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IMP Reference Guide  2.13.0
The Integrative Modeling Platform
pmi/symmetry.py
1 ## \example pmi/symmetry.py
2 """Clone molecules and use a symmetry constrant
3 """
4 
5 import IMP
6 import IMP.atom
7 import IMP.rmf
8 import IMP.pmi
9 import IMP.pmi.topology
10 import IMP.pmi.dof
11 import IMP.pmi.macros
13 import math
14 import sys
15 
16 IMP.setup_from_argv(sys.argv, "Symmetry constraint example")
17 
18 # Create System and State
19 mdl = IMP.Model()
21 st = s.create_state()
22 
23 # Create a simple all-bead molecule
24 mol = st.create_molecule("mymol",sequence='A'*10,chain_id='A')
25 mol.add_representation(mol,
26  resolutions=[1])
27 
28 # Clone the molecule multiple times
29 # Calling molecule.create_clone makes a new molecule with the same name, sequence,
30 # initial structure, and choice of representations
31 # Note: another function, molecule.create_copy(), just copies the name and sequence
32 mols = [mol]
33 chains='BCDEFGHI'
34 for nc in range(7):
35  clone = mol.create_clone(chains[nc])
36  mols.append(clone)
37 
38 hier = s.build()
39 
40 # Create a symmetry constraint
41 # A constrant is invariant: IMP will automatically move all clones to match the reference
42 # If instead you want some more flexiblity, consider IMP.pmi.restraints.stereochemistry.SymmetryRestraint
44 center = IMP.algebra.Vector3D([50,0,0])
45 for nc in range(7):
46  rot = IMP.algebra.get_rotation_about_axis([0,0,1],2*math.pi*(nc+1)/8)
47  transform = IMP.algebra.get_rotation_about_point(center,rot)
48  dof.constrain_symmetry(mols[0],mols[nc+1],transform)
49 mdl.update() # propagates coordinates
50 
51 
52 ############ Make stuff look cool with restraints ###########
53 
54 # set up the original molecule as flexible beads
55 dof.create_flexible_beads(mols[0])
56 
57 # Create a connectivity restraint for the first molecule
59 cr.add_to_model()
60 
61 # Create excluded volume for all particles
63 evr.add_to_model()
64 
65 # Quickly move all flexible beads into place
66 dof.optimize_flexible_beads(100)
67 
68 # write a single-frame RMF to view the helix
70 out.init_rmf("example_symmetry.rmf3",hierarchies=[hier])
71 out.write_rmf("example_symmetry.rmf3")