distance_bounds now floats

CHANGELOG.rst

@@ -5,6 +5,7 @@ Changelog
 v0.8.3dev1
 ----------
 
+- Distance definitions accept floating point values
 - Bug fix in ``PconsParser`` class to accept negative ``raw_score`` values
 - Bug fix in ``SequenceFile.neff`` which returned ``float`` instead of ``int``
 - ``requirements.txt`` file re-added for easier dependency installation

conkit/core/contact.py

@@ -118,7 +118,7 @@ def __init__(self, res1_seq, res2_seq, raw_score, distance_bound=(0, 8)):
            The residue sequence number of residue 2
 
         """
-        self._distance_bound = [0, 8]
+        self._distance_bound = [0., 8.]
         self._raw_score = 1.0
         self._res1 = 'X'
         self._res2 = 'X'
@@ -195,7 +195,7 @@ def lower_bound(self, value):
 
         Parameters
         ----------
-        value : int
+        value : int, float 
 
         Raises
         ------
@@ -209,7 +209,7 @@ def lower_bound(self, value):
             raise ValueError('Lower bound must be positive')
         elif value >= self.upper_bound:
             raise ValueError('Lower bound must be smaller than upper bound')
-        self._distance_bound[0] = value
+        self._distance_bound[0] = float(value)
 
     @property
     def upper_bound(self):
@@ -222,7 +222,7 @@ def upper_bound(self, value):
 
         Parameters
         ----------
-        value : int
+        value : int, float
 
         Raises
         ------
@@ -236,7 +236,7 @@ def upper_bound(self, value):
             raise ValueError('Upper bound must be positive')
         elif value <= self.lower_bound:
             raise ValueError('Upper bound must be larger than lower bound')
-        self._distance_bound[1] = value
+        self._distance_bound[1] = float(value)
 
     @property
     def raw_score(self):
@@ -249,7 +249,7 @@ def raw_score(self, score):
 
         Parameters
         ----------
-        score : float
+        score : int, float
 
         """
         self._raw_score = float(score)

conkit/io/casp.py

@@ -155,7 +155,7 @@ def read(self, f_handle, f_id="casp"):
                             res2_chain, res2_seq = res2_split[1], res2_split[2]
 
                         contact = Contact(int(res1_seq), int(res2_seq), float(raw_score),
-                                          distance_bound=(int(lb), int(ub)))
+                                          distance_bound=(float(lb), float(ub)))
                         contact.res1_chain = res1_chain
                         contact.res2_chain = res2_chain
                         contact.res1_altseq = int(res1_seq)
@@ -221,9 +221,10 @@ def write(self, f_handle, hierarchy):
                 else:
                     res1_chain = contact.res1_chain
                     res2_chain = contact.res2_chain
+                lb = int(contact.lower_bound) if float(contact.lower_bound).is_integer() else contact.lower_bound
+                ub = int(contact.upper_bound) if float(contact.upper_bound).is_integer() else contact.upper_bound
                 s = s.format(res1_chain=res1_chain, res1_seq=contact.res1_seq, res2_chain=res2_chain,
-                             res2_seq=contact.res2_seq, lb=contact.distance_bound[0], ub=contact.distance_bound[1],
-                             raw_score=contact.raw_score)
+                             res2_seq=contact.res2_seq, lb=lb, ub=ub, raw_score=contact.raw_score)
                 content += s + os.linesep
             content += "ENDMDL" + os.linesep
 

conkit/io/epcmap.py

@@ -74,7 +74,7 @@ def read(self, f_handle, f_id="epcmap"):
 
             elif line[0].isdigit():
                 _contact = Contact(int(line[0]), int(line[1]), float(line[4]),
-                                   distance_bound=(int(line[2]), int(line[3])))
+                                   distance_bound=(float(line[2]), float(line[3])))
                 _map.add(_contact)
 
         hierarchy.method = 'Contact map predicted using EPC-Map'
@@ -108,8 +108,10 @@ def write(self, f_handle, hierarchy):
         for contact_map in contact_file:
             for contact in contact_map:
                 line = "{res1_seq} {res2_seq} {lb} {ub} {raw_score:.6f}"
+                lb = int(contact.lower_bound) if float(contact.lower_bound).is_integer() else contact.lower_bound
+                ub = int(contact.upper_bound) if float(contact.upper_bound).is_integer() else contact.upper_bound
                 line = line.format(res1_seq=contact.res1_seq, res2_seq=contact.res2_seq, raw_score=contact.raw_score,
-                                   lb=contact.distance_bound[0], ub=contact.distance_bound[1])
+                                   lb=lb, ub=ub)
                 content += line + os.linesep
 
         f_handle.write(content)

conkit/io/pdb.py

@@ -182,7 +182,7 @@ def _read(self, structure, f_id, distance_cutoff, atom_type):
                         atom1.resseq,
                         atom2.resseq,
                         round(1.0-(distance/100), 6),
-                        distance_bound=(0, distance_cutoff)
+                        distance_bound=(0., float(distance_cutoff))
                     )
 
                     contact.res1_altseq = atom1.resseq_alt

conkit/io/psicov.py

@@ -75,7 +75,7 @@ def read(self, f_handle, f_id="psicov"):
 
             elif line[0].isdigit():
                 _contact = Contact(int(line[0]), int(line[1]), float(line[4]),
-                                   distance_bound=(int(line[2]), int(line[3])))
+                                   distance_bound=(float(line[2]), float(line[3])))
                 _map.add(_contact)
 
         hierarchy.method = 'Contact map predicted using PSICOV'
@@ -109,8 +109,10 @@ def write(self, f_handle, hierarchy):
         for contact_map in contact_file:
             for contact in contact_map:
                 line = "{res1_seq} {res2_seq} {lb} {ub} {raw_score:.6f}"
+                lb = int(contact.lower_bound) if float(contact.lower_bound).is_integer() else contact.lower_bound
+                ub = int(contact.upper_bound) if float(contact.upper_bound).is_integer() else contact.upper_bound
                 line = line.format(res1_seq=contact.res1_seq, res2_seq=contact.res2_seq, raw_score=contact.raw_score,
-                                   lb=contact.distance_bound[0], ub=contact.distance_bound[1])
+                                   lb=lb, ub=ub)
                 content += line + os.linesep
 
         f_handle.write(content)