merge

Author: hcji

Example/test_fingerprint.py

@@ -8,7 +8,7 @@
 import numpy as np
 from PyFingerprint.fingerprint import get_fingerprint, get_fingerprints
 
-cdktypes = ['standard', 'extended', 'graph', 'maccs', 'pubchem', 'estate', 'hybridization', 'lingo', 'klekota-roth', 'shortestpath', 'cdk-substructure', 'circular', 'atompairs', 'signature']
+cdktypes = ['standard', 'extended', 'graph', 'maccs', 'pubchem', 'estate', 'hybridization', 'lingo', 'klekota-roth', 'shortestpath', 'cdk-substructure', 'circular', 'cdk-atompairs', 'signature']
 rdktypes = ['rdkit', 'morgan', 'rdk-maccs', 'topological-torsion', 'avalon', 'atom-pair', 'rdk-descriptor']
 babeltypes = ['fp2', 'fp3', 'fp4', 'spectrophore']
 vectypes = ['mol2vec']
@@ -48,4 +48,4 @@
 
 output_np = output.copy()
 for k, fps in output.items():
-    output_np[k] = np.array([fp.to_numpy() for fp in fps])
+    output_np[k] = np.array([fp.to_numpy() for fp in fps])

PyFingerprint/rdk.py

@@ -29,7 +29,7 @@ def calcDescriptors(mol):
 def rdk_fingerprint(smi, fp_type="rdkit", depth=None, size=None):
 
     mol = Chem.MolFromSmiles(smi)
-    mol = Chem.AddHs(mol)
+    mol = Chem.RemoveHs(mol)
 
     if not depth == None:
 	    if fp_type == "avalon":