Hi Greg, Thank you so much for the help!
Pure RDKit functionality really helpful! Thanks, Xuan ________________________________ 发件人: Greg Landrum <greg.land...@gmail.com> 发送时间: 2019年1月4日 0:08 收件人: Cao Xuan 抄送: rdkit-discuss@lists.sourceforge.net 主题: Re: [Rdkit-discuss] 转发: Reading the fingerprint 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<mailto: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<mailto: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<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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