Pdbstat distance type functionnal

ariaec/conf/config.ini

@@ -72,26 +72,20 @@ hb_dplus:                                   0.5
 ;                                 use all, heavy atms or from a minimized
 ;                                 list (CA, CB, SC) for contribution list for
 ;                                 each distance restraint
-; pair_product                  : True, False [True]
-;                                 Define if there is more than one contribution
-;                                 per atom type. If True, compute pairwise
-;                                 product between contribution lists of the 2
-;                                 residues. Otherwise, pair_list will be a
+; atoms_type                    : all, heavy, min [min]
+;                                 use all, heavy atms or from a minimized
+;                                 list (CA, CB, SC) for contribution list for
+;                                 each distance restraint
+; contributions_type            : same, allvsall, onevsall [same]
+;                                 By default contributions list will be a
 ;                                 simple list between atoms of the same type
-;                                 (CA-CA, CB-CB, ...)
-; ambiguous_distance_restraint  : True, False [False]
-;                                 Generate Ambiguous Distance Restraints.
-;                                 Otherwise, each distance restraints will have
-;                                 only one contribution (unambiguous distance
-;                                 restraints)
-; ambiguous_distance_type       : min, deff [min]
-;                                 compute Deff or min distance as target
-;                                 distance if reference structure given
-; ambiguous_restraint_type      : allvsall, onevsall [allvsall]
-;                                 generate one ADR for all contribution pairs or
-;                                 one ADR foreach atom in first res against all
-;                                 the others in second res defined by
-;                                 contribution list
+;                                 (CA-CA, CB-CB, ...). Otherwise, compute
+;                                 pairwise product between contribution
+;                                 lists of the 2 residues (onevsall and
+;                                 allvsall). In the case of ADR, onevsall will
+;                                 generate one ADR for all contribution pairs
+;                                 between an atom of the first residue against
+;                                 all the other atoms in the second residue
 ; distance_type                 : fixed, pdbstat, distfile [fixed]
 ;                                 Define distance use for target distance. By
 ;                                 default the target distance is fixed by
@@ -100,22 +94,25 @@ hb_dplus:                                   0.5
 ;                                 (not yet implemented) or given by the user can
 ;                                 be used.
 ; pdbdistance_level             : ss, res,
-; groupby_method                : mean, min [min]
+; groupby_method                : mean, min, deff [min]
 ;                                 If a distance map is used for setting distance
-;                                 target, define if we use min or mean distance
-;                                 values at residu level.
+;                                 target, define if we use min, mean or deff
+;                                 distance on all the possible values.
+; ambiguous_distance_restraint  : True, False [False]
+;                                 Generate Ambiguous Distance Restraints.
+;                                 Otherwise, each distance restraints will have
+;                                 only one contribution (unambiguous distance
+;                                 restraints)
 native_reliable:                            False
 evfold_weight:                              False
 neighborhood_contact:                       False
-pair_list:                                  min
-pair_product:                               True
-ambiguous_distance_restraint:               False
-ambiguous_restraint_type:                   onevsall
-ambiguous_distance_type:                    min
-deffpow:                                    6
+atoms_type:                                 min
+contributions_type:                         same
 distance_type:                              fixed
-pdbdistance_level:                          ss
 groupby_method:                             min
+deffpow:                                    6
+pdbdistance_level:                          ss
+ambiguous_distance_restraint:               False
 ; Parameters below used only when distance_type is set to "fixed"
 restraint_distance:                         2.5
 lower_bound:                                1.0

ariaec/protein.py

@@ -61,6 +61,19 @@ class SsList(object):
         else:
             return []
 
+    @property
+    def sequence(self):
+        """
+        
+        Returns
+        -------
+
+        """
+        if self.ss_matrix:
+            return [_ for _ in zip(*self.ss_matrix)[2]]
+        else:
+            return []
+
     def check_filetype(self, filename):
         """
         

ariaec/protmap.py

@@ -936,10 +936,10 @@ class ProteinMap(Map):
                 if scoremap is not None:
                     score = scoremap.iat[(int(contact[0]) - offset,
                                           int(contact[1]) - offset)]
-                    outfile.write("%d %d %.4f" %
+                    outfile.write("%d %d %.4f\n" %
                                   (contact[0], contact[1], score))
                 else:
-                    outfile.write("%d %d" % (contact[0], contact[1]))
+                    outfile.write("%d %d\n" % (contact[0], contact[1]))
 
 
 class ResAtmMap(ProteinMap):

ariaec/reader.py

@@ -849,8 +849,10 @@ class MapFileListReader(object):
             if os.path.exists(filepath):
                 # TODO: check_type functionstr
                 LOG.debug("Adding %s file to watchlist", maptypes[i])
-                if maptypes[i].lower() == "pdb" and \
-                        os.path.splitext(filepath)[1][1:] == "pdb":
+                if (maptypes[i].lower() == "pdb" and
+                        os.path.splitext(filepath)[1][1:] == "pdb") or (
+                    maptypes[i].lower() == "distfile" and
+                        os.path.splitext(filepath)[1][1:] == "pdb"):
                         self.maps.append(PDBFile(filepath))
                 else:
                     self.maps.append(ContactMapFile(filepath,