This function fragment both acyclic and cyclic bonds of the molecule
(any)
(object
= {})
| Name | Description |
|---|---|
options.calculateHoseCodes boolean
(default false)
|
calculating hose code for bonds is quite time consuming |
options.cyclic boolean
(default true)
|
calculate cyclic fragmentation |
options.acyclic boolean
(default true)
|
calculate acyclic fragmentation |
options.full boolean
(default true)
|
calculate the molecular formula of the full molecule |
object:
In-Silico fragmentation results
The function performs the fragmentation of all single linear bonds
(any)
any:
Results fragmentation of acyclic bonds
The function performs the fragmentation of all single ring bonds not belonging to aromatic rings
(any)
any:
Array with results for the fragmentation of ring bonds
This function returns an array of objects with all combination of 2 bonds who can be fragmented in the same ring
(any)
any:
All combination of 2 bonds who can be fragmented in the same ring
This function returns ringBond, and object that contains information about the bonds of each ring
(any)
any:
Information of ring bonds for each ring in the molecule
Fragment a molecule by applying reactions from a custom database of reactions
(any)
(Object
= {})
| Name | Description |
|---|---|
options.ionizations Array<(
(default ['esi'])
|
The ionization technique to be used |
options.modes Array<(
(default ['positive'])
|
The ionization mode to be used |
options.maxDepth number
(default 5)
|
The maximum depth of the overall fragmentation tree |
options.limitReactions number
(default 200)
|
The maximum number of reactions to be applied to each branch |
options.dwar string?
|
The dwar entry to be used, if not provided, the default one will be used |
options.maxIonizations number
(default 1)
|
The maximum depth of the ionization tree |
options.minIonizations number
(default 1)
|
The minimum depth of the ionization tree |
options.minReactions number
(default 0)
|
The minimum depth of the reaction tree |
options.maxReactions number
(default 3)
|
The maximum depth of the reaction tree |
object:
In-Silico fragmentation results with the following properties:
get array of mz from fragmentation nodes
(Array)
valid nodes of fragmentation process
Array:
array of unique mz values
Type: object
Get the default databases of reactions for positive and negative mode
(Object
= {})
Options for database selection
| Name | Description |
|---|---|
options.kind Array<(
(default ['ionization','resonance','reaction'])
|
The kind of database to be used |
options.ionizations Array<(
(default ['esi','ei'])
|
The ionization technique to be used |
options.modes Array<(
(default ['positive','negative'])
|
The ionization mode to be used |
options.dwar string?
|
The dwar file to use. Default will use an included mass fragmentation database |