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Converting TOP scripts from old MODELLER versions

Previous versions of MODELLER used TOP as their scripting language. TOP is a language similar in syntax to FORTRAN, which is also used by ASGL. For increased power and flexibility, interoperability with other programs, and improved ease of use, MODELLER now uses Python 2.3 for its control language.

Subsections

- Running old scripts unchanged
- Converting TOP scripts to Python
  - TOP commands and variables
  - TOP models and alignments
  - TOP to Python correspondence