pyopenms 2.3.0__zip

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (166) hide show
  1. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/License.txt +52 -0
  2. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/__init__.py +54 -0
  3. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/__init__.pyc +0 -0
  4. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/all_modules.py +4 -0
  5. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/all_modules.pyc +0 -0
  6. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/docompile.py +35 -0
  7. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/docompile.pyc +0 -0
  8. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/libOpenMS.so +0 -0
  9. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/libOpenSwathAlgo.so +0 -0
  10. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/libSuperHirn.so +0 -0
  11. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/pyopenms_1.so +0 -0
  12. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/pyopenms_2.so +0 -0
  13. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/pyopenms_3.so +0 -0
  14. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/pyopenms_4.so +0 -0
  15. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/python_extras.py +22 -0
  16. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/python_extras.pyc +0 -0
  17. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/qt_version_info.py +2 -0
  18. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/qt_version_info.pyc +0 -0
  19. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/Elements.xml +1221 -0
  20. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/Enzymes.xml +269 -0
  21. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/HMDBMappingFile.tsv +10104 -0
  22. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModel.scale +6 -0
  23. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModel.svm +626 -0
  24. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised2.scale +4 -0
  25. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised2.svm +559 -0
  26. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised5.scale +4 -0
  27. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised5.svm +1010 -0
  28. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MissedCleavage.model +229 -0
  29. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/NegativeAdducts.tsv +15 -0
  30. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/OMSSA_modification_mapping +158 -0
  31. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/PSI-MOD.obo +23804 -0
  32. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/PositiveAdducts.tsv +33 -0
  33. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/Residues.xml +470 -0
  34. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/XLMOD.obo +623 -0
  35. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/XTandem_default_input.xml +181 -0
  36. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml +38885 -0
  37. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/brenda.obo +22923 -0
  38. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/goslim_goa.obo +823 -0
  39. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/psi-ms.obo +17899 -0
  40. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/psi-mzdata.obo +2920 -0
  41. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/qc-cv.obo +471 -0
  42. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/quality.obo +12581 -0
  43. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/unimod.obo +13214 -0
  44. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/unit.obo +2585 -0
  45. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/TOPPAS.appdata.xml +33 -0
  46. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/TOPPAS.desktop +10 -0
  47. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/TOPPView.appdata.xml +35 -0
  48. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/TOPPView.desktop +11 -0
  49. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/readme.txt +5 -0
  50. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/GUISTYLE/qtStyleSheet.qss +9 -0
  51. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/IDPool/IDPool.txt +0 -0
  52. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/IDPool/README +29 -0
  53. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/MAPPING/TraML-mapping.xml +171 -0
  54. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/MAPPING/ms-mapping.xml +187 -0
  55. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/MAPPING/mzIdentML-mapping.xml +221 -0
  56. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/MAPPING/mzdata-mapping.xml +158 -0
  57. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/PIP/codebooks.data +2 -0
  58. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/PIP/linearMapping.data +2 -0
  59. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/CTD_0_3.xsd +168 -0
  60. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_0.xsd +376 -0
  61. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_1.xsd +381 -0
  62. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_2.xsd +202 -0
  63. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_3.xsd +686 -0
  64. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_4.xsd +694 -0
  65. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_5.xsd +698 -0
  66. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_6.xsd +613 -0
  67. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_7.xsd +618 -0
  68. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/CvMapping.xsd +157 -0
  69. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_0.xsd +737 -0
  70. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_1.xsd +770 -0
  71. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_2.xsd +770 -0
  72. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_3.xsd +660 -0
  73. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_4.xsd +660 -0
  74. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_5.xsd +670 -0
  75. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_6.xsd +674 -0
  76. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_7.xsd +679 -0
  77. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_8.xsd +587 -0
  78. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_9.xsd +592 -0
  79. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FuGElightv1.0.0.xsd +1118 -0
  80. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_0.xsd +340 -0
  81. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_1.xsd +345 -0
  82. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_2.xsd +354 -0
  83. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_3.xsd +367 -0
  84. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_4.xsd +371 -0
  85. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_5.xsd +371 -0
  86. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_0.xsd +91 -0
  87. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_1.xsd +101 -0
  88. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_2.xsd +168 -0
  89. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_3.xsd +173 -0
  90. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_4.xsd +149 -0
  91. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_6_2.xsd +99 -0
  92. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ToolDescriptor_1_0.xsd +232 -0
  93. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/TraML0.9.3.xsd +552 -0
  94. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/TraML1.0.0.xsd +622 -0
  95. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/TrafoXML_1_0.xsd +102 -0
  96. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/general_types_1.0.xsd +17 -0
  97. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzData_1_05.xsd +631 -0
  98. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzIdentML1.0.0.xsd +1339 -0
  99. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzIdentML1.1.0.xsd +1845 -0
  100. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzML_1_00.xsd +921 -0
  101. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzML_1_10.xsd +1119 -0
  102. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzML_idx_1_00.xsd +992 -0
  103. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzML_idx_1_10.xsd +1201 -0
  104. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzQCML_0_0_5.xsd +220 -0
  105. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzQuantML_1_0_0-rc2.xsd +1557 -0
  106. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzXML_2_1.xsd +1 -1
  107. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzXML_3.1.xsd +1 -1
  108. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzXML_3.1_mod.xsd +686 -0
  109. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzXML_idx_3.1.xsd +60 -0
  110. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/pepXML_v114.xsd +1448 -0
  111. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/protXML_v6.xsd +935 -0
  112. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd +235 -0
  113. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/separation_technique_1.0.xsd +10 -0
  114. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/xQuest_1_0.xsd +210 -0
  115. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/InternalCalibration_Models.R +40 -0
  116. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/InternalCalibration_Residuals.R +57 -0
  117. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_acc.R +28 -0
  118. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_idmap.R +39 -0
  119. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_inj.R +27 -0
  120. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_rt_acc.R +31 -0
  121. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_setid.R +27 -0
  122. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_tic.R +23 -0
  123. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/Rscript_generic_example.R +88 -0
  124. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PEP.R +47 -0
  125. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PRT.R +104 -0
  126. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PSM.R +80 -0
  127. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/plot_trafo.R +126 -0
  128. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/THIRDPARTY/ReadMe.txt +9 -0
  129. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Hardkloer.ttd +109 -0
  130. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/LINUX/TPP_ProteinProphet.ttd +46 -0
  131. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/LINUX/mail.ttd +22 -0
  132. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/MSGFtoPercolator.ttd +30 -0
  133. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/MascotPercolator.ttd +42 -0
  134. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Percolator.ttd +29 -0
  135. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/QCExporter.ttd +51 -0
  136. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/RawDirConvert.ttd +25 -0
  137. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/ReadMe.txt +72 -0
  138. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_generic.ttd +42 -0
  139. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PEP.ttd +26 -0
  140. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PRT.ttd +26 -0
  141. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PSM.ttd +26 -0
  142. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_acc.ttd +30 -0
  143. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_idmap.ttd +33 -0
  144. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_rt_acc.ttd +30 -0
  145. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_setid.ttd +30 -0
  146. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_tic.ttd +30 -0
  147. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_trapfill.ttd +30 -0
  148. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/TEMPLATE.ttd_ +52 -0
  149. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/TPP_RefreshParser.ttd +28 -0
  150. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/WINDOWS/TPP_ProteinProphet.ttd +46 -0
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media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/PositiveAdducts.tsv ADDED
@@ -0,0 +1,33 @@
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+ M+3H;3+
2
+ M+2H+Na;3+
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+ M+H+2Na;3+
4
+ M+3Na;3+
5
+ M+2H;2+
6
+ M+H+NH4;2+
7
+ M+H+Na;2+
8
+ M+H+K;2+
9
+ M+CH3CN+2H;2+
10
+ M+2Na;2+
11
+ M+2CH3CN+2H;2+
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+ M+3CH3CN+2H;2+
13
+ M+H;1+
14
+ M;1+
15
+ M+NH4;1+
16
+ M+Na;1+
17
+ M+CH3OH+H;1+
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+ M+K;1+
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+ M+CH3CN+H;1+
20
+ M+2Na-H;1+
21
+ M+C3H8O;1+
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+ M+CH3CN+Na;1+
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+ M+2K-H;1+
24
+ M+C2H6OS;1+
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+ M+2CH3CN+H;1+
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+ M+C3H8O+Na+H;1+
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+ 2M+H;1+
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+ 2M+NH4;1+
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+ 2M+Na;1+
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+ 2M+3H2O+2H;2+
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+ 2M+K;1+
32
+ 2M+CH3CN+H;1+
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+ 2M+CH3CN+Na;1+
media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/Residues.xml ADDED
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+ <?xml version="1.0" encoding="ISO-8859-1"?>
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+ <PARAMETERS>
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+ <NODE name="Residues">
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+ <NODE name="Alanine">
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+ <ITEM name="Name" value="Alanine" type="string" />
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+ <ITEM name="ShortName" value="Ala" type="string" />
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+ <ITEM name="ThreeLetterCode" value="ALA" type="string" />
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+ <ITEM name="Formula" value="C3H7NO2" type="string" />
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+ <NODE name="Synonyms">
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+ <ITEM name="L-Alanine" value="L-Alanine" type="string" />
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+ <ITEM name="alanine" value="alanine" type="string" />
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+ <ITEM name="Alanin" value="Alanin" type="string" />
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+ <ITEM name="Ala" value="Ala" type="string" />
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+ </NODE>
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+ <NODE name="Cysteine">
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+ <ITEM name="ThreeLetterCode" value="CYS" type="string" />
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+ <ITEM name="OneLetterCode" value="C" type="string" />
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+ <ITEM name="Formula" value="C3H7NO2S" type="string" />
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+ <NODE name="Synonyms">
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+ <ITEM name="Cystine" value="Cystine" type="string" />
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+ <ITEM name="Formula" value="C4H7NO4" type="string" />
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+ <ITEM name="pkc" value="3.90" type="string" />
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+ <ITEM name="ResidueSets" value="All,Natural20,Natural19WithoutI,Natural19WithoutL,Natural19J,AmbiguousWithoutX,Ambiguous,AllNatural" type="string" />
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+ <NODE name="Synonyms">
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+ <ITEM name="Asp" value="Asp" type="string" />
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+ </NODE>
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+ <NODE name="Losses">
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+ <ITEM name="LossName" value="water" type="string" />
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+ <ITEM name="LossFormula" value="H2O" type="string" />
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+ <NODE name="Glutamate">
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+ <ITEM name="ShortName" value="Glu" type="string" />
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+ <ITEM name="Formula" value="C5H9NO4" type="string" />
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+ <ITEM name="pka" value="2.10" type="string" />
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+ <ITEM name="pkb" value="9.47" type="string" />
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+ <ITEM name="pkc" value="4.07" type="string" />
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+ <ITEM name="ResidueSets" value="All,Natural20,Natural19WithoutI,Natural19WithoutL,Natural19J,AmbiguousWithoutX,Ambiguous,AllNatural" type="string" />
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+ <NODE name="Synonyms">
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+ <ITEM name="Glu" value="Glu" type="string" />
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+ </NODE>
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+ <NODE name="Losses">
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+ <ITEM name="LossName" value="water" type="string" />
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+ <ITEM name="LossFormula" value="H2O" type="string" />
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+ </NODE>
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+ <NODE name="NTermLosses">
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+ <ITEM name="LossName" value="water" type="string" />
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+ <ITEM name="LossFormula" value="H2O" type="string" />
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+ </NODE>
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+ </NODE>
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+ <NODE name="Phenylalanine">
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+ <ITEM name="Name" value="Phenylalanine" type="string" />
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+ <ITEM name="ShortName" value="Phe" type="string" />
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+ <ITEM name="ThreeLetterCode" value="PHE" type="string" />
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+ <ITEM name="OneLetterCode" value="F" type="string" />
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+ <ITEM name="Formula" value="C9H11NO2" type="string" />
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+ <NODE name="Synonyms">
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+ <ITEM name="Phe" value="Phe" type="string" />
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+ </NODE>
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+ </NODE>
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+ <NODE name="Glycine">
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+ <ITEM name="ShortName" value="Gly" type="string" />
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+ <ITEM name="ThreeLetterCode" value="GLY" type="string" />
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+ <ITEM name="OneLetterCode" value="G" type="string" />
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+ <ITEM name="Formula" value="C2H5NO2" type="string" />
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+ <NODE name="Synonyms">
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+ <ITEM name="Gly" value="Gly" type="string" />
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+ </NODE>
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+ <NODE name="Histidine">
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+ <ITEM name="ShortName" value="His" type="string" />
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+ <ITEM name="pkc" value="6.04" type="string" />
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+ <NODE name="Synonyms">
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+ <ITEM name="His" value="His" type="string" />
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+ <NODE name="Synonyms">
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+ <ITEM name="Ile" value="Ile" type="string" />
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+ </NODE>
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+ </NODE>
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+ </NODE>
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+ <NODE name="Synonyms">
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+ <ITEM name="Leu" value="Leu" type="string" />
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+ </NODE>
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+ <ITEM name="Name" value="Methionine" type="string" />
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+ <ITEM name="pkc" value="5.73" type="string" />
298
+ <ITEM name="GB_SC" value="0.00" type="string" />
299
+ <ITEM name="GB_BB_L" value="880.99" type="string" />
300
+ <ITEM name="GB_BB_R" value="0.12" type="string" />
301
+ <ITEM name="ResidueSets" value="All,AmbiguousWithoutX,Ambiguous,AllNatural" type="string" />
302
+ <NODE name="Synonyms">
303
+ <ITEM name="Sec" value="Sec" type="string" />
304
+ </NODE>
305
+ </NODE>
306
+ <NODE name="Serine">
307
+ <ITEM name="Name" value="Serine" type="string" />
308
+ <ITEM name="ShortName" value="Ser" type="string" />
309
+ <ITEM name="ThreeLetterCode" value="SER" type="string" />
310
+ <ITEM name="OneLetterCode" value="S" type="string" />
311
+ <ITEM name="GB_SC" value="775.0" type="string" />
312
+ <ITEM name="GB_BB_L" value="881.08" type="string" />
313
+ <ITEM name="GB_BB_R" value="0.98" type="string" />
314
+ <ITEM name="Formula" value="C3H7NO3" type="string" />
315
+ <ITEM name="pka" value="2.19" type="string" />
316
+ <ITEM name="pkb" value="9.21" type="string" />
317
+ <ITEM name="ResidueSets" value="All,Natural20,Natural19WithoutI,Natural19WithoutL,Natural19J,AmbiguousWithoutX,Ambiguous,AllNatural" type="string" />
318
+ <NODE name="Synonyms">
319
+ <ITEM name="Ser" value="Ser" type="string" />
320
+ </NODE>
321
+ <NODE name="Losses">
322
+ <ITEM name="LossName" value="water" type="string" />
323
+ <ITEM name="LossFormula" value="H2O" type="string" />
324
+ </NODE>
325
+ </NODE>
326
+ <NODE name="Threonine">
327
+ <ITEM name="Name" value="Threonine" type="string" />
328
+ <ITEM name="ShortName" value="Thr" type="string" />
329
+ <ITEM name="ThreeLetterCode" value="THR" type="string" />
330
+ <ITEM name="OneLetterCode" value="T" type="string" />
331
+ <ITEM name="Formula" value="C4H9NO3" type="string" />
332
+ <ITEM name="pka" value="2.09" type="string" />
333
+ <ITEM name="pkb" value="9.10" type="string" />
334
+ <ITEM name="GB_SC" value="780.0" type="string" />
335
+ <ITEM name="GB_BB_L" value="881.14" type="string" />
336
+ <ITEM name="GB_BB_R" value="1.21" type="string" />
337
+ <ITEM name="ResidueSets" value="All,Natural20,Natural19WithoutI,Natural19WithoutL,Natural19J,AmbiguousWithoutX,Ambiguous,AllNatural" type="string" />
338
+ <NODE name="Synonyms">
339
+ <ITEM name="Thr" value="Thr" type="string" />
340
+ </NODE>
341
+ <NODE name="Losses">
342
+ <ITEM name="LossName" value="water" type="string" />
343
+ <ITEM name="LossFormula" value="H2O" type="string" />
344
+ </NODE>
345
+ </NODE>
346
+ <NODE name="Valine">
347
+ <ITEM name="Name" value="Valine" type="string" />
348
+ <ITEM name="ShortName" value="Val" type="string" />
349
+ <ITEM name="ThreeLetterCode" value="VAL" type="string" />
350
+ <ITEM name="OneLetterCode" value="V" type="string" />
351
+ <ITEM name="Formula" value="C5H11NO2" type="string" />
352
+ <ITEM name="pka" value="2.39" type="string" />
353
+ <ITEM name="pkb" value="9.74" type="string" />
354
+ <ITEM name="GB_SC" value="0.0" type="string" />
355
+ <ITEM name="GB_BB_L" value="881.17" type="string" />
356
+ <ITEM name="GB_BB_R" value="-0.90" type="string" />
357
+ <ITEM name="ResidueSets" value="All,Natural20,Natural19WithoutI,Natural19WithoutL,Natural19J,AmbiguousWithoutX,Ambiguous,AllNatural" type="string" />
358
+ <NODE name="Synonyms">
359
+ <ITEM name="Val" value="Val" type="string" />
360
+ </NODE>
361
+ </NODE>
362
+ <NODE name="Tryptophan">
363
+ <ITEM name="Name" value="Tryptophan" type="string" />
364
+ <ITEM name="ShortName" value="Trp" type="string" />
365
+ <ITEM name="ThreeLetterCode" value="TRP" type="string" />
366
+ <ITEM name="OneLetterCode" value="W" type="string" />
367
+ <ITEM name="Formula" value="C11H12N2O2" type="string" />
368
+ <ITEM name="pka" value="2.46" type="string" />
369
+ <ITEM name="pkb" value="9.41" type="string" />
370
+ <ITEM name="GB_SC" value="909.53" type="string" />
371
+ <ITEM name="GB_BB_L" value="881.31" type="string" />
372
+ <ITEM name="GB_BB_R" value="0.10" type="string" />
373
+ <ITEM name="ResidueSets" value="All,Natural20,Natural19WithoutI,Natural19WithoutL,Natural19J,AmbiguousWithoutX,Ambiguous,AllNatural" type="string" />
374
+ <NODE name="Synonyms">
375
+ <ITEM name="Trp" value="Trp" type="string" />
376
+ </NODE>
377
+ </NODE>
378
+ <NODE name="Tyrosine">
379
+ <ITEM name="Name" value="Tyrosine" type="string" />
380
+ <ITEM name="ShortName" value="Tyr" type="string" />
381
+ <ITEM name="ThreeLetterCode" value="TYR" type="string" />
382
+ <ITEM name="OneLetterCode" value="Y" type="string" />
383
+ <ITEM name="Formula" value="C9H11NO3" type="string" />
384
+ <ITEM name="pka" value="2.20" type="string" />
385
+ <ITEM name="pkb" value="9.21" type="string" />
386
+ <ITEM name="pkc" value="10.46" type="string" />
387
+ <ITEM name="GB_SC" value="790.0" type="string" />
388
+ <ITEM name="GB_BB_L" value="881.20" type="string" />
389
+ <ITEM name="GB_BB_R" value="-0.38" type="string" />
390
+ <ITEM name="ResidueSets" value="All,Natural20,Natural19WithoutI,Natural19WithoutL,Natural19J,AmbiguousWithoutX,Ambiguous,AllNatural" type="string" />
391
+ <NODE name="Synonyms">
392
+ <ITEM name="Tyr" value="Tyr" type="string" />
393
+ </NODE>
394
+ </NODE>
395
+ <NODE name="Pyrrolysine">
396
+ <ITEM name="Name" value="Pyrrolysine" type="string" />
397
+ <ITEM name="ShortName" value="Pyr" type="string" />
398
+ <ITEM name="ThreeLetterCode" value="PYR" type="string" />
399
+ <ITEM name="OneLetterCode" value="O" type="string" />
400
+ <ITEM name="Formula" value="C12H21N3O3" type="string" />
401
+ <ITEM name="pka" value="0.0" type="string" />
402
+ <ITEM name="pkb" value="0.0" type="string" />
403
+ <ITEM name="pkc" value="0.0" type="string" />
404
+ <ITEM name="GB_SC" value="0.0" type="string" />
405
+ <ITEM name="GB_BB_L" value="0.0" type="string" />
406
+ <ITEM name="GB_BB_R" value="0.0" type="string" />
407
+ <ITEM name="ResidueSets" value="All,AmbiguousWithoutX,Ambiguous,AllNatural" type="string" />
408
+ <NODE name="Synonyms">
409
+ <ITEM name="Pyr" value="Pyr" type="string" />
410
+ </NODE>
411
+ </NODE>
412
+ <NODE name="Ambiguous_ASN_or_ASP" >
413
+ <ITEM name="Name" value="Asparagine/Aspartate" type="string" />
414
+ <ITEM name="ShortName" value="Asx" type="string" />
415
+ <ITEM name="ThreeLetterCode" value="ASX" type="string" />
416
+ <ITEM name="OneLetterCode" value="B" type="string" />
417
+ <ITEM name="Formula" value="" type="string" />
418
+ <ITEM name="GB_SC" value="0" type="string" />
419
+ <ITEM name="GB_BB_L" value="0" type="string" />
420
+ <ITEM name="GB_BB_R" value="0" type="string" />
421
+ <ITEM name="ResidueSets" value="All,AmbiguousWithoutX,Ambiguous" type="string" />
422
+ <NODE name="Synonyms">
423
+ <ITEM name="Asx" value="Asx" type="string" />
424
+ </NODE>
425
+ </NODE>
426
+ <NODE name="Ambiguous_GLN_or_GLU" >
427
+ <ITEM name="Name" value="Glutamine/Glutamate" type="string" />
428
+ <ITEM name="ShortName" value="Glx" type="string" />
429
+ <ITEM name="ThreeLetterCode" value="GLX" type="string" />
430
+ <ITEM name="OneLetterCode" value="Z" type="string" />
431
+ <ITEM name="Formula" value="" type="string" />
432
+ <ITEM name="GB_SC" value="0" type="string" />
433
+ <ITEM name="GB_BB_L" value="0" type="string" />
434
+ <ITEM name="GB_BB_R" value="0" type="string" />
435
+ <ITEM name="ResidueSets" value="All,AmbiguousWithoutX,Ambiguous" type="string" />
436
+ <NODE name="Synonyms">
437
+ <ITEM name="Glx" value="Glx" type="string" />
438
+ </NODE>
439
+ </NODE>
440
+ <NODE name="Ambiguous_ILE_or_LEU" >
441
+ <ITEM name="Name" value="Isoleucine/Leucine" type="string" />
442
+ <ITEM name="ShortName" value="Xle" type="string" />
443
+ <ITEM name="ThreeLetterCode" value="XLE" type="string" />
444
+ <ITEM name="OneLetterCode" value="J" type="string" />
445
+ <ITEM name="Formula" value="C6H13NO2" type="string" />
446
+ <ITEM name="GB_SC" value="0" type="string" />
447
+ <ITEM name="GB_BB_L" value="880.99" type="string" />
448
+ <ITEM name="GB_BB_R" value="-1.17" type="string" />
449
+ <ITEM name="ResidueSets" value="All,AmbiguousWithoutX,Ambiguous" type="string" />
450
+ <NODE name="Synonyms">
451
+ <ITEM name="Xle" value="Xle" type="string" />
452
+ </NODE>
453
+ </NODE>
454
+ <NODE name="Ambiguous_Unspecified_or_Unknown" >
455
+ <ITEM name="Name" value="Unspecified/Unknown" type="string" />
456
+ <ITEM name="ShortName" value="Xaa" type="string" />
457
+ <ITEM name="ThreeLetterCode" value="XAA" type="string" />
458
+ <ITEM name="OneLetterCode" value="X" type="string" />
459
+ <ITEM name="Formula" value="" type="string" />
460
+ <ITEM name="GB_SC" value="0" type="string" />
461
+ <ITEM name="GB_BB_L" value="0" type="string" />
462
+ <ITEM name="GB_BB_R" value="0" type="string" />
463
+ <ITEM name="ResidueSets" value="All,Ambiguous" type="string" />
464
+ <NODE name="Synonyms">
465
+ <ITEM name="Xaa" value="Xaa" type="string" />
466
+ <ITEM name="Unk" value="Unk" type="string" />
467
+ </NODE>
468
+ </NODE>
469
+ </NODE>
470
+ </PARAMETERS>