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:
ct
)len
)o
)t
)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 |
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 0bond.customType >= 0
(short version: b.ct >= 0
): matches bonds with custom type larger than 0bond.customType >= 0 and bond.customType <= 2
(short version: b.ct >= 0 and b.ct <= 2
): matches bonds with custom type between 0 and 2The 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 angstromsbond.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 angstromsThe 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 2bond.order >= 2 and b.order <= 3
(short version: b.o >= 2 and b.o <= 3
): matches all bonds with order between 2 and 3The bond.type
attribute (short name b.t
) matches bonds with one of the specific types:
single
(short name s
) - single bondsdouble
(short name d
) - double bondstriple
(short name t
) - triple bondsamide
(short name am
) - amide bondsaromatic
(short name ar
) - aromatic bondsdummy
(short name du
) - dummy bondsundefined
(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 bondsbond.type double
(short name b.t d
): matches all double bondsbond.type triple
(short name b.t t
): matches all triple bondsbond.type amide
(short name b.t am
): matches all amide bondsbond.type aromatic
(short name b.t ar
): matches all aromatic bondsbond.type dummy
(short name b.t du
): matches all dummy bondsbond.type undefined
(short name b.t un
): matches all undefined bondsbond.type single or bond.type double
(short name b.t s or b.t d
): matches all single and double bondsbond.type dummy or bond.type undefined
(short name b.t du or b.t un
): matches all dummy and undefined bonds