Greetings,
Could someone please clarify how can I pass atomic partial charges to the
ECFP fingerprint generator along with the default atomic properties that it
considers? Can I pass the real charge values or do I have to group them
into bins and pass the bin identifier? I found a function in utilsFP.py
file which generates invariants as follows:
def generateAtomInvariant(mol):
"""
>>> generateAtomInvariant(Chem.MolFromSmiles("Cc1ncccc1"))
[341294046, 3184205312, 522345510, 1545984525, 1545984525,
1545984525, 1545984525]
"""
num_atoms = mol.GetNumAtoms()
invariants = [0]*num_atoms
for i,a in enumerate(mol.GetAtoms()):
descriptors=[]
descriptors.append(a.GetAtomicNum())
descriptors.append(a.GetTotalDegree())
descriptors.append(a.GetTotalNumHs())
descriptors.append(a.IsInRing())
descriptors.append(a.GetIsAromatic())
invariants[i]=hash(tuple(descriptors))& 0xffffffff
return invariants
And then generate the fingerprint like this:
fp = AllChem.GetMorganFingerprint(mol, radius=3,
invariants=generateAtomInvariant(mol))
Would just suffice to add this extra line in generateAtomInvariant() function?
descriptors.append(a.GetFormalCharge())
I thank you in advance.
Thomas
--
======================================================================
Dr. Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
&
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic
email: teva...@gmail.com, Twitter: tevangelidis
<https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
<https://www.linkedin.com/in/thomas-evangelidis-495b45125/>
website: https://sites.google.com/site/thomasevangelidishomepage/
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