add calcConvergenceRMSDs

prody/dynamics/adaptive.py

@@ -20,7 +20,7 @@
 from prody.atomic import Atomic, AtomMap
 from prody.utilities import getCoords, createStringIO, importLA, checkCoords, copy
 
-from prody.measure.transform import calcTransformation, superpose, applyTransformation, calcRMSD
+from prody.measure.transform import calcTransformation, superpose, applyTransformation, calcRMSD, getRMSD
 from prody.measure.measure import calcDeformVector, calcDistance
 
 from prody.ensemble.ensemble import Ensemble
@@ -717,6 +717,32 @@ def getRMSDsB(self):
 
         return calcRMSD(self._atomsB, self._confs[:, indices], weights)
 
+    def getConvergenceRMSDs(self):
+        if self._confs is None or self._coords is None:
+            return None
+
+        indices = self._indices
+        if indices is None:
+            indices = np.arange(self._confs.shape[1])
+
+        weights = self._weights[indices] if self._weights is not None else None
+
+        n_confs = self.numConfs()
+        confsA = self._confs[::2]
+        if n_confs % 2:
+            confsB = self._confs[-2::-2]
+        else:
+            confsB = self._confs[-1::-2]
+
+        n_confsA = len(confsA)
+        n_confsB = len(confsB)
+        RMSDs = zeros((n_confsA, n_confsB))
+        for i in range(n_confsA):
+            for j in range(n_confsB):
+                RMSDs[i, j] = getRMSD(confsA[i, indices], confsB[j, indices], weights)
+
+        return RMSDs
+
     def _generate(self, confs, **kwargs):
 
         LOGGER.info('Sampling conformers in generation %d ...' % self._cycle)

prody/dynamics/comd.py

@@ -1,6 +1,6 @@
 from prody.proteins.pdbfile import parsePDB, writePDBStream, parsePDBStream
-from prody.measure.transform import calcRMSD, calcTransformation, superpose, applyTransformation
-from prody.measure.measure import buildDistMatrix, calcDeformVector, calcDistance
+from prody.measure.transform import calcRMSD, calcTransformation, getRMSD, applyTransformation
+from prody.measure.measure import buildDistMatrix, calcDeformVector
 from prody.ensemble.ensemble import Ensemble
 from prody.utilities import createStringIO, importLA, checkCoords, copy
 
@@ -537,6 +537,32 @@ def getRMSDsB(self):
 
         return calcRMSD(self._atomsB, self._confs[:, indices], weights)
 
+    def getConvergenceRMSDs(self):
+        if self._confs is None or self._coords is None:
+            return None
+
+        indices = self._indices
+        if indices is None:
+            indices = np.arange(self._confs.shape[1])
+
+        weights = self._weights[indices] if self._weights is not None else None
+
+        n_confs = self.numConfs()
+        confsA = self._confs[::2]
+        if n_confs % 2:
+            confsB = self._confs[-2::-2]
+        else:
+            confsB = self._confs[-1::-2]
+
+        n_confsA = len(confsA)
+        n_confsB = len(confsB)
+        RMSDs = zeros((n_confsA, n_confsB))
+        for i in range(n_confsA):
+            for j in range(n_confsB):
+                RMSDs[i, j] = getRMSD(confsA[i, indices], confsB[j, indices], weights)
+
+        return RMSDs
+
     def run(self, cutoff=15., n_modes=20, gamma=1., n_confs=50, rmsd=1.0,
             n_gens=5, solvent='imp', sim=False, force_field=None, temp=303.15,
             t_steps_i=1000, t_steps_g=7500,