[Rdkit-discuss] non-element elements

[Brian Peterson]

Hello RDKit people,

Is it possible to modify the properties of elements in the periodic 
table or to create new ones?  Use case: Suppose one had some molecules 
defined in terms of functional groups or united atoms or some other 
entities that are not pure elemental atoms. Could one map these things 
on to unused elements (e.g. my_functional_group --> U) and fix up the 
properties of U so that it had the appropriate valence etc. and could be 
present both in a molecule and in SMARTS patterns so that one could do 
substructure matches within RDKit?


Thanks,
Brian

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Re: [Rdkit-discuss] Atom object comparison in python

[Brian Peterson]

Thanks Paolo. Makes sense.

On 1/8/2021 4:54 AM, Paolo Tosco wrote:

Hi Brian,

when you fetch a Chem.Atom object from a Chem.Mol a Python object is 
created on-the-fly that wraps the underlying C++ object.
Every time you do this, a new Python object is created. This does not 
apply only to GetNeighbors(); please see an example below:


In [1]: from rdkit import Chem

In [2]: mol = Chem.MolFromSmiles("C")

In [3]: a0_1 = mol.GetAtomWithIdx(0)

In [4]: a0_2 = mol.GetAtomWithIdx(0)

In [5]: a0_1 == a0_2
Out[5]: False

In [6]: a0_1
Out[6]: 

In [7]: a0_2
Out[7]: 

In [8]: a0_1.GetIdx() == a0_2.GetIdx()
Out[8]: True

In short, you cannot rely on comparing Chem.Atom object identity, but 
you can certainly rely on their index.


Cheers,
p.

On Fri, Jan 8, 2021 at 5:00 AM Brian Peterson 
mailto:brian.peter...@molsight.com>> wrote:


Hello all. When traversing a molecule's atoms with
atom.GetNeighbors(),
the object returned for an atom is not necessarily the same object
returned when the atom is indexed directly from the molecule. This
means
one can't directly compare two atoms as objects found while
traversing a
molecule via neighbors to see if they are the same atom. It seems
a new
object is created for the atom returned by .GetNeighbors(). Is this
expected behavior and what is the reason for this? I've found that
the
comparison can be done by using atom.GetIdx(), but wanted to use the
objects themselves for various reasons. Thanks.

Example:
-

from rdkit import Chem

m = Chem.MolFromSmiles('C(F)(Cl)(Br)(I)')
atoms = [myatom for myatom in m.GetAtoms()]
for myatom in atoms:
 print(myatom.GetIdx(),myatom.GetSymbol(),myatom)

print("The neighbors of {} are:".format(atoms[1].GetSymbol()))
for newatom in atoms[1].GetNeighbors():
 print(newatom.GetIdx(),newatom.GetSymbol(),newatom)

print("C0 == C0 ?")
print(atoms[0] == newatom)

Output:

0 C 
1 F 
2 Cl 
3 Br 
4 I 
The neighbors of F are:
0 C 
C0 == C0 ?
False






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[Rdkit-discuss] Atom object comparison in python

[Brian Peterson]

Hello all. When traversing a molecule's atoms with atom.GetNeighbors(), 
the object returned for an atom is not necessarily the same object 
returned when the atom is indexed directly from the molecule. This means 
one can't directly compare two atoms as objects found while traversing a 
molecule via neighbors to see if they are the same atom. It seems a new 
object is created for the atom returned by .GetNeighbors(). Is this 
expected behavior and what is the reason for this? I've found that the 
comparison can be done by using atom.GetIdx(), but wanted to use the 
objects themselves for various reasons. Thanks.


Example:
-

from rdkit import Chem

m = Chem.MolFromSmiles('C(F)(Cl)(Br)(I)')
atoms = [myatom for myatom in m.GetAtoms()]
for myatom in atoms:
    print(myatom.GetIdx(),myatom.GetSymbol(),myatom)

print("The neighbors of {} are:".format(atoms[1].GetSymbol()))
for newatom in atoms[1].GetNeighbors():
    print(newatom.GetIdx(),newatom.GetSymbol(),newatom)

print("C0 == C0 ?")
print(atoms[0] == newatom)

Output:

0 C 
1 F 
2 Cl 
3 Br 
4 I 
The neighbors of F are:
0 C 
C0 == C0 ?
False






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