2 """This script shows how to create a system with multiple copies of the
4 We also create some cross-links which take into account the ambiguity.
5 The key to ambiguity is using the same molecule name for ambiguous copies.
6 That way when you perform Selection it automatically finds all relevant
31 st1 = s.create_state()
32 st2 = s.create_state()
37 m1A = st1.create_molecule(
'ProtA', sequence, chain_id=
'A')
38 m1A.add_representation(m1A, resolutions=[1])
43 m1B = m1A.create_clone(chain_id=
'B')
44 m1C = st1.create_molecule(
'ProtC', sequence, chain_id=
'C')
45 m1C.add_representation(m1C, resolutions=[1])
48 m2A = st2.create_molecule(
'ProtA', sequence, chain_id=
'A')
49 m2A.add_representation(m2A, resolutions=[1])
50 m2C = st2.create_molecule(
'ProtC', sequence, chain_id=
'C')
51 m2C.add_representation(m2C, resolutions=[1])
61 for mol
in (m1A, m1B, m1C, m2A, m2C):
62 dof.create_flexible_beads(mol, max_trans=0.1)
63 dof.create_super_rigid_body(mol)
72 lines =
'''id,mol1,res1,mol2,res2,score
75 tf = tempfile.NamedTemporaryFile(delete=
False, mode=
'w')
81 kw.set_unique_id_key(
"id")
82 kw.set_protein1_key(
"mol1")
83 kw.set_protein2_key(
"mol2")
84 kw.set_residue1_key(
"res1")
85 kw.set_residue2_key(
"res2")
86 kw.set_id_score_key(
"score")
88 xldb.create_set_from_file(tf.name)
100 output_objects.append(xlr)
102 dof.get_nuisances_from_restraint(xlr)
106 for mol
in (m1A, m1B, m1C, m2A, m2C):
109 output_objects.append(cr)
113 included_objects=(m1A, m1B, m1C))
115 output_objects.append(evr1)
117 included_objects=(m2A, m2C))
119 output_objects.append(evr2)
137 monte_carlo_sample_objects=dof.get_movers(),
138 global_output_directory=
'ambiguity_output/',
139 output_objects=output_objects,
140 monte_carlo_steps=10,
Simplify creation of constraints and movers for an IMP Hierarchy.
Setup cross-link distance restraints from mass spectrometry data.
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.
A macro to help setup and run replica exchange.
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)
GenericHierarchies get_leaves(Hierarchy mhd)
Get all the leaves of the bit of hierarchy.
Protocols for sampling structures and analyzing them.
Represent the root node of the global IMP.atom.Hierarchy.
This class is needed to convert the keywords from a generic database to the standard ones...
Class for storing model, its restraints, constraints, and particles.
void transform(XYZ a, const algebra::Transformation3D &tr)
Apply a transformation to the particle.
A decorator for a particle with x,y,z coordinates.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Create a restraint between consecutive TempResidue objects or an entire PMI Molecule object...
Create movers and set up constraints for PMI objects.
A class to create an excluded volume restraint for a set of particles at a given resolution.
Restraints for handling cross-linking data.
Python classes to represent, score, sample and analyze models.
Functionality for loading, creating, manipulating and scoring atomic structures.
this class handles a cross-link dataset and do filtering operations, adding cross-links, merge datasets...
Support for the RMF file format for storing hierarchical molecular data and markup.