WolframChemistry/ChemistryFunctions

WolframChemistry`ChemistryFunctions`

MoleculeScaffold

MoleculeScaffold [mol]
	returns a version of mol in which all terminal atoms have been iteratively removed,leaving only the ring systems and the bonds that connect them.

MoleculeScaffold [mol,"type"]
	returns the scaffold of the given type.

Details and Options



Examples

(4)

Basic Examples

(1)

Find the scaffold for a molecule:

In[1]:=

MoleculeScaffold

m=Molecule

Formula:

C

14

H

16

Cl

N

5

Atoms:

36

Bonds:

38



Out[1]=

Molecule

Formula:

C

9

H

6

N

4

Atoms:

19

Bonds:

21



Highlight the substructure in a plot:

In[2]:=

MoleculePlot[m,%]

Out[2]=

Set all the atoms in the scaffold to carbon and the bonds to single:

In[3]:=

MoleculeScaffold

[m,"AllCarbonMolecule"]

Out[3]=

Molecule

Formula:

C

13

H

22

Atoms:

35

Bonds:

37



Scope

(1)



Applications

(2)



SeeAlso

Molecule

▪

MoleculePattern

RelatedGuides

▪

Wolfram Chemistry Functions

RelatedLinks

▪

Bemis G. W.; Murcko M. A. The Properties of Known Drugs. 1. Molecular Frameworks. J. Med. Chem. 1996, 39, 2887–2893. 10.1021/jm9602928.

▪

Buehler Y, Reymond JL. Molecular Framework Analysis of the Generated Database GDB-13s. J Chem Inf Model. 2023 Jan 23;63(2):484-492. doi: 10.1021/acs.jcim.2c01107.

""