bug fixes when template or contactfilter fields are empty in ini file

ariaec/conf/aria_ec.ini

@@ -7,10 +7,10 @@ ariaproject_template:
 
 [contactdef]
 ; Contact definition section used to define contactmap from pdb file
-default_cutoff:                             8.0
-ca_ca:
-cb_cb:
-sc_sc:
+default_cutoff:                             7.0
+ca_ca:                                      7.0
+cb_cb:                                      7.0
+sc_sc:                                      5.0
 ; Add other contact cutoff below folowwing the syntax atm1_atm2
 
 [setup]
@@ -60,9 +60,10 @@ cb_upper_bound:                             7.0
 ; ---------------------------- Filter parameters ----------------------------- #
 ; n_factor      : Number of EC selected: n * n_factor (n: sequence length)
 ; contactfilter : all or combinaison of pos, cons, cys, ssclash, nd
-;                 separated by "+" character [all]
+;                 separated by "+" character [all]. If empty, use only position
+;                 filter (avoid short range restraints)
 n_factor:                                   1.0
-contactfilter:
+contactfilter:                              all
 conservation_treshold:                      95
 position_treshold:                          5
 nd_beta:                                    0.99

ariaec/econverter.py

@@ -13,7 +13,7 @@ import os
 import sys
 import json
 import re
-
+import pkg_resources as pkgr
 import aria.legacy.AminoAcid as AminoAcid
 import aria.ConversionTable as ConversionTable
 import aria.conversion
@@ -127,6 +127,7 @@ reliable="{reliable}" list_name="{list_name}">
             for contrib_id in restraint_dict[restraint_id]["contrib"]:
                 res_id = restraint_dict[restraint_id]["contrib"][contrib_id][
                     "spin_pair"].keys()
+                print(res_id)
                 xml_file.write('''\
     <contribution id="{id}" weight="{weight}">
       <spin_pair>
@@ -500,7 +501,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
 
         for contactidx, contact in enumerate(pair_list):
             # /!\ humanidx in contact must start at 1 !n_factor
-
+            print(contact)
             # Add neighbors if neigh_flag
             resx_idx = range(min_ind(contact[0] - 1),
                              max_ind(contact[0] + 2, max_seqidx)) if \
@@ -610,6 +611,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
                         }
         xml_file = self.settings.infra["xml"] + "/" + "_".join((
             self.outprefix, listname)) + ".xml"
+        print(restraint_dict)
         self.write_dist_xml(restraint_dict, xml_file)
         return xml_file, pair_list
 
@@ -685,14 +687,20 @@ class AriaEcXMLConverter(AriaXMLConverter):
 
     def write_project(self, aria_template, seqfile, dist_files, tbl_files,
                       desc=""):
-        template = os.path.abspath(aria_template)
+        if aria_template:
+            template = os.path.abspath(aria_template)
 
-        try:
-            t = open(template, 'r')
-        except IOError:
-            sys.exit("""Can't open "%s" file.""" % template)
+            try:
+                t = open(template, 'r')
+            except IOError:
+                sys.exit("""Can't open "%s" file.""" % template)
 
-        aria_project_template = t.read()
+            aria_project_template = t.read()
+            t.close()
+        else:
+            logger.info("Reading default aria template file %s" % self.settings.ARIAPROJ_TEMPLATE)
+            aria_project_template = pkgr.resource_string(
+                __name__, self.settings.ARIAPROJ_TEMPLATE)
 
         aria_project_dict = {}
 
@@ -794,5 +802,3 @@ class AriaEcXMLConverter(AriaXMLConverter):
         with open(proj_file, 'w') as proj_xml:
             logger.info("Writing ARIA project file (%s)" % proj_file)
             proj_xml.write(aria_project_template % aria_project_dict)
-
-        t.close()

ariaec/protmap.py

@@ -946,8 +946,7 @@ class MapFilter:
         if mapfilters == "all":
             mapfilters = self.filter_types
         elif not mapfilters:
-            logger.info("No filter with %s map!" % mtype)
-            return mapdict
+            mapfilters = ("pos",)
         else:
             mapfilters = [elm for elm in mapfilters if elm in self.filter_types]
         logger.info("Filtering %s contact map" % mtype)

ariaec/setup.py

@@ -154,8 +154,9 @@ class AriaEcSetup:
 
         # ---------------------- ARIA XML project file ----------------------- #
         aria_template = self.settings.main.config["ariaproject_template"] if \
+            self.settings.main.config["ariaproject_template"] and \
             os.path.exists(self.settings.main.config["ariaproject_template"])\
-            else self.settings.template
+            else None
         self.converter.write_project(aria_template,
                                      seq_file, dist_files, tbl_files,
                                      desc="_".join(sorted(self.allresmap.keys())))