from rdkit import Chem from rdkit.Chem import AllChem, Draw import cairosvg mol_with_atom_index 这个函数用于产生带 index 的 Molecule 对象。 def mol_with_atom_index(mol): for atom in mol.GetAtoms(): atom.SetAtomMapNum(atom.GetIdx()) return mol smiles2png 这个函数通过给定的smiles,保存为...
可以通过minFontSize和maxFontSize来控制绘制分子图片时atom label 的大小,代码如下所示: from rdkit.Chem import rdDepictor from rdkit.Chem.Draw import rdMolDraw2D from rdkit import Chem smiles = 'FC1OC2N3C4[Si]5=C6B7C(C=CC6=CC4=CC2=CC1)C=CC=C7C=C5C=C3' mol = Chem.MolFromSmiles(...
►rdkit.Chem.rdchem.Atom - The Atom Classrdkit.Chem.rdchem.Bond - The Bond Classrdkit.Chem.rdchem.RWMol - The RWMol Classrdkit.Chem.rdmolfiles - Molecular File Modulerdkit.Chem.rdDepictor - Compute 2D Coordinatesrdkit.Chem.Draw - Handle Molecule Images...
- rdkit.Chem.Draw.MolDrawing.DrawingOptions class prepresents a set of molecule drawing options. You can use them to control the appearance of molecule images. rdkit.Chem.Draw.MolDrawing.DrawingOptions contains the following attributes as molecule drawing options: atomLabelDeuteriumTritium = False a...
Fix chirality handling when the chiral atom is the first one in a SMARTS (github pull #6730 from johnmay) ConnectTheDots can segfault if all atoms do not have residue info (github issue #6756 from jasondbiggs) _moltoimg() should honor drawOptions.prepareMolsBeforeDrawing (github issue #67...
What Is RDKit- RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. The current release supports the following packages: rdkit.Avalon package rdkit.Chem package rdkit.Chem.AtomPairs package rdkit.Chem.ChemUtils package rdkit.Chem.Draw package rdkit....
draw_mols.py extract_mol_by_name.py extractsdf.py filter_conf.py filter_conf_adv.py filter_mols.py frags2mols.py gen_conf_rdkit.py gen_stereo_rdkit.py get_mol_center.py get_sdf_from_db.py get_substr.py get_total_charge.py ...
The biggest drawback about the PDBQT format is that it does not encode for the bond order in molecules explicitly. Instead, the bond order is inferred based on the atom type, distance and angle to nearby atoms in the molecule. For normal sp3 carbons and molecules with mostly single bonds ...
Molecular database cartridge for PostgreSQL Cheminformatics nodes for KNIME (distributed from the KNIME community site) PolarDB 通过rdkit插件实现生物、化学分子结构数据存储与计算、分析. (相似搜索、子结构或精确匹配搜索、分子比较等) 链接 数据类型
MolDraw2D now does a much better job of handling query features like common query bond types, atom lists, variable attachment points, and link nodes. It also supports adding annotations at the molecule level, displaying brackets for Sgroups, rendering the ABS flag for stereochemistry, and a ...