Reference

• Classes
  • Linker
    • Linker.__init__()
    • Linker.arch
    • Linker.cage_template
    • Linker.dr
    • Linker.get_xmotif_coordinates()
    • Linker.set_ranked_linker_possibilities()
    • Linker.x_atoms
    • Linker.x_motifs
  • Cage
    • Cage.__init__()
    • Cage.get_cavity_vol()
    • Cage.get_centroid()
    • Cage.get_charges()
    • Cage.get_esp_cube()
    • Cage.get_m_m_dist()
    • Cage.get_max_escape_sphere()
    • Cage.get_metal_atom_ids()
    • Cage.get_num_h_bond_acceptors()
    • Cage.get_num_h_bond_donors()
    • Cage.get_num_rot_bonds()
    • Cage.print_esp_cube_file()
  • Substrate
    • Substrate.__init__()
    • Substrate.gen_confs()
  • CageSubstrateComplex
    • CageSubstrateComplex.__init__()
  • BaseStruct
    • BaseStruct.__init__()
    • BaseStruct.atoms
    • BaseStruct.centre()
    • BaseStruct.charge
    • BaseStruct.com
    • BaseStruct.energy
    • BaseStruct.mult
    • BaseStruct.n_atoms
    • BaseStruct.name
    • BaseStruct.optimise()
    • BaseStruct.print_xyz_file()
    • BaseStruct.reasonable_geometry
    • BaseStruct.set_atoms()
    • BaseStruct.singlepoint()
    • BaseStruct.solvent
  • Molecule
    • Molecule.__init__()
    • Molecule.bonds
    • Molecule.conformers
    • Molecule.get_charges()
    • Molecule.mol_obj
    • Molecule.n_confs
    • Molecule.n_h_acceptors
    • Molecule.n_h_donors
    • Molecule.n_rot_bonds
    • Molecule.smiles
    • Molecule.volume
• Input Output
  • xyz_file_to_atoms()
  • atoms_to_xyz_file()
  • get_atoms_from_file()
  • xyzfile_to_atoms()
  • molfile_to_atoms()
  • mol2file_to_atoms()
• Geometry Utilities
  • calc_com()
  • calc_normalised_vector()
  • is_geom_reasonable()
  • rotation_matrix()
  • get_rot_mat_kabsch()
  • get_centered_matrix()
  • spherical_to_cart()
• Config
  • Config
    • Config.allow_permutations
    • Config.n_cores
• Templates
  • Template
    • Template.__init__()
    • Template.save_template()
  • Linker
    • Linker.__init__()
    • Linker.atoms
    • Linker.bonds
    • Linker.com
    • Linker.coords
    • Linker.x_atoms
    • Linker.x_motifs
  • Metal
    • Metal.__init__()
    • Metal.atom_id
    • Metal.coord
    • Metal.label
    • Metal.shift_vec
  • find_mols_in_xyzs()
  • get_template()