RDKit计算分子属性

RDKit计算分子属性

  分子属性的计算在化学、药物研发和生物信息学等领域中具有重要意义。这些属性包括分子的物理化学性质、生物活性、构象信息和其他关键特征，它们对于药物筛选、分子设计、毒理学评估以及生物分子研究等任务至关重要。RDKit，作为一款强大的开源工具包，被广泛应用于计算和分析分子属性。本文将探讨如何使用RDKit来计算和分析分子属性。

  RDKit是一个Python库，专注于化学信息学和药物化学领域。它提供了丰富的功能，可以用于处理、分析和可视化分子数据。从计算分子的物化性质，如溶解度和分配系数，到生成分子的二维和三维结构，RDKit都提供了一系列功能强大的工具。这些功能使研究人员和科学家能够更好地理解和设计分子，为药物发现和生物学研究提供有力支持。

  在本文中，我们将探讨常见的分子属性计算方法以及如何使用RDKit库进行分子属性计算。

1. 计算脚本

from rdkit.Chem import Descriptors 
from rdkit import Chem 
#读入smiles格式的分子 
m = Chem.MolFromSmiles('c1ccccc1C(=O)O') 
#计算属性 
Descriptors.Kappa2(m)

2. RDKit能够计算的属性

Index	Descriptor/Descriptor Family	Details
Class1	GraphDescriptors	Topological/topochemical descriptors
1	BalabanJ	This method calculates the Balaban J index，which is a type of topological index.
2	BertzCT	A topological index meant to quantify “complexity” of molecules.
3	Ipc	This returns the information content of the coefficients of the characteristic polynomial of the adjacency matrix of a hydrogen-suppressed graph of a molecule.
4	HallKierAlpha	The Hall-Kier alpha value for a molecule.
5	Kappa1 - Kappa3	Hall-Kier Kappa1 value.
6	Chi0, Chi1	From equations (1),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991).
7	Chi0n - Chi4n	Similar to Hall Kier Chi0v, but uses nVal instead of valence. This makes a big difference after we get out of the first row.
8	Chi0v - Chi4v	From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991).
Class2	Descriptors	General descriptors
9	MolLogP	Wildman-Crippen LogP value.
10	MolMR	Wildman-Crippen MR value.
11	MolWt	The average molecular weight of the molecule.
12	ExactMolWt	The exact molecular weight of the molecule.
13	HeavyAtomCount	Thenumber of the molecule ignoring hydrogens.
14	HeavyAtomMolWt	The average molecular weight of the molecule ignoring hydrogens.
15	NHOHCount	The number of NHs or OHs.
16	NOCount	The number of Nitrogens and Oxygens.
17	NumHAcceptors	The number of Hydrogen Bond Acceptors.
18	NumHDonors	The number of Hydrogen Bond Donors.
19	NumHeteroatoms	The number of Heteroatoms.
20	NumRotatableBonds	The number of Rotatable Bonds.
21	NumValenceElectrons	The number of valence electrons the molecule has.
22	NumAromaticRings	The number of aromatic rings for a molecule.
23	NumSaturatedRings	The number of saturated rings for a molecule.
24	NumAliphaticRings	The number of aliphatic (containing at least one non-aromatic bond) rings for a molecule.
25	NumAromaticHeterocycles	The number of aromatic heterocycles for a molecule.
26	NumAromaticCarbocycles	The number of aromatic carbocycles for a molecule.
27	NumSaturatedHeterocycles	The number of saturated heterocycles for a molecule.
28	NumSaturatedCarbocycles	The number of saturated carbocycles for a molecule.
28	NumAliphaticHeterocycles	The number of aliphatic (containing at least one non-aromatic bond) heterocycles for a molecule.
30	NumAliphaticCarbocycles	The number of aliphatic (containing at least one non-aromatic bond) carbocycles for a molecule.
31	RingCount	Ring count.
32	FractionCSP3	The fraction of C atoms that are SP3 hybridized.
33	TPSA	The polar surface area of a molecule based upon fragments.
34	LabuteASA	Labute’s Approximate Surface Area.