Below a number of installation recipes is presented, with varying degree of complexity. Cross-platform using Conda Introduction to Conda Conda is an open-source, cross-platform, software package manager. It supports the packaging and distribution of software components, and manages their installation ...
查看各种描述符的含义:GetDescriptorSummaries() >>>calculator.GetDescriptorSummaries()['The average molecular weight of the molecule','Number of Hydrogen Bond Acceptors','Number of Hydrogen Bond Donors','Wildman-Crippen LogP value','Number of Rotatable Bonds'] 获取所有描述符:Descriptors._descList >...
m2 = Chem.Mol(m) for at in m2.GetAtoms(): lbl = '%.2f'%(at.GetDoubleProp("_GasteigerCharge")) at.SetProp('atomNote',lbl) m2 图六 上图原子标号与电荷数值有点重合。 3. 寻找公共骨架 Rdkit 可以分析大量smiles字符串,并统计出现次数最多的骨架。首先,需要创建一个字符串的集合mlist, 注意...
Dear RDKit users, The function *GetMMFFAtomType* from the *rdForceField *module returns a number describing the assigned atom type by the forcefield of the queried atom. I want to get the definition of the atom type which the number represents. I wonder if there's a dictionary or a d...
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(mol, highlightAtoms=range(bg.number_of_nodes()), highlightBonds=[], highlightAtomColors=atom_colors) drawer.FinishDrawing() svg = drawer.GetDrawingText() svg = svg.replace('svg:', '') if torch.cuda.is_available(): atom_weights = atom_weights.to('cpu') return (Chem.MolFromSmiles...
a.GetNumRadicalElectrons() does have the right number. If it set all the atoms to not have implicit hydrogens with for atom in mol.GetAtoms(): atom.SetNoImplicit(True) then I still get a sanitization error with >>> Chem.SanitizeMol(mol) ...
Batched DGLGraphslabels:Tensorofdtype float32 andshape(B,T)Batched datapoint labels.Bislen(data)andTis the numberoftotal tasks.masks:Tensorofdtype float32 andshape(B,T)Batched datapoint binary mask,indicating the existenceoflabels.If binary masks are not ...
Here is the definition of the method: rdkit.Chem.rdMolDescriptors.GetHashedMorganFingerprint((Mol)mol, (int)radius [, (int)nBits=2048 [, (AtomPairsParameters)invariants=[] [, (AtomPairsParameters)fromAtoms=[] [, (bool)useChirality=False [, (bool)useBondTypes=True [, (bool)useFeatures=...
GetAtoms(): nodes_dict['~id'].append('Node-'+ caffeine_smiles + str(atom.GetIdx())) nodes_dict['~label'].append(atom.GetSymbol()) nodes_dict['idx'].append(atom.GetIdx()) nodes_dict['atomicNumber'].append(atom.GetAtomicNum()) nodes_dict['isAromatic'].append(atom.GetIsAromatic(...