Search

28 Mar 2024: 3.82 | 949 | aromatic-aliphatic amide [2, 6, 1, 8, 18, 7, 20, 14] | any OH [19, 13] 3.00 | 112 | aromatic-aliphatic amide [2, 6, 1, 8, 18, 7, 20, ... amide N-H [8, 1, 7, 20, 18, 14] 2.41 | 1810 | aromatic-aliphatic amide [2, 6, 1, 8, 18, 7, 20, 14] | any

28 Mar 2024: print(len(fxa_cavities[0].features)) 50 >>> print(fxa_cavities[0].features) (Feature(acceptor at Coordinates(x=30.506, y=20.947, z=20.879)),. It is possible to find out ... f = fxa_cavities[0].features[0] >>> print(f.type) acceptor >>>

28 Mar 2024: Distance 0.45 contacts 23 Distance 0.46 contacts 22 Distance 0.47 contacts 20 Distance 0.48 contacts 25 Distance 0.49 contacts 11. ... print(hit.match_atoms()) [Atom(C1), Atom(C3), Atom(C2), Atom(C9), Atom(C8), Atom(O3), Atom(O4)] >>>

28 Mar 2024: up Axes fig = plt.figure(figsize=(10., 10.)) # 3D graph instance ax = fig.add_subplot(111, projection='3d') # 3D Axes ax.set_xlim3d(-20, 20) ax.set_ylim3d(-20, 20) ... set_zlim3d(-20, 20) ax.set_xlabel('X axis') ax.set_ylabel('Y axis') ax.set_zlabel('Z

28 Mar 2024: that the angle between the planes defined above should be between 0 and 20 degrees:. >>> ... After 20 seconds the search will be terminated, and we can inspect the hits:. >>>

28 Mar 2024: settings = Pharmacophore.Search.Settings() >>> settings.max_hit_structures = 20 >>> settings.max_hits_per_structure = 1 >>> settings.max_hit_rmsd = 1.0 >>> searcher = Pharmacophore.Search(settings). ... database=feature_db) >>> print(len(hits)) 20 >>>

28 Mar 2024: 1.0, End: 1.0, NBins: 20, Bin width: 0.1. ... at_point(mol.atom('C10').coordinates) >>> print(round(v, 2)) 2.64 >>> v = grid.value(20, 25, 10) >>> print(round(v, 2)) 0.66.

28 Mar 2024: rotamer = Docker.Settings.Rotamer(3) rotamer.energy = 10 rotamer.chi1 = (-60,) rotamer.chi2 = (-75, 10) rotamer.chi3 = (-90, 10, 20) assert(rotamer.chi1.angle, -60) assert(rotamer.chi2.min_delta, 10) ... assert(rotamer.chi3.max_delta, 20).

28 Mar 2024: 20, inclusion='AnyAtomIncluded') >>> print(len(sliced.components)) 84 >>> sliced = crystal.slicing(MolecularDescriptors.atom_plane(crystal.molecule.heavy_atoms)) >>> print(len(sliced.components)) 20.

28 Mar 2024: For each of the 20 most similar cavities the PDB identifiers of the bound ligands are printed. ... pockets. Usage: python cavity_compare_db_screening_ligands.py --query query_cavity --db_path database_file --max_comparisons 20 ''' ########################