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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.resolution -- resolution of protein structure
model.last_energy -- last objective function value
model.remark -- text remark(s)
model.restraints -- all static restraints which act on the model
model.group_restraints -- all restraints which act on atom groups
model.atoms -- all atoms in the model
model.residues -- all residues in the model
model.chains -- all chains in the model
model.point() -- return a point in Cartesian space
model.atom_range() -- return a subset of all atoms
model.residue_range() -- return a subset of all residues
model.get_insertions() -- return a list of all insertions
model.get_deletions() -- return a list of all deletions
model.loops() -- return a list of all loops
model.read() -- read coordinates for MODEL
model.build_sequence() -- build model from a sequence of one-letter codes
model.write() -- write MODEL
model.clear_topology() -- clear model topology
model.generate_topology() -- generate MODEL topology
model.write_psf() -- write molecular topology to PSF file
model.patch() -- patch MODEL topology
model.patch_ss_templates() -- guess MODEL disulfides from templates
model.patch_ss() -- guess MODEL disulfides from model structure
model.build() -- build MODEL coordinates from topology
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.to_iupac() -- standardize certain dihedral angles
model.reorder_atoms() -- standardize order of MODEL atoms
model.orient() -- center and orient MODEL
model.write_data() -- write derivative MODEL data
model.make_region() -- define a random surface patch of atoms
model.color() -- color MODEL according to alignment
model.make_chains() -- Fetch sequences from PDB file
model.saxs_intens() -- Calculate SAXS intensity from model
model.saxs_pr() -- Calculate of model
model.saxs_chifun() -- Calculate SAXS score chi from model
model.assess_ga341() -- assess a model with the GA341 method

Ben Webb 2008-02-01

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

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