[Rdkit-discuss] 答复: 转发: Reading the fingerprint

[Cao Xuan]

Hi Greg,

Thank you so much for the help!

Pure RDKit functionality really helpful!

Thanks,
Xuan


发件人: Greg Landrum 
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 
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=).

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
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] 转发: Reading the fingerprint

[Cao Xuan]

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=).

Thank you for help!
Xuan
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Method about calculating Pi electro negativity in rdkit

[Cao Xuan]

Hi,

Is there a method that can calculates the pi electronegativity of a given atom 
in rdkit package?

Thanks!
Xuan 



___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Is that possible to get features/descriptors for single atoms in a molecule

[Cao Xuan]

Hi,


I am just wondering does rdkit support the functionality of get descriptors 
value for single atoms of a molecules.


For example, in cdk, they have following function:

// mol is molecule object; atoms.get(i) returns a single atoms

// descriptor.calculate will calculate the descriptor value for the 
atoms.get(i) in mol

IDescriptorResult res = descriptor.calculate(atoms.get(i), mol).getValue();



For example, I want to calculate the RDF of the molecules 
(rdkit.Chem.rdMolDescriptors.CalcRDF),

After I called Chem.rdMolDescriptors.CalcRDF(mol), I got a large list with RDF 
values; then I tried the following


>>> Chem.rdMolDescriptors.CalcRDF(mol,2)
Traceback (most recent call last):
  File "", line 1, in 
ValueError: Bad Conformer Id


So I assume that the Conformer Id correspond to each individual atoms?



Thank you so much!

Xuan
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss