x.parent
the System object that contains this polymer
x.residues
a list of AminoAcid or Nucleotide objects
x.residue_dict
a dictionary of residues; indexed by residue number
x.selected
a boolean indicator for selection
x.key
the single letter chain designator of the polymer
x.default_chain_color
default chain color, from self.get_chain_color_word()
x.vtk_arg_list
visualization arguments. Described in MolecularViewer.
x.add_residue(res)
adds a residue to both x.residues and x.residue_dict
x.len()
returns the number of residues in the polymer
x.pdb_print()
calls pdb_print() for all residues
x.select()
calls select() on all residues
x.deselect()
calls deselect() on all residues
x.get_chain_color()
accesses 'colormap' (or 'colorblind_colormap') to obtain the chain color. Returns a RGB triple.
x.locate_termini()
set the .is_Nterm and .is_Cterm for all residues. .is_*term is 0 for most residues, unless the residue is a literal terminus (first or last residue), or is a terminal residue due to disordered atoms in an xray structure.
x.res_number_to_residues_index(res_number)
OUTDATED. Uses a residue number, from the PDB file, to locate a residue in the .residues list attribute. Use residue_dict instead.
x.assign_atom_distances(mindist=0.0, maxdist=12.0)
for each central atom (alpha carbon or 'C3' atom), add a 'nearby_cps' index to the atom's .data dictionary attribute. This is a list of actual atoms that are between mindist and maxdist from each query central atom.
x.get_central_point_list()
returns a list of all of the central atoms as points.
x.get_central_atom_list()
returns a list of all of the central atoms as atoms.
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