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RRD: A Reactivity-Related bond/atom-wise Descriptors (RRD) package

Project description

PyPI version

A package to compute the Reactivity-Related bond/atom-wise Descriptors (RRD).

Installation

# 安装依赖
pip install RRD

Usage

from RRD import RRDCalculator
RRDC = RRDCalculator(scale=True)
smiles = 'CCCC'

## one smiles
dfa, dfb = RRDC.transform(smiles)

## many smiles: compute in parallel
smiles_list = [smiles for i in range(20)]
res = RRDC.batch_transform(smiles_list, n_jobs=-1)

TODO list

  • Buried Volume: trained model-based
  • Frontier orbital energy

List of descriptors in our RRD package

Descriptor Description Atom/Bond Ref. Package
PC Hirshfeld partial charge Atom [1] qmdesc
FN Neucleuphilic Fukui indices Atom [1] qmdesc
FE Electrophilic Fukui indices Atom [1] qmdesc
NSC NMR shielding constants Atom [1] qmdesc
GC GasteigerCharge Atom [2] Rdkit
MR Molar refractivity Atom [3] Rdkit
Apol Atomic polarizability Atom [4] Rdkit
SHI Steric hindrance index Atom [5] -
TSEI Toplogical steric effect index Atom [5] -
OV Occupied volume Atom [7] Trained, DBSTEP
PBV Percent buried volume Atom [7] Trained, DBSTEP
PSV Percent shell volume Atom [7] Trained, DBSTEP
SB Single bond Bond - -
DB Double bond Bond - -
TB Triple bond Bond - -
AB Aromatic bond Bond - -
CB Conjugation bond Bond - -
RB Ring bond Bond - -
SN Stereo-None Bond - -
SA Stereo-Any Bond - -
SS Stereo-S Bond - -
SR Stereo-R Bond - -
BO Bond order Bond [1] qmdesc
BL Bond length Bond [1] qmdesc
BDE Bond dissociation enthalpies Bond [6] alfabet
BDFE Bond dissociation free energies Bond [6] alfabet

Refernces

  • [1]. Guan, Yanfei, et al. "Regio-selectivity prediction with a machine-learned reaction representation and on-the-fly quantum mechanical descriptors." Chemical science 12.6 (2021): 2198-2208.
  • [2]. J.Gasteiger, M. Marseli, Iterative Equalization of Oribital Electronegatiity A Rapid Access to Atomic Charges, Tetrahedron Vol 36 p3219 1980
  • [3]. Wildman, Scott A., and Gordon M. Crippen. "Prediction of physicochemical parameters by atomic contributions." Journal of chemical information and computer sciences 39.5 (1999): 868-873.
  • [4]. Miller and Savchik, JACS 101(24) 7206-7213, 1979.
  • [5]. Cao, Chenzhong, and Li Liu. "Topological steric effect index and its application." Journal of chemical information and computer sciences 44.2 (2004): 678-687.
  • [6]. St John, Peter C., et al. "Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost." Nature communications 11.1 (2020): 1-12.
  • [7]. A. Poater, F. Ragone, R. Mariz, R. Dorta and L. Cavallo, Chem. Eur. J. 2010, 16, 14348–14353.

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