matches = product.GetSubstructMatches(pharm_feats) print('Pharmacophore matches:', matches) 分子筛选 rdkit 可以用于筛选化合物库,寻找具有特定性质或活性的化合物。 from rdkit.Chem import Descriptors # Filter molecules by molecular weight filtered_mols = [mol for mol in molecules if Descriptors.MolWt...
properties = ['iupacname', 'molecularformula', 'molecularweight', 'xlogp', 'tpsa', 'canonicalsmiles'] #需要获得的属性 return_list = [] for n in cid_list: cid = n x = pcp.get_properties(properties, cid, 'cid') #通过cid检索相关属性 if len(x) == 1: return_list.append(x[0]) ...
molecular_weight fp - bit-vector fingerprint in form of indexes of positive bits ("1 4 19 23") fp_ones - count of positive bits mdlmol Additional reserved property names: smiles If the graph was fulfilled with nodes before the extension was loaded, it is possible to apply a procedure:...
atomChiralTypeFromBondDirPseudo3D fails for poorly scaled molecular coordinates (github issue #7509 from d-b-w) EnumerateStereoisomers cannot give enumeration on certain rings and nitrogens (github issue #7516 from qcxia20) rdkit-stubs/Chem/rdchem.pyi: Mol.GetAtoms and Mol.GetBonds are wrong...
2019年8月13日JMC(Journal of Medicinal Chemistry)刊登了一篇文章“Pushing theBoundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism”,介绍了一种基于注意力机制的图神经网络模型(Attentive FP)。该模型可以用于分子表征,在多个药物发现相关的数据集上的预测表现达到当前最优,并...
RDKit_Overview
GetProp('_Name') for mol in database]) 计算分子指纹 代码语言:javascript 复制 fps= [FingerprintMols.FingerprintMol(mol) for mol in database] 代码语言:javascript 复制 print(len(database))print(len(fps)) 1000 1000 相似度计算 代码语言:javascript 复制 DataStructs.FingerprintSimilarity(fps[0],fps...
2019年8月13日JMC(Journal of Medicinal Chemistry)刊登了一篇文章“Pushing theBoundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism”,介绍了一种基于注意力机制的图神经网络模型(Attentive FP)。该模型可以用于分子表征,在多个药物发现相关的数据集上的预测表现达到当前最优,并...
Molecular Functionality Input/Output: SMILES/SMARTS, mol, SDF, TDT “Cheminformatics”: • Substructure searching • Canonical SMILES • Chirality support • Chemical transformations • Chemical reactions • Molecular serialization (e.g. mol - text) 2D depiction, including ...
>>> for i in range(m.GetNumConformers()): ... w.write(m,confId=i) ... >>> w.flush() Molecular Miscellany >>> from rdkit import Chem >>> from rdkit.Chem import Crippen >>> Crippen.MolLogP(Chem.MolFromSmiles('c1ccccn1')) ...