Added configuration file converter

.gitignore

@@ -6,6 +6,7 @@ build/
 dist/
 *.egg-info/
 .eggs/
+docs.old*
 docs/_static/
 docs/_templates/
 .svn/

README.md

@@ -5,7 +5,7 @@
 
                  A software for automated NOE assignment
 
-                               Version 2.3
+                               Version 2.4
 
 ===============================================================================
 
@@ -43,15 +43,12 @@ structure calculation. Bioinformatics 23:381-382
 
 Contents:
 
-1. What's new in version 2.3 ?
+1. What's new in version 2.4 ?
 
-   1.1 Support of CCPNMR version 2
-   1.2 Symmetric oligomers (C3, C5 and D2)
-   1.3 Log-harmonic potential for distance restraints (Nilges et al. Structure, 2008)
-   1.4 Import of CCPN Models/Structure Ensembles
-   1.5 Zinc ions coordination
-   1.6 Automated Molprobilty clashlist analysis
-   1.7 Old aria1.x features added
+   1.1 Potential of Mean Forces for dihedral angles () and H-bonds ()
+   1.2 Clustering step during the iterative process
+   1.3 Extended scoring function including PMF, coulombic and full Lennard Jones functions
+   1.4 Restraints generation from evolutionary couplings and secondary structure prediction 
 
 2. Installation
 
@@ -98,7 +95,7 @@ Contents:
   (go to "Add > Zinc Coordination")
 
 - Automated Molprobilty (clashlist) analysis
-  (go to "Analyses > Molprobity Classhlist")
+  (go to "Analyses > Molprobity Clashlist")
 
 - addition of old aria1.x features (keep_structures, only fully assigned peaks)
 

aria/aria2.py

@@ -1043,7 +1043,6 @@ def run_aria(project_file, log_file=None, debug=0, test_commands=1,
     #    is turned of once a project has been set up.
 
     Settings.Path.global_mandatory = 0
-
     project = load_project(project_file)
 
     project.check(test_commands)

aria/conbox/commands.py

@@ -12,7 +12,8 @@ from . import __doc__
 from .common import format_dict, CustomLogging
 from .settings import AriaEcSettings
 from .maplot import AriaEcContactMap
-from .converter import AriaEcBbConverter, AriaEcXMLConverter
+from .converter import AriaEcBbConverter, AriaEcXMLConverter, \
+    AriaEcConfigConverter
 from .setup import AriaEcSetup
 from .pdbqual import AriaEcPdbqual
 from .pdbdist import PDBDist
@@ -69,7 +70,7 @@ class AriaEcCommands(object):
     """Argparse interface for aria_ec"""
 
     command_list = ("setup", "bbconv", "maplot", "pdbqual", "analysis",
-                    "tbl2xml", "pdbdist", "pdbstat")
+                    "tbl2xml", "pdbdist", "pdbstat", "iniconv")
     desc_list = (u"Setup ARIA infrastructure with contact maps translated "
                  u"into ARIA restraints",
                  u"Convert a contact map in bbcontact format",
@@ -78,7 +79,8 @@ class AriaEcCommands(object):
                  u"Extended ARIA ensemble analysis on a specific iteration ",
                  u"XML converter for tbl distance restraint",
                  u"Extract distance distribution from culled list of pdb files",
-                 u"Analyze distance distribution with GMM, ...")
+                 u"Analyze distance distribution with GMM",
+                 u"Convert configuration files into a unique csv file")
     contact_types = ("evfold", "plmev", "plm", "plmdca", "plmc", "bbcontacts",
                      "pconsc", "pconsc1", "pconsc2", "psicov", "metapsicovhb",
                      "metapsicov_stg1", "metapsicov_stg2", "gremlin", "pdb",
@@ -119,9 +121,9 @@ class AriaEcCommands(object):
             log.welcome()
 
     def _create_argparser(self):
-        """ """
-        parser = argp.ArgumentParser(description=__doc__,
-                                     formatter_class=argp.ArgumentDefaultsHelpFormatter)
+        parser = argp.ArgumentParser(
+            description=__doc__,
+            formatter_class=argp.ArgumentDefaultsHelpFormatter)
         parser.add_argument("-o", "--output", dest="output_directory",
                             type=str, help="Output directory", required=True)
         parser.add_argument("-c", "--conf", action=ReadableFile,
@@ -179,7 +181,7 @@ class AriaEcCommands(object):
                            help="sequence file [FASTA]")
         # group.add_argument("sspred", action=ReadableFile,
         #                    help="secondary structure prediction file")
-        group.add_argument("infiles", nargs="+", metavar="infile",
+        group.add_argument("infiles", nargs="*", metavar="infile",
                            action=ReadableFile,
                            help="contact or pdb file(s) used to build aria "
                                 "distance restraints")
@@ -195,8 +197,8 @@ class AriaEcCommands(object):
                            action=ReadableFile,
                            help="ARIA project file. This file will be used as"
                                 "an initialization file if")
-        group.add_argument("-t", "--type", required=True,
-                           nargs="+", dest="contact_types",
+        group.add_argument("-t", "--type",
+                           nargs="*", dest="contact_types",
                            choices=self.contact_types, help="Infile(s) contact "
                                                             "type(s)")
         group.add_argument("-r", "--ref", dest="ref",
@@ -244,6 +246,28 @@ class AriaEcCommands(object):
                                                              "type")
         return parser
 
+    @staticmethod
+    def _iniconv_argparser(desc=None):
+        """
+        iniconv opt & args
+
+        Parameters
+        ----------
+        desc :
+            command descriptor (Default value = None)
+
+        Returns
+        -------
+
+
+        """
+        parser = argp.ArgumentParser(description=desc,
+                                     add_help=False)
+        # args
+        parser.add_argument("confiles", nargs='+',
+                            type=str, help="config files")
+        return parser
+
     def _maplot_argparser(self, desc=None):
         """
         maplot opt & args
@@ -454,26 +478,26 @@ class AriaEcCommands(object):
         if self.args.verbose:
             LOG.info("Toggle on debug mode")
             logging.getLogger().setLevel(logging.DEBUG)
-        LOG.debug("Create AriaEcSettings")
+        LOG.info("Initialize settings")
         settings = AriaEcSettings(self.args.command)
-        LOG.info("Loading default config file")
+        LOG.debug("Loading default config file")
         settings.load_config(self.default_confile, pkg=True)
         if self.args.conf_file:
-            LOG.info("Updating settings with conf file")
+            LOG.info("Updating settings according to config file")
             settings.load_config(self.args.conf_file)
         # Update settings associated to command section
-        LOG.info("Updating %s args settings", self.args.command)
+        LOG.debug("Updating %s args settings", self.args.command)
         LOG.debug(self.args.__dict__)
         getattr(settings, self.args.command).args.update(format_dict(self.args.__dict__))
         LOG.debug(getattr(settings, self.args.command).args)
         if self.args.output_directory:
-            LOG.info("Updating output directory %s", self.args.output_directory)
+            LOG.debug("Output directory: %s", self.args.output_directory)
             settings.infra = self.args.output_directory
         return settings
 
     def run(self):
         """call method relative to args.command"""
-        LOG.info("Run %s command", self.args.command)
+        LOG.debug("Run %s command", self.args.command)
         getattr(self, self.args.command)()
 
     def setup(self):
@@ -516,6 +540,10 @@ class AriaEcCommands(object):
         inst = EnsembleAnalysis(self.create_settings())
         inst.run()
 
+    def iniconv(self):
+        inst = AriaEcConfigConverter(self.create_settings())
+        inst.run()
+
 
 def main():
     """Launch ariaec command interface"""

aria/conbox/converter.py

@@ -17,7 +17,6 @@ import pickle
 import pkg_resources as pkgr
 import random
 import re
-import sys
 import textwrap
 from ..core.AriaXML import AriaXMLPickler
 from ..core.ConversionTable import ConversionTable
@@ -36,6 +35,7 @@ from .common import get_filename, TqdmToLogger
 from .protein import Protein
 from .protmap import (ResAtmMap, ResMap, SsAaAtmMap)
 from .reader import MapFileListReader, TblDistFile
+from .settings import AriaEcSettings
 
 LOG = logging.getLogger(__name__)
 
@@ -1818,3 +1818,99 @@ class AriaEcXMLConverter(AriaXMLConverter):
         list_name = self.settings.tbl2xml.args["listname"]
 
         self.tbl2xml(outdir_path, molecule_path, tbl_paths, list_name)
+
+
+class AriaEcConfigConverter(object):
+    OUTFILE = "configs.csv"
+
+    def __init__(self, settings):
+        self.settings = settings
+
+    @staticmethod
+    def formatcell(value):
+        """
+        Format value in order to save it into a panda dataframe
+
+        Parameters
+        ----------
+        value: object
+            Instance which has to be saved into a unique pandas cell
+
+        Returns
+        -------
+        value: object
+            Instance compatible to value of ONE cell
+
+        """
+        if isinstance(value, list):
+            return ';'.join(value)
+        elif value is None:
+            return np.NaN
+        else:
+            return value
+
+    def conftodf(self, path=None):
+        """
+        Convert config file into panda dataframe
+
+        Parameters
+        ----------
+        path: str
+            Path to the config file
+
+        Returns
+        -------
+        config: pd.Dataframe object
+            pandas dataframe with all options saved as a 1xn matrix
+            (n corresponding to the number of columns)
+        """
+        conf = AriaEcSettings('config')
+        conf.load_config(path)
+        columns = ['config']
+        row = [
+            os.path.splitext(os.path.basename(path))[0] if path else "default"]
+        for section in conf.SECTIONS:
+            tmpcols = getattr(getattr(conf, section), 'config').keys()
+            columns += tmpcols
+            row += [self.formatcell(
+                getattr(getattr(conf, section), 'config')[key])
+                for key in tmpcols]
+        confdf = pd.DataFrame([row], columns=columns)
+        return confdf
+
+    def confstodf(self, paths):
+        """
+        Read several config files and convert them into a unique pandas
+        dataframe
+
+        Parameters
+        ----------
+        paths: list
+            list of config files
+
+        Returns
+        -------
+        maindf: pd.Dataframe object
+        """
+        maindf = None
+        for i, path in enumerate(paths):
+            df = self.conftodf(path)
+            maindf = pd.merge(maindf, df, how='outer', on='config') \
+                if i != 0 else df
+        return maindf
+
+    def run(self):
+        """
+        Fetch config files and convert them into a unique csv file
+        """
+        confiles = [None] + [confile for confile in
+                             self.settings.iniconv.args.get("confiles")]
+        LOG.info("Reading configuration file(s)")
+        configs = self.confstodf(confiles)
+        LOG.info("Generate output csv file (%s)", self.OUTFILE)
+        configs.to_csv(
+            os.path.join(self.settings.iniconv.args.get("output_directory"),
+                         self.OUTFILE)
+            if os.path.exists(
+                self.settings.iniconv.args.get("output_directory"))
+            else self.OUTFILE, index=False)

aria/conbox/settings.py

@@ -116,7 +116,8 @@ class Settings(object):
         return "<Settings object>\n    sections: %s" % self._sections
 
 
-# TODO: AriaEcSettings should probably be an astract class.
+# TODO: AriaEcSettings should be an astract class. Sections are actually
+# duplicated with AriaEcCommands
 class AriaEcSettings(Settings):
     """
     Settings object for ariaec
@@ -127,6 +128,7 @@ class AriaEcSettings(Settings):
     # TODO: move these constant variable in objects which can read these file !!
     # TODO: Baseclass inspired from this class and ariabase class. All
     # objects in this package should extend the base object
+    DEFAULT_CONFIG = "conf/config.ini"
     ARIAPROJ_TEMPLATE = 'templates/aria_project_v2.3.0.xml'
     SS_DIST = 'data/ss_dist.txt'
     SCSC_MIN = 'data/scsc_min.p'
@@ -141,7 +143,8 @@ class AriaEcSettings(Settings):
     # TODO: Should define sections in one object, actually we have to define
     # sections in settings and also command objects ...
     SECTIONS = ("main", "setup", "maplot", "bbconv", "contactdef",
-                "pdbqual", "pdbdist", "analysis", "tbl2xml", "pdbstat")
+                "pdbqual", "pdbdist", "analysis", "tbl2xml", "pdbstat",
+                "iniconv")
     # TODO: options in main section should be accessible from all sections ! DO
     #  not use this a other section as it is done actually
 
@@ -296,7 +299,7 @@ class AriaEcSettings(Settings):
             if not os.path.exists(self.infra[direct]):
                 os.makedirs(os.path.abspath(self.infra[direct]))
 
-    def load_config(self, configpath, **kwargs):
+    def load_config(self, configpath=None, **kwargs):
         """
         
 
@@ -312,7 +315,11 @@ class AriaEcSettings(Settings):
 
         
         """
-        super(AriaEcSettings, self).load_config(configpath, **kwargs)
+        if configpath:
+            super(AriaEcSettings, self).load_config(configpath, **kwargs)
+        else:
+            super(AriaEcSettings, self).load_config(
+                self.DEFAULT_CONFIG, pkg=True)
 
     def __getitem__(self, item):
         for section in self._sections:

aria/core/JobManager.py

@@ -285,8 +285,8 @@ class Job(Thread, AriaBaseClass):
             d['check_script'] = os.path.basename(d['check_script'])
 
         command = self.cmd_template % d
-        msg = 'Starting job %s'
-        self.message(msg % job_desc)
+        # msg = 'Starting job %s'
+        # self.message(msg % job_desc)
         self.debug(command)
 
         process = subprocess.Popen(command, shell=True,
@@ -331,11 +331,15 @@ class Job(Thread, AriaBaseClass):
             time.sleep(5.)
 
         if retcode or checkcode:
-            error = subprocess.CalledProcessError(
-                retcode, command.split(), output=out) if retcode else \
-                subprocess.CalledProcessError(checkcode, checkcmd.split(),
-                                              output=out)
-            self.error(str(error))
+            therror = subprocess.CalledProcessError(
+                    returncode=retcode,
+                    cmd=command,
+                    output=out) if retcode else \
+                subprocess.CalledProcessError(
+                    returncode=checkcode,
+                    cmd=checkcmd,
+                    output=out)
+            self.error(msg=str(therror))
 
         # Remove if exists updated checkpoint script
         try:
@@ -344,9 +348,9 @@ class Job(Thread, AriaBaseClass):
             pass
 
         if not self.isStopped() and terminated and checkpoint:
-            self.message('Job "%s" completed.' % job_desc)
+            self.message('Job %s completed.' % job_desc)
         else:
-            self.debug('Job "%s" has been canceled.\n' % job_desc)
+            self.debug('Job %s has been canceled.\n' % job_desc)
             self.debug('%s' % command)
 
         # notify that we are done.

aria/core/Project.py

@@ -1534,7 +1534,6 @@ class Project(AriaBaseClass):
         return iteration
 
     def load_and_preprocess_data(self):
-
         self.read_data()
         self.preprocess_data()
 

aria/core/Protocol.py

@@ -812,7 +812,6 @@ class Protocol(AriaBaseClass):
 
         
         """
-        from .Singleton import ProjectSingleton
 
         if kept_structures is None:
             kept_structures = []
@@ -2275,7 +2274,7 @@ class Protocol(AriaBaseClass):
             #
 
             # set spectrum-specific parametes for Calibrator
-            # TODO [FALLAIN]: User ERROR with wml distance files
+            # TODO [FALLAIN]: User ERROR with xml distance files
             self._updateSpectrumSettings(spectrum)
 
             if ensemble is None:

aria/core/ccpn_conversion.py

@@ -27,7 +27,6 @@ $Date: 2010/03/23 15:27:24 $
 """
 
 
-
 from .ariabase import AriaBaseClass
 from .Topology import TYPE_AMINO_ACID, TYPE_DNA_BASE, TYPE_RNA_BASE, \
      TERMINUS_N_STANDARD, TERMINUS_C_STANDARD, TERMINUS_N_AMINYL, \
@@ -45,7 +44,6 @@ if ccpn_path not in sys.path: sys.path.insert(0, ccpn_path)
 # TODO [FALLAIN] ccpn in ccpnmr package ?
 # noinspection PyUnresolvedReferences
 from ccpn.Global import false
-
 import ccpn.Api as api
 
 

docs.olds/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = AriaEc
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

docs.olds/_build/html/.buildinfo

+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: cbf8f1a8c4c0d68994ae9bd4f214590d
+tags: 645f666f9bcd5a90fca523b33c5a78b7