Updated to python 3.5 syntax

ariaec/base.py

@@ -13,7 +13,7 @@ import sys
 import numpy as np
 import pkg_resources as pkgr
 import matplotlib.artist as art
-from cStringIO import StringIO
+from io import StringIO
 
 
 logger = logging.getLogger()
@@ -289,10 +289,8 @@ class Capturing(list):
         sys.stdout = self._stringio = StringIO()
         return self
 
-    def __exit__(self, *args):
+    def __exit__(self,):
         """
-
-        :param args:
         :return:
         """
         self.extend("\n".join(self._stringio.getvalue().splitlines()))

ariaec/commands.py

@@ -27,6 +27,9 @@ def check_file(prospective_file):
 
 class ReadableFile(argp.Action):
 
+    def __init__(self, *args, **kwargs):
+        super(ReadableFile, self).__init__(*args, **kwargs)
+
     def __call__(self, parser, namespace, values, option_string=None):
         if type(values) == list:
             for prospective_file in values:

ariaec/econverter.py

@@ -13,7 +13,6 @@ import os
 import sys
 import json
 import re
-import pkg_resources as pkgr
 import aria.legacy.AminoAcid as AminoAcid
 from .base import get_filename, Capturing
 from .protein import Protein
@@ -307,7 +306,7 @@ assign (resid {res1} and name o) (resid {res2} and name hn)  1.8 {dminus} {dplus
         # Build global secondary structure distance restraints (H-H+4, E-E+1,
         #  ...)
         with open(outfile, 'w') as outfile:
-            for a in xrange(len(sec_struct) - 1):
+            for a in range(len(sec_struct) - 1):
                 for b in range(a + 1, len(sec_struct)):
                     ss1 = sec_struct[a][2]
                     ss2 = sec_struct[b][2]
@@ -331,7 +330,7 @@ assign (resid {res1} and name {atm1}) (resid {res2} and name {atm2})  {dist} {sd
     def write_dihedral_tbl(sec_struct, outfile, k=0.5, e=2):
         # Build dihedral angle restraints (phi, psi)
         with open(outfile, "w") as outfile:
-            for i in xrange(len(sec_struct)):
+            for i in range(len(sec_struct)):
                 if (i + 1) != len(sec_struct):
                     if sec_struct[i][2] == sec_struct[i + 1][2]:
                         # Si ss identique
@@ -396,6 +395,12 @@ assign (resid {res1} and name n) (resid {res1} and name ca) (resid {res1} and na
 
 
 class AriaEcXMLConverter(AriaXMLConverter):
+
+    @staticmethod
+    def _write_hbmap_tbl(hbmap, outfile, dminus, dplus, n_hb=None, hb_type="main", topo=None):
+        AriaXMLConverter._write_hbmap_tbl(hbmap, outfile, dminus, dplus, n_hb=None, hb_type="main",
+                                          topo=None)
+
     def __init__(self, *args, **kwargs):
         self.restraint_list = []
         super(AriaEcXMLConverter, self).__init__(*args, **kwargs)
@@ -711,7 +716,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
             self._pickler.dump(self.molecule, self._mol_set[
                 'output'])
 
-        except Exception, msg:
+        except Exception as msg:
 
             logger.error("Error writing xml seq file : %s" % msg)
 
@@ -732,7 +737,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
 
         templatepath = os.path.abspath(aria_template)
         ariaproj_template = Template(filename=templatepath,
-                                    module_directory="/tmp/mako_modules")
+                                     module_directory="/tmp/mako_modules")
 
         try:
             t = open(templatepath, 'r')

ariaec/ecsettings.py

@@ -5,9 +5,9 @@ from __future__ import absolute_import, division, print_function
 
 import logging
 import os
-import ConfigParser
+from configparser import SafeConfigParser
 import collections
-import cPickle as Pickle
+import pickle
 import pkg_resources as pkgr
 
 from .base import format_dict
@@ -42,7 +42,7 @@ class Settings(object):
         elif not pkg:
             logger.error("Configuration file not found (%s)" % configpath)
             return None
-        config = ConfigParser.SafeConfigParser(allow_no_value=True)
+        config = SafeConfigParser(allow_no_value=True)
         if pkg:
             with pkgr.resource_stream(__name__, configpath) as conf:
                 config.readfp(conf)
@@ -62,7 +62,7 @@ class Settings(object):
     def write_config(self, filename):
         # Ecrit les config de toutes les sections dans un autre fichier
         logger.info("Writing .ini file (%s)" % filename)
-        config = ConfigParser.SafeConfigParser(allow_no_value=True)
+        config = SafeConfigParser(allow_no_value=True)
         iniout = open(filename, mode="w")
         for section in self._sections:
             config.add_section(section)
@@ -151,12 +151,12 @@ class AriaEcSettings(Settings):
             try:
                 # Read scsc_min_file given in aria_ec.ini
                 with open(self.main.config["scsc_min_file"]) as scsc:
-                    scsc_min = Pickle.load(scsc)
+                    scsc_min = pickle.load(scsc)
             except (IOError, KeyError, TypeError):
                 # If file can't be open or given key is invalid, load default
                 # package file
                 with pkgr.resource_stream(__name__, self.SCSC_MIN) as scsc:
-                    scsc_min = Pickle.load(scsc)
+                    scsc_min = pickle.load(scsc)
             scsc_min = dict(
                 (aa1, dict((aa2, tuple(atm_pair.split(', ')))
                            for aa2, atm_pair in atm_pairs.items()))

ariaec/protein.py

@@ -11,6 +11,7 @@ import logging
 import pkg_resources as pkgr
 import aria.legacy.SequenceList as SequenceList
 import aria.legacy.AminoAcid as AmnAcd
+from six import iteritems
 from .base import (reg_load, Capturing, ppdict)
 # import skbio.Protein as skprot
 # TODO: interface skbio ??
@@ -211,7 +212,7 @@ class SsList:
         try:
             with open(filename) as f:
                 self._read_ssdist(f, filename=filename)
-        except Exception, message:
+        except Exception as message:
             logger.error("%s" % message)
             logger.error("Can't load given ss dist file...")
             logger.error("Loading default ss dist file")
@@ -242,7 +243,7 @@ class SsList:
     # TODO: read_dssp
 
 
-class AminoAcidSequence(SequenceList.SequenceList):
+class AminoAcidSequence(SequenceList.SequenceList, object):
 
     startres_reg = re.compile(r"^\s*residue\s+(?P<name>[A-Za-z]{1,4})", flags=re.I)
     end_reg = re.compile(r"^\s*end", flags=re.I)
@@ -277,7 +278,7 @@ class AminoAcidSequence(SequenceList.SequenceList):
         :param kwargs:
         :return:
         """
-        SequenceList.SequenceList.__init__(self, *args, **kwargs)
+        super(AminoAcidSequence, self).__init__(*args, **kwargs)
         self._topfile = topologyfile
         self._topology = None
         self._topok = False
@@ -303,7 +304,7 @@ class AminoAcidSequence(SequenceList.SequenceList):
                 self._topology = [(aa, topo[aa]) for aa in self.aalist]
                 self._topok = True
             else:
-                self._topology = list(topo.iteritems())
+                self._topology = list(iteritems(topo))
         return self._topology
 
     def __getitem__(self, key):
@@ -324,7 +325,7 @@ class AminoAcidSequence(SequenceList.SequenceList):
 
     def readtopo(self):
         """
-
+        Parse topology file for amino acids
         :return:
         """
         topo = {}
@@ -346,24 +347,24 @@ class AminoAcidSequence(SequenceList.SequenceList):
                         resname = ""
                         continue
                     # Walk along reg dict
-                    for regid, reg in self.restatement_reg.iteritems():
+                    for regid, reg in iteritems(self.restatement_reg):
+                        if regid not in topo[resname]:
+                            topo[resname][regid] = []
                         if regid == "bond":
                             match = re.findall(reg, line)
+                            if match:
+                                topo[resname][regid] += match
+                                break
                         else:
                             match = reg.search(line)
-                        if match:
-                            if regid not in topo[resname]:
-                                topo[resname][regid] = []
-                            if regid == "bond":
-                                # Add 2-tuple
-                                topo[resname][regid] += match
-                            elif regid in ("improper", "dihedral"):
-                                # Add tuple into list since we need atm order
-                                topo[resname][regid].append(match.groups())
-                            else:
-                                # Add dict
-                                topo[resname][regid].append(match.groupdict())
-                            break
+                            if match:
+                                if regid in ("improper", "dihedral"):
+                                    # Add tuple into list since we need atm order
+                                    topo[resname][regid].append(match.groups())
+                                else:
+                                    # Add dict
+                                    topo[resname][regid].append(match.groupdict())
+                                break
         logger.debug("Topology used:\n%s" % ppdict(topo))
         return topo
 

ariaec/protmap.py

@@ -41,8 +41,11 @@ class Map(pd.DataFrame):
 
     mtype_choices = {'contact': bool, 'distance': float, "score": float}
 
-    def _constructor_expanddim(self):
-        super(Map, self)._constructor_expanddim()
+    def update(self, *args, **kwargs):
+        super(Map, self).update(*args, **kwargs)
+
+    # def _constructor_expanddim(self):
+    #     super(Map, self)._constructor_expanddim()
 
     def __init__(self, index=None, columns=None, mtype='distance',
                  duplicate_levels=False, data=None, dtype=None, sym=True,
@@ -660,7 +663,7 @@ class ResAtmMap(ProteinMap):
                                    "the default cutoff)" % str(pair))
                 logger.info(
                     "Filtering values in matrix related to %s (%s)" %
-                    (str(pair), str(treshold)))
+                    (str(pair), str(treshold) if treshold else def_cutoff))
                 if pair in (("SC", "SC"), ("sc", "sc")):
                     # Use scsc_min to apply treshold updateonly for selected atom
                     # sidechain
@@ -757,8 +760,8 @@ class AaMap(Map):
     Amino Acid Distance Matrix
     """
 
-    def _constructor_expanddim(self):
-        super(AaMap, self)._constructor_expanddim()
+    # def _constructor_expanddim(self):
+    #     super(AaMap, self)._constructor_expanddim()
 
     def __init__(self, *args, **kwargs):
         if ("humanidx", "columns") not in kwargs:
@@ -781,8 +784,8 @@ class AtmMap(Map):
     Atom Distance Matrix
     """
 
-    def _constructor_expanddim(self):
-        super(AtmMap, self)._constructor_expanddim()
+    # def _constructor_expanddim(self):
+    #     super(AtmMap, self)._constructor_expanddim()
 
     def __init__(self, *args, **kwargs):
         super(AtmMap, self).__init__(*args, **kwargs)
@@ -1037,7 +1040,7 @@ class MapFilter:
         ss_start_end = collections.defaultdict(lambda: [None, None])
 
         # TODO: deplacer construction du dic ss_start_end dans SsList
-        for res_ind in xrange(len(ss_matrix)):
+        for res_ind in range(len(ss_matrix)):
             # Construction du dict ss_start_end
             if res_ind == 0:
                 # If first residue
@@ -1082,7 +1085,7 @@ class MapFilter:
                 for n in (1, 2, 3, 4):
 
                     # Search type of the bond (H-1 H, E-2 E, ...)
-                    for i in xrange(2):
+                    for i in range(2):
                         # Test both sides
 
                         resi = contact[i]
@@ -1331,8 +1334,7 @@ class MapFilter:
                 else:
                     op = "added"
                     ctype = clash
-                meta_clash[clash_t]["warn"] += "\n/!\ Clash: {clash_desc} {" \
-                                               "clash} flag for contact " \
+                meta_clash[clash_t]["warn"] += "\n/!\ Clash: {clash_desc} {clash} flag for contact " \
                                                "{res_pos} ({res1}, {res2})".format(
                     clash_desc=op, clash=ctype, res_pos=icontact + 1,
                     res1=contact[0], res2=contact[1])

setup.py

@@ -97,7 +97,7 @@ setup(
         'seaborn',
         'scipy',
         'sklearn',
-        'colorlog',
+        'colorlog', 'mako',
         # 'scikit-bio==0.4.0',
         # 'aria==2.3'
     ],

version.py

 # Do not edit this file, pipeline versioning is governed by git tags
-__version__=v0.1.11-dev2-8-g4239f50
\ No newline at end of file
+__version__=v0.1.11-dev2-16-gb1e477c
\ No newline at end of file