Note: this section makes extensive use of OTF-specific terminology that is explained in detail in the design concepts page. If you haven't read that page, you should do so before continuing.
In the broadest terms, the procedure for using the OTF in writing a biochemical application is as follows:
This section will lay out the general procedure of developing your genlib input and may gloss over fine detail. Questions of exact syntax, etc., can be resolved by consulting the genlib reference page.
The first step in input preparation is to decide which available toolkit components to request for inclusion in the generated classes. Requests for inclusion are typically found at the top of the input and are composed of the keyword implementation followed by the name of an implementation of that component, e.g.:
The name of the implementation is composed of the toolkit name and the component implementation file name, separated by a '/'. If the component is in a subtoolkit, then the subtoolkit name (or names, for sub-subtoolkits) would follow the main toolkit name but proceed the component name, with '/'s separating the names.
If a genlib input file contained only implementation statements, then genlib would generate code for a set of classes (e.g. Molecule, Atom, etc.) with the specified genericly useful features included. To make these classes useful to a particular application, specialized features need to be added...
The vast bulk of the application-specific customization is in the form of C++ code written by the application developer, specially marked up so that genlib knows where to place the code in the generated classes. The code markup tags are:
code, except inlined.
Besides code markup tags, there are some other statements that genlib interprets that are pertinent to class customization. They are:
containerstatement is employed to communicate a custom container's syntax and semantics to genlib, so that the container can be used in other genlib statements.
After creating an input file, running genlib with that file as input and no command line options will do the following:
Via command line options, it is possible to override the default library name (lib), the default compiler (g++), etc. The Command Line Use section of the genlib manual page covers these options in detail and should be perused in any case.
There are two types of errors that can result from running genlib: errors from genlib itself, and errors from the compilation of the assembled C++ code. Errors from genlib itself should be fairly self-explanatory. If you encounter a genlib error that you don't understand, please send mail to email@example.com so that we can explain the error and also improve the error text to make it more understandable in the future.
Errors during compilation will refer to line numbers in the composed code modules, rather than in the genlib input file. To correct the errors, you should refer to the code module mentioned in the error message, identify the error and its correction and then go back to the input file and make the correction and rerun genlib. Making the correction directly in the code module and running make will work to recompile the library, but in the long run it is better to correct the input file so that if you decide to add or subtract components, etc., then rerunning genlib will generate correct code and you won't have to redo all your corrections.
To employ the class library created by genlib, it is necessary to include the lib/lib.h file in any code modules that use the generated classes, and to link the object files with the lib/liblib.a archive. That's all there is to it.