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molecular_hierarchy.py
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## \example atom/molecular_hierarchy.py
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## In this example, we read a protein from a PDB file and set the center and radius of each residue to enclose the atoms in that residue.
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##
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## Then a second copy of the protein is loaded and they are both added to the same hierarchy
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## to define a hypothetical assembly.
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##
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import
IMP
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import
IMP.core
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import
IMP.atom
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m =
IMP.Model
()
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mp0=
IMP.atom.read_pdb
(
IMP.atom.get_example_path
(
'example_protein.pdb'
), m)
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# get the 16th residue of the first chain
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hchain=
IMP.atom.get_by_type
(mp0, IMP.atom.CHAIN_TYPE)[0]
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# decorate the chain particle with an IMP.atom.Chain decorator.
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# unfortunately, our python wrapper does not handle converseions properly
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# as a result you have to manually get the particle for that chain
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chain=
IMP.atom.Chain
(hchain.get_particle())
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r16 =
IMP.atom.get_residue
(chain, 16)
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r16.show()
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# get all the atoms
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atoms=
IMP.atom.get_by_type
(mp0, IMP.atom.ATOM_TYPE)
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# I didn't really have anything interesting to do with them...
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# create a new version of the protein that is coarsened (one particle per residue)
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smp0=
IMP.atom.create_simplified_along_backbone
(chain, 1)
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# we don't need mp0 any more
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IMP.atom.destroy
(mp0)
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# load another copy
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mp1=
IMP.atom.read_pdb
(
IMP.atom.get_example_path
(
'example_protein.pdb'
), m)
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# create a graph from the hierarchy
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mp1t=
IMP.atom.get_hierarchy_tree
(mp1)
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# process the file with dot like
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# dot -Tpdf hierarchy.dot > hierarchy.pdf
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mp1t.show_graphviz(open(
"hierarchy.dot"
,
"w"
))
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# try to display it graphically, assuming altgraph is installed
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try
:
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mp1t.show_with_altgraph()
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except
:
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pass
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# make this one rigid
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IMP.atom.create_rigid_body
(mp1)
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# create a hierarchy which contains the two proteins
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p =
IMP.Particle
(m)
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rmp=
IMP.atom.Hierarchy.setup_particle
(p)
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rmp.add_child(smp0)
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rmp.add_child(mp1)