OpenMS
Constants.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg$
6 // $Authors: Marc Sturm $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/config.h>
12 #include <string>
13 
19 namespace OpenMS
20 {
42  namespace Constants
43  {
47 
49  inline const double PI = 3.14159265358979323846;
50 
52  inline const double E = 2.718281828459045235;
53 
57  inline double EPSILON = 1e-6;
59 
63 
67  inline const double ELEMENTARY_CHARGE = 1.60217738E-19; // C
68 
70  inline const double e0 = ELEMENTARY_CHARGE;
71 
75  inline const double ELECTRON_MASS = 9.1093897E-31; // kg
76 
80  inline const double ELECTRON_MASS_U = 1.0 / 1822.8885020477; // u
81 
85  inline const double PROTON_MASS = 1.6726230E-27; // kg
86 
90  inline const double PROTON_MASS_U = 1.0072764667710; // u
91 
95  inline const double C13C12_MASSDIFF_U = 1.0033548378; // u
96 
100  inline const double ISOTOPE_MASSDIFF_55K_U = 1.002371; // u
101 
105  inline const double NEUTRON_MASS = 1.6749286E-27; // kg
106 
110  inline const double NEUTRON_MASS_U = 1.00866491566; // u
111 
115  inline const double AVOGADRO = 6.0221367E+23; // 1 / mol
116 
119  inline const double NA = AVOGADRO;
120 
123  inline const double MOL = AVOGADRO;
124 
128  inline const double BOLTZMANN = 1.380657E-23; // J / K
129 
132  inline const double k = BOLTZMANN;
133 
137  inline const double PLANCK = 6.6260754E-34; // J * sec
138 
141  inline const double h = PLANCK;
142 
145  inline const double GAS_CONSTANT = NA * k;
146 
149  inline const double R = GAS_CONSTANT;
150 
153  inline const double FARADAY = NA * e0;
154 
157  inline const double F = FARADAY;
158 
162  inline const double BOHR_RADIUS = 5.29177249E-11; // m
163 
166  inline const double a0 = BOHR_RADIUS;
167 
168  // the following values from:
169  // P.W.Atkins: Physical Chemistry, 5th ed., Oxford University Press, 1995
170 
174  inline const double VACUUM_PERMITTIVITY = 8.85419E-12; // C^2 / (J * m)
175 
179  inline const double VACUUM_PERMEABILITY = (4 * PI * 1E-7); // J s^2 / (C^2 * m)
180 
184  inline const double SPEED_OF_LIGHT = 2.99792458E+8; // m / s
185 
188  inline const double c = SPEED_OF_LIGHT;
189 
193  inline const double GRAVITATIONAL_CONSTANT = 6.67259E-11; // N m^2 / kg^2
194 
198  inline const double FINE_STRUCTURE_CONSTANT = 7.29735E-3; // 1
200 
204 
208  inline const double DEG_PER_RAD = 57.2957795130823209;
209 
213  inline const double RAD_PER_DEG = 0.0174532925199432957;
214 
218  inline const double MM_PER_INCH = 25.4;
219 
223  inline const double M_PER_FOOT = 3.048;
224 
228  inline const double JOULE_PER_CAL = 4.184;
229 
233  inline const double CAL_PER_JOULE = (1 / 4.184);
234 
235  namespace UserParam
236  {
240  inline const std::string CONCAT_PEPTIDE = "concatenated_peptides";
241 
244  inline const std::string LOCALIZED_MODIFICATIONS_USERPARAM = "localized_modifications";
245 
249  inline const std::string MERGED_CHROMATOGRAM_MZS = "merged_chromatogram_mzs";
250 
254  inline const std::string PRECURSOR_ERROR_PPM_USERPARAM = "precursor_mz_error_ppm";
255 
259  inline const std::string FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM = "fragment_mz_error_median_ppm";
260 
261 
265  inline const std::string FRAGMENT_ERROR_PPM_USERPARAM = "fragment_mass_error_ppm";
266 
270  inline const std::string FRAGMENT_ERROR_DA_USERPARAM = "fragment_mass_error_da";
271 
275  inline const std::string FRAGMENT_ANNOTATION_USERPARAM = "fragment_annotation";
276 
280  inline const std::string PSM_EXPLAINED_ION_CURRENT_USERPARAM = "PSM_explained_ion_current";
281 
282  // User parameter name for the fraction of prefix ions that have been matched
283  inline const std::string MATCHED_PREFIX_IONS_FRACTION = "matched_prefix_ions_fraction";
284 
285  // User parameter name for the fraction of suffix ions that have been matched
286  inline const std::string MATCHED_SUFFIX_IONS_FRACTION = "matched_suffix_ions_fraction";
287 
291  inline const std::string SPECTRUM_REFERENCE = "spectrum_reference";
292 
297  inline const std::string ID_MERGE_INDEX = "id_merge_index";
298 
302  inline const std::string TARGET_DECOY = "target_decoy";
303 
307  inline const std::string DELTA_SCORE = "delta_score";
308 
312  inline const std::string ISOTOPE_ERROR = "isotope_error";
313 
314  // Cross-Linking Mass Spectrometry user parameters
318  inline const std::string OPENPEPXL_SCORE = "OpenPepXL:score";
319 
323  inline const std::string OPENPEPXL_BETA_SEQUENCE = "sequence_beta";
324 
328  inline const std::string OPENPEPXL_BETA_ACCESSIONS = "accessions_beta";
329 
333  inline const std::string OPENPEPXL_XL_POS1 = "xl_pos1";
334 
338  inline const std::string OPENPEPXL_XL_POS2 = "xl_pos2";
339 
343  inline const std::string OPENPEPXL_XL_POS1_PROT = "xl_pos1_protein";
344 
348  inline const std::string OPENPEPXL_XL_POS2_PROT = "xl_pos2_protein";
349 
353  inline const std::string OPENPEPXL_XL_TYPE = "xl_type";
354 
358  inline const std::string OPENPEPXL_XL_RANK = "xl_rank";
359 
363  inline const std::string OPENPEPXL_XL_MOD = "xl_mod";
364 
368  inline const std::string OPENPEPXL_XL_MASS = "xl_mass";
369 
373  inline const std::string OPENPEPXL_XL_TERM_SPEC_ALPHA = "xl_term_spec_alpha";
374 
378  inline const std::string OPENPEPXL_XL_TERM_SPEC_BETA = "xl_term_spec_beta";
379 
383  inline const std::string OPENPEPXL_HEAVY_SPEC_RT = "spec_heavy_RT";
384 
388  inline const std::string OPENPEPXL_HEAVY_SPEC_MZ = "spec_heavy_MZ";
389 
393  inline const std::string OPENPEPXL_HEAVY_SPEC_REF = "spectrum_reference_heavy";
394 
398  inline const std::string OPENPEPXL_TARGET_DECOY_ALPHA = "xl_target_decoy_alpha";
399 
403  inline const std::string OPENPEPXL_TARGET_DECOY_BETA = "xl_target_decoy_beta";
404 
408  inline const std::string OPENPEPXL_BETA_PEPEV_PRE = "BetaPepEv:pre";
409 
413  inline const std::string OPENPEPXL_BETA_PEPEV_POST = "BetaPepEv:post";
414 
418  inline const std::string OPENPEPXL_BETA_PEPEV_START = "BetaPepEv:start";
419 
423  inline const std::string OPENPEPXL_BETA_PEPEV_END = "BetaPepEv:end";
424 
429 
433  inline const std::string SIRIUS_MZ = "mz";
434 
438  inline const std::string SIRIUS_EXACTMASS = "exact_mass";
439 
443  inline const std::string SIRIUS_EXPLANATION = "explanation";
444 
448  inline const std::string SIRIUS_SCORE = "score";
449 
453  inline const std::string SIRIUS_PEAKMZ = "peak_mz";
454 
458  inline const std::string SIRIUS_ANNOTATED_SUMFORMULA = "annotated_sumformula";
459 
463  inline const std::string SIRIUS_ANNOTATED_ADDUCT = "annotated_adduct";
464 
468  inline const std::string SIRIUS_DECOY = "decoy";
469 
473  inline const std::string SIRIUS_FEATURE_ID = "feat_id";
474 
476 
480  inline const std::string XFDR_FDR = "XFDR:FDR";
481 
485  inline const std::string IIMN_BEST_ION = "best ion";
486 
491  inline const std::string IIMN_ADDUCT_PARTNERS = "partners";
492 
496  inline const std::string IIMN_ROW_ID = "row ID";
497 
501  inline const std::string IIMN_ANNOTATION_NETWORK_NUMBER = "annotation network number";
502 
506  inline const std::string ADDUCT_GROUP = "Group";
507 
511  inline const std::string IIMN_LINKED_GROUPS = "LinkedGroups";
512 
516  inline const std::string DC_CHARGE_ADDUCTS = "dc_charge_adducts";
517 
521  inline const std::string NUM_OF_MASSTRACES = "num_of_masstraces";
522 
526  inline const std::string NUM_OF_DATAPOINTS = "num_of_datapoints";
527 
531  inline const std::string MSM_METABOLITE_NAME = "Metabolite_Name";
532 
536  inline const std::string MSM_INCHI_STRING = "Inchi_String";
537 
541  inline const std::string MSM_SMILES_STRING = "SMILES_String";
542 
546  inline const std::string MSM_PRECURSOR_ADDUCT = "Precursor_Ion";
547 
551  inline const std::string MSM_SUM_FORMULA = "Sum_Formula";
552  }
553 
555  }
556 }
const std::string TARGET_DECOY
Definition: Constants.h:302
const std::string SIRIUS_EXPLANATION
Definition: Constants.h:443
const std::string MATCHED_PREFIX_IONS_FRACTION
Definition: Constants.h:283
const std::string OPENPEPXL_XL_POS2
Definition: Constants.h:338
const std::string OPENPEPXL_HEAVY_SPEC_RT
Definition: Constants.h:383
const std::string SIRIUS_SCORE
Definition: Constants.h:448
const std::string OPENPEPXL_BETA_PEPEV_PRE
Definition: Constants.h:408
const std::string ADDUCT_GROUP
Definition: Constants.h:506
const std::string OPENPEPXL_XL_POS2_PROT
Definition: Constants.h:348
const std::string OPENPEPXL_HEAVY_SPEC_REF
Definition: Constants.h:393
const std::string OPENPEPXL_BETA_SEQUENCE
Definition: Constants.h:323
const std::string SIRIUS_DECOY
Definition: Constants.h:468
const std::string SIRIUS_EXACTMASS
Definition: Constants.h:438
const std::string DELTA_SCORE
Definition: Constants.h:307
const std::string ISOTOPE_ERROR
Definition: Constants.h:312
const std::string IIMN_LINKED_GROUPS
Definition: Constants.h:511
const std::string OPENPEPXL_SCORE
Definition: Constants.h:318
const std::string NUM_OF_DATAPOINTS
Definition: Constants.h:526
const std::string SPECTRUM_REFERENCE
Definition: Constants.h:291
const std::string DC_CHARGE_ADDUCTS
Definition: Constants.h:516
const std::string MATCHED_SUFFIX_IONS_FRACTION
Definition: Constants.h:286
const std::string PRECURSOR_ERROR_PPM_USERPARAM
Definition: Constants.h:254
const std::string MSM_SMILES_STRING
Definition: Constants.h:541
const std::string OPENPEPXL_XL_TYPE
Definition: Constants.h:353
const std::string SIRIUS_FEATURE_ID
Definition: Constants.h:473
const std::string OPENPEPXL_XL_TERM_SPEC_BETA
Definition: Constants.h:378
const std::string OPENPEPXL_XL_RANK
Definition: Constants.h:358
const std::string OPENPEPXL_XL_MASS
Definition: Constants.h:368
const std::string IIMN_BEST_ION
Definition: Constants.h:485
const std::string IIMN_ANNOTATION_NETWORK_NUMBER
Definition: Constants.h:501
const std::string OPENPEPXL_BETA_PEPEV_POST
Definition: Constants.h:413
const std::string SIRIUS_ANNOTATED_SUMFORMULA
Definition: Constants.h:458
const std::string OPENPEPXL_BETA_PEPEV_END
Definition: Constants.h:423
const std::string FRAGMENT_ANNOTATION_USERPARAM
Definition: Constants.h:275
const std::string FRAGMENT_ERROR_DA_USERPARAM
Definition: Constants.h:270
const std::string FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM
Definition: Constants.h:259
const std::string SIRIUS_ANNOTATED_ADDUCT
Definition: Constants.h:463
const std::string OPENPEPXL_XL_TERM_SPEC_ALPHA
Definition: Constants.h:373
const std::string ID_MERGE_INDEX
Definition: Constants.h:297
const std::string IIMN_ROW_ID
Definition: Constants.h:496
const std::string OPENPEPXL_TARGET_DECOY_ALPHA
Definition: Constants.h:398
const std::string FRAGMENT_ERROR_PPM_USERPARAM
Definition: Constants.h:265
const std::string OPENPEPXL_TARGET_DECOY_BETA
Definition: Constants.h:403
const std::string OPENPEPXL_XL_POS1_PROT
Definition: Constants.h:343
const std::string SIRIUS_PEAKMZ
Definition: Constants.h:453
const std::string MERGED_CHROMATOGRAM_MZS
Definition: Constants.h:249
const std::string OPENPEPXL_HEAVY_SPEC_MZ
Definition: Constants.h:388
const std::string SIRIUS_MZ
Definition: Constants.h:433
const std::string CONCAT_PEPTIDE
Definition: Constants.h:240
const std::string OPENPEPXL_XL_POS1
Definition: Constants.h:333
const std::string MSM_SUM_FORMULA
Definition: Constants.h:551
const std::string IIMN_ADDUCT_PARTNERS
Definition: Constants.h:491
const std::string OPENPEPXL_BETA_PEPEV_START
Definition: Constants.h:418
const std::string LOCALIZED_MODIFICATIONS_USERPARAM
Definition: Constants.h:244
const std::string MSM_INCHI_STRING
Definition: Constants.h:536
const std::string XFDR_FDR
Definition: Constants.h:480
const std::string MSM_PRECURSOR_ADDUCT
Definition: Constants.h:546
const std::string NUM_OF_MASSTRACES
Definition: Constants.h:521
const std::string OPENPEPXL_XL_MOD
Definition: Constants.h:363
const std::string OPENPEPXL_BETA_ACCESSIONS
Definition: Constants.h:328
const std::string MSM_METABOLITE_NAME
Definition: Constants.h:531
const std::string PSM_EXPLAINED_ION_CURRENT_USERPARAM
Definition: Constants.h:280
const double R
Definition: Constants.h:149
const double NEUTRON_MASS
Definition: Constants.h:105
const double ELECTRON_MASS
Definition: Constants.h:75
const double CAL_PER_JOULE
Definition: Constants.h:233
const double ISOTOPE_MASSDIFF_55K_U
Definition: Constants.h:100
const double MOL
Definition: Constants.h:123
double EPSILON
Definition: Constants.h:57
const double F
Definition: Constants.h:157
const double e0
Elementary charge (alias)
Definition: Constants.h:70
const double VACUUM_PERMITTIVITY
Definition: Constants.h:174
const double AVOGADRO
Definition: Constants.h:115
const double PROTON_MASS
Definition: Constants.h:85
const double DEG_PER_RAD
Definition: Constants.h:208
const double GAS_CONSTANT
Definition: Constants.h:145
const double PROTON_MASS_U
Definition: Constants.h:90
const double GRAVITATIONAL_CONSTANT
Definition: Constants.h:193
const double c
Definition: Constants.h:188
const double k
Definition: Constants.h:132
const double PI
PI.
Definition: Constants.h:49
const double NEUTRON_MASS_U
Definition: Constants.h:110
const double JOULE_PER_CAL
Definition: Constants.h:228
const double M_PER_FOOT
Definition: Constants.h:223
const double h
Definition: Constants.h:141
const double ELEMENTARY_CHARGE
Definition: Constants.h:67
const double SPEED_OF_LIGHT
Definition: Constants.h:184
const double VACUUM_PERMEABILITY
Definition: Constants.h:179
const double E
Euler's number - base of the natural logarithm.
Definition: Constants.h:52
const double FARADAY
Definition: Constants.h:153
const double BOHR_RADIUS
Definition: Constants.h:162
const double a0
Definition: Constants.h:166
const double C13C12_MASSDIFF_U
Definition: Constants.h:95
const double MM_PER_INCH
Definition: Constants.h:218
const double FINE_STRUCTURE_CONSTANT
Definition: Constants.h:198
const double RAD_PER_DEG
Definition: Constants.h:213
const double BOLTZMANN
Definition: Constants.h:128
const double ELECTRON_MASS_U
Definition: Constants.h:80
const double NA
Definition: Constants.h:119
const double PLANCK
Definition: Constants.h:137
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22