Add rdkit op

Signed-off-by: shiyu22 <shiyu.chen@zilliz.com>

README.md

@@ -1,2 +1,99 @@
-# rdkit
+# Molecular Fingerprinting
 
+*author: shiyu*
+
+<br />
+
+## Desription
+
+Molecular Fingerprinting encodes a Simplified Molecular Input Line Entry Specification (SMILES) as a fingerprint. The fingerprint can represent elements, atom pairs, or functional groups, etc., and are often used for substructure searches and similarity searches in drug discovery. 
+
+This operator uses [RDKit](https://www.rdkit.org/docs/index.html) to generate the molecular fingerprint.
+
+
+
+<br />
+
+
+
+## Code Example
+
+> Before running the following code, you need to install rdkit, refer to https://www.rdkit.org/docs/Install.html.
+>
+> ```
+> # install rdkit with conda
+> $ conda install -c conda-forge rdkit
+> ```
+
+An example that use the Morgan algorithm to generate a fingerprint of the molecular formula 'Cc1ccc(cc1)S(=O)(=O)N'.
+
+ *Write the pipeline in simplified style:*
+
+```python
+import towhee
+
+towhee.dc(['Cc1ccc(cc1)S(=O)(=O)N']) \
+  .molecular_fingerprinting.rdkit() \
+  .show()
+```
+<img src="./result1.png" height="35px"/>
+
+*Write a same pipeline with explicit inputs/outputs name specifications:*
+
+```python
+import towhee
+
+towhee.dc['smiles'](['Cc1ccc(cc1)S(=O)(=O)N']) \
+  .molecular_fingerprinting.rdkit['smiles', 'fingerprint']() \
+  .show()
+```
+<img src="./result2.png" height="75px"/>
+
+
+
+<br />
+
+
+
+## Factory Constructor
+
+Create the operator via the following factory method:
+
+***molecular_fingerprinting.rdkit( algorithm: str = 'morgan', size: int = 2048)***
+
+
+
+**Parameters:**
+
+***algorithm:*** *str*
+
+Which algorithm to use for fingerprinting, including 'morgan', 'daylight', 'ap', 'maccs', defaluts to 'morgan', and there is the [list of available fingerprints](https://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-fingerprints).
+
+
+
+***size:*** *int*
+
+The bit vector size just for morgan and daylight algorithm, defaults to 2048.
+
+
+
+<br />
+
+
+
+## Interface
+
+An molecular fingerprinting operator takes a SMILES as input.
+It uses the RDKit specified by algorithm name to generate a SMILES fingerprint.
+
+**Parameters:**
+
+***smiles:*** *str*
+
+A Simplified Molecular Input Line Entry Specification (SMILES).
+
+
+
+**Returns:** *bytes*
+
+The molecular fingerprint.

__init__.py

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+# Copyright 2021 Zilliz. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from .rdkit import Rdkit
+
+
+def rdkit(**kwargs):
+    return Rdkit(**kwargs)

rdkit.py

@@ -0,0 +1,53 @@
+# Copyright 2021 Zilliz. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from towhee import register
+from towhee.operator import Operator
+
+from rdkit import DataStructs, Chem
+
+@register(output_schema=['fingerprint'])
+class Rdkit(Operator):
+    """
+    Generate molecular fingerprint with RDKit.
+    
+    Args:
+        algorithm (`str`):
+            Which algorithm to use for fingerprinting, including morgan, daylight, ap, maccs, and defaluts to 'morgan'.
+        size (`int`):
+            The bit vector size, defaults to 2048.
+    """
+
+    def __init__(self, algorithm: str = 'morgan', size: int = 2048):
+        self.algorithm = algorithm
+        self.size = size
+
+    def __call__(self, smiles: str):
+        mols = Chem.MolFromSmiles(smiles)
+        if self.algorithm == 'daylight':
+            fp = Chem.RDKFingerprint(mols, fpSize=self.size)
+        elif self.algorithm == 'morgan':
+            from rdkit.Chem import AllChem
+            AllChem.GetMorganFingerprint
+            fp = AllChem.GetMorganFingerprintAsBitVect(mols, 2, self.size)
+        elif self.algorithm == 'ap':
+            from rdkit.Chem.AtomPairs import Pairs
+            fp = Pairs.GetAtomPairFingerprintAsBitVect(mols)
+        elif self.algorithm == 'maccs':
+            from rdkit.Chem import MACCSkeys
+            fp = MACCSkeys.GenMACCSKeys(mols)
+
+        hex_fp = DataStructs.BitVectToFPSText(fp)
+        fingerprint = bytes.fromhex(hex_fp)
+        return fingerprint