aria integration update

COPYRIGHT

+"""
+          ARIA -- Ambiguous Restraints for Iterative Assignment
+
+                 A software for automated NOE assignment
+
+                               Version 2.3
+
+
+Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,
+              Wolfgang Rieping, and Michael Nilges
+
+All rights reserved.
+
+
+NO WARRANTY. This software package is provided 'as is' without warranty of
+any kind, expressed or implied, including, but not limited to the implied
+warranties of merchantability and fitness for a particular purpose or
+a warranty of non-infringement.
+
+Distribution of substantively modified versions of this module is
+prohibited without the explicit permission of the copyright holders.
+
+$Author: bardiaux $
+$Revision: 1.1.1.1 $
+$Date: 2010/03/23 15:27:16 $
+"""
+

MANIFEST.in

-graft ariaec/conf
-graft ariaec/templates
-graft ariaec/data
+graft aria
 graft docs
+include *.md
+include COPYRIGHT
+prune examples-dev*
 prune examples*

aria/Analyser.py

+# coding=utf-8
+"""
+
+          ARIA -- Ambiguous Restraints for Iterative Assignment
+
+                 A software for automated NOE assignment
+
+                               Version 2.3
+
+
+Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,
+              Wolfgang Rieping, and Michael Nilges
+
+All rights reserved.
+
+
+NO WARRANTY. This software package is provided 'as is' without warranty of
+any kind, expressed or implied, including, but not limited to the implied
+warranties of merchantability and fitness for a particular purpose or
+a warranty of non-infringement.
+
+Distribution of substantively modified versions of this module is
+prohibited without the explicit permission of the copyright holders.
+
+$Author: bardiaux $
+$Revision: 1.1.1.1 $
+$Date: 2010/03/23 15:27:24 $
+"""
+
+
+from aria.ariabase import *
+from aria.xmlutils import XMLBasePickler
+from aria.xmlutils import XMLElement
+
+import aria.Settings as Settings
+
+
+class AnalysisParameters(Settings.Settings):
+
+    def create(self):
+
+        # TODO: delete hack for paths; enable check for existence
+
+        d = {'procheck_executable': Settings.Path(exists=0),
+             'procheck_enabled': Settings.YesNoChoice(),
+             'whatif_executable': Settings.Path(exists=0),
+             'whatif_enabled': Settings.YesNoChoice(),
+             'prosa_executable': Settings.Path(exists=0),
+             'prosa_enabled': Settings.YesNoChoice(),
+             'clashlist_executable': Settings.Path(exists=0),
+             'clashlist_enabled': Settings.YesNoChoice()}
+
+        descr = 'If enabled, ARIA runs a number of scripts to analyse ' + \
+                'the structures in last iteration and solvent refinement.'
+
+        d['cns_analyses'] = Settings.YesNoChoice(description=descr)
+
+        return d
+
+    def create_default_values(self):
+
+        defaults = {'procheck_enabled': YES,
+                    'whatif_enabled': YES,
+                    'prosa_enabled': YES,
+                    'clashlist_enabled': YES,
+                    'procheck_executable': 'procheck',
+                    'prosa_executable': 'prosaII',
+                    'whatif_executable': 'whatif',
+                    'clashlist_executable': 'clashlist',
+                    'cns_analyses': YES}
+
+        return defaults
+
+
+class Analyser(AriaBaseClass):
+
+    def __init__(self, settings):
+        AriaBaseClass.__init__(self, settings=settings, name='Analyser')
+
+        self.solvent_ensemble = None
+
+    def isEnabled(self):
+        """
+        convenience function. returns 1 if any of the analyses
+        is enabled.
+
+        Parameters
+        ----------
+
+        Returns
+        -------
+
+        """
+
+        entities = ('procheck_enabled', 'whatif_enabled',
+                    'prosa_enabled')
+
+        s = self.getSettings()
+
+        for e in entities:
+            if s[e] == YES:
+                return 1
+
+        return 0
+
+    def quality_checks(self, pdb_path, n_structures):
+        from aria.Singleton import ProjectSingleton
+        from .legacy.QualityChecks import QualityChecks as checker
+        from os.path import exists 
+
+        # BARDIAUX 2.2
+        from aria.WhatifProfile import WhatifProfile
+        
+        check_string(pdb_path)
+
+        project = ProjectSingleton()
+        infra = project.getInfrastructure()
+
+        temp_path = infra.get_temp_path()
+
+        s = self.getSettings()
+
+        procheck_enabled = s['procheck_enabled'] == YES
+        prosa_enabled = s['prosa_enabled'] == YES
+        whatif_enabled = s['whatif_enabled'] == YES
+        clashlist_enabled = s['clashlist_enabled'] == YES
+
+        # check whether executables exist
+
+        msg = 'Could not find executable for %s ("%s"). Quality-check ' + \
+            'has been disabled.'
+
+        if procheck_enabled and not exists(s['procheck_executable']):
+            self.message(msg % ('Procheck', s['procheck_executable']))
+            procheck_enabled = 0
+
+        if prosa_enabled and not exists(s['prosa_executable']):
+            self.message(msg % ('Prosa II', s['prosa_executable']))
+            prosa_enabled = 0
+
+        if whatif_enabled and not exists(s['whatif_executable']):
+            self.message(msg % ('WhatIf', s['whatif_executable']))
+            whatif_enabled = 0
+
+        if clashlist_enabled and not exists(s['clashlist_executable']):
+            self.message(msg % ('Clashlist', s['clashlist_executable']))
+            clashlist_enabled = 0
+            
+        if not(procheck_enabled or prosa_enabled or whatif_enabled or
+                clashlist_enabled):
+            return
+
+        msg = 'Running quality checks on structures in %s'
+        self.message(msg % pdb_path)
+
+        try:
+
+            checker.runChecks(workingDirectory=pdb_path,
+                              trashDirectory=temp_path,
+                              procheckOnOff=procheck_enabled,
+                              prosaOnOff=prosa_enabled,
+                              whatifOnOff=whatif_enabled,
+                              clashlistOnOff=clashlist_enabled,
+                              procheckExe=s['procheck_executable'],
+                              prosaExe=s['prosa_executable'],
+                              whatIfExe=s['whatif_executable'],
+                              clashlistExe=s['clashlist_executable'],
+                              howManyPdb=n_structures,
+                              skipPrefix='fitted_')
+            
+            # BARDIAUX 2.2
+            if whatif_enabled:
+                w_prof = WhatifProfile(pdb_path,
+                                       whatIfExe=s['whatif_executable'])
+                w_prof.makeProfiles()
+
+        except Exception as msg:
+            from aria.tools import last_traceback
+            self.message(last_traceback())
+            s = 'Could not run quality-checks: %s'
+            self.warning(s % msg)
+
+        self.message('Quality checks done.')
+        
+    # BARDIAUX 2.2
+    def _getSolventEnsemble(self, iteration, settings):
+        """
+        
+
+        Parameters
+        ----------
+        iteration :
+            
+        settings :
+            
+
+        Returns
+        -------
+        type
+            
+
+        """
+
+        if self.solvent_ensemble is not None:
+            return self.solvent_ensemble
+        
+        from aria.Singleton import ProjectSingleton
+        import os
+        project = ProjectSingleton()
+        infra = project.getInfrastructure()
+        
+        n_structures = settings['n_structures']
+        solvent_type = settings['solvent']
+        
+        ensemble = iteration.getStructureEnsemble()
+        files = ensemble.getFiles()[:n_structures]
+        
+        pdb_name_template = os.path.join(infra.get_refinement_path(),
+                                         infra.get_file_root() + '_%d' +
+                                         '_%s.pdb' % solvent_type)
+
+        float_name_template = os.path.join(infra.get_refinement_path(),
+                                           infra.get_file_root() + '_%d' +
+                                           '_%s.float' % solvent_type)
+        counters = []
+        structures = []
+        float_files = []
+        
+        for i in range(len(files)):
+
+            src = files[i]
+            
+            counter = os.path.basename(src)
+            counter = counter.replace(infra.get_file_root() + '_', '')
+            counter = counter.replace('.pdb', '')
+            counter = int(counter)
+            
+            if os.path.exists(pdb_name_template % counter):
+                structures.append(pdb_name_template % counter)
+                continue
+
+            if os.path.exists(float_name_template % counter):
+                float_files.append(float_name_template % counter)
+                continue
+
+            counters.append(counter)
+
+        # if float_files == []:
+        if not float_files:
+            float_files = None
+
+        if float_files is not None:
+            
+            from aria.FloatFile import FloatFile
+
+            parser = FloatFile()
+            swapped_atoms = [parser.parse(f) for f in float_files]
+            
+        else:
+            swapped_atoms = None
+
+        # create structure-ensemble from given 'structures'
+        import aria.StructureEnsemble as SE
+        
+        molecule = project.getMolecule()
+        
+        se_settings = SE.StructureEnsembleSettings()
+        se_settings['number_of_best_structures'] = n_structures
+        solv_ensemble = SE.StructureEnsemble(se_settings)
+        solv_ensemble.read(structures, molecule, 'cns', swapped_atoms)
+
+        return solv_ensemble        
+            
+    def cns_analyses(self, iteration, is_water=0):  # BARDIAUX 2.2
+        
+        check_type(iteration, 'Iteration')
+
+        if self.getSettings()['cns_analyses'] != YES:
+            return
+
+        if is_water:
+            msg = 'water refinement'
+        else:
+            msg = 'iteration %d' % iteration.getNumber()
+        s = 'Running CNS analyses for %s.'
+        self.message(s % msg)
+        
+        from aria.Singleton import ProjectSingleton
+
+        project = ProjectSingleton()
+        
+        protocol_settings = project.getProtocol().getSettings()
+        engine = project.getStructureEngine()
+        
+        if is_water:
+            ensemble = self._getSolventEnsemble(
+                iteration, protocol_settings['water_refinement'])
+
+        else:
+            ensemble = iteration.getStructureEnsemble()
+        
+        engine.analysis(protocol_settings, ensemble, is_water)
+        
+#     def cns_analyses(self, iteration):
+#         check_type(iteration, 'Iteration')
+
+#         if self.getSettings()['cns_analyses'] <> YES:
+#             return
+
+#         s = 'Running CNS analyses for iteration %d.'
+#         self.message(s % iteration.getNumber())
+        
+#         from Singleton import ProjectSingleton
+
+#         project = ProjectSingleton()
+        
+#         protocol_settings = project.getProtocol().getSettings()
+#         engine = project.getStructureEngine()
+#         ensemble = iteration.getStructureEnsemble()
+        
+#         engine.analysis(protocol_settings, ensemble)
+
+
+class AnalyserXMLPickler(XMLBasePickler):
+
+    order = ('structures_analysis', 'procheck', 'prosa', 'whatif', 'clashlist')
+
+    def _xml_state(self, x):
+
+        x = x.getSettings()
+
+        procheck = XMLElement()
+        procheck.enabled = x['procheck_enabled']
+        procheck.executable = x['procheck_executable']
+
+        whatif = XMLElement()
+        whatif.enabled = x['whatif_enabled']
+        whatif.executable = x['whatif_executable']
+
+        prosa = XMLElement()
+        prosa.enabled = x['prosa_enabled']
+        prosa.executable = x['prosa_executable']
+
+        clashlist = XMLElement()
+        clashlist.enabled = x['clashlist_enabled']
+        clashlist.executable = x['clashlist_executable']        
+
+        cns = XMLElement()
+        cns.enabled = x['cns_analyses']
+
+        e = XMLElement(tag_order=self.order)
+
+        e.structures_analysis = cns
+        e.procheck = procheck
+        e.whatif = whatif
+        e.prosa = prosa
+        e.clashlist = clashlist
+
+        return e
+
+    def load_from_element(self, e):
+
+        s = AnalysisParameters()
+        
+        s['procheck_executable'] = str(e.procheck.executable)
+        s['procheck_enabled'] = str(e.procheck.enabled)
+        s['whatif_executable'] = str(e.whatif.executable)
+        s['whatif_enabled'] = str(e.whatif.enabled)
+        s['prosa_executable'] = str(e.prosa.executable)
+        s['prosa_enabled'] = str(e.prosa.enabled)
+        s['cns_analyses'] = str(e.structures_analysis.enabled)
+
+        if hasattr(e, 'clashlist'):
+            s['clashlist_executable'] = str(e.clashlist.executable)
+            s['clashlist_enabled'] = str(e.clashlist.enabled)
+        else:
+            s['clashlist_executable'] = ''
+            s['clashlist_enabled'] = NO
+
+        return Analyser(s)
+
+Analyser._xml_state = AnalyserXMLPickler()._xml_state

aria/AriaXML.py

+# coding=utf-8
+"""
+
+          ARIA -- Ambiguous Restraints for Iterative Assignment
+
+                 A software for automated NOE assignment
+
+                               Version 2.3
+
+
+Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,
+              Wolfgang Rieping, and Michael Nilges
+
+All rights reserved.
+
+
+NO WARRANTY. This software package is provided 'as is' without warranty of
+any kind, expressed or implied, including, but not limited to the implied
+warranties of merchantability and fitness for a particular purpose or
+a warranty of non-infringement.
+
+Distribution of substantively modified versions of this module is
+prohibited without the explicit permission of the copyright holders.
+
+$Author: bardiaux $
+$Revision: 1.1.1.1 $
+$Date: 2010/03/23 15:27:24 $
+"""
+
+from __future__ import absolute_import
+# from .ariabase import AriaBaseClass
+from .TypeChecking import is_type, check_elements, LIST, TUPLE
+from .xmlutils import *
+from .tools import last_traceback
+
+# TODO[FALLAIN]: actually no function/ class of ariabase called here
+from aria.ariabase import *
+from aria.xmlutils import *
+# TODO[FALLAIN]: import Exception is not necessary all exceptions are provided
+# in the built in namespace. Furthermore, this package do not exist in python 3
+# from exceptions import Exception
+from aria.tools import last_traceback
+
+# DTD base names
+
+DTD_CHEMICAL_SHIFT_LIST = 'chemical_shift_list'
+DTD_MOLECULE = 'molecule'
+DTD_NOESY_SPECTRUM = 'noesy_spectrum'
+DTD_PROJECT = 'project'
+DTD_NOE_RESTRAINT = 'noe_restraint'
+DTD_DIST_RESTRAINT = 'distance_restraint'
+
+# DOCTYPEs
+
+DOCTYPE_NOE_RESTRAINTS = 'noe_restraint_list'
+DOCTYPE_DIST_RESTRAINTS = 'distance_restraint_list'
+
+
+class DOCManager(AriaBaseClass):
+    VERSION = 1.0
+
+    def __init__(self):
+
+        from .Project import Project
+        from .AriaPeak import AriaPeak, DistanceRestraint
+        from .Topology import Topology
+        from .Molecule import Molecule
+        from .NOESYSpectrum import NOESYSpectrum
+        from .ChemicalShiftList import ChemicalShiftList
+        from .Project import ProjectSingleton
+        from .conversion import ConverterSettings
+
+        AriaBaseClass.__init__(self)
+
+        # DTD base names
+
+        d = {Project: DTD_PROJECT,
+             AriaPeak: DTD_NOE_RESTRAINT,
+             DistanceRestraint: DTD_DIST_RESTRAINT,
+             Topology: 'topology',
+             Molecule: DTD_MOLECULE,
+             NOESYSpectrum: DTD_NOESY_SPECTRUM,
+             ChemicalShiftList: DTD_CHEMICAL_SHIFT_LIST,
+             ProjectSingleton: DTD_PROJECT,
+             ConverterSettings: 'conversion'}
+
+        for key, value in d.items():
+            # Compile dtd file names with DOCManager version
+            d[key] = self._compile_name(value)
+
+        self.__dtd_base_names = d
+
+        # DOCTYPEs
+
+        d = {Project: 'project',
+             AriaPeak: DOCTYPE_NOE_RESTRAINTS,
+             DistanceRestraint: DOCTYPE_DIST_RESTRAINTS,
+             Topology: 'topology',
+             Molecule: 'molecule',
+             NOESYSpectrum: 'spectrum',
+             ChemicalShiftList: 'chemical_shift_list',
+             ProjectSingleton: 'project',
+             ConverterSettings: 'conversion'}
+
+        self.__doc_types = d
+
+    def _compile_name(self, base):
+        return '%s%s.dtd' % (base, self.VERSION)
+
+    def getDOCTypes(self):
+        return self.__doc_types.values()
+
+    def getDTDs(self):
+        return self.__dtd_base_names.values()
+
+    def is_validDOCType(self, name):
+        return name in self.getDOCTypes()
+
+    def is_validDTD(self, name):
+        return name in self.getDTDs()
+
+    def getDTD(self, c, is_class=0):
+        """
+        returns DTD for class 'c'
+
+        Parameters
+        ----------
+        c :
+            
+        is_class :
+             (Default value = 0)
+
+        Returns
+        -------
+
+        """
+
+        if not is_class:
+
+            if not type(c) == type(self):
+                s = 'Instance expected, "%s" given.' % str(type(c))
+                self.error(msg=s)
+
+            c = c.__class__
+
+        if c not in self.__dtd_base_names:
+            s = 'DTD for class "%s" unknown'
+            self.error(ValueError, s % c.__name__)
+
+        dtd_name = self.__dtd_base_names[c]
+
+        return dtd_name
+
+    def getDOCType(self, c, is_class=0):
+
+        if not is_class:
+
+            if not type(c) == type(self):
+                s = 'Instance expected, "%s" given.' % str(type(c))
+                self.error(msg=s)
+
+            c = c.__class__
+
+        if c not in self.__doc_types:
+            s = 'DOCTYPE for class "%s" unknown'
+            self.error(ValueError, s % c.__class__.__name__)
+
+        return self.__doc_types[c]
+
+
+class AriaXMLContentHandler(XMLContentHandler):
+    """Define all ARIA xml content handler (picklers)"""
+
+    def __init__(self):
+
+        from .Project import ProjectXMLPickler
+        from .AriaPeak import AriaPeakXMLPickler, DistanceRestraintXMLPickler
+        from .Topology import TopologyXMLPickler
+        from .Molecule import MoleculeXMLPickler
+        from .NOESYSpectrum import NOESYSpectrumXMLPickler
+        from .ChemicalShiftList import ChemicalShiftListXMLPickler
+        from .conversion import ConverterSettingsXMLPickler
+
+        XMLContentHandler.__init__(self)
+
+        pickler = {'project': ProjectXMLPickler(),
+                   DOCTYPE_NOE_RESTRAINTS: AriaPeakXMLPickler(),
+                   DOCTYPE_DIST_RESTRAINTS: DistanceRestraintXMLPickler(),
+                   'topology': TopologyXMLPickler(),
+                   'molecule': MoleculeXMLPickler(),
+                   'spectrum': NOESYSpectrumXMLPickler(),
+                   'chemical_shift_list': ChemicalShiftListXMLPickler(),
+                   'conversion': ConverterSettingsXMLPickler()}
+
+        # register pickler for different DOCTYPEs
+
+        self.pickler = pickler
+
+    def select(self, doc_type):
+        if doc_type in self.pickler.keys():
+            self.sub_pickler = self.pickler[doc_type]
+        else:
+            self.sub_pickler = None
+
+    def load_from_element(self, name, e):
+        """