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| generate_dummy_atoms(self) |
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findVectorAtoms(self)
Return a list of 2 atom numbers for the vector dummy atoms |
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remove_dummy_atoms(self)
Delete the vector atoms and other dummy atoms |
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| get_vector_atoms_from_internal_coords(self) |
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update_internal_coords_to_vector_atoms(self,
coords1,
coords2)
Update internal coordinates from 2 numpy arrays containing the x,y,z
coordinates of two atoms defining the membrane. |
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updateFromVector(self)
Update internal coordinates from vector dummy atoms in self.ct |
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createVectorAtoms(self)
Add vector dummy atoms to the specified Structure based on membrane
coordinates |
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deleteVectorAtoms(self)
Delete the vector atoms |
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| getCenterOrientationOfAtoms(self,
atom_list) |
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autoPlaceByMolecule(self,
mol_atom_lists)
Auto places the membrane based on the average vector between all
specified molecules (list of atom iterators) |
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findHydrophobicCenter(self)
Returns coordinates of center of mass of all hydrophobic residues |
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autoPlace(self)
Automatically orient the membrane according to the protein in self.ct |
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rotateProteinToMembrane(self,
rotate_membrane=True)
Translate the protein so that the membrane will be located at the
origin and rotate the protein so that membrane is along the z-axis. |
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calculateMembraneBox(self)
Stores OpenGL representation of the membrane box (2 red squares) in
this instance. |
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draw(self)
Draws the red membrane squires to the workspace. |
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clear(self)
Remove the 3D objects from the group, which removes them from
Maestro's fit bounds. |
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| write_structure(self,
filename) |
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| write_parameter_file(self,
filename) |
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