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/Enzymes.xml ADDED
@@ -0,0 +1,269 @@
1
+ <?xml version="1.0" encoding="ISO-8859-1"?>
2
+ <PARAMETERS>
3
+ <NODE name="Enzymes">
4
+ <NODE name="Trypsin">
5
+ <ITEM name="Name" value="Trypsin" type="string" />
6
+ <ITEM name="RegEx" value="(?&lt;=[KR])(?!P)" type="string" />
7
+ <ITEM name="RegExDescription" value="Trypsin cleaves following a K or R residue unless the next residue is P." type="string" />
8
+ <ITEM name="NTermGain" value="H" type="string" />
9
+ <ITEM name="CTermGain" value="OH" type="string" />
10
+ <ITEM name="PSIID" value="MS:1001251" type="string" />
11
+ <ITEM name="XTandemID" value="[KR]|{P}" type="string" />
12
+ <ITEM name="OMSSAID" value="0" type="int" />
13
+ <ITEM name="CometID" value="1" type="int" />
14
+ </NODE>
15
+ <NODE name="Arg-C">
16
+ <ITEM name="Name" value="Arg-C" type="string" />
17
+ <ITEM name="RegEx" value="(?&lt;=R)(?!P)" type="string" />
18
+ <ITEM name="RegExDescription" value="Arg-C cleaves following R residue unless the next residue is P." type="string" />
19
+ <ITEM name="NTermGain" value="H" type="string" />
20
+ <ITEM name="CTermGain" value="OH" type="string" />
21
+ <ITEM name="PSIID" value="MS:1001303" type="string" />
22
+ <ITEM name="XTandemID" value="[R]|{P}" type="string" />
23
+ <ITEM name="OMSSAID" value="1" type="int" />
24
+ <ITEM name="CometID" value="5" type="int" />
25
+ <NODE name="Synonyms">
26
+ <ITEM name="Clostripain" value="Clostripain" type="string" />
27
+ <ITEM name="argc" value="argc" type="string" />
28
+ </NODE>
29
+ </NODE>
30
+ <NODE name="Arg-C/P">
31
+ <ITEM name="Name" value="Arg-C/P" type="string" />
32
+ <ITEM name="RegEx" value="(?&lt;=R)" type="string" />
33
+ <ITEM name="RegExDescription" value="Arg-C/P cleaves after R residues." type="string" />
34
+ <ITEM name="NTermGain" value="H" type="string" />
35
+ <ITEM name="CTermGain" value="OH" type="string" />
36
+ <ITEM name="XTandemID" value="[R]|[X]" type="string" />
37
+ <ITEM name="MSGFID" value="6" type="int" />
38
+ </NODE>
39
+ <NODE name="Asp-N">
40
+ <ITEM name="Name" value="Asp-N" type="string" />
41
+ <ITEM name="RegEx" value="(?=[BD])" type="string" />
42
+ <ITEM name="RegExDescription" value="Asp-N cleaves before B or D." type="string" />
43
+ <ITEM name="NTermGain" value="H" type="string" />
44
+ <ITEM name="CTermGain" value="OH" type="string" />
45
+ <ITEM name="PSIID" value="MS:1001304" type="string" />
46
+ <ITEM name="XTandemID" value="[X]|[BD]" type="string" />
47
+ <ITEM name="OMSSAID" value="12" type="int" />
48
+ <ITEM name="CometID" value="6" type="int" />
49
+ </NODE>
50
+ <NODE name="Asp-N/B">
51
+ <ITEM name="Name" value="Asp-N/B" type="string" />
52
+ <ITEM name="RegEx" value="(?=[D])" type="string" />
53
+ <ITEM name="RegExDescription" value="Asp-N/B cleaves before D." type="string" />
54
+ <ITEM name="NTermGain" value="H" type="string" />
55
+ <ITEM name="CTermGain" value="OH" type="string" />
56
+ <ITEM name="XTandemID" value="[X]|[D]" type="string" />
57
+ <ITEM name="MSGFID" value="7" type="int" />
58
+ </NODE>
59
+ <NODE name="Asp-N_ambic">
60
+ <ITEM name="Name" value="Asp-N_ambic" type="string" />
61
+ <ITEM name="RegEx" value="(?=[DE])" type="string" />
62
+ <ITEM name="RegExDescription" value="Asp-N Ammonium bicarbonate cleaves before D or E." type="string" />
63
+ <ITEM name="NTermGain" value="H" type="string" />
64
+ <ITEM name="CTermGain" value="OH" type="string" />
65
+ <ITEM name="PSIID" value="MS:1001305" type="string" />
66
+ <ITEM name="XTandemID" value="[X]|[DE]" type="string" />
67
+ <ITEM name="OMSSAID" value="19" type="int" />
68
+ </NODE>
69
+ <NODE name="Chymotrypsin">
70
+ <ITEM name="Name" value="Chymotrypsin" type="string" />
71
+ <ITEM name="RegEx" value="(?&lt;=[FLWY])(?!P)" type="string" />
72
+ <ITEM name="RegExDescription" value="Chymotrypsin cleaves following F, Y, W or L residue unless the next residue is P." type="string" />
73
+ <ITEM name="NTermGain" value="H" type="string" />
74
+ <ITEM name="CTermGain" value="OH" type="string" />
75
+ <ITEM name="PSIID" value="MS:1001306" type="string" />
76
+ <ITEM name="XTandemID" value="[FYWL]|{P}" type="string" />
77
+ <ITEM name="OMSSAID" value="3" type="int" />
78
+ <ITEM name="CometID" value="10" type="int" />
79
+ </NODE>
80
+ <NODE name="Chymotrypsin/P">
81
+ <ITEM name="Name" value="Chymotrypsin/P" type="string" />
82
+ <ITEM name="RegEx" value="(?&lt;=[FLWY])" type="string" />
83
+ <ITEM name="RegExDescription" value="Chymotrypsin cleaves following F, Y, W or L residue." type="string" />
84
+ <ITEM name="NTermGain" value="H" type="string" />
85
+ <ITEM name="CTermGain" value="OH" type="string" />
86
+ <ITEM name="XTandemID" value="[FYWL]|[X]" type="string" />
87
+ <ITEM name="MSGFID" value="2" type="int" />
88
+ </NODE>
89
+ <NODE name="CNBr">
90
+ <ITEM name="Name" value="CNBr" type="string" />
91
+ <ITEM name="RegEx" value="(?&lt;=M)" type="string" />
92
+ <ITEM name="RegExDescription" value="CNBr cleaves following M." type="string" />
93
+ <ITEM name="NTermGain" value="H" type="string" />
94
+ <ITEM name="CTermGain" value="OH" type="string" />
95
+ <ITEM name="PSIID" value="MS:1001307" type="string" />
96
+ <ITEM name="XTandemID" value="[M]|[X]" type="string" />
97
+ <ITEM name="OMSSAID" value="2" type="int" />
98
+ <ITEM name="CometID" value="7" type="int" />
99
+ </NODE>
100
+ <NODE name="Formic_acid">
101
+ <ITEM name="Name" value="Formic_acid" type="string" />
102
+ <ITEM name="RegEx" value="((?&lt;=D))|((?=D))" type="string" />
103
+ <ITEM name="RegExDescription" value="Formic_acid cuts after D and next residue is D." type="string" />
104
+ <ITEM name="NTermGain" value="H" type="string" />
105
+ <ITEM name="CTermGain" value="OH" type="string" />
106
+ <ITEM name="PSIID" value="MS:1001308" type="string" />
107
+ <ITEM name="XTandemID" value="[D]|[D]" type="string" />
108
+ <ITEM name="OMSSAID" value="4" type="int" />
109
+ </NODE>
110
+ <NODE name="Lys-C">
111
+ <ITEM name="Name" value="Lys-C" type="string" />
112
+ <ITEM name="RegEx" value="(?&lt;=K)(?!P)" type="string" />
113
+ <ITEM name="RegExDescription" value="Lys-C cuts after K if not followed by P." type="string" />
114
+ <ITEM name="NTermGain" value="H" type="string" />
115
+ <ITEM name="CTermGain" value="OH" type="string" />
116
+ <ITEM name="PSIID" value="MS:1001309" type="string" />
117
+ <ITEM name="XTandemID" value="[K]|{P}" type="string" />
118
+ <ITEM name="OMSSAID" value="5" type="int" />
119
+ <ITEM name="CometID" value="3" type="int" />
120
+ </NODE>
121
+ <NODE name="Lys-N">
122
+ <ITEM name="Name" value="Lys-N" type="string" />
123
+ <ITEM name="RegEx" value="(?=K)" type="string" />
124
+ <ITEM name="RegExDescription" value="Lys-N cuts before K" type="string" />
125
+ <ITEM name="NTermGain" value="H" type="string" />
126
+ <ITEM name="CTermGain" value="OH" type="string" />
127
+ <ITEM name="PSIID" value="" type="string" />
128
+ <ITEM name="XTandemID" value="[X]|[K]" type="string" />
129
+ <ITEM name="CometID" value="4" type="int" />
130
+ <ITEM name="MSGFID" value="4" type="int" />
131
+ </NODE>
132
+ <NODE name="Lys-C/P">
133
+ <ITEM name="Name" value="Lys-C/P" type="string" />
134
+ <ITEM name="RegEx" value="(?&lt;=K)" type="string" />
135
+ <ITEM name="RegExDescription" value="Lys-C/P cuts after K." type="string" />
136
+ <ITEM name="NTermGain" value="H" type="string" />
137
+ <ITEM name="CTermGain" value="OH" type="string" />
138
+ <ITEM name="PSIID" value="MS:1001310" type="string" />
139
+ <ITEM name="XTandemID" value="[K]|[X]" type="string" />
140
+ <ITEM name="OMSSAID" value="6" type="int" />
141
+ <ITEM name="MSGFID" value="3" type="int" />
142
+ </NODE>
143
+ <NODE name="PepsinA">
144
+ <ITEM name="Name" value="PepsinA" type="string" />
145
+ <ITEM name="RegEx" value="(?&lt;=[FL])" type="string" />
146
+ <ITEM name="RegExDescription" value="PepsinA cuts after F or L." type="string" />
147
+ <ITEM name="NTermGain" value="H" type="string" />
148
+ <ITEM name="CTermGain" value="OH" type="string" />
149
+ <ITEM name="PSIID" value="MS:1001311" type="string" />
150
+ <ITEM name="XTandemID" value="[FL]|[X]" type="string" />
151
+ <ITEM name="OMSSAID" value="7" type="int" />
152
+ <ITEM name="CometID" value="9" type="int" />
153
+ </NODE>
154
+ <NODE name="TrypChymo">
155
+ <ITEM name="Name" value="TrypChymo" type="string" />
156
+ <ITEM name="RegEx" value="(?&lt;=[KRFLWY])(?!P)" type="string" />
157
+ <ITEM name="RegExDescription" value="TrypChymo cuts after F, Y, W, L, K or R if not followed by P." type="string" />
158
+ <ITEM name="NTermGain" value="H" type="string" />
159
+ <ITEM name="CTermGain" value="OH" type="string" />
160
+ <ITEM name="PSIID" value="MS:1001312" type="string" />
161
+ <ITEM name="XTandemID" value="[FYWLKR]|{P}" type="string" />
162
+ <ITEM name="OMSSAID" value="9" type="int" />
163
+ </NODE>
164
+ <NODE name="Trypsin/P">
165
+ <ITEM name="Name" value="Trypsin/P" type="string" />
166
+ <ITEM name="RegEx" value="(?&lt;=[KR])" type="string" />
167
+ <ITEM name="RegExDescription" value="Trypsin/P cuts after K or R." type="string" />
168
+ <ITEM name="NTermGain" value="H" type="string" />
169
+ <ITEM name="CTermGain" value="OH" type="string" />
170
+ <ITEM name="PSIID" value="MS:1001313" type="string" />
171
+ <ITEM name="XTandemID" value="[KR]|[X]" type="string" />
172
+ <ITEM name="OMSSAID" value="10" type="int" />
173
+ <ITEM name="CometID" value="2" type="int" />
174
+ <ITEM name="MSGFID" value="1" type="int" />
175
+ </NODE>
176
+ <NODE name="V8-DE">
177
+ <ITEM name="Name" value="V8-DE" type="string" />
178
+ <ITEM name="RegEx" value="(?&lt;=[BDEZ])(?!P)" type="string" />
179
+ <ITEM name="RegExDescription" value="V8-DE cuts after B, D, E or Z if not followed by P." type="string" />
180
+ <ITEM name="NTermGain" value="H" type="string" />
181
+ <ITEM name="CTermGain" value="OH" type="string" />
182
+ <ITEM name="PSIID" value="MS:1001314" type="string" />
183
+ <ITEM name="XTandemID" value="[BDEZ]|{P}" type="string" />
184
+ </NODE>
185
+ <NODE name="V8-E">
186
+ <ITEM name="Name" value="V8-E" type="string" />
187
+ <ITEM name="RegEx" value="(?&lt;=[EZ])(?!P)" type="string" />
188
+ <ITEM name="RegExDescription" value="V8-E cuts after E or Z if not followed by P." type="string" />
189
+ <ITEM name="NTermGain" value="H" type="string" />
190
+ <ITEM name="CTermGain" value="OH" type="string" />
191
+ <ITEM name="PSIID" value="MS:1001315" type="string" />
192
+ <ITEM name="XTandemID" value="[EZ]|{P}" type="string" />
193
+ </NODE>
194
+ <NODE name="leukocyte elastase">
195
+ <ITEM name="Name" value="leukocyte elastase" type="string" />
196
+ <ITEM name="RegEx" value="(?&lt;=[AILV])(?!P)" type="string" />
197
+ <ITEM name="RegExDescription" value="leukocyte elastase cuts after A, L, I or V if not followed by P." type="string" />
198
+ <ITEM name="NTermGain" value="H" type="string" />
199
+ <ITEM name="CTermGain" value="OH" type="string" />
200
+ <ITEM name="PSIID" value="MS:1001915" type="string" />
201
+ <ITEM name="XTandemID" value="[ALIV]|{P}" type="string" />
202
+ </NODE>
203
+ <NODE name="proline endopeptidase">
204
+ <ITEM name="Name" value="proline endopeptidase" type="string" />
205
+ <ITEM name="RegEx" value="(?&lt;=[HKR]P)(?!P)" type="string" />
206
+ <ITEM name="RegExDescription" value="proline endopeptidase cuts after HP, KP or RP if not followed by P." type="string" />
207
+ <ITEM name="NTermGain" value="H" type="string" />
208
+ <ITEM name="CTermGain" value="OH" type="string" />
209
+ <ITEM name="PSIID" value="MS:1001916" type="string" />
210
+ </NODE>
211
+ <NODE name="glutamyl endopeptidase">
212
+ <ITEM name="Name" value="glutamyl endopeptidase" type="string" />
213
+ <ITEM name="RegEx" value="(?&lt;=[DE])" type="string" />
214
+ <ITEM name="RegExDescription" value="glutamyl endopeptidase cuts after D or E." type="string" />
215
+ <ITEM name="NTermGain" value="H" type="string" />
216
+ <ITEM name="CTermGain" value="OH" type="string" />
217
+ <ITEM name="PSIID" value="MS:1001917" type="string" />
218
+ <ITEM name="XTandemID" value="[DE]|[X]" type="string" />
219
+ <ITEM name="OMSSAID" value="20" type="int" />
220
+ <ITEM name="CometID" value="8" type="int" />
221
+ <ITEM name="MSGFID" value="5" type="int" />
222
+ <NODE name="Synonyms">
223
+ <ITEM name="Glu-C" value="Glu-C" type="string" />
224
+ <ITEM name="staphylococcal protease" value="staphylococcal protease" type="string" />
225
+ </NODE>
226
+ </NODE>
227
+ <NODE name="alphaLP">
228
+ <ITEM name="Name" value="Alpha-lytic protease" type="string" />
229
+ <ITEM name="RegEx" value="(?&lt;=[TASV])" type="string" />
230
+ <ITEM name="RegExDescription" value="Alpha-lytic protease (aLP) cuts after T, A, S, and V." type="string" />
231
+ <ITEM name="NTermGain" value="H" type="string" />
232
+ <ITEM name="CTermGain" value="OH" type="string" />
233
+ <ITEM name="XTandemID" value="[ASTV]|[X]" type="string" />
234
+ <ITEM name="MSGFID" value="8" type="int" />
235
+ </NODE>
236
+ <NODE name="2-iodobenzoate">
237
+ <ITEM name="Name" value="2-iodobenzoate" type="string" />
238
+ <ITEM name="RegEx" value="(?&lt;=W)" type="string" />
239
+ <ITEM name="RegExDescription" value="2-iodobenzoate cuts after W." type="string" />
240
+ <ITEM name="NTermGain" value="H" type="string" />
241
+ <ITEM name="CTermGain" value="OH" type="string" />
242
+ <ITEM name="PSIID" value="MS:1001918" type="string" />
243
+ <ITEM name="XTandemID" value="[W]|[X]" type="string" />
244
+ </NODE>
245
+ <NODE name="no cleavage">
246
+ <ITEM name="Name" value="no cleavage" type="string" />
247
+ <ITEM name="RegEx" value="()" type="string" />
248
+ <ITEM name="RegExDescription" value="no cleavage." type="string" />
249
+ <ITEM name="NTermGain" value="H" type="string" />
250
+ <ITEM name="CTermGain" value="OH" type="string" />
251
+ <ITEM name="PSIID" value="MS:1001955" type="string" />
252
+ <ITEM name="XTandemID" value="" type="string" />
253
+ <ITEM name="OMSSAID" value="11" type="int" />
254
+ <ITEM name="MSGFID" value="9" type="int" />
255
+ </NODE>
256
+ <NODE name="unspecific cleavage">
257
+ <ITEM name="Name" value="unspecific cleavage" type="string" />
258
+ <ITEM name="RegEx" value="(?&lt;=[A-Z])" type="string" />
259
+ <ITEM name="RegExDescription" value="unspecific cleavage cuts at every site." type="string" />
260
+ <ITEM name="NTermGain" value="H" type="string" />
261
+ <ITEM name="CTermGain" value="OH" type="string" />
262
+ <ITEM name="PSIID" value="MS:1001956" type="string" />
263
+ <ITEM name="XTandemID" value="[X]|[X]" type="string" />
264
+ <ITEM name="OMSSAID" value="17" type="int" />
265
+ <ITEM name="CometID" value="0" type="int" />
266
+ <ITEM name="MSGFID" value="0" type="int" />
267
+ </NODE>
268
+ </NODE>
269
+ </PARAMETERS>