3.3.16A class that deals with database of monoisotopic mass and molecular formula
Add a new database using the KnapSack content
(any
= {})
Add a new database of 12000 commercial products
(any
= {})
Generates a database 'generated' from an array of molecular formula
(array)
Array of string or Array of array containing the parts to combine
(object
= {})
| Name | Description |
|---|---|
options.estimate boolean
(default false)
|
estimate the number of MF without filters |
options.databaseName string
(default 'generated')
|
|
options.onStep function?
|
Callback to do after each step |
options.limit number
(default 10000000)
|
Maximum number of results |
options.canonizeMF boolean
(default true)
|
Canonize molecular formula |
options.uniqueMFs boolean
(default true)
|
Force canonization and make MF unique |
options.ionizations string
(default '')
|
Comma separated list of ionizations (to charge the molecule) |
options.filter object
(default {})
|
|
options.filter.minMass number
(default 0)
|
Minimal monoisotopic mass |
options.filter.maxMass number
(default +Infinity)
|
Maximal monoisotopic mass |
options.filter.minEM number
(default 0)
|
Minimal neutral monoisotopic mass |
options.filter.maxEM number
(default +Infinity)
|
Maximal neutral monoisotopic mass |
options.filter.minMSEM number
(default 0)
|
Minimal observed monoisotopic mass |
options.filter.maxMSEM number
(default +Infinity)
|
Maximal observed monoisotopic mass |
options.filter.minCharge number
(default -Infinity)
|
Minimal charge |
options.filter.maxCharge number
(default +Infinity)
|
Maximal charge |
options.filter.absoluteCharge boolean
(default false)
|
If true, the charge is absolute (so between 0 and +Infinity by default) |
options.filter.unsaturation object
(default {})
|
|
options.filter.unsaturation.min number
(default -Infinity)
|
Minimal unsaturation |
options.filter.unsaturation.max number
(default +Infinity)
|
Maximal unsaturation |
options.filter.unsaturation.onlyInteger boolean
(default false)
|
Integer unsaturation |
options.filter.unsaturation.onlyNonInteger boolean
(default false)
|
Non integer unsaturation |
options.filter.atoms object?
|
object of atom:{min, max} |
options.filter.callback function?
|
a function to filter the MF |
options.filterFct string?
|
A string representing a function |
const {EMDB} = require('emdb');
let emdb = new EMDB();
let array = ['C1-10', 'H1-10'];
emdb.fromArray(array); // create a database 'generated' combining all possibilies
console.log(emdb.get('generated').length); // 100
const {EMDB} = require('emdb');
let emdb = new EMDB();
let array = ['C1-10 H1-10'];
emdb.fromArray(array); // create a database 'generated' combining all possibilies
console.log(emdb.get('generated').length); // 100
const {EMDB} = require('emdb');
let emdb = new EMDB();
// in case of an array of array, one of the group is allwed
let array = [['C1-10','H1-10'],'Cl0-1 Br0-1'];
emdb.fromArray(array); // create a database 'generated' combining all possibilies
console.log(emdb.get('generated').length); // 80
<script src="https://www.lactame.com/lib/mass-tools/HEAD/mass-tools.js" />
<script>
let emdb = new MassTools.EMDB();
let array = ['C1-10', 'H1-10'];
emdb.fromArray(array); // create a database 'generated' combining all possibilities
console.log(emdb.get('generated').length); // 100
</script>
// from the browser
(any)
(any)
(object
= {})
| Name | Description |
|---|---|
options.onStep function?
|
Callback to do after each step |
options.allowNeutral boolean
(default true)
|
|
options.ionizations string
(default '')
|
string containing a comma separated list of modifications |
options.precision number
(default 100)
|
Allowed mass range based on precision |
options.groupResults boolean
(default false)
|
Should we group the results if they have the same monoisotopic mass and experimental mass |
options.fragmentation object
(default {})
|
|
options.fragmentation.acyclic object
(default false)
|
|
options.fragmentation.cyclic object
(default false)
|
|
options.fragmentation.full object
(default true)
|
Promise:
We could group the results and replace the property 'fragment' by 'fragments'
(any)
(object)
(any)
Generates a database 'monoisotopic' from a monoisotopic mass and various options
(object
= {})
| Name | Description |
|---|---|
options.maxIterations number
(default 10000000)
|
Maximum number of iterations |
options.onStep function?
|
Callback to do after each step |
options.allowNeutral boolean
(default true)
|
|
options.uniqueMFs boolean
(default true)
|
|
options.limit number
(default 1000)
|
Maximum number of results |
options.ionizations string
(default '')
|
string containing a comma separated list of modifications |
options.ranges string
(default 'C0-100 H0-100 O0-100 N0-100')
|
range of mfs to search |
options.precision number
(default 100)
|
Allowed mass range based on precision |
options.filter object
(default {})
|
|
options.filter.minCharge number
(default -Infinity)
|
Minimal charge |
options.filter.maxCharge number
(default +Infinity)
|
Maximal charge |
options.filter.absoluteCharge boolean
(default false)
|
If true, the charge is absolute (so between 0 and +Infinity by default) |
options.filter.unsaturation object
(default {})
|
|
options.filter.unsaturation.min number
(default -Infinity)
|
Minimal unsaturation |
options.filter.unsaturation.max number
(default +Infinity)
|
Maximal unsaturation |
options.filter.unsaturation.onlyInteger boolean
(default false)
|
Integer unsaturation |
options.filter.unsaturation.onlyNonInteger boolean
(default false)
|
Non integer unsaturation |
options.filter.atoms object?
|
object of atom:{min, max} |
options.filter.callback function?
|
a function to filter the MF |
Promise:
Add a database starting from a peptidic sequence
(string?)
Sequence as a string of 1 letter or 3 letters code. Could also be a correct molecular formula respecting uppercase, lowercase
(object
= {})
| Name | Description |
|---|---|
options.estimate boolean
(default false)
|
estimate the number of MF without filters |
options.onStep function?
|
Callback to do after each step |
options.limit number
(default 100000)
|
|
options.ionizations string
(default '')
|
|
options.info object
(default {})
|
|
options.info.kind string?
|
rna, ds-dna or dna. Default if contains U: rna, otherwise ds-dna |
options.info.fivePrime string
(default monophosphate)
|
alcohol, monophosphate, diphosphate, triphosphate |
options.info.circular string
(default false)
|
|
options.mfsArray array
(default [])
|
|
options.fragmentation object
(default {})
|
Object defining options for fragmentation |
options.fragmentation.a boolean
(default false)
|
If true allow fragments of type 'a' |
options.fragmentation.ab boolean
(default false)
|
If true allow fragments of type 'a' minus base |
options.fragmentation.b boolean
(default false)
|
If true allow fragments of type 'b' |
options.fragmentation.c boolean
(default false)
|
If true allow fragments of type 'c' |
options.fragmentation.d boolean
(default false)
|
If true allow fragments of type 'd' |
options.fragmentation.dh2o boolean
(default false)
|
If true allow fragments of type 'd' with water loss |
options.fragmentation.w boolean
(default false)
|
If true allow fragments of type 'w' |
options.fragmentation.x boolean
(default false)
|
If true allow fragments of type 'x' |
options.fragmentation.y boolean
(default false)
|
If true allow fragments of type 'y' |
options.fragmentation.z boolean
(default false)
|
If true allow fragments of type 'z' |
options.baseLoss boolean
(default false)
|
If true allow base loss at all the positions |
options.filter object
(default {})
|
Object defining options for molecular formula filter |
options.filter.minMass number
(default 0)
|
Minimal monoisotopic mass |
options.filter.maxMass number
(default +Infinity)
|
Maximal monoisotopic mass |
options.filter.minEM number
(default 0)
|
Minimal neutral monoisotopic mass |
options.filter.maxEM number
(default +Infinity)
|
Maximal neutral monoisotopic mass |
options.filter.minMSEM number
(default 0)
|
Minimal observed monoisotopic mass |
options.filter.maxMSEM number
(default +Infinity)
|
Maximal observed monoisotopic mass |
options.filter.minCharge number
(default -Infinity)
|
Minimal charge |
options.filter.maxCharge number
(default +Infinity)
|
Maximal charge |
options.filter.absoluteCharge boolean
(default false)
|
If true, the charge is absolute (so between 0 and +Infinity by default) |
options.filter.unsaturation object
(default {})
|
|
options.filter.unsaturation.min number
(default -Infinity)
|
Minimal unsaturation |
options.filter.unsaturation.max number
(default +Infinity)
|
Maximal unsaturation |
options.filter.unsaturation.onlyInteger boolean
(default false)
|
Integer unsaturation |
options.filter.unsaturation.onlyNonInteger boolean
(default false)
|
Non integer unsaturation |
Promise:
Add a database starting from a peptidic sequence
(string?)
Sequence as a string of 1 letter or 3 letters code. Could also be a correct molecular formula respecting uppercase, lowercase. It can be comma separated if you have many peptide sequences
(object
= {})
| Name | Description |
|---|---|
options.estimate boolean
(default false)
|
estimate the number of MF without filters |
options.ionizations string
(default '')
|
|
options.onStep function?
|
Callback to do after each step |
options.mfsArray array
(default [])
|
|
options.protonation boolean
(default false)
|
|
options.protonationPH number
(default 7)
|
|
options.allowNeutralLoss boolean
(default false)
|
|
options.limit number
(default 100000)
|
|
options.digestion object
(default {})
|
Object defining options for digestion |
options.digestion.minMissed number
(default 0)
|
Minimal number of allowed missed cleavage |
options.digestion.maxMissed number
(default 0)
|
Maximal number of allowed missed cleavage |
options.digestion.minResidue number
(default 0)
|
Minimal number of residues |
options.digestion.maxResidue number
(default +Infinity)
|
Maximal number of residues |
options.digestion.enzyme string?
|
Mandatory field containing the name of the enzyme among: chymotrypsin, trypsin, glucph4, glucph8, thermolysin, cyanogenbromide |
options.fragmentation object
(default {})
|
Object defining options for fragmentation |
options.fragmentation.a boolean
(default false)
|
If true allow fragments of type 'a' |
options.fragmentation.b boolean
(default false)
|
If true allow fragments of type 'b' |
options.fragmentation.c boolean
(default false)
|
If true allow fragments of type 'c' |
options.fragmentation.x boolean
(default false)
|
If true allow fragments of type 'x' |
options.fragmentation.y boolean
(default false)
|
If true allow fragments of type 'y' |
options.fragmentation.z boolean
(default false)
|
If true allow fragments of type 'z' |
options.fragmentation.ya boolean
(default false)
|
If true allow fragments of type 'ya' |
options.fragmentation.yb boolean
(default false)
|
If true allow fragments of type 'yb' |
options.fragmentation.yc boolean
(default false)
|
If true allow fragments of type 'yc' |
options.fragmentation.zc boolean
(default false)
|
If true allow fragments of type 'zc' |
options.fragmentation.minInternal number
(default 0)
|
Minimal internal fragment length |
options.fragmentation.maxInternal number
(default +Infinity)
|
Maximal internal fragment length |
options.filter object
(default {})
|
Object defining options for molecular formula filter |
options.filter.precision number
(default 1000)
|
The precision on the experimental mass |
options.filter.targetMass number?
|
Target mass, allows to calculate error and filter results |
options.filter.targetMasses Array<number>?
|
Target masses: SORTED array of numbers |
options.filter.targetIntensities Array<number>?
|
Target intensities: SORTED array of numbers |
options.filter.minEM number
(default 0)
|
Minimal neutral monoisotopic mass |
options.filter.maxEM number
(default +Infinity)
|
Maximal neutral monoisotopic mass |
options.filter.minMSEM number
(default 0)
|
Minimal observed monoisotopic mass |
options.filter.maxMSEM number
(default +Infinity)
|
Maximal observed monoisotopic mass |
options.filter.minCharge number
(default -Infinity)
|
Minimal charge |
options.filter.maxCharge number
(default +Infinity)
|
Maximal charge |
options.filter.absoluteCharge boolean
(default false)
|
If true, the charge is absolute (so between 0 and +Infinity by default) |
options.filter.unsaturation object
(default {})
|
|
options.filter.unsaturation.min number
(default -Infinity)
|
Minimal unsaturation |
options.filter.unsaturation.max number
(default +Infinity)
|
Maximal unsaturation |
options.filter.unsaturation.onlyInteger boolean
(default false)
|
Integer unsaturation |
options.filter.unsaturation.onlyNonInteger boolean
(default false)
|
Non integer unsaturation |
options.filter.callback function?
|
a function to filter the MF |
Promise:
Generates a database 'generated' from an array of molecular formula
(string)
a string representing the range to search
(object
= {})
| Name | Description |
|---|---|
options.estimate boolean
(default false)
|
estimate the number of MF without filters |
options.onStep function?
|
Callback to do after each step |
options.databaseName string
(default 'generated')
|
|
options.limit number
(default 100000)
|
Maximum number of results |
options.canonizeMF boolean
(default true)
|
Canonize molecular formula |
options.uniqueMFs boolean
(default true)
|
Force canonization and make MF unique |
options.ionizations string
(default '')
|
Comma separated list of ionizations (to charge the molecule) |
options.filter object
(default {})
|
|
options.filter.minMass number
(default 0)
|
Minimal monoisotopic mass |
options.filter.maxMass number
(default +Infinity)
|
Maximal monoisotopic mass |
options.filter.minEM number
(default 0)
|
Minimal neutral monoisotopic mass |
options.filter.maxEM number
(default +Infinity)
|
Maximal neutral monoisotopic mass |
options.filter.minMSEM number
(default 0)
|
Minimal observed monoisotopic mass |
options.filter.maxMSEM number
(default +Infinity)
|
Maximal observed monoisotopic mass |
options.filter.minCharge number
(default -Infinity)
|
Minimal charge |
options.filter.maxCharge number
(default +Infinity)
|
Maximal charge |
options.filter.absoluteCharge boolean
(default false)
|
If true, the charge is absolute (so between 0 and +Infinity by default) |
options.filter.unsaturation object
(default {})
|
|
options.filter.unsaturation.min number
(default -Infinity)
|
Minimal unsaturation |
options.filter.unsaturation.max number
(default +Infinity)
|
Maximal unsaturation |
options.filter.unsaturation.onlyInteger boolean
(default false)
|
Integer unsaturation |
options.filter.unsaturation.onlyNonInteger boolean
(default false)
|
Non integer unsaturation |
options.filter.callback function?
|
a function to filter the MF |
options.filter.atoms object?
|
object of atom:{min, max} |
Promise:
list of possible molecular formula
const {EMDB} = require('emdb');
let emdb = new EMDB();
// semi-columns separated for combination, comma for 'or'
emdb.fromRange('C1-10, H1-10; Cl0-1 Br0-1'); // create a database 'generated' combining all possibilies
console.log(emdb.get('generated').length); // 80
Searching by various criteria. This mass will not take into account the mass of the mass of the electron
(any)
(object
= {})
| Name | Description |
|---|---|
filter.minMW number
(default 0)
|
Minimal molecular weight |
filter.maxMW number
(default +Infinity)
|
Maximal molecular weight |
filter.minEM number
(default 0)
|
Minimal monoisotopic mass |
filter.maxEM number
(default +Infinity)
|
Maximal monoisotopic mass |
filter.minCharge number
(default -Infinity)
|
Minimal charge |
filter.maxCharge number
(default +Infinity)
|
Maximal charge |
filter.absoluteCharge boolean
(default false)
|
If true, the charge is absolute (so between 0 and +Infinity by default) |
filter.unsaturation object
(default {})
|
|
filter.unsaturation.min number
(default -Infinity)
|
Minimal unsaturation |
filter.unsaturation.max number
(default +Infinity)
|
Maximal unsaturation |
filter.unsaturation.onlyInteger boolean
(default false)
|
Integer unsaturation |
filter.unsaturation.onlyNonInteger boolean
(default false)
|
Non integer unsaturation |
filter.atoms object?
|
object of atom:{min, max} |
Search for an experimental monoisotopic mass
(any)
(number)
The observed monoisotopic mass
Search for an experimental monoisotopic mass and calculate the similarity
(any)
(object
= {})
| Name | Description |
|---|---|
options.databases array?
|
an array containing the name of the databases so search, by default all |
options.flatten boolean?
|
should we return the array as a flat result |
options.onStep function?
|
Callback to do after each step |
options.ionizations string
(default '')
|
Comma separated list of ionizations (to charge the molecule) |
options.minSimilarity object
(default 0.5)
|
min similarity value |
options.filter object
(default {})
|
|
options.filter.forceIonization boolean
(default false)
|
If true ignore existing ionizations |
options.filter.msem number?
|
Observed monoisotopic mass in mass spectrometer |
options.filter.precision number
(default 1000)
|
The precision on the experimental mass |
options.filter.minCharge number
(default -Infinity)
|
Minimal charge |
options.filter.maxCharge number
(default +Infinity)
|
Maximal charge |
options.filter.absoluteCharge boolean
(default false)
|
If true, the charge is absolute (so between 0 and +Infinity by default) |
options.filter.unsaturation object
(default {})
|
|
options.filter.unsaturation.min number
(default -Infinity)
|
Minimal unsaturation |
options.filter.unsaturation.max number
(default +Infinity)
|
Maximal unsaturation |
options.filter.unsaturation.onlyInteger boolean
(default false)
|
Integer unsaturation |
options.filter.unsaturation.onlyNonInteger boolean
(default false)
|
Non integer unsaturation |
options.filter.atoms object?
|
object of atom:{min, max} |
options.filter.callback object?
|
a function to filter the MF |
options.similarity object
(default {})
|
|
options.similarity.widthBottom number?
|
|
options.similarity.widthTop number?
|
|
options.similarity.widthFunction object?
|
function called with mass that should return an object width containing top and bottom |
options.similarity.zone object
(default {})
|
|
options.similarity.zone.low number
(default -0.5)
|
window shift based on observed monoisotopic mass |
options.similarity.zone.high number
(default 2.5)
|
to value for the comparison window |
options.similarity.zone.auto boolean
(default false)
|
if true, low / high is determined based on the isotopic distribution and the threshold |
options.similarity.common string?
|
|
options.similarity.threshold number
(default 0.001)
|
when calculating similarity we only use the isotopic distribution with peaks over this relative threshold |
options.similarity.limit number?
|
We may define the maximum number of peaks to keep |
Promise:
Calculates a function that allows post-calibration on mass spectra based on the error in assignment
(any)
(object
= {})