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
HOWTO's
  1. Call CDL functions and objects from ORACLE
Clients executables that provide CDL functionality :
  1. Nails
  2. sdf_helper
  3. multicats
  4. rdf_helper
  5. smarts
Applications :
  1. Miscellaneous
  2. Fragments and pKa
  3. Evolution of novel HIV-protease inhibitors. In the T22 poster from the 4th Joint Sheffield Conference on Chemoinformatics. Note is a 2.4MB PDF document
Other morpho libraries :
  1. Neural Networks Template Library
  2. Support Vector Machines Template Library

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