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x.pdb_line
the original line from the PDB file that the atom was built from
x.atom_number
PDB atom number
x.atom_type
PDB atom type
x.extra_type1
position 12 in a PDB atom record. If numeric, appended to atom_type. If alphabetic, insert instead as the first character of atom_type.
x.res_type
PDB residue type
x.chain_name
PDB chain name
x.res_number
PDB residue number
x.x
atom x-coordinate
x.y
atom y-coordinate
x.z
atom z-coordinate
x.occupancy
PDB occupancy record
x.b_factor
PDB temperature factor record
x.selected
whether or not the atom is currently selected
x.visible
whether or not the atom has already been visualized in a molecular viewer.
x.bonds_list
a list of atoms to which this one is covalently bound.
x.vtk_arg_list
a dictionary of attributes for visualization of this atom in a molecular viewer. Note that neither this dictionary, nor any MolecularSystem components contain any VTK Class objects, so MolecularSystem does not require VTK to compile.
x.radius
Van der Wall's radius is available here for simple types.
x.features
A location for users to store atom-based numerical values that can be applied by generalized visualization and algorithm tools. Contents should be real decimal values only.
x.data
A location for users to store non-numerical data. For convenience purposes only.
x.reduce_for_storage()
Removes redundant terms for smaller pickled MolecularSystem objects. Not currently implemented though, requires some level of stabilization.
x.rebuild_from_storage()
Designed to complement .reduce_for_storage()
x.get_selected()
Returns whether this atom is currently selected.
x.pdb_print()
Constructs a PDB-formatted string that represents this atom's current information and prints it to screen.
x.get_pdb_line()
Constructs a PDB-formatted string that represents this atom's current information and returns it.
x.select()
Set x.selected to 1.
x.deselect()
Set x.selected to 0.
point_line_distance(a1, a2)
This function is used primarily by the Shielding algorithm to determine if this atom is perpendicular to a line between class Atom input arguments a1 and a2.
Copyright © 2001