Merge pull request #1823 from jamesmkrieger/kmedoids

add kmedoid clustering

prody/utilities/catchall.py

@@ -11,7 +11,8 @@
 __all__ = ['calcTree', 'clusterMatrix', 'showLines', 'showMatrix', 
            'reorderMatrix', 'findSubgroups', 'getCoords',  
            'getLinkage', 'getTreeFromLinkage', 'clusterSubfamilies', 
-           'calcRMSDclusters', 'calcGromosClusters', 'calcGromacsClusters']
+           'calcRMSDclusters', 'calcGromosClusters', 'calcGromacsClusters',
+           'calcKmedoidClusters']
 
 class LinkageError(Exception):
     pass
@@ -1032,3 +1033,15 @@ def calcRMSDclusters(rmsd_matrix, c, labels=None):
 
 calcGromosClusters = calcRMSDclusters
 calcGromacsClusters = calcRMSDclusters
+
+def calcKmedoidClusters(coordsets, nClusters):
+    try:
+        from sklearn_extra.cluster import KMedoids
+    except ImportError:
+        raise ImportError('Please install scikit-learn-extra to run this function')
+
+    X = coordsets.reshape(coordsets.shape[0], -1)
+    c = KMedoids(n_clusters=nClusters, random_state=0).fit(X)
+    labels = c.labels_
+    _, counts = np.unique(labels, return_counts=True)
+    return c.medoid_indices_, labels, counts