Indigo | Indigo（Python）简介、安装与入门

Indigo简介

Bingo: 针对Oracle，Microsoft SQL Server和PostgreSQL数据库的化学搜索引擎
Indigo: U具有与.NET，Java和Python绑定的通用化学信息库，以及以下工具：
Legio: 组合化学GUI应用程序
ChemDiff: SDF或SMILES文件的可视化比较
indigo-depict: 分子和反应渲染工具
indigo-cano: Canonical SMILES 生成器
indigo-deco: R-Group反卷积实用程序

Indigo安装

Indigo的Python绑定安装

pip install epam.indigo

Indigo入门

from indigo import *indigo = Indigo()

获取版本

print ("Indigo version " + indigo.version())

Accessing Neighbor Atoms

for atom in mol.iterateAtoms():print ("atom %d: %d neighbors" % (atom.index(), atom.degree()))for nei in atom.iterateNeighbors():print ("neighbor atom %d is connected by bond %d\n" % (nei.index(), nei.bond().index()))

Accessing R-Groups

for rg in mol.iterateRGroups():print ("RGROUP #" + rg.index())for frag in rg.iterateRGroupFragments():print ("  FRAGMENT #" + rg.index())print (frag.molfile())

Stereochemistry

The following methods of IndigoObject are available for accessing molecule’s stereo configuration:

countStereocenters returns the number of the chiral atoms in a molecule
iterateStereocenters returns an iterator for molecule’s atoms that are stereocenters
countAlleneCenters returns the number of allene-like stereo fragments
iterateAlleneCenters returns an iterator for molecule’s atoms that are centers of allene fragments (the middle ‘C’ in ‘C=C=C’)
bondStereo returns one of the following constants:
- Indigo.UP — stereo “up” bond
- Indigo.DOWN — stereo “down” bond
- Indigo.EITHER — stereo “either” bond
- Indigo.CIS — “Cis” double bond
- Indigo.TRANS — “Trans” double bond
- zero — not a stereo bond of any kind
stereocenterType returns one of the following constants:
- Indigo.ABS — “absolute” stereocenter
- Indigo.OR — “or” stereocenter
- Indigo.AND — “and” stereocenter
- Indigo.EITHER — “any” stereocenter
- zero — not a stereocenter
invertStereo inverts the stereo configuration of an atom
resetStereo resets the stereo configuration of an atom or a bond
changeStereocenterType(newType) changes current stereocenter type to a specified type
addStereocenter(type, idx1, idx2, idx3, [idx4]) adds new stereocenter build on a atom pyramid with a specified atom indices
clearStereocenters resets the chiral configurations of a molecule’s atoms
clearAlleneCenters resets the chiral configurations of a molecule’s allene-like fragments
clearCisTrans resets the cis-trans configurations of a molecule’s bonds

The following methods are useful for keeping cis-trans stereochemistry intact when converting to/from SMILES:

resetSymmetricCisTrans can be called on a molecule loaded from a Molfile or CML. After this call, the cis-trans configurations remain only on nonsymmetric cis-trans bonds. The method returns the number of bonds that have been reset.
markEitherCisTrans can be called prior to saving a molecule loaded from SMILES to Molfile format. It guarantees that the bonds that have no cis-trans configuration in SMILES will not have a cis-trans configuration in the resulting Molfile.

IndigoObject mol = indigo.loadMolecule("chiral.mol");print mol.countStereocenters(), "chiral atoms"
for atom in mol.iterateStereocenters():print "atom", atom.index(), "-- stereocenter type", atom.stereocenterType()atom.invertStereo();for bond in mol.iterateBonds():if bond.bondStereo() != 0:print "bond", bond.index(), "-- stereo type", bond.bondStereo()print mol.smiles()
mol.clearStereocenters()
mol.clearCisTrans()
print mol.smiles()

Reaction Products Enumeration

reaction = indigo.loadQueryReaction("Cl[C:1]([*:3])=O.[OH:2][*:4]>>[*:4][O:2][C:1]([*:3])=O")monomers_table = indigo.createArray()monomers_table.arrayAdd(indigo.createArray())
monomers_table.at(0).arrayAdd(indigo.loadMolecule("CC(Cl)=O"))
monomers_table.at(0).arrayAdd(indigo.loadMolecule("OC1CCC(CC1)C(Cl)=O"))monomers_table.arrayAdd(indigo.createArray())
monomers_table.at(1).arrayAdd(indigo.loadMolecule("O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O"))output_reactions = indigo.reactionProductEnumerate(reaction, monomers_table)indigo.setOption("render-comment", "Results")
rxn_array = indigo.createArray();
for elem in output_reactions.iterateArray():rxn = elem.clone();rxn_array.arrayAdd(rxn)indigoRenderer.renderGridToFile(rxn_array, None, 2, 'result_rpe.png')

Reaction-based Molecule Transformations

reaction = indigo.loadQueryReaction("[*+:1][*-:2]>>[*:2]=[*:1]")
molecule = indigo.loadMolecule("[O-][C+]1CCCC1[N+]([O-])=O")
indigo.transform(reaction, molecule)
print(molecule.smiles())

运行结果

O=N(C1CCCC1=O)=O

参考

1. https://github.com/epam/Indigo

2. https://lifescience.opensource.epam.com/

3. https://pypi.org/project/epam.indigo/

4. https://lifescience.opensource.epam.com/indigo/api/index.html

Indigo | Indigo（Python）简介、安装与入门相关推荐

Python学习1——python简介和基础入门
转载原文Python学习之路[第一篇]-Python简介和基础入门:https://www.cnblogs.com/linupython/p/5713324.html 1.python3.7.2下 ...
python 简介+安装（搬运廖雪峰网站）
Python简介 Python是著名的"龟叔"Guido van Rossum在1989年圣诞节期间,为了打发无聊的圣诞节而编写的一个编程语言. 现在,全世界差不多有600多种编程 ...
Python学习-Python简介和基础入门
1.Python简介 1.1 Python是什么相信混迹IT界的很多朋友都知道,Python是近年来最火的一个热点,没有之一.从性质上来讲它和我们熟知的C.java.php等没有什么本质的区别,也是 ...
Python学习之路【第一篇】-Python简介和基础入门
1.Python简介 1.1 Python是什么相信混迹IT界的很多朋友都知道,Python是近年来最火的一个热点,没有之一.从性质上来讲它和我们熟知的C.java.php等没有什么本质的区别,也是 ...
Xfce4和Python的安装 | AidLux入门操作②
自从"AidLux开发者社区"推出后,有很多用户聚集在社区里探讨各类话题,其中不乏如何在平台内安装.配置各种常用软件和编程语言的相关内容.今天我们就以社区讨论热度较高的两个对象为例 ...
Python|Python简介|安装Python解释器|运行|开发工具|Python之禅|turtle绘制五星红旗|绘制方块|绘制小猪佩奇|语言100课：学习（1）
文章目录源项目地址初识Python Python简介 Python的历史 Python的优缺点 Python的应用领域安装Python解释器运行Python程序确认Python的版本编写P ...
linux安装python_VTK：华为笔记本电脑+深度deepin-linux+python下安装和入门
1 说明: ===== 1.1 vtk,(visualization toolkit)是一个开源的免费软件系统,主要用于三维计算机图形学.图像处理和可视化. 1.2 是一个开源.跨平台.可自由获取.支 ...
循序渐进学Python 1 安装与入门
1 安装 2 使用 2.1 运行程序 3 艺搜参考 by 2013年10月16日安装 Windows安装版,源码,帮助文档: 使用打开开始菜单中的Python GUI启动Python解释器: 启动 ...
python pdb 安装_入门 Python 调试器 pdb
前言调试线上的 Python 程序时,虽然 PyCharm 可以实现远程调试,但 pdb 才是最便捷的方式,本文简单介绍 pdb 工具的使用,希望各位除了掌握 PyCharm 调试技巧外,还可以掌握 ...