Updated sphinx documentation

ariaec/analysis.py

@@ -24,15 +24,25 @@ LOG = logging.getLogger(__name__)
 
 
 class EnsembleAnalysis(object):
-    """
-    ARIA extended ensemble analysis
-    """
+    """ARIA extended ensemble analysis"""
 
     def __init__(self, settings):
         self.settings = settings
 
     @staticmethod
     def _get_pdblist(iteration_path):
+        """
+
+        Parameters
+        ----------
+        iteration_path :
+            
+
+        Returns
+        -------
+
+        
+        """
         # Get the list of all the generated structures in iteration path if no
         # clustering. Otherwise, get the list of the lowest energy cluster
         if os.path.exists(os.path.join(iteration_path, "report.clustering")):
@@ -56,23 +66,31 @@ class EnsembleAnalysis(object):
         return list_of_pdb
 
     @staticmethod
-    def violation_analysis(project, iteration_id, restraints, dists, out_file,
+    def violation_analysis(project, iteration_id, restraints, ensemble, out_file,
                            dists_ref=None, headerflag=True):
         """
 
         Parameters
         ----------
-        project
-        iteration_id
-        restraints
-        dists
-        out_file
-        dists_ref
-        headerflag
+        project :
+            
+        iteration_id :
+            
+        restraints :
+            
+        ensemble :
+            
+        out_file :
+            
+        dists_ref :
+            (Default value = None)
+        headerflag :
+            (Default value = True)
 
         Returns
         -------
 
+        
         """
         protein_id = project.getSettings()['name']
         nbest = project.getProtocol().getIterationSettings(iteration_id)[
@@ -93,7 +111,8 @@ class EnsembleAnalysis(object):
 
                         dist = None
                         try:
-                            dist = [dists(*sp.getAtoms()) for sp in contrib]
+                            dist = [ensemble.getDistances(*sp.getAtoms())
+                                    for sp in contrib]
                             # Liste des distances pour la contribution c pour
                             # chaque structure de l'ensemble (une ou plusieur
                             # distance(s) par structure de l'ensemble si contribution
@@ -209,14 +228,19 @@ class EnsembleAnalysis(object):
 
         Parameters
         ----------
-        iter_dir
-        ensemble
-        molecule
-        atmask
+        iter_dir :
+            
+        ensemble :
+            
+        molecule :
+            
+        atmask :
+            (Default value = "CA")
 
         Returns
         -------
 
+        
         """
         mask = [a.getId() for c in molecule.get_chains() for r in c.getResidues()
                 for a in r.getAtoms() if a.getName() == atmask]
@@ -238,9 +262,7 @@ class EnsembleAnalysis(object):
         # return fitcoords, infos
 
     def run(self):
-        """
-        Execute Violation analysis
-        """
+        """Execute Violation analysis"""
         # Args
         project_path = self.settings.analysis.args["project"]
         # restraints_path = self.settings.analysis.args["restraints"]
@@ -331,13 +353,13 @@ class EnsembleAnalysis(object):
 
             dists_ref = native.getDistances
 
-        # We get here the distance of ALL THE STRUCTURES IN THE CLUSTER for viol
-        # analysis
-        dists = ensemble.getDistances
+        # We get here the distance of 'number_of_best_structures' in the
+        #  ensemble
+        # ens_getdists = ensemble.getDistances
 
         LOG.info("Violation analysis")
         out_file = os.path.join(out_path, 'violations.csv')
-        self.violation_analysis(project, iteration_id, restraints, dists,
+        self.violation_analysis(project, iteration_id, restraints, ensemble,
                                 out_file, dists_ref=dists_ref)
 
         infos = [inf for inf in ensemble.getInfo()]

ariaec/base.py

@@ -24,22 +24,39 @@ LOG = logging.getLogger(__name__)
 
 
 def addtup(tup, inc=1):
-    """
-    Increment all values by 1 in a tuple
-    :param tup:
-    :param inc:
-    :return:
+    """Increment all values by 1 in a tuple
+
+    Parameters
+    ----------
+    tup :
+        param inc:
+    inc :
+        (Default value = 1)
+
+    Returns
+    -------
+
+    
     """
     return tuple((val + inc for val in tup))
 
 
 def titleprint(outfile, progname='', desc=''):
-    """
-    Init log file
-    :param outfile:
-    :param progname: docstring
-    :param desc:
-    :return:
+    """Init log file
+
+    Parameters
+    ----------
+    outfile :
+        param progname: docstring
+    desc :
+        return: (Default value = '')
+    progname :
+        (Default value = '')
+
+    Returns
+    -------
+
+    
     """
     out = '''
 ================================================================================
@@ -51,10 +68,17 @@ def titleprint(outfile, progname='', desc=''):
 
 
 def get_filename(path):
-    """
-    Search filename in the given path
-    :param path:
-    :return:
+    """Search filename in the given path
+
+    Parameters
+    ----------
+    path :
+        return:
+
+    Returns
+    -------
+
+    
     """
     return "_".join(path.split("/")[-1].split(".")[:-1])
 
@@ -62,10 +86,19 @@ def get_filename(path):
 def reg_load(regex, filepath, sort=None):
     """
 
-    :param regex:
-    :param filepath:
-    :param sort:
-    :return:
+    Parameters
+    ----------
+    regex :
+        param filepath:
+    sort :
+        return: (Default value = None)
+    filepath :
+        
+
+    Returns
+    -------
+
+    
     """
 
     lines_dict = {}
@@ -83,12 +116,21 @@ def reg_load(regex, filepath, sort=None):
 
 
 def sort_2dict(unsort_dict, key, reverse=True):
-    """
-    Sort 2d dict by key
-    :param reverse:
-    :param key:
-    :param unsort_dict:
-    :return: sorted dict
+    """Sort 2d dict by key
+
+    Parameters
+    ----------
+    reverse :
+        param key: (Default value = True)
+    unsort_dict :
+        return: sorted dict
+    key :
+        
+
+    Returns
+    -------
+
+    
     """
     sorted_index = sorted(unsort_dict, key=lambda x: float(unsort_dict[x][key]),
                           reverse=reverse)
@@ -101,20 +143,35 @@ def sort_2dict(unsort_dict, key, reverse=True):
 
 
 def cart_dist(vectx, vecty):
-    """
-    Evaluate cartesian distance beetween 2 points x, vecty
-    :param vectx: numpy array (len = n dimensions)
-    :param vecty: numpy array (len = n dimensions)
-    :return:
+    """Evaluate cartesian distance beetween 2 points x, vecty
+
+    Parameters
+    ----------
+    vectx :
+        numpy array (len = n dimensions)
+    vecty :
+        numpy array (len = n dimensions)
+
+    Returns
+    -------
+
+    
     """
     return np.sqrt(sum(np.power(vectx - vecty, 2)))
 
 
 def format_str(string):
-    """
-    Convert str in bool, float, int or str
-    :param string:
-    :return:
+    """Convert str in bool, float, int or str
+
+    Parameters
+    ----------
+    string :
+        return:
+
+    Returns
+    -------
+
+    
     """
     if re.search(r"^\s*(true)\s*$", string, re.I):
         return True
@@ -154,8 +211,15 @@ def format_str(string):
 def format_dict(indict):
     """
 
-    :param indict:
-    :return:
+    Parameters
+    ----------
+    indict :
+        return:
+
+    Returns
+    -------
+
+    
     """
     for key in indict:
         if isinstance(indict[key], str):
@@ -166,21 +230,39 @@ def format_dict(indict):
 def ppdict(indict, indent=2):
     """
 
-    :param indict:
-    :param indent:
-    :return:
+    Parameters
+    ----------
+    indict :
+        param indent:
+    indent :
+        (Default value = 2)
+
+    Returns
+    -------
+
+    
     """
     return json.dumps(indict, indent=indent)
 
 
 def tickmin(pandata, ntick=None, shift=0, offset=5):
-    """
-    Minimise number of ticks labels for matplotlib or seaborn plot
-    :param offset:
-    :param shift:
-    :param pandata: pandas dataframe
-    :param ntick: number of ticks wanted per axes
-    :return:
+    """Minimise number of ticks labels for matplotlib or seaborn plot
+
+    Parameters
+    ----------
+    offset :
+        param shift: (Default value = 5)
+    pandata :
+        pandas dataframe
+    ntick :
+        number of ticks wanted per axes (Default value = None)
+    shift :
+        (Default value = 0)
+
+    Returns
+    -------
+
+    
     """
     yticks = [_ + shift for _ in range(0, len(pandata.index))]
     xticks = [_ + shift for _ in range(0, len(pandata.columns))]
@@ -206,14 +288,25 @@ def tickmin(pandata, ntick=None, shift=0, offset=5):
 
 
 def tickrot(axes, figure, rotype='horizontal', xaxis=True, yaxis=True):
-    """
-    Matplot rotation of ticks labels
-    :param axes:
-    :param figure:
-    :param rotype:
-    :param xaxis:
-    :param yaxis:
-    :return:
+    """Matplot rotation of ticks labels
+
+    Parameters
+    ----------
+    axes :
+        param figure:
+    rotype :
+        param xaxis: (Default value = 'horizontal')
+    yaxis :
+        return: (Default value = True)
+    figure :
+        
+    xaxis :
+        (Default value = True)
+
+    Returns
+    -------
+
+    
     """
     if yaxis:
         art.setp(axes.get_yticklabels(), rotation=rotype)
@@ -224,6 +317,7 @@ def tickrot(axes, figure, rotype='horizontal', xaxis=True, yaxis=True):
 
 # TODO: Add another level when we use verbose options instead of displaying debug messages
 class CustomLogging(object):
+    """ """
     # default_file = os.path.join(os.path.abspath(os.path.dirname(__file__)),
     #                             "conf/logging.json")
     """
@@ -249,8 +343,15 @@ class CustomLogging(object):
     def update_msg(self, desc):
         """
 
-        :param desc:
-        :return:
+        Parameters
+        ----------
+        desc :
+            return:
+
+        Returns
+        -------
+
+        
         """
         if isinstance(self.msg, list):
             self.msg += desc
@@ -259,10 +360,7 @@ class CustomLogging(object):
             self.msg = " - ".join((self.msg, desc.capitalize()))
 
     def default_config(self):
-        """
-
-        :return:
-        """
+        """:return:"""
         # with open(self.default_file, 'rt') as f:
         conf = pkgr.resource_stream(__name__, self.default_file).read().decode()
         config = json.loads(conf)
@@ -270,10 +368,17 @@ class CustomLogging(object):
         return config
 
     def set_outdir(self, outdir):
-        """
-        Create log directory and change log files location
-        :param outdir: path output directory
-        :return:
+        """Create log directory and change log files location
+
+        Parameters
+        ----------
+        outdir :
+            path output directory
+
+        Returns
+        -------
+
+        
         """
         outdir = os.path.join(outdir,
                               "log") if "log" not in outdir else outdir
@@ -295,10 +400,7 @@ class CustomLogging(object):
             logging.config.dictConfig(self.config)
 
     def welcome(self):
-        """
-
-        :return:
-        """
+        """:return:"""
         desc = '''
 ================================================================================
 
@@ -315,9 +417,7 @@ class CustomLogging(object):
 
 
 class Capturing(list):
-    """
-    Capture output
-    """
+    """Capture output"""
     def __enter__(self):
         """
 
@@ -344,9 +444,7 @@ class Capturing(list):
 
 
 class RedirectStdStreams(object):
-    """
-    Redirect standard ouput and errors
-    """
+    """Redirect standard ouput and errors"""
     def __init__(self, stdout=None, stderr=None):
         self._stdout = stdout or sys.stdout
         self._stderr = stderr or sys.stderr
@@ -366,9 +464,7 @@ class RedirectStdStreams(object):
 
 
 class CommandProtocol(object):
-    """
-    Abstract class for subcommand protocol
-    """
+    """Abstract class for subcommand protocol"""
     __metaclass__ = ABCMeta
 
     def __init__(self, settings):
@@ -376,29 +472,35 @@ class CommandProtocol(object):
 
     @abstractmethod
     def run(self):
-        """
-        main method to launch protocol
+        """main method to launch protocol
         :return:
+
+        Parameters
+        ----------
+
+        Returns
+        -------
+
+        
         """
         raise NotImplementedError
 
 
 class NotDisordered(Select):
-    """
-    Define an atom as disordered or not in pdb selection
-    """
+    """Define an atom as disordered or not in pdb selection"""
     def accept_atom(self, atom):
-        """
-        Accept or not the atom if it does not correspond to an alternative
+        """Accept or not the atom if it does not correspond to an alternative
         location
 
         Parameters
         ----------
-        atom
+        atom :
+            
 
         Returns
         -------
 
+        
         """
         return not atom.is_disordered() or atom.get_altloc() == 'A'
 

ariaec/commands.py

@@ -25,7 +25,15 @@ LOG = logging.getLogger(__name__)
 def check_file(prospective_file):
     """
 
-    :param prospective_file:
+    Parameters
+    ----------
+    prospective_file :
+        
+
+    Returns
+    -------
+
+    
     """
     LOG.debug("Checking if %s is a readable file", prospective_file)
     if not os.path.exists(prospective_file):
@@ -37,9 +45,7 @@ def check_file(prospective_file):
 
 
 class ReadableFile(argp.Action):
-    """
-    Class used with argparse action to check if a file is readable
-    """
+    """Class used with argparse action to check if a file is readable"""
 
     def __init__(self, *args, **kwargs):
         super(ReadableFile, self).__init__(*args, **kwargs)
@@ -58,9 +64,7 @@ class ReadableFile(argp.Action):
 # TODO: Make parent Command class with _create_argparser, self.args,
 # update_logger and run
 class AriaEcCommands(object):
-    """
-    Argparse interface for aria_ec
-    """
+    """Argparse interface for aria_ec"""
 
     command_list = ("setup", "bbconv", "maplot", "pdbqual", "analysis",
                     "tbl2xml", "pdbdist")
@@ -87,6 +91,18 @@ class AriaEcCommands(object):
         self._update_logger(custom_logging)
 
     def _update_logger(self, log):
+        """
+
+        Parameters
+        ----------
+        log :
+            
+
+        Returns
+        -------
+
+        
+        """
         if log and hasattr(self.args, "output_directory"):
             if not self.args.nolog:
                 # Don't generate log files
@@ -99,6 +115,7 @@ class AriaEcCommands(object):
             log.welcome()
 
     def _create_argparser(self):
+        """ """
         parser = argp.ArgumentParser(description=__doc__,
                                      formatter_class=argp.ArgumentDefaultsHelpFormatter)
         parser.add_argument("-o", "--output", dest="output_directory",
@@ -116,10 +133,17 @@ class AriaEcCommands(object):
         return parser
 
     def _create_subparsers(self, parser):
-        """
-        Generate subcommands
-        :param parser: argparser object
-        :return:
+        """Generate subcommands
+
+        Parameters
+        ----------
+        parser :
+            argparser object
+
+        Returns
+        -------
+
+        
         """
         for index, command in enumerate(self.command_list):
             # Create subparser defined in command list
@@ -128,10 +152,17 @@ class AriaEcCommands(object):
             parser.add_parser(command, parents=[subcommand])
 
     def _setup_argparser(self, desc=None):
-        """
-        setup opt & args
-        :param desc: command descriptor
-        :return: argparser object
+        """setup opt & args
+
+        Parameters
+        ----------
+        desc :
+            command descriptor (Default value = None)
+
+        Returns
+        -------
+
+        
         """
         parser = argp.ArgumentParser(description=desc,
                                      add_help=False)
@@ -167,10 +198,17 @@ class AriaEcCommands(object):
         return parser
 
     def _bbconv_argparser(self, desc=None):
-        """