2 """This script demonstrates a few different ways you can perform selection
4 In PMI we first set up molecules at various resolutions.
5 Then you call System.build() and this creates all requested representations.
30 mol = st.create_molecule(
"Rpb4", seqs[
"1WCM:D"], chain_id=
"D")
41 myres2 = mol.residue_range(
'1',
'10')
49 atomic = mol.get_atomic_residues()
50 non_atomic = mol.get_non_atomic_residues()
54 myres3 = mol[0:50] - atomic
55 myres4 = mol[0:50] & atomic
58 mol.add_representation(
62 mol.add_representation(myres4,
86 dof.create_rigid_body(mol, nonrigid_parts=non_atomic,
94 residue_indexes=range(1, 10))
95 particles = sel.get_selected_particles()
99 all_mol_copies = st.molecules[
"Rpb4"]
100 mol = all_mol_copies[0]
Simplify creation of constraints and movers for an IMP Hierarchy.
Restraints for keeping correct stereochemistry.
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
Set of Python classes to create a multi-state, multi-resolution IMP hierarchy.
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Protocols for sampling structures and analyzing them.
Represent the root node of the global IMP.atom.Hierarchy.
Class for storing model, its restraints, constraints, and particles.
Classes to handle different kinds of restraints.
Create a restraint between consecutive TempResidue objects or an entire PMI Molecule object...
Create movers and set up constraints for PMI objects.
Python classes to represent, score, sample and analyze models.
A dictionary-like wrapper for reading and storing sequence data.
Functionality for loading, creating, manipulating and scoring atomic structures.
Select hierarchy particles identified by the biological name.
Support for the RMF file format for storing hierarchical molecular data and markup.