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IMP Reference Guide  develop.98212aac1f,2024/11/04
The Integrative Modeling Platform
pmi/symmetry.py
1 ## \example pmi/symmetry.py
2 """Clone molecules and use a symmetry constraint
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, resolutions=[1])
26 
27 # Clone the molecule multiple times
28 # Calling molecule.create_clone makes a new molecule with the same name,
29 # sequence, initial structure, and choice of representations
30 # Note: another function, molecule.create_copy(), just copies the name
31 # 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 constraint is invariant: IMP will automatically move all clones to
42 # match the reference
43 # If instead you want some more flexibility, consider
44 # IMP.pmi.restraints.stereochemistry.SymmetryRestraint
46 center = IMP.algebra.Vector3D([50, 0, 0])
47 for nc in range(7):
48  rot = IMP.algebra.get_rotation_about_axis([0, 0, 1], 2*math.pi*(nc+1)/8)
49  transform = IMP.algebra.get_rotation_about_point(center, rot)
50  dof.constrain_symmetry(mols[0], mols[nc+1], transform)
51 mdl.update() # propagates coordinates
52 
53 
54 # ########### Make stuff look cool with restraints ###########
55 
56 # set up the original molecule as flexible beads
57 dof.create_flexible_beads(mols[0])
58 
59 # Create a connectivity restraint for the first molecule
61 cr.add_to_model()
62 
63 # Create excluded volume for all particles
65  included_objects=mols)
66 evr.add_to_model()
67 
68 # Quickly move all flexible beads into place
69 dof.optimize_flexible_beads(100)
70 
71 # write a single-frame RMF to view the helix
73 out.init_rmf("example_symmetry.rmf3", hierarchies=[hier])
74 out.write_rmf("example_symmetry.rmf3")