RDkit画分子结构

 输入为包含分子的SMILES表示符，输出为.png或.svg格式的图片，其中凯库勒式分子结构的样式，包含键长、键宽、图大小、原子和键的高亮表示等功能，具体参考了RDkit的手册------The RDKit Documentation — The RDKit 2023.03.1 documentation

''' SMILES is used to create tailored 2D molecular pictures to assist reaxFF
    reaction network analysis, the mol image format supports png and svg ,
    Written by Rui Zhou, UCAS '''

import os
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D

def createPng(sms_content):
    for i in range(len(sms_content)):
        mol = Chem.MolFromSmiles(sms_content[i])
        drawer = rdMolDraw2D.MolDraw2DCairo(150, 350)
        do = rdMolDraw2D.MolDrawOptions()
        do.bondLineWidth = 5                    # 键宽
        do.fixedBondLength = 50                # 键长
        do.rotate = 0                                   # 顺时针旋转0度
        #do.atomLabels[9] = 'ester group'    # 修改原子标签，[atom ID]
        drawer.SetDrawOptions(do)
        rdMolDraw2D.PrepareAndDrawMolecule(d, mol)  # 准备并绘制分子
        drawer.FinishDrawing()                        # 结束绘制
        drawer.WriteDrawingText('./' + str(i + 1) + 'reax.png')   # 图片命名从1开始

def createSvg(sms_content):
    for i in range(len(sms_content)):
        mol = Chem.MolFromSmiles(sms_content[i])
        substructure = Chem.MolFromSmarts('C(=O)O')
        #rdDepictor.Compute2DCoords(mol)  # for generating conformer ID
        drawer = rdMolDraw2D.MolDraw2DSVG(400, 200)
        do = rdMolDraw2D.MolDrawOptions()
        #do.addAtomIndices = True                        # adds atom indices to drawings
        #do.addBondIndices  = True                         # adds bond indices to drawings
        do.bondLineWidth = 5                    # 键宽
        do.fixedBondLength = 40                 # 键长
        do.baseFontSize = 1.2                      # relative size of font
        #do.annotationFontScale = 10          # Scale of font for atom and bond annotation relative to atomlabel font. Default=0.75.
        # do.explicitMethyl = True                  # Draw terminal methyls explictly. Default is false.
        do.setHighlightColour((0,1,0))           # HighlightColour (0.95,0.7,0.95)-紫红色 (0,1,0)-草绿色
        #do.variableBondWidthMultiplier = 10 #  what to multiply standard bond width by for variable attachment points.
        do.rotate = 0                                   # 顺时针旋转0度
        #do.atomLabels[9] = 'ester group'    # 修改原子标签，[atom ID]
        drawer.SetDrawOptions(do)
        rdMolDraw2D.PrepareAndDrawMolecule(drawer, mol, highlightAtoms=[], highlightBonds=[])  # 准备并绘制分子, 代码跨行
        drawer.FinishDrawing()          # 结束绘制
        svg = drawer.GetDrawingText()
        with open('./' + str(i + 24) + 'reax.svg', "w") as f:
           f.write(svg)

def reactionSvg(sms_content):
    for i in range(len(sms_content)):
        mol = AllChem.ReactionFromSmarts(sms_content[i])
        drawer = rdMolDraw2D.MolDraw2DSVG(800, 300)
        do = rdMolDraw2D.MolDrawOptions()
        do.bondLineWidth = 2                    # 键宽
        do.fixedBondLength = 30                # 键长
        do.rotate = 0                                   # 顺时针旋转0度
        #do.atomLabels[9] = 'ester group'    # 修改原子标签，[atom ID]
        drawer.SetDrawOptions(do)
        drawer.DrawReaction(mol, highlightByReactant=Ture)  # 准备并绘制分子
        drawer.FinishDrawing()              # 结束绘制
        svg = drawer.GetDrawingText()
        with open('./' + str(i + 1) + 'reaction.svg', "w") as f:
           f.write(svg)

#sms_file_path = './reaction.sms'
sms_file_path = './species.sms'
sms = open(sms_file_path, 'r')
sms_content = sms.readlines()
#createPng(sms_content)
createSvg(sms_content)
#reactionSvg(sms_content)
sms.close()

print('********* finished **********')

species.sms文件内容示例如下：

[H]C([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]
[H]C([H])C([H])([H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])C([H])[H]
[H]C([H])C([H])([H])C([H])([H])C([H])([H])[H]
[H]C([H])=C([H])[H]

reaction.sms 文件内容示例如下：

[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])O.[N-:13]=[N+:14]=[N-:15]>C(Cl)Cl.C(=O)(C(=O)Cl)Cl>[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])[N:13]=[N+:14]=[N-:15]