from __future__ import absolute_import, division, print_function import scitbx.graph.utils as graph_utils from scitbx import matrix from libtbx.utils import Sorry class pdb_extract(object): def __init__(O, tag, pdb, bonds, clusters=None, hinge_edges=None, loop_edges=None, loop_edge_bendings=None, find_cluster_loop_repeats=0, merge_clusters_with_multiple_connections_passes=1): O.index = None O.tag = tag O.labels, O.sites = [], [] for line in pdb.splitlines(): O.labels.append(line[22:26].strip()+"."+line[12:16].strip()) O.sites.append(matrix.col([float(line[30+i*8:38+i*8]) for i in [0,1,2]])) O.bonds = bonds O.clusters = clusters O.hinge_edges = hinge_edges O.loop_edges = loop_edges O.loop_edge_bendings = loop_edge_bendings O.find_cluster_loop_repeats = find_cluster_loop_repeats O.merge_clusters_with_multiple_connections_passes = \ merge_clusters_with_multiple_connections_passes def angles(O): return graph_utils.extract_edge_list( graph_utils.bond_bending_edge_sets( edge_sets=graph_utils.construct_edge_sets( n_vertices=len(O.sites), edge_list=O.bonds), omit_bonds=True)) def tardy_tree_construct(O, fixed_vertex_lists=[]): from scitbx.graph import tardy_tree tt = tardy_tree.construct( sites=O.sites, edge_list=O.bonds, fixed_vertex_lists=fixed_vertex_lists) if (len(fixed_vertex_lists) != 0): return tt cm = tt.cluster_manager if (O.clusters is None): print("tag:", O.tag) if (O.clusters is None): print("clusters:", cm.clusters) else: assert cm.clusters == O.clusters if (O.hinge_edges is None): print("hinge_edges:", cm.hinge_edges) else: assert cm.hinge_edges == O.hinge_edges if (O.loop_edges is None): print("loop_edges:", cm.loop_edges) else: assert cm.loop_edges == O.loop_edges if (O.loop_edge_bendings is None): print("loop_edge_bendings:", cm.loop_edge_bendings) else: assert cm.loop_edge_bendings == O.loop_edge_bendings assert tt.find_cluster_loop_repeats == O.find_cluster_loop_repeats assert cm.merge_clusters_with_multiple_connections_passes \ == O.merge_clusters_with_multiple_connections_passes if (O.clusters is None): print() return tt test_cases = [ pdb_extract( tag="point", pdb="""\ ATOM 0 FE FE A 1 10.949 12.815 15.189 0.00 0.00 FE """, bonds=[], clusters=[[0]], hinge_edges=[(-1, 0)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="gly_no_h", pdb="""\ ATOM 0 N GLY A 1 10.949 12.815 15.189 0.00 0.00 N ATOM 1 CA GLY A 1 10.405 13.954 15.917 0.00 0.00 C ATOM 2 C GLY A 1 10.779 15.262 15.227 0.00 0.00 C ATOM 3 O GLY A 1 9.916 16.090 14.936 0.00 0.00 O """, bonds=[(0,1),(1,2),(2,3)], clusters=[[0, 1, 2], [3]], hinge_edges=[(-1, 1), (1, 2)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="gly_with_nh", pdb="""\ ATOM 0 N GLY A 1 10.949 12.815 15.189 0.00 0.00 N ATOM 1 CA GLY A 1 10.405 13.954 15.917 0.00 0.00 C ATOM 2 C GLY A 1 10.779 15.262 15.227 0.00 0.00 C ATOM 3 O GLY A 1 9.916 16.090 14.936 0.00 0.00 O ATOM 4 H GLY A 1 11.792 12.691 15.311 0.00 0.00 H """, bonds=[(0,1),(0,4),(1,2),(2,3)], clusters=[[0, 1, 4], [2], [3]], hinge_edges=[(-1, 0), (0, 1), (1, 2)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="ala_no_h", pdb="""\ ATOM 0 N ALA A 1 10.949 12.815 15.189 0.00 0.00 N ATOM 1 CA ALA A 1 10.405 13.954 15.917 0.00 0.00 C ATOM 2 C ALA A 1 10.779 15.262 15.227 0.00 0.00 C ATOM 3 CB ALA A 1 10.908 13.950 17.351 0.00 0.00 C ATOM 4 O ALA A 1 9.916 16.090 14.936 0.00 0.00 O """, bonds=[(0,1),(1,2),(1,3),(2,4)], clusters=[[0, 1, 2, 3], [4]], hinge_edges=[(-1, 1), (1, 2)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="ala_with_h", pdb="""\ ATOM 0 N ALA A 1 10.949 12.815 15.189 0.00 0.00 N ATOM 1 CA ALA A 1 10.405 13.954 15.917 0.00 0.00 C ATOM 2 C ALA A 1 10.779 15.262 15.227 0.00 0.00 C ATOM 3 HA ALA A 1 9.428 13.887 15.936 0.00 0.00 H ATOM 4 O ALA A 1 9.916 16.090 14.936 0.00 0.00 O ATOM 5 H ALA A 1 11.792 12.691 15.311 0.00 0.00 H ATOM 6 CB ALA A 1 10.908 13.950 17.351 0.00 0.00 C ATOM 7 HB1 ALA A 1 10.627 13.138 17.778 0.00 0.00 H ATOM 8 HB2 ALA A 1 10.540 14.707 17.813 0.00 0.00 H ATOM 9 HB3 ALA A 1 11.867 14.004 17.346 0.00 0.00 H """, bonds=[(0,1),(0,5),(1,2),(1,3),(1,6),(2,4),(6,7),(6,8),(6,9)], clusters=[[0, 1, 2, 3, 6], [7, 8, 9], [5], [4]], hinge_edges=[(-1, 1), (1, 6), (1, 0), (1, 2)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="tyr_with_h", pdb="""\ ATOM 0 CG TYR A 1 11.007 9.417 9.446 1.00 0.79 C ATOM 1 CD1 TYR A 1 9.923 10.155 8.940 1.00 1.42 C ATOM 2 CD2 TYR A 1 10.765 8.288 10.238 1.00 1.41 C ATOM 3 CE1 TYR A 1 8.612 9.760 9.229 1.00 1.61 C ATOM 4 CE2 TYR A 1 9.453 7.895 10.525 1.00 1.42 C ATOM 5 CZ TYR A 1 8.377 8.631 10.021 1.00 1.11 C ATOM 6 HD1 TYR A 1 10.092 11.024 8.328 1.00 2.14 H ATOM 7 HD2 TYR A 1 11.596 7.718 10.630 1.00 2.21 H ATOM 8 HE1 TYR A 1 7.780 10.329 8.841 1.00 2.44 H ATOM 9 HE2 TYR A 1 9.270 7.023 11.135 1.00 2.13 H ATOM 10 OH TYR A 1 7.083 8.244 10.304 1.00 1.32 O ATOM 11 HH TYR A 1 6.494 8.723 9.717 1.00 2.00 H ATOM 12 CB TYR A 1 12.440 9.818 9.148 1.00 0.74 C ATOM 13 HB2 TYR A 1 12.827 9.193 8.358 1.00 0.78 H ATOM 14 HB3 TYR A 1 13.036 9.677 10.037 1.00 0.78 H ATOM 15 N TYR A 1 11.593 12.101 9.550 1.00 0.82 N ATOM 16 CA TYR A 1 12.527 11.286 8.721 1.00 0.75 C ATOM 17 C TYR A 1 12.160 11.413 7.239 1.00 0.76 C ATOM 18 HA TYR A 1 13.536 11.638 8.870 1.00 0.85 H ATOM 19 O TYR A 1 12.298 12.462 6.643 1.00 0.83 O ATOM 20 H TYR A 1 10.948 12.701 9.122 1.00 0.88 H """, bonds=[ (0, 1), (0, 2), (0, 12), (1, 3), (1, 6), (2, 4), (2, 7), (3, 5), (3, 8), (4, 5), (4, 9), (5, 10), (10, 11), (12, 13), (12, 14), (12, 16), (15, 16), (15, 20), (16, 17), (16, 18), (17, 19)], clusters=[ [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12], [13, 14, 16], [15, 17, 18], [11], [20], [19]], hinge_edges=[ (-1, 0), (0, 12), (12, 16), (5, 10), (16, 15), (16, 17)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="van_fragment", # PDB code 1qd8 pdb="""\ HETATM 47 C44 VAN 1 0.718 5.411 2.269 1.00 3.66 C HETATM 48 C47 VAN 1 0.913 3.899 2.010 1.00 3.90 C HETATM 49 C48 VAN 1 1.937 3.222 2.700 1.00 3.87 C HETATM 50 C50 VAN 1 2.013 1.800 2.726 1.00 4.31 C HETATM 51 C52 VAN 1 1.044 1.071 2.004 1.00 4.71 C HETATM 52 O53 VAN 1 1.077 -0.297 2.083 1.00 6.04 O HETATM 53 C51 VAN 1 0.066 1.767 1.246 1.00 5.04 C HETATM 54 C49 VAN 1 0.006 3.153 1.237 1.00 4.22 C HETATM 55 C45 VAN 1 -0.704 5.507 2.917 1.00 3.80 C HETATM 56 O46 VAN 1 -1.666 5.899 2.216 1.00 4.55 O HETATM 57 N54 VAN 1 -0.869 5.098 4.194 1.00 4.02 N HETATM 58 C55 VAN 1 0.141 4.679 5.156 1.00 4.23 C HETATM 69 C56 VAN 1 0.045 3.151 5.360 1.00 4.51 C HETATM 70 O57 VAN 1 -1.022 2.542 5.259 1.00 5.51 O HETATM 71 N68 VAN 1 1.226 2.525 5.641 1.00 4.67 N HETATM 72 C69 VAN 1 1.340 1.069 5.484 1.00 5.14 C HETATM 73 C72 VAN 1 2.754 0.737 4.924 1.00 4.58 C HETATM 74 C73 VAN 1 3.049 1.131 3.577 1.00 4.34 C HETATM 75 C75 VAN 1 4.354 0.899 3.099 1.00 4.29 C HETATM 76 O79 VAN 1 4.736 1.286 1.834 1.00 4.73 O HETATM 77 C76 VAN 1 5.342 0.269 3.883 1.00 4.57 C HETATM 78 C77 VAN 1 5.023 -0.107 5.195 1.00 4.56 C HETATM 79 O78 VAN 1 5.912 -0.707 6.053 1.00 5.51 O HETATM 80 C74 VAN 1 3.724 0.123 5.713 1.00 4.95 C HETATM 81 C70 VAN 1 1.069 0.287 6.838 1.00 5.82 C HETATM 82 O71 VAN 1 1.149 0.912 7.924 1.00 7.21 O HETATM 83 O80 VAN 1 0.816 -0.957 6.693 1.00 8.10 O """, bonds=[ (0, 1), (0, 8), (1, 2), (1, 7), (2, 3), (3, 4), (3, 17), (4, 5), (4, 6), (6, 7), (8, 9), (8, 10), (10, 11), (11, 12), (12, 13), (12, 14), (14, 15), (15, 16), (15, 24), (16, 17), (16, 23), (17, 18), (18, 19), (18, 20), (20, 21), (21, 22), (21, 23), (24, 25), (24, 26)], clusters=[ [3, 15, 16, 17, 18, 19, 20, 21, 22, 23], [0, 1, 2, 4, 5, 6, 7], [14, 24], [25, 26], [8], [9, 10], [11], [12], [13]], hinge_edges=[ (-1, 16), (17, 3), (16, 15), (15, 24), (1, 0), (0, 8), (8, 10), (10, 11), (11, 12)], loop_edges=[(12, 14)], loop_edge_bendings=[(11, 14), (12, 15), (13, 14)]), pdb_extract( tag="ZINC00000015", # C[C@@H](C(=O)[O-])[NH+](CCCl)CCCl pdb="""\ ATOM 1 C00 LIG A 1 2.209 1.054 0.461 1.00 20.00 A C ATOM 2 C01 LIG A 1 0.708 1.054 0.461 1.00 20.00 A C ATOM 3 C02 LIG A 1 0.094 1.054 1.832 1.00 20.00 A C ATOM 4 O03 LIG A 1 -0.670 1.994 2.178 1.00 20.00 A O ATOM 5 O04 LIG A 1 0.433 0.179 2.672 1.00 20.00 A O-1 ATOM 6 N05 LIG A 1 0.121 0.117 -0.463 1.00 20.00 A N+1 ATOM 7 C06 LIG A 1 0.808 -1.157 -0.363 1.00 20.00 A C ATOM 8 C07 LIG A 1 1.154 -1.925 -1.637 1.00 20.00 A C ATOM 9 CL08 LIG A 1 1.969 -3.508 -1.515 1.00 20.00 A CL ATOM 10 C09 LIG A 1 -1.281 -0.063 -0.144 1.00 20.00 A C ATOM 11 C10 LIG A 1 -2.233 -0.595 -1.214 1.00 20.00 A C ATOM 12 CL11 LIG A 1 -3.974 -0.726 -0.854 1.00 20.00 A CL ATOM 13 H12 LIG A 1 0.449 2.022 0.057 1.00 20.00 A H ATOM 14 H13 LIG A 1 0.214 0.498 -1.470 1.00 20.00 A H """, bonds=[ (0, 1), (1, 2), (1, 5), (1, 12), (2, 3), (2, 4), (5, 6), (5, 9), (5, 13), (6, 7), (7, 8), (9, 10), (10, 11)], clusters=[[0, 1, 2, 5, 12], [6, 9, 13], [3, 4], [7], [8], [10], [11]], hinge_edges=[(-1, 1), (1, 5), (1, 2), (5, 6), (6, 7), (5, 9), (9, 10)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="C1CCCCCCC1", pdb="""\ ATOM 1 C01 LIG A 1 -0.602 0.044 -1.758 1.00 20.00 A C ATOM 2 C02 LIG A 1 0.946 0.044 -1.758 1.00 20.00 A C ATOM 3 C03 LIG A 1 1.549 0.044 -0.333 1.00 20.00 A C ATOM 4 C04 LIG A 1 0.985 1.155 0.557 1.00 20.00 A C ATOM 5 C05 LIG A 1 0.430 0.619 1.870 1.00 20.00 A C ATOM 6 C06 LIG A 1 -0.536 -0.585 1.672 1.00 20.00 A C ATOM 7 C07 LIG A 1 -1.590 -0.345 0.547 1.00 20.00 A C ATOM 8 C08 LIG A 1 -1.184 -0.969 -0.799 1.00 20.00 A C ATOM 9 H011 LIG A 1 -0.949 -0.183 -2.755 1.00 20.00 A H ATOM 10 H012 LIG A 1 -0.952 1.028 -1.483 1.00 20.00 A H ATOM 11 H021 LIG A 1 1.293 -0.834 -2.283 1.00 20.00 A H ATOM 12 H022 LIG A 1 1.293 0.921 -2.283 1.00 20.00 A H ATOM 13 H031 LIG A 1 2.618 0.172 -0.411 1.00 20.00 A H ATOM 14 H032 LIG A 1 1.349 -0.911 0.130 1.00 20.00 A H ATOM 15 H041 LIG A 1 1.773 1.861 0.775 1.00 20.00 A H ATOM 16 H042 LIG A 1 0.196 1.666 0.025 1.00 20.00 A H ATOM 17 H051 LIG A 1 1.254 0.304 2.494 1.00 20.00 A H ATOM 18 H052 LIG A 1 -0.102 1.413 2.373 1.00 20.00 A H ATOM 19 H061 LIG A 1 -1.057 -0.766 2.600 1.00 20.00 A H ATOM 20 H062 LIG A 1 0.045 -1.461 1.425 1.00 20.00 A H ATOM 21 H071 LIG A 1 -2.531 -0.775 0.857 1.00 20.00 A H ATOM 22 H072 LIG A 1 -1.722 0.718 0.413 1.00 20.00 A H ATOM 23 H081 LIG A 1 -0.452 -1.743 -0.620 1.00 20.00 A H ATOM 24 H082 LIG A 1 -2.056 -1.415 -1.253 1.00 20.00 A H """, bonds=[ (0, 1), (0, 7), (0, 8), (0, 9), (1, 2), (1, 10), (1, 11), (2, 3), (2, 12), (2, 13), (3, 4), (3, 14), (3, 15), (4, 5), (4, 16), (4, 17), (5, 6), (5, 18), (5, 19), (6, 7), (6, 20), (6, 21), (7, 22), (7, 23)], clusters=[ [0, 1, 7, 8, 9], [2, 10, 11], [3, 12, 13], [4, 14, 15], [5, 16, 17], [6, 18, 19], [20, 21], [22, 23]], hinge_edges=[ (-1, 0), (0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6), (0, 7)], loop_edges=[(6, 7)], loop_edge_bendings=[(0, 6), (5, 7), (6, 22), (6, 23), (7, 20), (7, 21)]), pdb_extract( tag="c1cc2ccc1CCc3ccc(cc3)CC2", pdb="""\ ATOM 1 C00 LIG A 1 -0.703 -1.478 -1.316 1.00 20.00 A C ATOM 2 C01 LIG A 1 0.705 -1.478 -1.316 1.00 20.00 A C ATOM 3 C02 LIG A 1 1.403 -1.478 -0.101 1.00 20.00 A C ATOM 4 C03 LIG A 1 0.695 -1.478 1.107 1.00 20.00 A C ATOM 5 C04 LIG A 1 -0.713 -1.478 1.095 1.00 20.00 A C ATOM 6 C05 LIG A 1 -1.400 -1.478 -0.101 1.00 20.00 A C ATOM 7 C06 LIG A 1 -2.732 -0.755 -0.050 1.00 20.00 A C ATOM 8 C07 LIG A 1 -2.724 0.768 0.057 1.00 20.00 A C ATOM 9 C08 LIG A 1 -1.389 1.474 0.106 1.00 20.00 A C ATOM 10 C09 LIG A 1 -0.698 1.663 -1.087 1.00 20.00 A C ATOM 11 C10 LIG A 1 0.700 1.663 -1.087 1.00 20.00 A C ATOM 12 C11 LIG A 1 1.392 1.474 0.106 1.00 20.00 A C ATOM 13 C12 LIG A 1 0.685 1.286 1.290 1.00 20.00 A C ATOM 14 C13 LIG A 1 -0.682 1.286 1.290 1.00 20.00 A C ATOM 15 C14 LIG A 1 2.727 0.768 0.057 1.00 20.00 A C ATOM 16 C15 LIG A 1 2.734 -0.755 -0.050 1.00 20.00 A C """, bonds=[ (0, 1), (0, 5), (1, 2), (2, 3), (2, 15), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8), (8, 9), (8, 13), (9, 10), (10, 11), (11, 12), (11, 14), (12, 13), (14, 15)], clusters=[[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]], hinge_edges=[(-1, 0)], loop_edges=[], loop_edge_bendings=[], find_cluster_loop_repeats=1, merge_clusters_with_multiple_connections_passes=2), pdb_extract( tag="ZINC04656480", # C[NH+]1CC2C[NH+](CC(C1)NC2=O)C pdb="""\ ATOM 1 C01 LIG A 1 3.508 -0.708 -0.412 1.00 20.00 A C ATOM 2 N02 LIG A 1 2.081 -0.708 -0.412 1.00 20.00 A N+1 ATOM 3 C03 LIG A 1 1.365 -0.708 0.929 1.00 20.00 A C ATOM 4 C04 LIG A 1 0.082 0.043 1.236 1.00 20.00 A C ATOM 5 C05 LIG A 1 -1.306 -0.550 0.994 1.00 20.00 A C ATOM 6 N06 LIG A 1 -2.192 -0.518 -0.222 1.00 20.00 A N+1 ATOM 7 C07 LIG A 1 -1.365 0.265 -1.189 1.00 20.00 A C ATOM 8 C08 LIG A 1 0.016 0.896 -1.052 1.00 20.00 A C ATOM 9 C09 LIG A 1 1.306 0.176 -1.376 1.00 20.00 A C ATOM 10 N10 LIG A 1 0.128 1.826 -0.060 1.00 20.00 A N ATOM 11 C11 LIG A 1 0.183 1.401 1.073 1.00 20.00 A C ATOM 12 O12 LIG A 1 0.029 2.140 1.997 1.00 20.00 A O ATOM 13 C13 LIG A 1 -3.570 -0.330 -0.116 1.00 20.00 A C ATOM 14 H021 LIG A 1 1.870 -1.698 -0.789 1.00 20.00 A H ATOM 15 H061 LIG A 1 -2.133 -1.527 -0.603 1.00 20.00 A H """, bonds=[ (0, 1), (1, 2), (1, 8), (1, 13), (2, 3), (3, 4), (3, 10), (4, 5), (5, 6), (5, 12), (5, 14), (6, 7), (7, 8), (7, 9), (9, 10), (10, 11)], clusters=[[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]], hinge_edges=[(-1, 1)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="ZINC00196949", # C1C[NH+]2C[NH+]3CC[NH+](C2)C[NH+]1C3 pdb="""\ ATOM 1 C01 LIG A 1 -0.794 -0.210 -2.068 1.00 20.00 A C ATOM 2 C02 LIG A 1 0.777 -0.210 -2.068 1.00 20.00 A C ATOM 3 N03 LIG A 1 1.469 -0.210 -0.777 1.00 20.00 A N+1 ATOM 4 C04 LIG A 1 1.272 1.121 0.048 1.00 20.00 A C ATOM 5 N05 LIG A 1 -0.055 1.295 0.938 1.00 20.00 A N+1 ATOM 6 C06 LIG A 1 -0.049 0.433 2.224 1.00 20.00 A C ATOM 7 C07 LIG A 1 -0.000 -0.931 1.970 1.00 20.00 A C ATOM 8 N08 LIG A 1 0.028 -1.145 0.699 1.00 20.00 A N+1 ATOM 9 C09 LIG A 1 1.169 -1.328 0.066 1.00 20.00 A C ATOM 10 C10 LIG A 1 -1.086 -1.335 0.014 1.00 20.00 A C ATOM 11 N11 LIG A 1 -1.435 -0.222 -0.800 1.00 20.00 A N+1 ATOM 12 C12 LIG A 1 -1.284 1.103 0.012 1.00 20.00 A C ATOM 13 H031 LIG A 1 2.523 -0.274 -1.003 1.00 20.00 A H ATOM 14 H051 LIG A 1 -0.075 2.324 1.264 1.00 20.00 A H ATOM 15 H081 LIG A 1 0.030 -0.086 0.488 1.00 20.00 A H ATOM 16 H111 LIG A 1 -2.490 -0.325 -1.006 1.00 20.00 A H """, bonds=[ (0, 1), (0, 10), (1, 2), (2, 3), (2, 8), (2, 12), (3, 4), (4, 5), (4, 11), (4, 13), (5, 6), (6, 7), (7, 8), (7, 9), (7, 14), (9, 10), (10, 11), (10, 15)], clusters=[[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]], hinge_edges=[(-1, 0)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="ZINC03847120", # c1ccc2ccccc(c1)C2(C#N)Br pdb="""\ ATOM 1 C01 LIG A 1 -0.432 0.012 -2.178 1.00 20.00 A C ATOM 2 C02 LIG A 1 0.935 0.041 -2.063 1.00 20.00 A C ATOM 3 C03 LIG A 1 1.687 0.100 -0.911 1.00 20.00 A C ATOM 4 C04 LIG A 1 1.243 0.139 0.405 1.00 20.00 A C ATOM 5 C05 LIG A 1 1.591 -1.206 0.440 1.00 20.00 A C ATOM 6 C06 LIG A 1 0.763 -2.304 0.362 1.00 20.00 A C ATOM 7 C07 LIG A 1 -0.604 -2.323 0.236 1.00 20.00 A C ATOM 8 C08 LIG A 1 -1.462 -1.249 0.162 1.00 20.00 A C ATOM 9 C09 LIG A 1 -1.152 0.105 0.202 1.00 20.00 A C ATOM 10 C10 LIG A 1 -1.368 0.038 -1.168 1.00 20.00 A C ATOM 11 C11 LIG A 1 0.001 0.809 0.965 1.00 20.00 A C ATOM 12 C12 LIG A 1 -0.253 2.219 0.533 1.00 20.00 A C ATOM 13 N13 LIG A 1 -0.445 3.287 0.205 1.00 20.00 A N ATOM 14 BR14 LIG A 1 -0.504 0.332 2.810 1.00 20.00 A BR """, bonds=[ (0, 1), (0, 9), (1, 2), (2, 3), (3, 4), (3, 10), (4, 5), (5, 6), (6, 7), (7, 8), (8, 9), (8, 10), (10, 11), (10, 13), (11, 12)], clusters=[[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13]], hinge_edges=[(-1, 0)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="-ZINC12362269", # C/C(=N\NC(=O)[C@H]1CC1(C2CC2)C3CC3)/c4cccc(c4)Br # atoms 16-23 removed pdb="""\ ATOM 1 C01 LIG A 1 -1.077 -0.498 -3.089 1.00 20.00 A C ATOM 2 C02 LIG A 1 -1.796 -0.766 -1.768 1.00 20.00 A C ATOM 3 N03 LIG A 1 -1.180 -0.649 -0.687 1.00 20.00 A N ATOM 4 N04 LIG A 1 0.179 -0.269 -0.687 1.00 20.00 A N ATOM 5 C05 LIG A 1 0.896 -0.141 0.569 1.00 20.00 A C ATOM 6 O06 LIG A 1 0.341 -0.355 1.593 1.00 20.00 A O ATOM 7 C07 LIG A 1 2.307 0.249 0.569 1.00 20.00 A C ATOM 8 C08 LIG A 1 2.760 -0.479 1.787 1.00 20.00 A C ATOM 9 C09 LIG A 1 3.212 0.911 1.550 1.00 20.00 A C ATOM 10 C10 LIG A 1 3.211 2.174 2.408 1.00 20.00 A C ATOM 11 C11 LIG A 1 3.039 3.693 2.491 1.00 20.00 A C ATOM 12 C12 LIG A 1 2.935 2.841 3.758 1.00 20.00 A C ATOM 13 C13 LIG A 1 4.738 0.961 1.496 1.00 20.00 A C ATOM 14 C14 LIG A 1 6.113 0.494 1.979 1.00 20.00 A C ATOM 15 C15 LIG A 1 6.006 1.517 0.846 1.00 20.00 A C """, bonds=[ (0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (4, 6), (6, 7), (6, 8), (7, 8), (8, 9), (8, 12), (9, 10), (9, 11), (10, 11), (12, 13), (12, 14), (13, 14)], clusters=[[4, 6, 7, 8, 9, 12], [10, 11], [13, 14], [3, 5], [2], [1], [0]], hinge_edges=[(-1, 6), (8, 9), (8, 12), (6, 4), (4, 3), (3, 2), (2, 1)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="ZINC01638508", # C1CC1C(C2CC2)(C3CC3)O pdb="""\ ATOM 1 C01 LIG A 1 -0.942 1.244 -2.155 1.00 20.00 A C ATOM 2 C02 LIG A 1 0.586 1.277 -2.221 1.00 20.00 A C ATOM 3 C03 LIG A 1 -0.120 1.216 -0.865 1.00 20.00 A C ATOM 4 C04 LIG A 1 -0.056 -0.069 -0.042 1.00 20.00 A C ATOM 5 C05 LIG A 1 -0.281 0.259 1.432 1.00 20.00 A C ATOM 6 C06 LIG A 1 -1.658 0.020 2.055 1.00 20.00 A C ATOM 7 C07 LIG A 1 -1.166 1.448 1.812 1.00 20.00 A C ATOM 8 C08 LIG A 1 1.316 -0.717 -0.216 1.00 20.00 A C ATOM 9 C09 LIG A 1 1.940 -1.483 0.953 1.00 20.00 A C ATOM 10 C10 LIG A 1 1.427 -2.242 -0.273 1.00 20.00 A C ATOM 11 O11 LIG A 1 -1.048 -0.953 -0.480 1.00 20.00 A O """, bonds=[ (0, 1), (0, 2), (1, 2), (2, 3), (3, 4), (3, 7), (3, 10), (4, 5), (4, 6), (5, 6), (7, 8), (7, 9), (8, 9)], clusters=[[2, 3, 4, 7, 10], [0, 1], [5, 6], [8, 9]], hinge_edges=[(-1, 3), (3, 2), (3, 4), (3, 7)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="ZINC01638509", # C1CC(OC1)(C2CC2)C3CC3 pdb="""\ ATOM 1 C01 LIG A 1 -1.976 0.015 -1.638 1.00 20.00 A C ATOM 2 C02 LIG A 1 -0.474 0.091 -1.532 1.00 20.00 A C ATOM 3 C03 LIG A 1 -0.172 0.077 -0.038 1.00 20.00 A C ATOM 4 O04 LIG A 1 -1.402 0.464 0.622 1.00 20.00 A O ATOM 5 C05 LIG A 1 -2.482 -0.041 -0.201 1.00 20.00 A C ATOM 6 C06 LIG A 1 0.849 1.194 0.167 1.00 20.00 A C ATOM 7 C07 LIG A 1 2.063 2.028 -0.248 1.00 20.00 A C ATOM 8 C08 LIG A 1 1.374 2.295 1.091 1.00 20.00 A C ATOM 9 C09 LIG A 1 0.546 -1.212 0.356 1.00 20.00 A C ATOM 10 C10 LIG A 1 1.137 -2.583 0.018 1.00 20.00 A C ATOM 11 C11 LIG A 1 0.535 -2.329 1.402 1.00 20.00 A C """, bonds=[ (0, 1), (0, 4), (1, 2), (2, 3), (2, 5), (2, 8), (3, 4), (5, 6), (5, 7), (6, 7), (8, 9), (8, 10), (9, 10)], clusters=[[0, 1, 2, 3, 4, 5, 8], [6, 7], [9, 10]], hinge_edges=[(-1, 0), (2, 5), (2, 8)], loop_edges=[], loop_edge_bendings=[]), pdb_extract( tag="ZINC00057527", # COc1cc2c(c(c1OC)OC)-c3ccc(c(=O)cc3[C@H](CC2)[NH3+])O pdb="""\ ATOM 1 C01 LIG A 1 -3.707 -1.073 -3.995 1.00 20.00 A C ATOM 2 O02 LIG A 1 -2.733 -0.091 -3.791 1.00 20.00 A O ATOM 3 C03 LIG A 1 -1.979 -0.103 -2.612 1.00 20.00 A C ATOM 4 C04 LIG A 1 -2.587 -0.442 -1.394 1.00 20.00 A C ATOM 5 C05 LIG A 1 -1.817 -0.515 -0.228 1.00 20.00 A C ATOM 6 C06 LIG A 1 -0.427 -0.384 -0.301 1.00 20.00 A C ATOM 7 C07 LIG A 1 0.172 0.035 -1.496 1.00 20.00 A C ATOM 8 C08 LIG A 1 -0.601 0.164 -2.656 1.00 20.00 A C ATOM 9 O09 LIG A 1 -0.012 0.608 -3.845 1.00 20.00 A O ATOM 10 C10 LIG A 1 -0.529 1.736 -4.489 1.00 20.00 A C ATOM 11 O11 LIG A 1 1.495 0.490 -1.488 1.00 20.00 A O ATOM 12 C12 LIG A 1 2.426 -0.085 -2.359 1.00 20.00 A C ATOM 13 C13 LIG A 1 0.459 0.004 0.693 1.00 20.00 A C ATOM 14 C14 LIG A 1 1.662 -0.498 0.151 1.00 20.00 A C ATOM 15 C15 LIG A 1 2.869 -0.758 0.803 1.00 20.00 A C ATOM 16 C16 LIG A 1 3.180 -0.590 2.138 1.00 20.00 A C ATOM 17 C17 LIG A 1 2.375 -0.122 3.157 1.00 20.00 A C ATOM 18 O18 LIG A 1 2.907 0.021 4.205 1.00 20.00 A O ATOM 19 C19 LIG A 1 1.045 0.298 3.092 1.00 20.00 A C ATOM 20 C20 LIG A 1 0.191 0.348 1.967 1.00 20.00 A C ATOM 21 C21 LIG A 1 -1.251 0.702 2.179 1.00 20.00 A C ATOM 22 C22 LIG A 1 -2.144 -0.498 2.330 1.00 20.00 A C ATOM 23 C23 LIG A 1 -2.468 -1.194 0.991 1.00 20.00 A C ATOM 24 N24 LIG A 1 -1.457 1.705 3.192 1.00 20.00 A N+1 ATOM 25 O25 LIG A 1 4.488 -0.926 2.503 1.00 20.00 A O ATOM 26 H211 LIG A 1 -1.563 1.168 1.254 1.00 20.00 A H """, bonds=[ (0, 1), (1, 2), (2, 3), (2, 7), (3, 4), (4, 5), (4, 22), (5, 6), (5, 12), (6, 7), (6, 10), (7, 8), (8, 9), (10, 11), (12, 13), (12, 19), (13, 14), (14, 15), (15, 16), (15, 24), (16, 17), (16, 18), (18, 19), (19, 20), (20, 21), (20, 23), (20, 25), (21, 22)], clusters=[ [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25], [0], [9], [11]], hinge_edges=[(-1, 2), (2, 1), (7, 8), (6, 10)], loop_edges=[], loop_edge_bendings=[], find_cluster_loop_repeats=1, merge_clusters_with_multiple_connections_passes=2), pdb_extract( # scitbx/rigid_body/essence/tst_tardy.py, exercise_near_singular_hinges() tag="collinear", pdb="""\ ATOM 1 C1 COL 1 -1.334 -0.770 0.000 1.00 0.00 ATOM 2 C2 COL 1 -1.334 0.770 0.000 1.00 0.00 ATOM 3 C3 COL 1 0.000 0.000 0.000 1.00 0.00 ATOM 4 C4 COL 1 1.540 0.000 0.000 1.00 0.00 ATOM 5 C5 COL 1 3.080 0.000 0.000 1.00 0.00 ATOM 6 C6 COL 1 4.620 0.000 0.000 1.00 0.00 ATOM 7 C7 COL 1 5.954 -0.770 0.000 1.00 0.00 """, bonds=[(0, 1), (0, 2), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6)], clusters=[[0, 1, 2, 3, 4, 5], [6]], hinge_edges=[(-1, 0), (4, 5)], loop_edges=[], loop_edge_bendings=[]), ] def _set_test_case_indices(): for i,test_case in enumerate(test_cases): test_case.index = i _set_test_case_indices() def select_test_cases(tags_or_indices): result = [] test_case_dict = dict([(test_case.tag,i) for i,test_case in enumerate(test_cases)]) for tag_or_index in tags_or_indices: i = test_case_dict.get(tag_or_index) if (i is None): try: i = int(tag_or_index) except ValueError: i = -1 if (i < 0 or i >= len(test_cases)): msg = "No such test case: %s" % tag_or_index print(msg) print("List of available test cases:") for i,test_case in enumerate(test_cases): print(" %2d: %s" % (i, test_case.tag)) raise Sorry(msg) result.append(test_cases[i]) if (len(result) == 0): result = test_cases return result