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IMP Reference Guide  2.15.0
The Integrative Modeling Platform
ambiguity.py
1 ## \example pmi/ambiguity.py
2 """This script shows how to create a system with multiple copies of the same molecule.
3 We also create some cross-links which take into account the ambiguity.
4 The key to ambiguity is using the same molecule name for ambiguous copies.
5 That way when you perform Selection it automatically finds all relevant molecules.
6 """
7 
8 import IMP
9 import IMP.atom
10 import IMP.algebra
11 import IMP.rmf
12 import IMP.pmi
13 import IMP.pmi.topology
14 import IMP.pmi.dof
15 import IMP.pmi.macros
18 import tempfile
19 import os
20 import sys
21 
22 IMP.setup_from_argv(sys.argv, "ambiguity example")
23 
24 ###################### SYSTEM SETUP #####################
25 
26 ### Setup multistate system
27 mdl = IMP.Model()
29 st1 = s.create_state()
30 st2 = s.create_state()
31 
32 ### For each state add some molecules - we'll make some bead only structures
33 # State 1: ProtA (chainA), ProtA (chainB), ProtC (chainC)
34 sequence = 'A'*10
35 m1A = st1.create_molecule('ProtA',sequence,chain_id='A')
36 m1A.add_representation(m1A,resolutions=[1])
37 m1B = m1A.create_clone(chain_id='B') # create_clone() will copy name/structure/representation
38  # You cannot edit it!
39  # There is also a function create_copy() which
40  # only copies the name, then you can change reps
41 m1C = st1.create_molecule('ProtC',sequence,chain_id='C')
42 m1C.add_representation(m1C,resolutions=[1])
43 
44 # State 2: ProtA (chainA), ProtC (chainC)
45 m2A = st2.create_molecule('ProtA',sequence,chain_id='A')
46 m2A.add_representation(m2A,resolutions=[1])
47 m2C = st2.create_molecule('ProtC',sequence,chain_id='C')
48 m2C.add_representation(m2C,resolutions=[1])
49 root_hier = s.build()
50 
51 ### Display all the states, molecules, representations
53 
54 ### Setup all molecules to move as flexible beads and super rigid bodies
55 # "Super rigid bodies" aren't really rigid, it's just a mover that moves the whole body together
57 for mol in (m1A,m1B,m1C,m2A,m2C):
58  dof.create_flexible_beads(mol,
59  max_trans=0.1)
60  dof.create_super_rigid_body(mol)
61 
62 
63 ###################### RESTRAINTS #####################
64 output_objects = [] # keep a list of functions that need to be reported
65 
66 ### Crosslinks setup
67 # 1) Create file. This one XL has 3 ambiguity options: State1 has 2, State2 has 1
68 lines = '''id,mol1,res1,mol2,res2,score
69 1,ProtA,3,ProtC,9,1.0
70 '''
71 tf = tempfile.NamedTemporaryFile(delete=False, mode='w')
72 tf.write(lines)
73 tf.close()
74 
75 # 2) Define the columns
77 kw.set_unique_id_key("id")
78 kw.set_protein1_key("mol1")
79 kw.set_protein2_key("mol2")
80 kw.set_residue1_key("res1")
81 kw.set_residue2_key("res2")
82 kw.set_id_score_key("score")
84 xldb.create_set_from_file(tf.name)
85 os.remove(tf.name)
86 
87 # 3) Add the restraint
89  root_hier=root_hier,
90  database=xldb,
91  length=21,
92  label="XL",
93  resolution=1,
94  slope=0.01)
95 xlr.add_to_model()
96 output_objects.append(xlr)
97 dof.get_nuisances_from_restraint(xlr) # needed to sample the nuisance particles (noise params)
98 
99 ### Connectivity keeps things connected along the backbone
100 crs = []
101 for mol in (m1A,m1B,m1C,m2A,m2C):
103  cr.add_to_model()
104  output_objects.append(cr)
105 
106 ### Excluded volume - one for each state (they don't interact)
107 evr1 = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(included_objects = (m1A,m1B,m1C))
108 evr1.add_to_model()
109 output_objects.append(evr1)
110 evr2 = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(included_objects = (m2A,m2C))
111 evr2.add_to_model()
112 output_objects.append(evr2)
113 
114 ###################### SAMPLING #####################
115 # randomize particles a bit
117  max_translation=20)
118 
119 # Shift state 2
120 # Even though the two states don't interact,
121 # it'll be easier to look at the RMF if we separate them
122 trans = IMP.algebra.Transformation3D([50,0,0])
123 for fb in IMP.core.get_leaves(m2A.get_hierarchy())+IMP.core.get_leaves(m2C.get_hierarchy()):
125 
126 # Run replica exchange Monte Carlo sampling
128  root_hier=root_hier, # pass the root hierarchy
129  monte_carlo_sample_objects=dof.get_movers(), # pass MC movers
130  global_output_directory='ambiguity_output/',
131  output_objects=output_objects,
132  monte_carlo_steps=10,
133  number_of_frames=1) # increase number of frames to get better results!
134 rex.execute_macro()
Simplify creation of constraints and movers for an IMP Hierarchy.
Setup cross-link distance restraints from mass spectrometry data.
Restraints for keeping correct stereochemistry.
Simple 3D transformation class.
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
def shuffle_configuration
Shuffle particles.
Definition: tools.py:1314
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.
Definition: macros.py:1
Represent the root node of the global IMP.atom.Hierarchy.
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:72
void transform(XYZ a, const algebra::Transformation3D &tr)
Apply a transformation to the particle.
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
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.
A macro to help setup and run replica exchange.
Definition: macros.py:59
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.