Constants.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <string>
 
namespace OpenMS
{
  namespace Constants
  {
 
    inline const double PI = 3.14159265358979323846;
 
    inline const double E = 2.718281828459045235;
 
    inline double EPSILON = 1e-6;
 
 
    inline const double ELEMENTARY_CHARGE = 1.60217738E-19; // C
 
    inline const double e0 = ELEMENTARY_CHARGE;
 
    inline const double ELECTRON_MASS = 9.1093897E-31; // kg
 
    inline const double ELECTRON_MASS_U = 1.0 / 1822.8885020477; // u
 
    inline const double PROTON_MASS = 1.6726230E-27; // kg
 
    inline const double PROTON_MASS_U = 1.0072764667710; // u
 
    inline const double C13C12_MASSDIFF_U = 1.0033548378; // u
 
    inline const double ISOTOPE_MASSDIFF_55K_U = 1.002371; // u
 
    inline const double NEUTRON_MASS = 1.6749286E-27; // kg
 
    inline const double NEUTRON_MASS_U = 1.00866491566; // u
 
    inline const double AVOGADRO = 6.0221367E+23; // 1 / mol
 
    inline const double NA = AVOGADRO;
 
    inline const double MOL = AVOGADRO;
 
    inline const double BOLTZMANN = 1.380657E-23; // J / K
 
    inline const double k = BOLTZMANN;
 
    inline const double PLANCK = 6.6260754E-34; // J * sec
 
    inline const double h = PLANCK;
 
    inline const double GAS_CONSTANT = NA * k;
 
    inline const double R = GAS_CONSTANT;
 
    inline const double FARADAY = NA * e0;
 
    inline const double F = FARADAY;
 
    inline const double BOHR_RADIUS = 5.29177249E-11; // m
 
    inline const double a0 = BOHR_RADIUS;
 
    //  the following values from:
    //  P.W.Atkins: Physical Chemistry, 5th ed., Oxford University Press, 1995
 
    inline const double VACUUM_PERMITTIVITY = 8.85419E-12; // C^2 / (J * m)
 
    inline const double VACUUM_PERMEABILITY = (4 * PI * 1E-7); // J s^2 / (C^2 * m)
 
    inline const double SPEED_OF_LIGHT = 2.99792458E+8; // m / s
 
    inline const double c = SPEED_OF_LIGHT;
 
    inline const double GRAVITATIONAL_CONSTANT = 6.67259E-11; // N m^2 / kg^2
 
    inline const double FINE_STRUCTURE_CONSTANT = 7.29735E-3; // 1
 
 
    inline const double DEG_PER_RAD = 57.2957795130823209;
 
    inline const double RAD_PER_DEG = 0.0174532925199432957;
 
    inline const double MM_PER_INCH = 25.4;
 
    inline const double M_PER_FOOT = 3.048;
 
    inline const double JOULE_PER_CAL = 4.184;
 
    inline const double CAL_PER_JOULE = (1 / 4.184);
 
    namespace UserParam
    {
      inline const std::string IM = "IM";
 
      inline const std::string FAIMS_CV = "FAIMS_CV";
 
      inline const std::string ION_MOBILITY = "Ion Mobility";
 
      inline const std::string INVERSE_REDUCED_ION_MOBILITY = "inverse reduced ion mobility";
 
      inline const std::string MEAN_INVERSE_REDUCED_ION_MOBILITY_ARRAY = "mean inverse reduced ion mobility array";
 
      inline const std::string ION_MOBILITY_CENTROID = "Ion Mobility Centroid";
 
 
      inline const std::string FWHM_IM = "IM Peak FWHM";
 
      inline const std::string FWHM_IM_AVG = "FWHM_im_avg";
 
      inline const std::string FWHM_MZ_ppm = "FWHM_ppm";
 
      inline const std::string FWHM_MZ_AVG = "FWHM_mz_avg";
 
      inline const std::string SD = "SD";
 
      inline const std::string SD_ppm = "SD_ppm";
 
      inline const std::string IonNames = "IonNames";
 
      inline const std::string CONCAT_PEPTIDE = "concatenated_peptides";
 
      inline const std::string LOCALIZED_MODIFICATIONS_USERPARAM = "localized_modifications";
 
      inline const std::string MERGED_CHROMATOGRAM_MZS = "merged_chromatogram_mzs";
 
      inline const std::string PRECURSOR_ERROR_PPM_USERPARAM = "precursor_mz_error_ppm";
 
      inline const std::string FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM = "fragment_mz_error_median_ppm";
 
 
      inline const std::string FRAGMENT_ERROR_PPM_USERPARAM = "fragment_mass_error_ppm";
 
      inline const std::string FRAGMENT_ERROR_DA_USERPARAM = "fragment_mass_error_da";
 
      inline const std::string FRAGMENT_ANNOTATION_USERPARAM = "fragment_annotation";
 
      inline const std::string   PSM_EXPLAINED_ION_CURRENT_USERPARAM = "PSM_explained_ion_current";
 
      // User parameter name for the fraction of prefix ions that have been matched
      inline const std::string MATCHED_PREFIX_IONS_FRACTION = "matched_prefix_ions_fraction";
 
      // User parameter name for the fraction of suffix ions that have been matched
      inline const std::string MATCHED_SUFFIX_IONS_FRACTION = "matched_suffix_ions_fraction";
 
      // User parameter name for the number of matched prefix ions (a/b/c, absolute count)
      inline const std::string MATCHED_PREFIX_IONS = "matched_prefix_ions";
 
      // User parameter name for the number of matched suffix ions (x/y/z, absolute count)
      inline const std::string MATCHED_SUFFIX_IONS = "matched_suffix_ions";
 
      // User parameter name for the total number of matched fragment ions
      inline const std::string NUM_MATCHED_PEAKS = "num_matched_peaks";
 
      // User parameter name for the longest consecutive prefix (a/b/c) or suffix (x/y/z) ion series
      inline const std::string LONGEST_PEPTIDE_ION_SEQUENCE = "longest_peptide_ion_sequence";
 
      // User parameter name for the matched ion current (sum of experimental
      // intensities over all matched fragment peaks, raw — not log-transformed)
      inline const std::string MATCHED_ION_CURRENT = "matched_ion_current";
 
      inline const std::string   SPECTRUM_REFERENCE = "spectrum_reference";
 
      inline const std::string   ID_MERGE_INDEX = "id_merge_index";
 
      inline const std::string   TARGET_DECOY = "target_decoy";
 
      inline const std::string   DELTA_SCORE = "delta_score";
 
      inline const std::string   ISOTOPE_ERROR = "isotope_error";
 
      // User parameter name for the standard score of the best candidate's score within
      // the pool of all candidates scored for the same spectrum. 0 when fewer than two
      // candidates were scored or when all of them tied.
      inline const std::string HYPERSCORE_ZSCORE = "hyperscore_zscore";
 
      // User parameter name for ln(1 + number of candidates scored for a spectrum).
      // The +1 offset keeps the value defined for spectra without any candidate; it is
      // order-preserving, so the feature stays monotone in the candidate count. The count
      // is capped by the search engine's per-spectrum candidate limit, so this saturates.
      inline const std::string LN_NUM_CANDIDATES = "ln_num_candidates";
 
      // User parameter name for the matched ion current normalized by the spectrum's total ion current
      inline const std::string MATCHED_ION_CURRENT_FRACTION = "matched_ion_current_fraction";
 
      // User parameter name for the fraction of cleavage sites where both a prefix ion and its
      // complementary suffix ion were matched
      inline const std::string COMPLEMENTARY_IONS_FRACTION = "complementary_ions_fraction";
 
      inline const std::string   PEPTIDE_Q_VALUE = "peptide q-value";
 
      // Cross-Linking Mass Spectrometry user parameters
      inline const std::string   OPENPEPXL_SCORE = "OpenPepXL:score";
 
      inline const std::string   OPENPEPXL_BETA_SEQUENCE = "sequence_beta";
 
      inline const std::string   OPENPEPXL_BETA_ACCESSIONS = "accessions_beta";
 
      inline const std::string   OPENPEPXL_XL_POS1 = "xl_pos1";
 
      inline const std::string   OPENPEPXL_XL_POS2 = "xl_pos2";
 
      inline const std::string   OPENPEPXL_XL_POS1_PROT = "xl_pos1_protein";
 
      inline const std::string   OPENPEPXL_XL_POS2_PROT = "xl_pos2_protein";
 
      inline const std::string   OPENPEPXL_XL_TYPE = "xl_type";
 
      inline const std::string   OPENPEPXL_XL_RANK = "xl_rank";
 
      inline const std::string   OPENPEPXL_XL_MOD = "xl_mod";
 
      inline const std::string   OPENPEPXL_XL_MASS = "xl_mass";
 
      inline const std::string   OPENPEPXL_XL_TERM_SPEC_ALPHA = "xl_term_spec_alpha";
 
      inline const std::string   OPENPEPXL_XL_TERM_SPEC_BETA = "xl_term_spec_beta";
 
      inline const std::string   OPENPEPXL_HEAVY_SPEC_RT = "spec_heavy_RT";
 
      inline const std::string   OPENPEPXL_HEAVY_SPEC_MZ = "spec_heavy_MZ";
 
      inline const std::string   OPENPEPXL_HEAVY_SPEC_REF = "spectrum_reference_heavy";
 
      inline const std::string   OPENPEPXL_TARGET_DECOY_ALPHA = "xl_target_decoy_alpha";
 
      inline const std::string   OPENPEPXL_TARGET_DECOY_BETA = "xl_target_decoy_beta";
 
      inline const std::string   OPENPEPXL_BETA_PEPEV_PRE = "BetaPepEv:pre";
 
      inline const std::string   OPENPEPXL_BETA_PEPEV_POST = "BetaPepEv:post";
 
      inline const std::string   OPENPEPXL_BETA_PEPEV_START = "BetaPepEv:start";
 
      inline const std::string   OPENPEPXL_BETA_PEPEV_END = "BetaPepEv:end";
 
 
      inline const std::string   SIRIUS_MZ = "mz";
 
      inline const std::string   SIRIUS_EXACTMASS = "exact_mass";
 
      inline const std::string   SIRIUS_EXPLANATION = "explanation";
 
      inline const std::string   SIRIUS_SCORE = "score";
 
      inline const std::string   SIRIUS_PEAKMZ = "peak_mz";
 
      inline const std::string   SIRIUS_ANNOTATED_SUMFORMULA = "annotated_sumformula";
 
      inline const std::string   SIRIUS_ANNOTATED_ADDUCT = "annotated_adduct";
 
      inline const std::string   SIRIUS_DECOY = "decoy";
 
      inline const std::string   SIRIUS_FEATURE_ID = "feat_id";
 
 
      inline const std::string   XFDR_FDR = "XFDR:FDR";
 
      inline const std::string   IIMN_BEST_ION = "best ion";
 
      inline const std::string   IIMN_ADDUCT_PARTNERS = "partners";
 
      inline const std::string   IIMN_ROW_ID = "row ID";
 
      inline const std::string   IIMN_ANNOTATION_NETWORK_NUMBER = "annotation network number";
 
      inline const std::string   ADDUCT_GROUP = "Group";
 
      inline const std::string   IIMN_LINKED_GROUPS = "LinkedGroups";
 
      inline const std::string   DC_CHARGE_ADDUCTS = "dc_charge_adducts";
 
      inline const std::string   NUM_OF_MASSTRACES = "num_of_masstraces";
 
      inline const std::string   NUM_OF_DATAPOINTS = "num_of_datapoints";
 
      inline const std::string   MSM_METABOLITE_NAME = "Metabolite_Name";
 
      inline const std::string   MSM_INCHI_STRING = "Inchi_String";
 
      inline const std::string   MSM_SMILES_STRING = "SMILES_String";
 
      inline const std::string   MSM_PRECURSOR_ADDUCT = "Precursor_Ion";
 
      inline const std::string   MSM_SUM_FORMULA = "Sum_Formula";
 
      inline const std::string   MSM_CCS = "CCS";
 
      inline const std::string   BASE_NAME = "base_name";
 
      inline const std::string   SIGNIFICANCE_THRESHOLD = "significance_threshold";
      
      inline const std::string   RANK = "rank";
 
      inline const std::string   NUM_PEAKS = "num_peaks";
 
      inline const std::string   MODIFICATION_DEFINITIONS = "modification_definitions";
    }
 
  }
}