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NEWS.md

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mzAnnotation 2.0.0

  • 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.

mzAnnotation 1.7.5

  • Fixed error in relationshipCalculator() for empty returns.

mzAnnotation 1.7.4

  • Remove modes argument form relationshipCalcualtor().

  • Speed uprelationshipCalculator() by ~x20.

mzAnnotation 1.7.3