All chemical structure (SMILES, InChI) and chemoinformatics functionality based on OpenBabel has now be moved to the cheminf package.
The adduct, isotope and transformation rules functions adduct()
, isotope()
and transformations()
have been renamed to adduct_rules()
, isotope_rules()
and transformation_rules()
respectively.
Added the adduct_names()
, isotope_names()
and transformation_names()
functions to list the available adducts, isotopes and transformations in the default rules tables.
Added suitableElementRanges()
to calculate minimum and maximum elemental ranges for a specified molecular mass, suitable for molecular formula generation.
Added elementRatios()
for calculating the ratio between all elements present in specified molecular formulas.
Added CHOproportion()
for calculating the proportion of CHO present in specified molecular formulas.
Added functions for calculating the rings plus double bonds equivalent (rdbe()
), LEWIS valence test lewis()
and senior()
molecular graph test for molecular formulas.
Added functions (goldenRules()
,elementCountCheck()
,elementRatioCheck()
) for calculating the Golden Rules 2, 3, 5 and 6 from Kind et al. 2007.
Added ipMF()
for generating molecular formulas for electrospray ionisation products.
Added transformationPossible()
to test if a transformation between two molecular formulas is possible.
count.elements()
is now re-exported from the CHNOSZ package.
The digits
option is now set to 7 on package load.
The specified adduct
, isotope
and transformation
arguments are now checked against the specified adduct_rules_table
, isotope_rules_table
and transformation_rules_table
in calcM()
and calcMZ()
. An error is thrown if an are not present.
Numerous function documentation improvements.
relationshipCalculator()
for empty returns. Remove modes
argument form relationshipCalcualtor()
.
Speed uprelationshipCalculator()
by ~x20.
Added a NEWS.md
file to track changes to the package.
Added a pkgdown
site available at https://jasenfinch.github.io/mzAnnotation/.
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