Merge pull request #1179 from jamesmkrieger/prody-master

Final changes before making release v1.11

prody/database/dali.py

@@ -165,6 +165,7 @@ def __init__(self, url, pdbId, chain, subset='fullPDB', localFile=False, **kwarg
         self._title = pdbId + '-' + chain
         self._alignPDB = None
         self._filterDict = None
+        self._max_index = None
         self.isSuccess = self.fetch(self._url, localFile=localFile, timeout=timeout, **kwargs)
 
     def fetch(self, url=None, localFile=False, **kwargs):
@@ -377,6 +378,10 @@ def filter(self, cutoff_len=None, cutoff_rmsd=None, cutoff_Z=None, cutoff_identi
         (3) Z score < cutoff_Z (must be a positive number);
         (4) Identity > cutoff_identity (must be an integer or a float between 0 and 1).
         """
+        if self._max_index is None:
+            LOGGER.warn('DaliRecord has no data. Please use the fetch() method.')
+            return None
+
         if cutoff_len == None:
             # cutoff_len = int(0.8*self._max_index)
             cutoff_len = 0

prody/dynamics/plotting.py

@@ -1148,9 +1148,9 @@ def showPerturbResponse(model, atoms=None, show_matrix=True, select=None, **kwar
     *model* and *atoms* must have the same number of atoms. *atoms* must 
     be an :class:`.Atomic` instance.
 
-    :arg model: any object with a calcCovariance method
-        e.g. :class:`.ANM` instance
-    :type model: :class:`.NMA`
+    :arg model: any object with a calcCovariance method from which to calculate
+         a PRS matrix (e.g. :class:`.ANM` instance) or a PRS matrix itself
+    :type model: :class:`.NMA`, :class:`~numpy.ndarray`
 
     :arg atoms: a :class: `AtomGroup` instance for matching residue numbers and chain 
         identifiers