schrodinger.application.desmond.reorder_atom module

Functions to reorder atoms.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.reorder_atom.Node(atom, parent=None)

Bases: object

add_child(atom)

atom_index()

children()

deproxy()

depth()

height(giveme_node=False)

is_leaf()

is_root()

parent()

print_tree(prefix='', drop='| ', node='+-', root=None)

+-1 | +-2 | | +-3 | | +-4 | +-5 | +-6

tree_index()

schrodinger.application.desmond.reorder_atom.add_atoms_onto_tree(atoms, nodes)

schrodinger.application.desmond.reorder_atom.atoms_within_3_bonds(atom)

schrodinger.application.desmond.reorder_atom.maid(ct)

schrodinger.application.desmond.reorder_atom.reorder_atom(cts, ct_indices)

schrodinger.application.desmond.reorder_atom.reroot(node)

schrodinger.application.desmond.reorder_atom.set_tree_index(level, index=1)

`level’ must be a list of `Node’ objects.

schrodinger.application.desmond.reorder_atom.treeify_indices(ct)