deprecation prep

prody/dynamics/heatmapper.py

@@ -6,7 +6,7 @@
 
 __author__ = 'Ahmet Bakan, Anindita Dutta'
 
-from numpy import arange, fromstring, array
+from numpy import arange, fromstring, frombuffer, array
 
 from prody.utilities import openFile, intorfloat, startswith, addext
 
@@ -131,7 +131,11 @@ def parseHeatmap(heatmap, **kwargs):
             numbers.append(items[:nnums])
         else:
             items = [arr]
-        heatmap.append(fromstring(items[-1], float, sep=';'))
+
+        try:
+            heatmap.append(fromstring(items[-1], float, sep=';'))
+        except:
+            heatmap.append(frombuffer(items[-1], float, sep=';'))
 
     heatmap = array(heatmap)
     if nnums:

prody/dynamics/nmdfile.py

@@ -272,7 +272,11 @@ def parseNMD(filename, type=NMA):
 
     line, coords = atomic.pop('coordinates', None)
     if coords is not None:
-        coords = np.fromstring(coords, dtype=float, sep=' ')
+        try:
+            coords = np.fromstring(coords, dtype=float, sep=' ')
+        except:
+            coords = np.frombuffer(coords, dtype=float, sep=' ')
+
         dof = coords.shape[0]
         if dof % 3 != 0:
             LOGGER.warn('Coordinate data in {0} at line {1} is corrupt '
@@ -325,7 +329,11 @@ def parseNMD(filename, type=NMA):
     eigvals = []
     count = 0
     for i, (line, mode) in enumerate(modes):
-        mode = np.fromstring(mode, dtype=float, sep=' ')
+        try:
+            mode = np.fromstring(mode, dtype=float, sep=' ')
+        except:
+            mode = np.frombuffer(mode, dtype=float, sep=' ')
+
         diff = len(mode) - dof
         if diff < 0 or diff > 2:
             LOGGER.warn('Mode data in {0} at line {1} is corrupt.'

prody/proteins/header.py

@@ -1100,15 +1100,28 @@ def buildBiomolecules(header, atoms, biomol=None):
         for times in range(int((len(mt)) / 4)):
             rotation = np.zeros((3, 3))
             translation = np.zeros(3)
-            line0 = np.fromstring(mt[times*4+1], sep=' ')
+
+            try:
+                line0 = np.fromstring(mt[times*4+1], sep=' ')
+            except:
+                line0 = np.frombuffer(mt[times*4+1], sep=' ')
             rotation[0, :] = line0[:3]
             translation[0] = line0[3]
-            line1 = np.fromstring(mt[times*4+2], sep=' ')
+
+            try:
+                line1 = np.fromstring(mt[times*4+2], sep=' ')
+            except:
+                line1 = np.frombuffer(mt[times*4+2], sep=' ')
             rotation[1, :] = line1[:3]
             translation[1] = line1[3]
-            line2 = np.fromstring(mt[times*4+3], sep=' ')
+
+            try:
+                line2 = np.fromstring(mt[times*4+3], sep=' ')
+            except:
+                line2 = np.frombuffer(mt[times*4+3], sep=' ')
             rotation[2, :] = line2[:3]
             translation[2] = line2[3]
+
             t = Transformation(rotation, translation)
 
             newag = atoms.select('chain ' + ' or chain '.join(mt[times*4+0]))

prody/sequence/msa.py

@@ -154,8 +154,16 @@ def __getitem__(self, index):
         if isinstance(rows, list):
             rows = self.getIndex(rows) or rows
         elif isinstance(rows, int):
-            return Sequence(self._msa[rows, cols].tobytes(),
-                            self._labels[rows])
+            if PY3K:
+                try:
+                    return Sequence(self._msa[rows, cols].tostring().decode(),
+                                    self._labels[rows])
+                except:
+                    return Sequence(self._msa[rows, cols].tobytes().decode(),
+                                    self._labels[rows])
+            else:
+                return Sequence(self._msa[rows, cols].tostring(),
+                                self._labels[rows])
         elif isinstance(rows, str):
             try:
                 rows = self._mapping[rows]
@@ -164,8 +172,12 @@ def __getitem__(self, index):
                                .format(index))
             else:
                 if isinstance(rows, int):
-                    return Sequence(self._msa[rows, cols].tobytes(),
-                                    self._labels[rows])
+                    try:
+                        return Sequence(self._msa[rows, cols].tostring(),
+                                        self._labels[rows])
+                    except:
+                        return Sequence(self._msa[rows, cols].tobytes(),
+                                        self._labels[rows])
 
         if cols is None:
             msa = self._msa[rows]
@@ -546,7 +558,16 @@ def refineMSA(msa, index=None, label=None, rowocc=None, seqid=None, colocc=None,
                 from prody.utilities import GAP_PENALTY, GAP_EXT_PENALTY, ALIGNMENT_METHOD
 
                 chseq = chain.getSequence()
-                algn = alignBioPairwise(pystr(arr[index].tobytes().upper()), pystr(chseq),
+
+                if PY3K:
+                    try:
+                        arr2 = arr[index].tostring().decode()
+                    except:
+                        arr2 = arr[index].tobytes().decode()
+                else:
+                    arr2 = arr[index].tostring()
+
+                algn = alignBioPairwise(pystr(arr2.upper()), pystr(chseq),
                                         "local",
                                         MATCH_SCORE, MISMATCH_SCORE,
                                         GAP_PENALTY, GAP_EXT_PENALTY,

prody/sequence/msafile.py

@@ -6,7 +6,7 @@
 
 from os.path import isfile, splitext, split, getsize
 
-from numpy import array, fromstring, empty
+from numpy import array, fromstring, empty, frombuffer
 
 from .sequence import splitSeqLabel, Sequence
 
@@ -425,15 +425,22 @@ def setSlice(self, slice):
             try:
                 seq[slice]
             except Exception:
-                arr = fromstring(seq, '|S1')
+                try:
+                    arr = fromstring(seq, '|S1')
+                except:
+                    arr = frombuffer(seq, '|S1')
                 try:
                     arr[slice]
                 except Exception:
                     raise TypeError('invalid slice: ' + repr(slice))
                 else:
                     self._slice = slice
-                    self._slicer = lambda seq, slc=slice: fromstring(seq,
-                                                        '|S1')[slc].tobytes()
+                    try:
+                        self._slicer = lambda seq, slc=slice: fromstring(seq,
+                                                            '|S1')[slc].tostring()
+                    except:
+                        self._slicer = lambda seq, slc=slice: fromstring(seq,
+                                                            '|S1')[slc].tobytes()
             else:
                 self._slice = slice
                 self._slicer = lambda seq, slc=slice: seq[slc]

prody/sequence/sequence.py

@@ -49,7 +49,10 @@ def _array(self):
     def __str__(self):
 
         if PY3K:
-            return self._array.tobytes().decode()
+            try:
+                return self._array.tostring().decode()
+            except:
+                return self._array.tobytes().decode()
         else:
             return self._array.tobytes()