RDKit 是一款开源化学信息学与机器学习工具包,提供C++ 和python 的API接口。 RDKit提供各种功能,如不同的化学I/O格式,包括SMILES/SMARTS,结构数据格式(SDF),Thor数据树(TDT),Sybyl线符号(SLN),Corina mol2和蛋白质数据库(PDB)。子结构搜索; 标准SMILES; 手性支持;化学转化;化学反应;分子序列化;相似性/多样性...
读取DataFrame中的SMILES:AddMoleculeColumnToFrame(frame, smilesCol, molCol, includeFingerprints) frame:DataFrame对象 smilesCol:SMILES所在列 molCol:新列名,将存放产生的rdkit mol对象 includeFingerprints:是否生成指纹 顺便计算下分子量:Descriptors.MolWt()...
rdkit_data_demo=# insert into public.test (smiles) values ('CC');【注意,字符串不要用"",要用'',踩过坑】 INSERT 0 1 验证RDKit功能,下面的语句是将smiles码转换成mol,生成inchikey的方法 rdkit_data_demo=# select mol_inchikey(mol_from_smiles(smiles::cstring)) from test limit 1; mol_inc...
Re: [Rdkit-discuss] Catching errors in SMILES filesGreg Landrum [Rdkit-discuss] NDonor Smarts in BaseFeatures.fdefChicago Ji [Rdkit-discuss] Read only first model of a pdb-fileIllimar Hugo Rekand Re: [Rdkit-discuss] Read only first model of a pdb-fileDimitri Maziuk via Rdkit-discuss...
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RDKit提供各种功能,如不同的化学I/O格式,包括SMILES/SMARTS,结构数据格式(SDF),Thor数据树(TDT),Sybyl线符号(SLN),mol2和蛋白质结构文件(PDB)。子结构搜索; 标准SMILES; 手性支持;化学转化;化学反应;分子序列化;相似性/多样性选择;二维药效团;三维维药效团;分层子图/片段分析; Bemis和Murcko骨架;逆合成组合...
Chem.MolToSmiles(mol, rootedAtAtom=pos), when the parameter rootedAtAtom is greater than or equal to 20, the range error is reported. (github issue #7572 from YOUNG-JAME) MergeQueryHs fails to detect explicit H involved in OR queries where there's more than 2 options in the query (git...
- mol: the molecule to assign bond orders to An example, start by generating a template from a SMILES and read in the PDB structure of the molecule """ refmol = MolFromSmiles(SMILES) refmol2 = rdchem.Mol(refmol) mol2 = rdchem.Mol(mol) ...
#定义一个反应,采用SMARTS格式 #解释这个SMARTS,第一个反应物限制:[C:1](=[O:2])-[OD1],羧基,侧链为(=[O:2]),O双键与C相连,第二个反应物限制:[N:3],基团带N原子 Draw.ReactionToImage(rxn) #画出反应式 pr = rxn.RunReactants((Chem.MolFromSmiles('CC(=O)O'),Chem.MolFromSmiles('NC'...
分子可以使用Python的pickle模块与文本之间转换: >>> m = Chem.MolFromSmiles('c1ccncc1') >>> im… 阅读全文 赞同 添加评论 分享 收藏 pip及conda安装rdkit出错时 Sunin 可尝试一下安装命令: conda install -c rdkit rdkit 2. conda install -c conda-forge rdki… ...