Next: automodel() prepare Up: Comparative modeling class reference Previous: Comparative modeling class reference Contents Index

`automodel` reference

All of the functions and data members of the automodel class are listed for reference below. Please note that the automodel class is derived from the model class, so all properties and commands of the model class are also available. Please see section 6.6 for more information.

Subsections

automodel() -- prepare to build one or more comparative models
automodel.library_schedule -- select optimization schedule
automodel.md_level -- control the model refinement level
automodel.outputs -- all output data for generated models
automodel.rand_method -- control initial model randomization
automodel.generate_method -- control initial model generation
automodel.max_var_iterations -- select length of optimizations
automodel.repeat_optimization -- number of times to repeat optimization
automodel.max_molpdf -- objective function cutoff
automodel.initial_malign3d -- initial template alignment
automodel.starting_model -- first model to build
automodel.ending_model -- last model to build
automodel.final_malign3d -- final template-model alignment
automodel.write_intermediates -- write intermediate files during optimization
automodel.trace_output -- control optimization output
automodel.max_ca_ca_distance -- Distance cutoff for CA-CA homology-derived restraints
automodel.max_n_o_distance -- Distance cutoff for N-O homology-derived restraints
automodel.max_sc_mc_distance -- Distance cutoff for sidechain-mainchain homology-derived restraints
automodel.max_sc_sc_distance -- Distance cutoff for sidechain-sidechain homology-derived restraints
automodel.get_optimize_actions() -- get actions to carry out during the initial optimization
automodel.get_refine_actions() -- get actions to carry out during the refinement
automodel.select_atoms() -- select region for optimization
automodel.auto_align() -- generate an automatic initial alignment
automodel.very_fast() -- request rapid optimization
automodel.make() -- build all models
automodel.cluster() -- cluster all built models
automodel.special_restraints() -- add additional restraints
automodel.nonstd_restraints() -- add restraints on ligands
automodel.special_patches() -- add additional patches to the topology
automodel.user_after_single_model() -- analyze or refine each model
automodel.get_model_filename() -- get the model PDB name
automodel.use_parallel_job() -- parallelize model building
automodel.guess_atom_types() -- automatically assign CHARMM atom types
automodel.guess_atom_type() -- automatically assign CHARMM atom type

Automatic builds 2014-02-11

automodel reference

`automodel` reference