emdbva 0.0.1.dev1__py3-none-any.whl

emdbva-0.0.1.dev1.dist-info/LICENSE

@@ -0,0 +1,201 @@
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emdbva-0.0.1.dev1.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: emdbva
+Version: 0.0.1.dev1
+Summary: CryoEM validation toolkit
+Home-page: https://test.pypi.org/project/va/
+Author: Zhe Wang
+Author-email: zhe@ebi.ac.uk
+License: Apache License
+Keywords: EMDB,Cryoem,Validation
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 2.7
+Description-Content-Type: text/x-rst; charset=UTF-8
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy >=0.14
+Requires-Dist: scikit-learn
+Requires-Dist: Pillow
+Requires-Dist: memory-profiler
+Requires-Dist: matplotlib
+Requires-Dist: pandas
+Requires-Dist: biopython
+Requires-Dist: mrcfile
+Requires-Dist: opencv-python
+
+CryoEM validation analysis pipeline
+

emdbva-0.0.1.dev1.dist-info/RECORD

@@ -0,0 +1,27 @@
+va/__init__.py,sha256=gHi6sjjnvd4J1-hcYShVW1RQAAZOcbHYxhQZzo7SX4E,268
+va/mainva.py,sha256=w0Xp6iTuzfSHVfm-QDAm7kmfhmYiWj9uUKytoCbJBh8,10026
+va/preparation.py,sha256=HzX6YUB345t84qe1sbWGPawpPEUuyOgN2mwBh98fRsE,72917
+va/qscores.csv,sha256=mZ28YdqnIRywBc6gq_iuiHYBc6zmESIhdXWfx8ZWm0A,902326
+va/validationanalysis.py,sha256=oBufOIl0oOESt_F14iKwgfP56fpab3kMnajWfdZICqQ,343456
+va/version.py,sha256=LCoemN7z7w1sFn6-Dndv1YBASgq8B-b8xYd2uEfNxDs,904
+va/metrics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+va/metrics/bars.py,sha256=WbW7xxbnXR8oXV482Vxiu0EfayDaxEMLe6LLXJ8sT3g,11710
+va/metrics/emda_mmcc.py,sha256=4PZUmPdKSCmsbQMnEXyNUJkyjL08_8vqxqww4sXtB9I,417
+va/metrics/emringer.py,sha256=IkybpIg2HG-qVfQvemouWpCLpSuVZem4tYYlnb4D4ig,1297
+va/metrics/phaserandomization.py,sha256=KtLYlBeusicpuWSxomGxSkJ3RJygWqbxM6NuiqZkMrI,15167
+va/metrics/phenix_cc.py,sha256=sJ-ftYsPDymLoKgD1NmN-6aphsJjgS60941E3hCLuLI,4406
+va/metrics/phenix_mm.py,sha256=rNIsbSqzsWE0wz47yvX9u37KVbh4jEtg3WyHxs9JAno,5916
+va/metrics/qscore.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+va/metrics/resmap.py,sha256=uTR048nnwVpYRt_FhVHGmfO7Pw77NArIy2uindOY-04,17951
+va/metrics/smoc.py,sha256=YZPXGLHRgvqJSmLBRkz2ig_Q6QIyXA-eGl48pr4nNxM,3670
+va/metrics/strudel.py,sha256=ki5ocH94U2GMFvDgBnVhDQcVE2CT7ejgrvSahqBthAo,4674
+va/metrics/threedfsc.py,sha256=-Lp91xy_HOLvOjcXrGI1qXw-tPW7NW7WAKy_J4T41XQ,1559
+va/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+va/utils/misc.py,sha256=IhcN1PdJr5eUsWXyXNblDV5HQKMcCAqTXKMoCxBbvXk,6753
+va/utils/stars.py,sha256=15yRUZ1nzRMzzw64DOA59q8mLYuCEQOfqGQAEmLToqI,5996
+emdbva-0.0.1.dev1.dist-info/LICENSE,sha256=EKRtSIAJIDq0FaOStnUlRfcyVCRaNuXBEZWfcjSoAYo,11338
+emdbva-0.0.1.dev1.dist-info/METADATA,sha256=iyvNqKAgs1C4glg8h0ITvMdIFnB7OLDHNyWAaxC4E1M,994
+emdbva-0.0.1.dev1.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+emdbva-0.0.1.dev1.dist-info/entry_points.txt,sha256=3GDgE_RPnedndxYSN7AbQ6ojnQR8dYM3VvJrR_mShSw,38
+emdbva-0.0.1.dev1.dist-info/top_level.txt,sha256=XkRzdik-cabgu1rSDVUmRKNy0pF_RGh-XAviUV9H0p8,3
+emdbva-0.0.1.dev1.dist-info/RECORD,,

emdbva-0.0.1.dev1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.41.2)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

emdbva-0.0.1.dev1.dist-info/entry_points.txt

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+[console_scripts]
+va = va.mainva:main

emdbva-0.0.1.dev1.dist-info/top_level.txt

@@ -0,0 +1 @@
+va

va/__init__.py

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+import os
+from os import path
+import sys
+from va.version import __version__
+
+sys.path.append(path.dirname(path.dirname(path.abspath(__file__))))
+# sys.path.append(path.dirname(path.abspath(__file__)))
+BASE_DIR = os.path.dirname(os.path.realpath(__file__))
+
+name = 'va'

va/mainva.py

@@ -0,0 +1,369 @@
+#!/usr/bin/env python
+
+"""
+mainva.py
+
+mainva class used to run the main function of validation
+analysis
+
+Copyright [2013] EMBL - European Bioinformatics Institute
+Licensed under the Apache License, Version 2.0 (the
+"License"); you may not use this file except in
+compliance with the License. You may obtain a copy of
+the License at
+http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing,
+software distributed under the License is distributed on
+an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+KIND, either express or implied. See the License for the
+specific language governing permissions and limitations
+under the License.
+
+"""
+
+
+__author__ = 'Zhe Wang'
+__email__ = 'zhe@ebi.ac.uk'
+__date__ = '2018-07-24'
+
+
+
+import timeit
+import os
+import sys
+from memory_profiler import memory_usage
+from va.validationanalysis import ValidationAnalysis
+from va.preparation import PreParation as prep
+from va.metrics.strudel import run_strudel
+import threading
+try:
+    from PATHS import MAP_SERVER_PATH
+except ImportError:
+    MAP_SERVER_PATH = None
+from memory_profiler import profile
+sys.stdout.flush()
+
+def allruns(validationobj, runs):
+    """
+        Each single run included here
+
+    :param validationobj: validation object from ValidationAnalysis module
+    :param runs: list of string which represent each of the function
+    :return: None
+    """
+
+    # Projections
+    if 'projection' in runs:
+        validationobj.orthogonal_projections()
+        validationobj.rawmap_projections()
+        validationobj.orthogonal_max()
+        validationobj.rawmap_max()
+        validationobj.orthogonal_min()
+        validationobj.rawmap_min()
+        validationobj.orthogonal_median()
+        validationobj.rawmap_median()
+        validationobj.orthogonal_std()
+        validationobj.rawmap_std()
+
+    # Central slice
+    if 'central' in runs:
+        validationobj.central_slice()
+        validationobj.rawmap_central_slice()
+
+    # Largest variance
+    if 'largestvariance' in runs:
+        validationobj.largest_variance()
+        validationobj.rawmap_largest_variance()
+
+    # Generate atom inclusion and residue inclusion json file
+    if 'inclusion' in runs:
+        validationobj.ai_bar()
+
+    # Sureface views
+    if 'surface' in runs:
+        validationobj.surfaces()
+
+    # Masks views
+    if 'mask' in runs:
+        validationobj.masks()
+
+    # Desnity distribution
+    if 'density' in runs:
+        validationobj.mapdensity_distribution()
+        validationobj.rawmapdensity_distribution()
+
+    # Contour level verses volume
+    if 'volume' in runs:
+        validationobj.volumecontour()
+
+    # rmcc/CCC
+    if 'rmmcc' in runs:
+        validationobj.real_mmcc()
+
+    # RAPS
+    if 'raps' in runs:
+        validationobj.rapss()
+
+    # FSC
+    if 'fsc' in runs:
+        validationobj.fscs()
+
+    # mmFSC
+    if 'mmfsc' in runs:
+        validationobj.phenix_mmfsc()
+
+    # Symmetry
+    if 'symmetry' in runs:
+        validationobj.symmetry()
+
+    # Strudel
+    if 'strudel' in runs:
+        validationobj.strudel()
+
+    # Q-score
+    if 'qscore' in runs:
+        validationobj.qscore_bar()
+
+    # SMOC
+    if 'smoc' in runs:
+        validationobj.smoc_bar()
+
+    # Phenix residue-wise CCC
+    if 'resccc' in runs:
+        validationobj.ccc_bar()
+    #
+    # if 'phrand' in runs:
+    #     validationobj.phrand()
+
+    # Resmap local resolution
+    if 'locres' in runs:
+        validationobj.locres_resmap()
+        validationobj.locres_histo()
+
+    # EMringer
+    if 'emringer' in runs:
+        validationobj.emringer()
+
+    # 3DFSC
+    # if '3dfsc' in runs:
+    #     validationobj.threedfsc()
+
+    return None
+
+
+def inallruns(validationobj, runs):
+    """
+        Each single run included here
+
+    :param validationobj: validation object from ValidationAnalysis module
+    :param runs: list of string which represent each of the function
+    :return: None
+    """
+
+    def without_strudel():
+        # Projections
+        if 'projection' in runs:
+            validationobj.orthogonal_projections()
+            validationobj.rawmap_projections()
+            validationobj.orthogonal_max()
+            validationobj.orthogonal_std()
+
+        # Central slice
+        if 'central' in runs:
+            validationobj.central_slice()
+            validationobj.rawmap_central_slice()
+
+        # Largest variance
+        if 'largestvariance' in runs:
+            validationobj.imgvariance()
+            validationobj.rawmap_imgvariance()
+
+        # Generate atom inclusion and residue inclusion json file
+        if 'inclusion' in runs:
+            validationobj.atom_inclusion()
+
+        # Sureface views
+        if 'surface' in runs:
+            validationobj.surfaces()
+
+        # Masks views
+        if 'mask' in runs:
+            validationobj.masks()
+
+        # Desnity distribution
+        if 'density' in runs:
+            validationobj.mapdensity_distribution()
+            validationobj.rawmapdensity_distribution()
+
+        # Contour level verses volume
+        if 'volume' in runs:
+            validationobj.volumecontour()
+
+        # rmcc/CCC
+        if 'rmmcc' in runs:
+            validationobj.real_mmcc()
+
+        # RAPS
+        if 'raps' in runs:
+            validationobj.raps()
+            validationobj.rawmap_raps()
+            # validationobj.pararaps()
+
+        # FSC
+        if 'fsc' in runs:
+            validationobj.fscs()
+
+        # mmFSC
+        if 'mmfsc' in runs:
+            validationobj.mmfsc()
+
+        # Symmetry
+        if 'symmetry' in runs:
+            validationobj.symmetry()
+
+        # # Strudel
+        # if 'strudel' in runs:
+        #     validationobj.strudel()
+
+        # Q-score
+        if 'qscore' in runs:
+            validationobj.qscore()
+
+        # SMOC
+        if 'smoc' in runs:
+            validationobj.smoc()
+
+        # EMringer
+        if 'emringer' in runs:
+            validationobj.emringer()
+
+        # 3DFSC
+        # if '3dfsc' in runs:
+        #     validationobj.threedfsc()
+
+        # Local resolution
+
+        return None
+
+    def strudel_only():
+        # Strudel
+        if 'strudel' in runs:
+            validationobj.strudel()
+
+        return None
+
+    t = threading.Thread(target=strudel_only)
+    t1 = threading.Thread(target=without_strudel)
+    t.start()
+    t1.start()
+    t.join()
+    t1.join()
+
+
+# @profile
+def main():
+
+    start_first = timeit.default_timer()
+
+    # Preparation
+    prepobj = prep()
+    position = prepobj.args.positions
+
+    if not prepobj.args.positions:
+        # Read map
+        inputmap, mapsize, mapdimension = prepobj.read_map()
+
+        # Read model
+        inputmodel, pid, modelsize = prepobj.read_model()
+
+        # Get model map names
+        # modelsmaps, _ = prepobj.modelstomaps()
+        modelsmaps = None
+        onlybar = prepobj.onlybar
+
+        # Read half map
+        halfeven, halfodd, rawmap, halfmapsize = prepobj.read_halfmaps()
+
+        # Contour level
+        contourlevel = prepobj.contourlevel
+
+        # Read run parameters
+        runs = prepobj.runs()
+
+        # EMDID
+        emdid = prepobj.emdid
+        dir = None if emdid is not None else prepobj.dir
+
+        # Resolution and EM method
+        resolution, emmethod = prepobj.resolution, prepobj.method
+
+        # fscfile
+        fscfile = prepobj.fscfile
+
+        # strudel lib
+        strudellib = prepobj.mofit_libpath
+
+        # 3DFSC root directory
+        threed_fsc_dir = prepobj.threedfscdir
+
+        # Masks
+        masks = prepobj.masks
+
+        # Memory prediction
+        memmsg = None
+        # if len(runs) == 10 and 'mask' not in runs:
+        memmsg = prepobj.memmsg(mapsize)
+
+        # Platform either wwpdb or emdb(default)
+        platform = prepobj.platform
+        print('Executed under: {} platform.'.format(platform))
+
+        # VA starts here on
+        print('%sValidation Analysis%s' % (20*'=', 20*'='))
+        validationobj = ValidationAnalysis(inputmap, inputmodel, pid, halfeven, halfodd, rawmap, contourlevel, emdid,
+                                           dir, emmethod, resolution, fscfile, masks, modelsmaps, onlybar, strudellib,
+                                           threed_fsc_dir, platform)
+
+        # Run all the validation piceces and give the peak memory consumption
+        if len(runs) == 9 and 'mask' not in runs:
+            mem = max(memory_usage((allruns, (validationobj, runs)), multiprocess=True, include_children=True))
+            print('The memory peak is: {}.'.format(mem))
+        else:
+            mem = 0.
+            allruns(validationobj, runs)
+
+        # Change cif file to the original one
+        prepobj.change_cifname()
+        # Merge all jsons
+        prepobj.finiliszejsons()
+
+        stop = timeit.default_timer()
+        alltime = stop - start_first
+        # print('Memory usage peak: %s.' % mem)
+        print('All time: %s' % alltime)
+
+
+        # Save data for memory prediction
+        #if runs['all'] is True:
+        if len(runs) == 9 and 'mask' not in runs:
+            if inputmodel is not None and modelsize is not None:
+                modelout = sum(modelsize)/len(modelsize) if len(inputmodel) != 0 else 0
+                vout = MAP_SERVER_PATH if emdid is not None else os.path.dirname(os.path.dirname(dir))
+                with open(vout + '/input.csv', 'a+') as f:
+                    if os.stat(vout + '/input.csv').st_size == 0:
+                        f.write('%s,%s,%s,%s,%s,%s,%s\n' % ('mapname', 'maprealsize', 'halfmapsize', 'modelrealsize', 'mapdimension', 'alltime', 'mem'))
+                    f.write('%s,%s,%s,%s,%s,%s,%s\n' % (prepobj.mapname, mapsize, halfmapsize, modelout, mapdimension, alltime, mem))
+                f.close()
+            else:
+                vout = MAP_SERVER_PATH if emdid is not None else os.path.dirname(os.path.dirname(dir))
+        else:
+            vout = None
+
+        return None
+    elif position == 'strudel':
+        run_strudel(prepobj.full_modelpath, prepobj.full_mappath, prepobj.mofit_libpath, prepobj.strdout)
+
+
+if __name__ == '__main__':
+    main()
+