使用
模块信息
介绍文档
| 编号 | 22 | |
| 名称 | Descriptors (RDKit) | |
| 封面 |  | |
| 描述 | 基于RDKit计算小分子的2D和3D描述符 | |
| 标签 |
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| 作者 | Manish Sud | |
| 发布时间 | 2021-10-22 09:00:29 | |
| 参考文献 | Sud M. MayaChemTools: An Open Source Package for Computational Drug Discovery. J Chem Inf Model. 2016 Dec 27;56(12):2292-2297. | |
目录导航
- 简介
- 参数说明
- Input File
- Output File
- Multiprocessing
- Type
- Descriptor Names
- 结果说明
- 参考文献
Descriptors (RDKit)
简介
Descriptors (RDKit)模块是计算分子的2D/3D描述符并将其写入SD或CSV/TSV文本文件中。2D描述符：Autocorr2D、MolWt、Ipc、NumRotatableBonds、qed等；3D描述符：Autocorr3D、RadiusOfGyration、Eccentricity等；以及FragmentCountOnly描述符：fr_Al_COO、fr_Al_OH、fr_Al_OH_noTert等。支持的输入文件格式为：Mol（.mol）、SD（.sdf、.sd）、SMILES（.smi、.txt、.csv、.tsv）。支持的输出文件格式为：SD文件（.sdf、.sd）、CSV/TSV（.csv、.tsv、.txt）。
参数说明
Input File
小分子结构文件，SDF或者SMILES格式。
Output File
输出文件以保存计算的描述符。
Multiprocessing
使用多进程处理（默认：yes）。
Type
计算分子描述符的类型，可选值有2D、3D、FragmentCountOnly和Specify。
2D描述符包括以下：
Autocorr2D, BalabanJ, BertzCT, Chi0, Chi1, Chi0n - Chi4n, Chi0v - Chi4v, EState_VSA1 - EState_VSA11, ExactMolWt, FpDensityMorgan1, FpDensityMorgan2, FpDensityMorgan3, FractionCSP3, HallKierAlpha, HeavyAtomCount, HeavyAtomMolWt, Ipc, Kappa1 - Kappa3, LabuteASA, MaxAbsEStateIndex, MaxAbsPartialCharge, MaxEStateIndex, MaxPartialCharge, MinAbsEStateIndex, MinAbsPartialCharge, MinEStateIndex, MinPartialCharge, MolLogP, MolMR, MolWt, NHOHCount, NOCount, NumAliphaticCarbocycles, NumAliphaticHeterocycles, NumAliphaticRings, NumAromaticCarbocycles, NumAromaticHeterocycles, NumAromaticRings, NumHAcceptors, NumHDonors, NumHeteroatoms, NumRadicalElectrons, NumRotatableBonds, NumSaturatedCarbocycles, NumSaturatedHeterocycles, NumSaturatedRings, NumValenceElectrons, PEOE_VSA1 - PEOE_VSA14, RingCount, SMR_VSA1 - SMR_VSA10, SlogP_VSA1 - SlogP_VSA12, TPSA, VSA_EState1 - VSA_EState10, qed
FragmentCountOnly描述符包括以下：
fr_Al_COO, fr_Al_OH, fr_Al_OH_noTert, fr_ArN, fr_Ar_COO, fr_Ar_N, fr_Ar_NH, fr_Ar_OH, fr_COO, fr_COO2, fr_C_O, fr_C_O_noCOO, fr_C_S, fr_HOCCN, fr_Imine, fr_NH0, fr_NH1, fr_NH2, fr_N_O, fr_Ndealkylation1, fr_Ndealkylation2, fr_Nhpyrrole, fr_SH, fr_aldehyde, fr_alkyl_carbamate, fr_alkyl_halide, fr_allylic_oxid, fr_amide, fr_amidine, fr_aniline, fr_aryl_methyl, fr_azide, fr_azo, fr_barbitur, fr_benzene, fr_benzodiazepine, fr_bicyclic, fr_diazo, fr_dihydropyridine, fr_epoxide, fr_ester, fr_ether, fr_furan, fr_guanido, fr_halogen, fr_hdrzine, fr_hdrzone, fr_imidazole, fr_imide, fr_isocyan, fr_isothiocyan, fr_ketone, fr_ketone_Topliss, fr_lactam, fr_lactone, fr_methoxy, fr_morpholine, fr_nitrile, fr_nitro, fr_nitro_arom, fr_nitro_arom_nonortho, fr_nitroso, fr_oxazole, fr_oxime, fr_para_hydroxylation, fr_phenol, fr_phenol_noOrthoHbond, fr_phos_acid, fr_phos_ester, fr_piperdine, fr_piperzine, fr_priamide, fr_prisulfonamd, fr_pyridine, fr_quatN, fr_sulfide, fr_sulfonamd, fr_sulfone, fr_term_acetylene, fr_tetrazole, fr_thiazole, fr_thiocyan, fr_thiophene, fr_unbrch_alkane, fr_urea
3D描述符包括以下：
Asphericity, Autocorr3D, Eccentricity, GETAWAY, InertialShapeFactor, MORSE, NPR1, NPR2, PMI1, PMI2, PMI3, RDF, RadiusOfGyration, SpherocityIndex, WHIM
Descriptor Names
此选项仅在Type为“Specify”时使用。当应用多个描述符时，由逗号分隔描述符，如MolWt, qed。
结果说明
得到各个分子指定描述符的数值在descriptors.csv文件中。
