schrodinger.structutils.rings module

Tools for detecting and characterizing rings in Structures.

schrodinger.structutils.rings.find_ring_systems(st, want_spiro=False, sort=False)

Find groups of atoms that are in conjoined rings.

If want_spiro is True, rings are part of the same system if they share any atom. If False, rings must share a bond.

Parameters:

  • st (Structure) – Molecule to identify ring systems in

  • want_spiro (bool) – True if a ring system can be defined by just a common atom (default False)

  • sort (bool) – True if ring systems should be sorted by minimum element

Returns:

List of the different ring systems defined by the index of the atoms, sorted by the minimum element in each set.

Return type:

tuple of tuple of int

schrodinger.structutils.rings.find_ring_atoms(st)

Find the set of all atoms which are in some ring

Parameters:

st (Structure) – Molecule to identify ring systems in

Returns:

tuple of atoms ids which are in some ring

Return type:

tuple of int

schrodinger.structutils.rings.find_rings(st, sort=True)

Return the smallest set of smallest rings (SSSR) in st.

See also the schrodinger.structure.Structure.find_rings method and the schrodinger.structure.Structure.ring iterator. This method may be deprecated at some point in favor of those methods.

The return value is a list of lists of ints. Each list of ints corresponds to a ring, and the integer values are the atom indices. Each ring is ordered by connectivity.

Parameters:

  • st (Structure) – Structure holding rings.

  • sort (bool) – Deprecated and unused

Return type:

list

Returns:

Each value is a list corresponding to the atom indices of a ring.

schrodinger.structutils.rings.find_ring_bonds(st, max_size=None)

Find all bonds that form the edge of a ring.

The return uses frozenset to represent each atom pair to allow comparisons without worrying about the order of the atoms. If it used a tuple you’d need to do both way checks.

Examples:

# Operate on each ring bond:
for atom_index0, atom_index1 in find_ring_bonds(st):
    atom0 = st.atom[atom_index0]
    atom1 = st.atom[atom_index1]
    # Do something with the atoms

# Operate on each non-ring bond:
ring_bonds = find_ring_bonds(st)
for bond in st.bond:
    # skip ring bonds. Use a set for comparison:
    if {bond.atom1.index, bond.atom2.index} in ring_bonds:
        continue
Parameters:

max_size (int or None) – if supplied, only include bonds that are in rings of size max_size or smaller

Return type:

set of frozenset of int

Returns:

set of pairs of atom indices that comprise a ring bond.

schrodinger.structutils.rings.find_all_rings(st, max_ring_size=50, max_seconds=1)

Find the set of all simple rings in a given structure. A simple ring is a cycle with no repeating atoms.

Parameters:

  • max_ring_size (int) – only include rings that are of max_ring_size or smaller. Default is max_ring_size = 50.

  • max_seconds (int) – time in seconds to run find_all_rings() before timing out. Throws a RuntimeError if max_seconds is exceeded.

Return type:

tuple of tuple of int

Returns:

set of all simple rings in st of size less than or equal to max_ring_size