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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 b.ct == 1
length len b.len > 1 A
order o b.o >= 1
type t single,
double,
triple,
amide,
aromatic,
dummy,
undefined
b.t s

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 and bond.customType <= 2 (short version: b.ct >= 0 and b.ct <= 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 all bonds with length larger than 1.5 angstroms
  • bond.length >= 1.2A and bond.length <= 1.4A (short version: b.len >= 1.2A and b.len <= 1.4A): matches all bonds with length between 1.2 and 1.4 angstroms

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

type#

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

  • single (short name s) - single bonds
  • double (short name d) - double bonds
  • triple (short name t) - 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 all single bonds
  • bond.type double (short name b.t d): matches all double bonds
  • bond.type triple (short name b.t t): matches all triple bonds
  • bond.type amide (short name b.t am): matches all amide bonds
  • bond.type aromatic (short name b.t ar): matches all aromatic bonds
  • bond.type dummy (short name b.t du): matches all dummy bonds
  • bond.type undefined (short name b.t un): matches all undefined bonds
  • bond.type single or bond.type double (short name b.t s or b.t d): matches all single and double bonds
  • bond.type dummy or bond.type undefined (short name b.t du or b.t un): matches all dummy and undefined bonds