23: 27, 24: 29, 25: 28, 26: 17, 27: 12, 28: 10,
+      29: 11, 30: 3, 31: 2, 32: 44, 33: 1, 40: 6, 41: 7, 42: 5, 44: 4, 45: 9, 46: 13,
+      47: 14, 48: 41, 49: 42}
+    score: '0.948'
+  edge_lig_1oiu_lig_1oiy:
+    ligand_a: lig_1oiu
+    ligand_b: lig_1oiy
+    atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10,
+      11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20,
+      21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30,
+      31: 43, 32: 44, 33: 41, 40: 35, 42: 33, 43: 34, 44: 31, 45: 32, 46: 45, 47: 46,
+      48: 47, 49: 48}
+    score: '0.901'
+  edge_lig_1oiu_lig_1h1q:
+    ligand_a: lig_1oiu
+    ligand_b: lig_1h1q
+    atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10,
+      11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20,
+      21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30,
+      31: 39, 32: 40, 33: 37, 40: 35, 41: 36, 42: 33, 43: 34, 44: 31, 45: 32, 46: 41,
+      47: 42, 48: 43, 49: 44}
+    score: '0.961'
+  edge_lig_1oi9_lig_1oiu:
+    ligand_a: lig_1oi9
+    ligand_b: lig_1oiu
+    atom mapping: {2: 40, 3: 33, 5: 31, 6: 32, 7: 30, 8: 28, 9: 29, 10: 27, 11: 26,
+      12: 4, 13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, 22: 14,
+      23: 16, 24: 15, 25: 17, 26: 18, 27: 19, 28: 20, 29: 22, 30: 21, 31: 23, 32: 24,
+      33: 25, 34: 3, 35: 2, 36: 1, 37: 0, 38: 48, 39: 49, 40: 47, 41: 46, 42: 44,
+      43: 45, 44: 42, 45: 43}
+    score: '0.936'
+  edge_lig_26_lig_1oiu:
+    ligand_a: lig_26
+    ligand_b: lig_1oiu
+    atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10,
+      11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20,
+      21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30,
+      31: 44, 32: 45, 33: 42, 34: 43, 35: 40, 41: 33, 43: 31, 44: 32, 45: 46, 46: 47,
+      47: 48, 48: 49}
+    score: '0.901'