Merge branch 'prody:main' into interactions

prody/database/dali.py

@@ -515,7 +515,7 @@ def getTitle(self):
 
         return self._title
 
-def daliFilterMultimer(atoms, dali_rec, n_chains=None):
+def daliFilterMultimer(atoms, dali_rec, n_chains=None, reverse=False):
     """
     Filters multimers to only include chains with Dali mappings.
 
@@ -524,6 +524,14 @@ def daliFilterMultimer(atoms, dali_rec, n_chains=None):
 
     :arg dali_rec: the DaliRecord object with which to filter chains
     :type dali_rec: :class:`.DaliRecord`
+
+    :arg n_chains: the number of chains in multimers to keep
+        Default is None, keeping all multimers
+    :arg n_chains: int
+
+    :arg reverse: whether to reverse filtering to exclude by n_chain
+        Default is False
+    :type reverse: bool
     """
     if not isinstance(atoms, Atomic):
         raise TypeError("atoms should be an Atomic object")
@@ -535,6 +543,12 @@ def daliFilterMultimer(atoms, dali_rec, n_chains=None):
     except:
         raise AttributeError("Dali Record does not have any data yet. Please run fetch.")
 
+    if not isinstance(n_chains, (int, type(None))):
+        raise TypeError('n_chains should be None or an integer')
+
+    if not isinstance(reverse, bool):
+        raise TypeError('reverse should be a Boolean')
+
     numChains = 0
     atommap = None
     for i, chain in enumerate(atoms.iterChains()):
@@ -546,17 +560,32 @@ def daliFilterMultimer(atoms, dali_rec, n_chains=None):
             else:
                 atommap += chain
 
-    if n_chains is None or numChains == n_chains:
-        return atommap
-    else:
-        return None
+    if n_chains is None or \
+        not reverse and numChains == n_chains or \
+            reverse and numChains != n_chains:
+        return atommap       
+    return None
 
-def daliFilterMultimers(structures, dali_rec, n_chains=None):
+def daliFilterMultimers(structures, dali_rec, n_chains=None, reverse=False):
     """A wrapper for daliFilterMultimer to apply to multiple structures.
+
+    :arg structures: a list of :class:`.Atomic` objects to be filtered
+    :type structures: list
+
+    :arg dali_rec: the DaliRecord object with which to filter chains
+    :type dali_rec: :class:`.DaliRecord`
+
+    :arg n_chains: the number of chains in multimers to keep
+        Default is None, keeping all multimers
+    :arg n_chains: int
+
+    :arg reverse: whether to reverse filtering to exclude by n_chain
+        Default is False
+    :type reverse: bool
     """
     dali_ags = []
     for entry in structures:
-        result = daliFilterMultimer(entry, dali_rec, n_chains)
+        result = daliFilterMultimer(entry, dali_rec, n_chains, reverse)
         if result is not None:
             dali_ags.append(result)
     return dali_ags

prody/dynamics/anmd.py

@@ -43,7 +43,7 @@
 
 __all__ = ['runANMD']
 
-def runANMD(atoms, num_modes=2, max_rmsd=2., num_steps=2, tolerance=10.0,
+def runANMD(atoms, num_modes=2, max_rmsd=2., num_steps=5, tolerance=10.0,
             **kwargs):
     """Runs the ANMD hybrid simulation method ([CM22]_), which generates conformations
     along single modes using :func:`.traverseModes` and minimises them. 
@@ -67,7 +67,7 @@ def runANMD(atoms, num_modes=2, max_rmsd=2., num_steps=2, tolerance=10.0,
     :type max_rmsd: float
 
     :arg num_steps: number of conformers in each direction for each mode
-        Default is 2
+        Default is 5
     :type num_steps: int
 
     :arg tolerance: tolerance for energy minimisation in OpenMM 

prody/tests/dynamics/test_anmd.py

@@ -32,12 +32,12 @@ def testAnmdAtomsWrongType(self):
     def testAnmdNumModesWrongType(self):
         """Test response to wrong type *num_modes* argument."""
         if prody.PY3K:
-            self.assertRaises(TypeError, self.runANMD, self.ATOMS, 'nogood')
+            self.assertRaises(TypeError, self.runANMD, self.ATOMS, 'nogood', num_steps=2)
 
     def testAnmdRmsdWrongType(self):
         """Test response to wrong type *max_rmsd* argument."""
         if prody.PY3K:
-            self.assertRaises(TypeError, self.runANMD, self.ATOMS, max_rmsd='nogood')
+            self.assertRaises(TypeError, self.runANMD, self.ATOMS, max_rmsd='nogood', num_steps=2)
 
     def testAnmdStepsWrongType(self):
         """Test response to wrong type *num_steps* argument."""
@@ -47,14 +47,14 @@ def testAnmdStepsWrongType(self):
     def testAnmdToleranceWrongType(self):
         """Test response to wrong type *tolerance* argument."""
         if prody.PY3K:
-            self.assertRaises(TypeError, self.runANMD, self.ATOMS, tolerance='nogood')
+            self.assertRaises(TypeError, self.runANMD, self.ATOMS, tolerance='nogood', num_steps=2)
 
 class TestAnmdResults(TestANMD):
 
     def testResults(self):
         """Test results with default parameters"""
         if prody.PY3K:
-            DEFAULT_RESULTS = runANMD(self.ATOMS)
+            DEFAULT_RESULTS = runANMD(self.ATOMS, num_steps=2)
             ens1 = DEFAULT_RESULTS[0]
 
             assert_equal(len(DEFAULT_RESULTS), 2,
@@ -70,7 +70,7 @@ def testResults(self):
     def testResultsNumModes1(self):
         """Test that num_modes=1 gives 1 ensemble"""
         if prody.PY3K:
-            RESULTS = runANMD(self.ATOMS, num_modes=1)
+            RESULTS = runANMD(self.ATOMS, num_modes=1, num_steps=2)
             assert_equal(len(RESULTS), 1,
                         'runANMD with num_modes=1 failed to give 1 ensemble')