Daylight Toolkit Programmers' Guide Daylight Toolkit Programmers' Guide Table of Contents Daylight Toolkit Programmers' Guide............................................................................................................1 1. Introduction..........................................................................................................................................1 1.1 Daylight Toolkit Modules...........................................................................................................1 1.2 Audience and Background..........................................................................................................2 1.3 Other References.........................................................................................................................2 1.4 Conventions.................................................................................................................................3 1.5 Compiling and Linking...............................................................................................................3 1.5.1 Compiling..........................................................................................................................3 1.5.2 Linking...............................................................................................................................4 1.5.3 Toolkit Libraries................................................................................................................5 1.5.4 Advanced Programming....................................................................................................5 2. Basics: Daylight Toolkit Objects.........................................................................................................6 2.1 Introduction to Objects................................................................................................................6 2.2 Handles........................................................................................................................................7 2.3 Object Types................................................................................................................................8 2.4 The NULL_OB Handle...............................................................................................................9 2.5 Daylight Version Handling.........................................................................................................9 3. Basics: Polymorphic Functions.........................................................................................................10 3.1 Polymorphism...........................................................................................................................10 3.2 Generic Functions......................................................................................................................11 3.3 Semi-Generic Functions............................................................................................................12 4. Error handling....................................................................................................................................13 4.1 Introduction...............................................................................................................................13 4.2 General approach.......................................................................................................................14 4.3 Function types...........................................................................................................................14 4.3.1 Functions which create objects........................................................................................14 4.3.2 Functions which get the properties of objects.................................................................15 4.3.3 Functions which modify the properties of objects...........................................................15 4.3.4. Exceptions.......................................................................................................................15 4.4 Function return types.................................................................................................................16 4.4.1 Functions which return dt_Boolean.................................................................................16 4.4.2 Functions which return dt_Integer...................................................................................16 4.4.3 Functions which return dt_Real.......................................................................................17 4.4.4 Functions which return dt_String....................................................................................17 4.4.5 Functions which return dt_Handle...................................................................................17 4.5 Error message facilities.............................................................................................................17 5. Basics: String and Number Objects...................................................................................................18 5.1 String Objects............................................................................................................................18 5.2 Integer and Real Number Objects.............................................................................................19 5.3 Binary-Data Functions..............................................................................................................19 6. Basics: Streams and Sequences.........................................................................................................20 6.1 Properties...................................................................................................................................20 6.1.1 Stream Properties.............................................................................................................20 6.1.2Sequence Properties..........................................................................................................21 6.1.3 Example...........................................................................................................................21 6.2 Functions on Streams and Sequences........................................................................................21 6.3 Functions on Sequences Only...................................................................................................22 7. SMILES Toolkit: Molecules..............................................................................................................23 i Daylight Toolkit Programmers' Guide Table of Contents Daylight Toolkit Programmers' Guide 7.1 Creating Molecules....................................................................................................................23 7.2 Constituents of a Molecule........................................................................................................23 7.3 Modifying Molecules................................................................................................................24 7.3.1 Derived Properties...........................................................................................................24 7.3.2 The Modify-on and Modify-off States.............................................................................24 7.3.3 Functions Applicable Only During Modify-On...............................................................25 7.3.4 Functions Applicable Only During Modify-Off..............................................................25 7.3.5 Functions Applicable At All Times.................................................................................25 7.4 Structural-Modification Functions............................................................................................26 7.5 Properties of Atoms...................................................................................................................26 7.6 Properties of Bonds...................................................................................................................27 7.7 Properties of Cycles...................................................................................................................28 7.8 Generating SMILES..................................................................................................................28 7.9 Aromaticity................................................................................................................................28 7.10 Symmetry................................................................................................................................28 7.11 Chirality...................................................................................................................................29 8. SMILES Toolkits: Substructures and Paths.......................................................................................30 8.1 Introduction...............................................................................................................................30 8.2 Functions on Substructures and Paths.......................................................................................31 9. SMARTS Toolkit: Structural Searching............................................................................................32 9.1 Introduction...............................................................................................................................32