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2.0.1
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structure_from_sequence.py
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## \example atom/structure_from_sequence.py
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## An atomic protein structure is created from primary (amino-acid) sequence.
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##
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import
IMP.atom
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# Use the CHARMM all-atom (i.e. including hydrogens) topology and parameters
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topology =
IMP.atom.CHARMMTopology
(
IMP.atom.get_all_atom_CHARMM_parameters
())
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# Create a single chain of amino acids and apply the standard C- and N-
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# termini patches
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topology.add_sequence(
'IACGACKPECPVNIIQGS'
)
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topology.apply_default_patches()
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# Make an IMP Hierarchy (atoms, residues, chains) that corresponds to
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# this topology
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m =
IMP.Model
()
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h = topology.create_hierarchy(m)
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# Generate coordinates for all atoms in the Hierarchy, using CHARMM internal
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# coordinate information (an extended chain conformation will be produced).
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# Since in some cases this information can be incomplete, better results will
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# be obtained if the atom types are assigned first and the CHARMM parameters
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# file is loaded, as we do here, so missing information can be filled in.
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# It will still work without that information, but will approximate the
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# coordinates.
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topology.add_atom_types(h)
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topology.add_coordinates(h)
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# Hierarchies in IMP must have radii
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IMP.atom.add_radii
(h)
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# Write out the final structure to a PDB file
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IMP.atom.write_pdb
(h,
'structure.pdb'
)