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Bond attributes#

Bond attributes are defined in the bond attribute space (short name: b). Bond attributes may only match bond nodes.

The following bond attributes are available in NSL:

Attribute name Short name Possible values Examples
customType ct integers b.ct 1
b.ct 1, 2
length len length b.len > 1.2 A
b.len 0.12nm:0.17nm
order o floats b.o >= 1
b.o 1:1.5
type t single (s, 1),
double (d, 2),
triple (t, 3),
amide (am),
aromatic (ar),
dummy (du),
undefined (un)		 b.t s
b.t s, d

customType#

The bond.customType attribute (short name: b.ct) matches bonds with specific custom types.

Possible values: an integer.

Examples:

  • bond.customType 0 (short version: b.ct 0): matches bonds with custom type 0
  • bond.customType >= 0 (short version: b.ct >= 0): matches bonds with custom type larger than 0
  • bond.customType 0:2 (short version: b.ct 0:2): matches bonds with custom type between 0 and 2

length#

The bond.length attribute (short name: b.len) matches bonds with specific bond length.

Possible values: floating-point values.

Examples:

  • bond.length >= 1.5A (short version: b.len >= 1.5A): matches bonds with length larger than 1.5 angstroms
  • bond.length 1.2A:1.4A (short version: b.len 1.2A:1.4A): matches bonds with length between 1.2 and 1.4 angstroms
  • bond.length 0.15nm:2.1nm (short version: b.len 0.15nm:2.1nm): matches bonds with length between 0.15 and 2.1 nanometers

order#

The bond.order attribute (short name: b.o) matches bonds with specific orders.

Possible values: floating-point values.

Examples:

  • bond.order >= 2 (short version: b.o >= 2): matches bonds with order larger than 2
  • bond.order 1.5:3 (short version: b.o 1.5:3): matches bonds with order between 1.5 and 3

type#

The bond.type attribute (short name: b.t) matches bonds with one of the specific types:

  • single (short names: s, 1) - single bonds
  • double (short names: d, 2) - double bonds
  • triple (short names: t, 3) - triple bonds
  • amide (short name: am) - amide bonds
  • aromatic (short name: ar) - aromatic bonds
  • dummy (short name: du) - dummy bonds
  • undefined (short name: un) - undefined bonds.

Note, that to use this a bond needs to have its bond type defined.

Examples:

  • bond.type single (short name: b.t s): matches single bonds
  • bond.type single, double (short name: b.t s,d): matches single and double bonds
  • bond.type dummy, undefined (short name: b.t du,un): matches dummy and undefined bonds