Merge branch 'main' of github.com:prody/ProDy into buildMSA_clustalo

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/measure/measure.py

@@ -5,7 +5,7 @@
 
 from numpy import ndarray, power, sqrt, array, zeros, arccos, dot
 from numpy import sign, tile, concatenate, pi, cross, subtract, var
-from numpy import unique, where
+from numpy import unique, where, divide, power
 
 from prody.atomic import Atomic, Residue, Atom, extendAtomicData
 from prody.kdtree import KDTree
@@ -16,11 +16,11 @@
 if PY2K:
     range = xrange
 
-__all__ = ['buildDistMatrix', 'calcDistance',
-           'calcCenter', 'calcGyradius', 'calcAngle',
-           'calcDihedral', 'calcOmega', 'calcPhi', 'calcPsi',
-           'calcMSF', 'calcRMSF',
-           'calcDeformVector',
+__all__ = ['buildDistMatrix', 'calcDistance', 'calcGyradius',
+           'calcCenter', 'calcAngle', 'calcDihedral',
+           'getCenter', 'getAngle', 'getDihedral',
+           'calcOmega', 'calcPhi', 'calcPsi',
+           'calcMSF', 'calcRMSF', 'calcDeformVector',
            'buildADPMatrix', 'calcADPAxes', 'calcADPs',
            'pickCentral', 'pickCentralAtom', 'pickCentralConf', 'getWeights',
            'calcInertiaTensor', 'calcPrincAxes', 'calcDistanceMatrix',
@@ -207,13 +207,17 @@ def getDihedral(coords1, coords2, coords3, coords4, radian=False):
     a3 = coords4 - coords3
 
     v1 = cross(a1, a2)
-    v1 = v1 / (v1 * v1).sum(-1)**0.5
+    v1 = divide(v1, power((v1 * v1).sum(-1), 0.5).reshape(-1,1))
     v2 = cross(a2, a3)
-    v2 = v2 / (v2 * v2).sum(-1)**0.5
+    v2 = divide(v2, power((v2 * v2).sum(-1), 0.5).reshape(-1,1))
     porm = sign((v1 * a3).sum(-1))
     rad = arccos((v1*v2).sum(-1) / ((v1**2).sum(-1) * (v2**2).sum(-1))**0.5)
-    if not porm == 0:
+    if not all(porm == 0):
         rad = rad * porm
+
+    if rad.shape[0] == 1:
+        rad = rad[0]
+
     if radian:
         return rad
     else:

prody/proteins/ciffile.py

@@ -312,12 +312,12 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
     stop = 0
     while not doneAtomBlock:
         line = lines[i]
-        if line[:11] == '_atom_site.':
+        if line.strip()[:11] == '_atom_site.':
             fieldCounter += 1
             fields[line.split('.')[1].strip()] = fieldCounter
             foundAtomFields = True
 
-        elif foundAtomFields and line.strip() != '#':
+        elif foundAtomFields and line.strip() not in ['#', '']:
             if not foundAtomBlock:
                 foundAtomBlock = True
                 start = i

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')