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