scopy.ScoVisualize package

Created on Fri May 15 22:47:38 2020

A module used for visualizing the screening result.

You can freely use and distribute it. If you have any problem, you could contact with us timely.

@Author: Zhi-Jiang Yang, Dong-Sheng Cao.

@Institution: CBDD Group, Xiangya School of Pharmaceutical Science, CSU, China.


@Mail: and


scopy.ScoVisualize.highlight module

scopy.ScoVisualize.highlight.HighlightAtoms(mol, highlightAtoms, figsize=[400, 200], kekulize=True)[source]

This function is used for showing which part of fragment matched the SMARTS by the id of atoms.

  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be visualized

  • highlightAtoms (tuple) – The atoms to be highlighted

  • figsize (list) – The resolution ratio of figure


a figure with highlighted molecule

Return type


scopy.ScoVisualize.mcloud module

scopy.ScoVisualize.mcloud.ShowMcloud(file, number=150, skip=0, savedir=None, hidden=False)[source]

Visualization of large molecular data sets using the Molecule Cloud approach.

  1. P. Ertl, B. Rohde (2012).

  • file (str) – the absolute path of file whose first column is the SMILES, and second one is frequnency correspondly. Delimit is ‘ ‘

  • number (int, optional) – process only first n molecules from the data file, defaults to 150

  • skip (int, optional) – skip first n structures (usually used 1 to skip large phenyl), defaults to 0

  • savedir (str, optional) – the path to save figure, defaults to None

  • hidden (bool, optional) – whether hidden the figure after finished, defaults to False



scopy.ScoVisualize.pc_depict module

scopy.ScoVisualize.pc_depict.PropMatrix(mols, n_jobs=1, items=['logP', 'TPSA', 'MW', 'nRot', 'nHD', 'nHA'])[source]

The proprty matrix can intuitively show the compounds’ distribution in Two-Dimension space, and diagonal of the matrix is the displot of property

  • mols (iterable object) – Molecules

  • n_jobs (int, optional) – The number of CPUs to use to do the computation, defaults to 1

  • items (list, optional) – The abbreviation name of property to be visualized, defaults to [‘logP’,’TPSA’,’MW’,’nRot’,’nHD’,’nHA’]


The proerty matrix

Return type


scopy.ScoVisualize.pc_depict.RuleRadar(mol, prop_kws={'HetRatio': (0.1, 1.1), 'MW': (100, 600), 'MaxRing': (0, 18), 'TPSA': (0, 180), 'fChar': (-4, 4), 'logP': (-3, 6), 'nC': (3, 35), 'nHA': (0, 12), 'nHD': (0, 7), 'nHet': (1, 15), 'nRig': (0, 30), 'nRing': (0, 6), 'nRot': (0, 11)})[source]

A radar plot positionning compound’s values within the selected filter ranges (pale blue and red). By default, the drug-like soft filter ranges are visualized.


mol (rdkit.Chem.rdchem.Mol) – molecular


A radar plot positionning compound’s values

Return type


Module contents