Daylight Toolkit Programmers' Guide

Table of Contents

1.1 Daylight Toolkit Modules
1.2 Audience and Background
1.3 Other References
1.4 Conventions
1.5 Compiling and Linking

2.1 Introduction to Objects
2.2 Handles
2.3 Object Types
2.4 The NULL_OB Handle

3.1 Polymorphism
3.2 Generic Functions
3.3 Semi-Generic Functions

4.1 Introduction
4.2 General approach
4.3 Function types

4.3.1 Functions which create objects
4.3.2 Functions which get the properties of objects
4.3.3 Functions which modify the properties of objects
4.3.4 Exceptions

4.4 Function return types

4.4.1 Functions which return dt_Boolean
4.4.2 Functions which return dt_Integer
4.4.3 Functions which return dt_Real
4.4.4 Functions which return dt_String
4.4.5 Functions which return dt_Handle

4.5 Error message facilities

5.1 String Objects
5.2 Integer and Real Number Objects
5.3 Binary-Data Functions

6.1 Properties

6.1.1 Stream Properties
6.1.2 Sequence Properties
6.1.3 Example

6.2 Functions on Streams and Sequences
6.3 Functions on Sequences Only
6.4 An Example

7.1 Creating Molecules
7.2 Constituents of a Molecule
7.3 Modifying Molecules

7.3.1 Derived Properties
7.3.2 The Modify-on and Modify-off States
7.3.3 Functions Applicable Only During Modify-On
7.3.4 Functions Applicable Only During Modify-Off
7.3.5 Functions Applicable At All Times

7.4 Structural-Modification Functions
7.5 Properties of Atoms
7.6 Properties of Bonds
7.7 Properties of Cycles
7.8 Generating SMILES
7.9 Aromaticity
7.10 Symmetry
7.11 Chirality

8.1 Introduction
8.2 Functions on Substructures and Paths

9.1 Introduction
9.2 Optimizing SMARTS
9.3 Allocating Patterns and Pathsets
9.4 Vector Bindings and Vbind Functions

9.4.1 Pattern Bindings
9.4.2 Pathset Bindings
9.4.3 Functions

9.5 Pattern Matching

10.1 Introduction
10.2 Fingerprint Functions

10.2.1 Global Settings
10.2.2 Creating Fingerprints
10.2.3 Properties
10.2.4 Fingerprint Bit Operations
10.2.5 Comparisons

11.1 Introduction
11.2 Depictions
11.3 Conformations
11.4 Modifying Depictions and Conformations
11.5 The Drawing Library

12.1 Introduction
12.2 Polymorphism in the Reaction Toolkit
12.3 Processing Reactions
12.4 Reaction Molecules
12.5 Atom Maps
12.6 Hydrogens in Reactions
12.7 Reaction Queries
12.8 Reactions and Other Objects

12.8.1 Paths and Substructs
12.8.2 Pathsets
12.8.3 Depictions
12.8.4 Conformations
12.8.5 Fingerprints

12.9 Transforms

13.1 Introduction
13.2 Using Program Objects

13.2.1 Welcome and Farewell Messages
13.2.2 Other Special Messages
13.2.3 Program Object Toolkit Functions

13.3 PIPETALK Protocol

13.3.1 Definitions
13.3.2 Receiving Messages
13.3.3 Sending Messages
13.3.4 Initial Response to Execution
13.3.5 Program Operation
13.3.6 Response to Special Messages
13.3.7 Program Termination
13.3.8 Naming Convention

14.1 Introduction: THOR and Merlin Objects
14.2 Connecting to a Server
14.3 Security

14.3.1 Restricted User DX_INFO_USER
14.3.2 Adding and Changing Users and Passwords

15.1 Introduction
15.2 Search Path
15.3 Creating and Configuring Databases

15.3.1 Database Creation
15.3.2 Database Configuration
15.3.3 Database Crunching

15.4 Opening and Closing Databases
15.5 Memory Usage: Cache and Hold

15.5.1 Merlin HOLD
15.5.2 THOR Caching

15.6 Database Security
15.7 Record Locking

16.1 Datatype and Fieldtype Objects
16.2 Getting Datatype and Fieldtype Objects

17.1 THOR Streams
17.2 Datatree Objects

17.2.1 Creating Datatree Objects
17.2.2 Destroying Datatrees and Datatree Objects
17.2.3 The Datatree Memory
17.2.4 Writing TDTs to a Database
17.2.5 Timestamps
17.2.6 Merging Datatrees
17.2.7 Cross-Referencing
17.2.8 Functions on TDT Objects

17.3 Dataitem and Datafield Objects

17.3.1 Functions on Dataitems and Datafields

18.1 Introduction
18.2 Tasks -- "Time Slicing"
18.3 Querying for Capabilities
18.4 Column Objects

18.4.1 Column "Functions"
18.4.2 Creating Columns
18.4.3 Information about Columns
18.4.4 Polymorphic Functions on Columns

18.5 Hitlist Objects

18.5.1 Creating Hitlists
18.5.2 Retrieving Data: Cells

18.6 Sorting
18.7 Searching

18.7.1 Actions
18.7.2 Parametric Searches
18.7.3 Structural Searches
18.7.4 Program-Object Searches

18.8 Other Hitlist Operations
18.9 Saving and Restoring Hitlists

19.1 Introduction
19.2 Widget Functional Interface
19.3 Widget Callback Functions
19.4 Options
19.5 The Widgets

19.5.1 3D or "Trackball" Widget
19.5.2 Depict Widget
19.5.3 Edgar Widget
19.5.4 File Widget
19.5.5 Font Utility
19.5.6 GRINS Widget
19.5.7 Help Widget
19.5.8 Message Widget
19.5.9 Status Widget
19.5.10 TDT Widget

19.6 Widget Programmer's Reference

20.1 The Application Programmer Interface

20.1.1 Create a Service (dt_http_alloc)
20.1.2 Receive a Request (dt_http_get)
20.1.3 Send a Response (dt_http_put)

20.2 The Structure of Programs

20.2.1 Build a CGI
20.2.2 Build a Server
20.2.3 Build a Dual-Purpose Server & CGI

20.3 The Essential Properties

20.3.1 Get a Request
20.3.2 Set a Response
20.3.3 Processing the GET Method: Hello World!

20.4 The Entire Set of Properties

20.4.1 Read-Only Properties of a CGI/Server
20.4.2 Read-Write Properties of a CGI/Server
20.4.3 Read-Only Properties of a Request
20.4.4 Read-Write Properties of a Response

20.5 Working With the Toolkit

20.5.1 Processing the POST Method

20.5.1.1 URL-Encoding (application/x-www-form-urlencoding)
20.5.1.2 Multipart Data (multipart/form-data)

20.5.2 Authenticating Access
20.5.3 Serving Files from Disk
20.5.4 Scripting With Java
20.5.5 Formatting With Automatic HTML
20.5.6 Adding Color to GIF Images
20.5.7 Avoiding Run-Time Problems With Compiler Definitions
20.5.8 Technical Specifications, Methods, Headers, and Status Codes

21.1 Introduction
21.2 Data Issues
21.3 Per-Thread Object Model
21.4 Global Object Model
21.5 Object Granularity
21.6 Thread Safety versus Reentrancy
21.7 Limitations