Hi Xuan, The easiest way to do this, and the one I'd recommend using most of the time, is using Python's builtin pickle mechanism:
In [5]: fp = Chem.RDKFingerprint(m) In [6]: import pickle In [7]: fp2 = pickle.loads(pickle.dumps(fp)) In [8]: fp == fp2 Out[8]: True But you can also use pure RDKit functionality if you want. This method uses an RDKit-internal format (the same used by pickling): In [9]: fp2 = DataStructs.ExplicitBitVect(fp.ToBinary()) In [10]: fp == fp2 Out[10]: True This method uses a binary string directly encoding the contents of the fingerprint: In [12]: fp2 = DataStructs.CreateFromBinaryText( DataStructs.BitVectToBinaryText(fp) ) In [13]: fp == fp2 Out[13]: True And, finally, the least efficient approach (using a string of 0s and 1s): In [14]: fp2 = DataStructs.CreateFromBitString(fp.ToBitString()) In [15]: fp == fp2 Out[15]: True I hope this helps, -greg On Thu, Jan 3, 2019 at 4:36 PM Cao Xuan <danis....@hotmail.com> wrote: > > ------------------------------ > *发件人:* Cao Xuan > *发送时间:* 2019年1月3日 0:25 > *收件人:* rdkit-discuss@lists.sourceforge.net > *主题:* Reading the fingerprint > > Hi All, > > Is that possible to store the fingerprint on disk in string or byte > format, and then read the fingerprint by initialize an > empty DataStructs.cDataStructs.ExplicitBitVect() (I tried to call SetBit() > and SetBitFromList() but no success). > > I also found the post > https://sourceforge.net/p/rdkit/mailman/message/28969251/ but it is using > C++, while I am using the python. > > # > bit_binary_text = DataStructs.cDataStructs.BitVectToBinaryText(fps) > temp_bitvect = DataStructs.cDataStructs.ExplicitBitVect(bit_binary_text) > > > ValueError: bad version in BitVect pickle > > The reason that I want to read fingerprint from disk is because I want to > do similarity check with rdkit.DataStructs.FingerprintSimilarity(fp1, fp2, > metric=<Boost.Python.function object>). > > Thank you for help! > Xuan > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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