pyopenms 2.3.0__zip

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/sysinfo.py

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+import sys
+
+if sys.platform.startswith("linux"):
+    import ctypes as c
+    import ctypes.util
+
+    libc = c.CDLL(ctypes.util.find_library("c"))
+
+    class SysInfo(c.Structure):
+
+         # for libc5: needs padding
+        padding = 20 - 2 * c.sizeof(c.c_long) - c.sizeof(c.c_int)
+
+        _fields_ = [("uptime", c.c_ulong),
+                    ("loads", 3 * c.c_ulong),
+                    ("totalram", c.c_ulong),
+                    ("freeram", c.c_ulong),
+                    ("sharedram", c.c_ulong),
+                    ("bufferram", c.c_ulong),
+                    ("totalswap", c.c_ulong),
+                    ("freeswap", c.c_ulong),
+                    ("procs", c.c_ushort),
+                    ("totalhigh", c.c_ulong),
+                    ("freehigh", c.c_ulong),
+                    ("mem_unit", c.c_ulong),
+                    ("_padding", padding * c.c_char)
+        ]
+
+    def free_mem():
+        sys_info = SysInfo()
+        libc.sysinfo(c.byref(sys_info))
+        return sys_info.freeram
+
+elif sys.platform == "win32":
+    try:
+        import win32api
+    except:
+        free_mem = lambda: 0 # memory will never change !
+    else:
+        def free_mem():
+            return win32api.GlobalMemoryStatus()['AvailPhys']
+
+else:
+    sys.stderr.write("Determination of memory status is not supported on this \n"
+                     " platform, measuring for memoryleaks will never fail\n")
+
+    free_mem = lambda: 0 # memory will never change !

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/version.py

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+version='2.3.0'

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/PKG-INFO

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+Metadata-Version: 1.1
+Name: pyopenms
+Version: 2.3.0
+Summary: Python wrapper for C++ LCMS library OpenMS
+Home-page: http://open-ms.de
+Author: Uwe Schmitt
+Author-email: uschmitt@mineway.de
+License: http://opensource.org/licenses/BSD-3-Clause
+Description-Content-Type: UNKNOWN
+Description: 
+        .. contents:: **Table of Contents**
+        
+        ------------
+        Introduction
+        ------------
+        
+        This package contains Python bindings for a large part of the OpenMS library
+        (http://www.openms.org) for mass spectrometry based proteomics.  It thus
+        provides providing facile access to a feature-rich, open-source algorithm
+        library for mass-spectrometry based proteomics analysis. These Python bindings
+        allow raw access to the data-structures and algorithms implemented in OpenMS,
+        specifically those for file access (mzXML, mzML, TraML, mzIdentML among
+        others), basic signal processing (smoothing, filtering, de-isotoping and
+        peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and
+        SWATH analysis tools).
+        
+        The pyOpenMS package runs - like OpenMS - on Windows, Linux and OSX.
+        
+        -----------
+        Publication
+        -----------
+        
+        The pyOpenMS bindings are described in the following publication:
+        
+          Rost HL, Schmitt U, Aebersold R and Malmstrom L.
+          pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.
+          Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246.
+        
+        Please also check `the pyOpenMS homepage`_ for updates and links.
+        
+        ------------
+        Installation
+        ------------
+        
+        We provide binary packages for Python 3.4, 3.5 and 3.6 on Windows (64 bit) and
+        Linux (64 bit) as well as Python 2.7 for Linux, which makes the installation
+        very straightforward with pip.  For other platforms, please refer to the
+        compilation instructions.
+        
+        Binary installation
+        ===================
+        
+        The current binaries require numpy **1.7.x**.  As we distribute the package as
+        binary wheels, you should use *pip* for installation::
+        
+            $ pip install pyopenms
+        
+        Source installation
+        ===================
+        
+        Please use the `the pyOpenMS homepage`_ for instructions on how to build pyOpenMS yourself.
+        
+        ---------------------
+        Questions and Support
+        ---------------------
+        
+        For questions and feature requests, please use `the OpenMS github page`_ which
+        contains a bug tracker, a wiki and describes multiple ways to contact the
+        developers.
+        
+        ------------
+        Testing
+        ------------
+        
+        pyOpenMS provides unittests, they are found under ./pyOpenMS/tests/ and can be
+        executed using nosetests::
+        
+            $ python run_nose.py
+        
+        ------------
+        License
+        ------------
+        
+        pyOpenMS is published under the 3-clause BSD licence, see ./pyOpenMS/License.txt
+        
+        -------------
+        Documentation
+        -------------
+        
+        pyOpenMS follows the `OpenMS documentation`_ very closely. Additionally, there is also a `pyOpenMS
+        Manual <http://proteomics.ethz.ch/pyOpenMS_Manual.pdf>`_ available. The online
+        manual contains a complete record of every wrapped class and function while the
+        documentation of the corresponding class or function can be inferred from the
+        OpenMS online documentation.
+        
+        
+        
+        .. _the pyOpenMS homepage: https://github.com/OpenMS/OpenMS/wiki/pyOpenMS
+        .. _the OpenMS documentation: http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html
+        .. _the OpenMS github page: https://github.com/OpenMS/OpenMS/
+        
+        
+Platform: any
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/SOURCES.txt

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+MANIFEST.in
+README.rst
+setup.py
+pyopenms/License.txt
+pyopenms/__init__.py
+pyopenms/all_modules.py
+pyopenms/docompile.py
+pyopenms/libOpenMS.so
+pyopenms/libOpenSwathAlgo.so
+pyopenms/libSuperHirn.so
+pyopenms/python_extras.py
+pyopenms/qt_version_info.py
+pyopenms/sysinfo.py
+pyopenms/version.py
+pyopenms.egg-info/PKG-INFO
+pyopenms.egg-info/SOURCES.txt
+pyopenms.egg-info/dependency_links.txt
+pyopenms.egg-info/not-zip-safe
+pyopenms.egg-info/top_level.txt
+pyopenms/share/OpenMS/CHEMISTRY/Elements.xml
+pyopenms/share/OpenMS/CHEMISTRY/Enzymes.xml
+pyopenms/share/OpenMS/CHEMISTRY/HMDBMappingFile.tsv
+pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModel.scale
+pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModel.svm
+pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised2.scale
+pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised2.svm
+pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised5.scale
+pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised5.svm
+pyopenms/share/OpenMS/CHEMISTRY/MissedCleavage.model
+pyopenms/share/OpenMS/CHEMISTRY/NegativeAdducts.tsv
+pyopenms/share/OpenMS/CHEMISTRY/OMSSA_modification_mapping
+pyopenms/share/OpenMS/CHEMISTRY/PSI-MOD.obo
+pyopenms/share/OpenMS/CHEMISTRY/PositiveAdducts.tsv
+pyopenms/share/OpenMS/CHEMISTRY/Residues.xml
+pyopenms/share/OpenMS/CHEMISTRY/XLMOD.obo
+pyopenms/share/OpenMS/CHEMISTRY/XTandem_default_input.xml
+pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
+pyopenms/share/OpenMS/CV/brenda.obo
+pyopenms/share/OpenMS/CV/goslim_goa.obo
+pyopenms/share/OpenMS/CV/psi-ms.obo
+pyopenms/share/OpenMS/CV/psi-mzdata.obo
+pyopenms/share/OpenMS/CV/qc-cv.obo
+pyopenms/share/OpenMS/CV/quality.obo
+pyopenms/share/OpenMS/CV/unimod.obo
+pyopenms/share/OpenMS/CV/unit.obo
+pyopenms/share/OpenMS/DESKTOP/TOPPAS.appdata.xml
+pyopenms/share/OpenMS/DESKTOP/TOPPAS.desktop
+pyopenms/share/OpenMS/DESKTOP/TOPPView.appdata.xml
+pyopenms/share/OpenMS/DESKTOP/TOPPView.desktop
+pyopenms/share/OpenMS/DESKTOP/readme.txt
+pyopenms/share/OpenMS/GUISTYLE/qtStyleSheet.qss
+pyopenms/share/OpenMS/IDPool/IDPool.txt
+pyopenms/share/OpenMS/IDPool/README
+pyopenms/share/OpenMS/MAPPING/TraML-mapping.xml
+pyopenms/share/OpenMS/MAPPING/ms-mapping.xml
+pyopenms/share/OpenMS/MAPPING/mzIdentML-mapping.xml
+pyopenms/share/OpenMS/MAPPING/mzdata-mapping.xml
+pyopenms/share/OpenMS/PIP/codebooks.data
+pyopenms/share/OpenMS/PIP/linearMapping.data
+pyopenms/share/OpenMS/SCHEMAS/CTD_0_3.xsd
+pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_0.xsd
+pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_1.xsd
+pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_2.xsd
+pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_3.xsd
+pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_4.xsd
+pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_5.xsd
+pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_6.xsd
+pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_7.xsd
+pyopenms/share/OpenMS/SCHEMAS/CvMapping.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_0.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_1.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_2.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_3.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_4.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_5.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_6.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_7.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_8.xsd
+pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_9.xsd
+pyopenms/share/OpenMS/SCHEMAS/FuGElightv1.0.0.xsd
+pyopenms/share/OpenMS/SCHEMAS/IdXML_1_0.xsd
+pyopenms/share/OpenMS/SCHEMAS/IdXML_1_1.xsd
+pyopenms/share/OpenMS/SCHEMAS/IdXML_1_2.xsd
+pyopenms/share/OpenMS/SCHEMAS/IdXML_1_3.xsd
+pyopenms/share/OpenMS/SCHEMAS/IdXML_1_4.xsd
+pyopenms/share/OpenMS/SCHEMAS/IdXML_1_5.xsd
+pyopenms/share/OpenMS/SCHEMAS/Param_1_0.xsd
+pyopenms/share/OpenMS/SCHEMAS/Param_1_1.xsd
+pyopenms/share/OpenMS/SCHEMAS/Param_1_2.xsd
+pyopenms/share/OpenMS/SCHEMAS/Param_1_3.xsd
+pyopenms/share/OpenMS/SCHEMAS/Param_1_4.xsd
+pyopenms/share/OpenMS/SCHEMAS/Param_1_6_2.xsd
+pyopenms/share/OpenMS/SCHEMAS/ToolDescriptor_1_0.xsd
+pyopenms/share/OpenMS/SCHEMAS/TraML0.9.3.xsd
+pyopenms/share/OpenMS/SCHEMAS/TraML1.0.0.xsd
+pyopenms/share/OpenMS/SCHEMAS/TrafoXML_1_0.xsd
+pyopenms/share/OpenMS/SCHEMAS/general_types_1.0.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzData_1_05.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzIdentML1.0.0.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzIdentML1.1.0.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzML_1_00.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzML_1_10.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzML_idx_1_00.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzML_idx_1_10.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzQCML_0_0_5.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzQuantML_1_0_0-rc2.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzXML_2_1.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzXML_3.1.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzXML_3.1_mod.xsd
+pyopenms/share/OpenMS/SCHEMAS/mzXML_idx_3.1.xsd
+pyopenms/share/OpenMS/SCHEMAS/pepXML_v114.xsd
+pyopenms/share/OpenMS/SCHEMAS/protXML_v6.xsd
+pyopenms/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd
+pyopenms/share/OpenMS/SCHEMAS/separation_technique_1.0.xsd
+pyopenms/share/OpenMS/SCHEMAS/xQuest_1_0.xsd
+pyopenms/share/OpenMS/SCRIPTS/InternalCalibration_Models.R
+pyopenms/share/OpenMS/SCRIPTS/InternalCalibration_Residuals.R
+pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_acc.R
+pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_idmap.R
+pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_inj.R
+pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_rt_acc.R
+pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_setid.R
+pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_tic.R
+pyopenms/share/OpenMS/SCRIPTS/Rscript_generic_example.R
+pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PEP.R
+pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PRT.R
+pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PSM.R
+pyopenms/share/OpenMS/SCRIPTS/plot_trafo.R
+pyopenms/share/OpenMS/THIRDPARTY/ReadMe.txt
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Hardkloer.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/MSGFtoPercolator.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/MascotPercolator.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Percolator.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/QCExporter.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/RawDirConvert.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/ReadMe.txt
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_generic.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PEP.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PRT.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PSM.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_acc.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_idmap.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_rt_acc.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_setid.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_tic.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_trapfill.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/TEMPLATE.ttd_
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/TPP_RefreshParser.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/XTandemToPercolator.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/msconvert.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/LINUX/TPP_ProteinProphet.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/LINUX/mail.ttd
+pyopenms/share/OpenMS/TOOLS/EXTERNAL/WINDOWS/TPP_ProteinProphet.ttd
+pyopenms/share/OpenMS/XSL/APML_to_CSV.xsl
+pyopenms/share/OpenMS/XSL/ConsensusXML.xsl
+pyopenms/share/OpenMS/XSL/IdXML.xsl
+pyopenms/share/OpenMS/XSL/QcML_report_sheet.xsl
+pyopenms/share/OpenMS/XSL/index.html

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/dependency_links.txt

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+

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/not-zip-safe

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+

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/top_level.txt

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+pyopenms
+pyopenms_1
+pyopenms_2
+pyopenms_3
+pyopenms_4