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The `model` class: handling of atomic coordinates, and model building

The model class holds all information about a 3D model (such as its Cartesian coordinates, topology, and optimization information). It also provides methods for reading, writing and transforming the model.

Subsections

model() -- create a new 3D model
model.seq_id -- sequence identity between the model and templates
model.restraints -- all restraints which act on the model
model.read() -- read coordinates for MODEL
model.write() -- write MODEL
model.generate_topology() -- generate MODEL topology
model.patch() -- patch MODEL topology
model.patch_ss_templates() -- guess MODEL disulfides from templates
model.patch_ss() -- guess MODEL disulfides from model structure
model.mutate() -- mutate selected MODEL residues
model.build() -- build MODEL coordinates from topology
model.unbuild() -- undefine MODEL coordinates
model.transfer_xyz() -- copy templates' coordinates to MODEL
model.res_num_from() -- residue numbers from MODEL2 to MODEL
model.rename_segments() -- rename MODEL segments
model.pick_atoms() -- select atoms in MODEL
model.pick_hot_atoms() -- pick atoms violating restraints
model.randomize_xyz() -- randomize MODEL coordinates
model.to_iupac() -- standardize certain dihedral angles
model.reorder_atoms() -- standardize order of MODEL atoms
model.rotate_dihedrals() -- change dihedral angles
model.orient() -- center and orient MODEL
model.rotate() -- rotate and translate MODEL
model.write_data() -- write derivative MODEL data
model.write_pdb_xref() -- write residue number/index correspondence
model.make_region() -- define a random surface patch of atoms
model.color() -- color MODEL according to alignment
model.superpose() -- superpose MODEL2 on MODEL given alignment
model.make_chains() -- Fetch sequences from PDB file
model.schedule.make() -- create optimization schedule
model.schedule.step -- current optimization schedule step
model.schedule.read() -- read optimization schedule
model.schedule.write() -- write optimization schedule
model.energy() -- evaluate MODEL given restraints
model.optimize() -- optimize MODEL given restraints
model.switch_trace() -- open new optimization trace file
model.debug_function() -- test code self-consistency
model.assess_ga341() -- assess a model with the GA341 method
model.assess_dope() -- assess a model with the DOPE method

Ben Webb 2005-04-21

The model class: handling of atomic coordinates, and model building

The `model` class: handling of atomic coordinates, and model building