Surge Filters ​

Surge has the facility to remove molecules which contain certain substructures using the -B option.

The argument of -B is a list of numbers separated by commas without spaces.

For example, -B2,3,8. Each number indicates a set of substructures that are forbidden.

You can use -B more than once, for example -B2,4,6 is the same as -B4 -B6

We will describe the meaning of each number separately below. In some cases it is necessary to understand the distinction between rings and cycles, as explained in Section 5.

In the pictures, a circle represents any type of atom, a simple join matches any bond, a double join matches a double or triple bond, and a triple join matches only a triple bond. Many of the families below were inspired by MOLGEN.

-B1 Rings of length up to 7 have no triple bonds. This is equivalent to cycles of length up to 7 having no triple bonds.

-B2 Consider rings of length r and s which share one bond (i.e. fused rings). Let e be the common bond and let f be any bond belonging to one of the rings and sharing exactly one atom with e. In the cases {r, s} = {3, 3}, {3, 4} and {3, 5}, both e and f must be single bonds. In the cases {r, s} = {3, 6}, {4, 4} and {4, 5}, f must be a 8 single bond.

-B3 Consider rings of length r and s which share two bonds. Let e be one of the shared bonds and let f be a bond belonging to one of the rings and sharing exactly one atom with e. In the cases {r, s} = {4, 4}, {4, 5}, {4, 6}, {5, 5} and {5, 6}, both e and f must be single bonds.

-B4 Consider two rings of length 6 that share three bonds. Then any bond which lies in one of the rings and has exactly one atom in the other ring must be a single bond.

-B5 No atom has two double or triple bonds unless it is also bonded to some other non-hydrogen atom. 9

-B6 No atom in a ring of length up to 8 has two double bonds unless it is also bonded to some other non-hydrogen atom.

-B7 These are forbidden: two atoms with four common neighbours, and three atoms with three common neighbours.

-B8 These are forbidden: a cycle of length 5 having an atom bonded to each of the other 4 atoms, a set of 4 atoms all bonded to each other sharing one bond with a cycle of length 4.

-B9 Every atom lies on at most one ring of length 3 or 4. Equivalently, every atom lies on at most one cycle of length 3 or 4.

process = Popen(
    ["surge", "-P", "-T", "-B1,2,3,4,5,7,8,9", "-t0", "-f0", "-S", <mf>],
    stdout=PIPE,
    stderr=PIPE,
)

process = Popen(
    ["surge", "-P", "-T", "-B1,2,3,4,5,7,8,9", "-t0", "-f0", "-S", <mf>],
    stdout=PIPE,
    stderr=PIPE,
)