Table of contents: Chemical Descriptors Library

1. Introduction to the CDL
2. Historic Background
3. Vision
4. Documentation assumptions
5. Library organization
6. Molecules, atoms and bonds
7. Quick tour of the CDL
8. Molecular Properties
9. Core library
   1. Basic Concepts
      1. Juice
      2. molecule class
      3. projected_molecule class
      4. indexed_molecule class
      5. reduced_molecule type and associated functions
   2. Free functions and algorithms
      1. Graph algorithms
         1. Ullmann algorithm for subgraph isomorphism
         2. Figueras algorithm for the calculation of the Smallest Set of Smallest Rings (SSSR)
         3. Maximum common edge subgraph
      2. For the molecule
         1. get_chiral_centers
         2. search_substructure
         3. add_cdl_implicit_H
         4. remove_hydrogens
         5. remove_cdl_implicit_hydrogens
         6. make_distance_matrix
         7. make_adjacency_matrix
         8. number_of_terminal_atoms
         9. number_non_h_atoms
         10. get_terminal_vertices
         11. count_atoms
      3. For the atoms
         1. valence_vertex_degree
         2. z_delta_num
         3. principal_quantum_num
         4. is_cdl_implicit_H
         5. num_implicit_hydrogens
         6. num_explicit_hydrogens
         7. num_hydrogens
   3. Function objects (Functors)
      1. For the molecule
         1. for_each_atom
         2. accumulate_atoms
         3. num_atoms
         4. num_bonds
         5. vertex_property_equals
         6. adjacent_vertices_property_equals
         7. is_vertex_ring_member
      2. For the atoms
         1. accumulate_atomic_prop
         2. accumulate_atomic_prop_if
         3. is_cdl_implicit_H_pred
         4. exclude_h_atom_filter
         5. preserve_selected_vertices
         6. exclude_implicit_h_filter
      3. For the bonds
         1. sum_bonds
         2. exclude_h_bond_filter
         3. preserve_selected_edges
         4. exclude_implicit_h_bond_filter
10. Client algorithms
    1. Molecular parsers
    2. Fingerprints
    3. Substructure search
    4. SMARTS language
    5. CDL Chemical Algebra
    6. Topological Pharmacophores
    7. Descriptors
    8. Atom Types Fingerprints
11. Error handling
12. Includes
13. FAQs
14. Style guide and programming policies
15. Building the CDL
16. Licence
17. References
18. Acknowledgements

1. Call CDL functions and objects from ORACLE

1. Nails
2. sdf_helper
3. multicats
4. rdf_helper
5. smarts

1. Miscellaneous
2. Fragments and pKa

1. Neural Networks Template Library
2. Support Vector Machines Template Library