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The `environ` class: MODELLER environment

The `environ` class contains most information about the MODELLER environment, such as the energy function and parameter and topology libraries (see section 6.1 for more information). Usually it is the first class to be used in a MODELLER script, as it provides methods to create the other main classes. In addition, some miscellaneous commands are also provided as methods of the `environ` class.

Subsections

- environ() — create a new MODELLER environment
- environ.io — default input parameters
- environ.edat — default objective function parameters
- environ.libs — MODELLER libraries
- environ.schedule_scale — energy function scaling factors
- environ.dendrogram() — clustering
- environ.principal_components() — clustering
- environ.system() — execute system command
- environ.make_pssmdb() — Create a database of PSSMs given a list of profiles