From e62f655d5868b7894fe68cb58dc1ba076b336067 Mon Sep 17 00:00:00 2001 From: David Hoekman Date: Wed, 20 Jun 2018 17:22:31 -0700 Subject: [PATCH] formatting test, son of redux --- README.md | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 9d95057..d36b247 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,28 @@ -# SMARTS is like a regular expression for chemical structures +## SMARTS is like a regular expression for chemical structures SMARTS is a tool for structure searching, the process of finding a particular pattern (a *subgraph*) in a molecule (a *graph*). Sub- (and super-) structure searches are used in virtually every computer-based chemistry application. -## Defining the terms +### Defining the terms * SMILES = __S__ implified __M__ olecular __I__ nput __L__ ine __E__ diting __S__ pecification - * SMARTS = __SM__ ILES __Ar__ bitrary __T__ arget __S__ pecification -A SMILES defines a specific chemical compound. A SMARTS is an expression that looks -for a match of a particular arrangement of atoms/bonds in that compound. +A SMILES defines a specific chemical compound, here the pesticide DDT: + +* Clc1ccc(cc1)C(c2ccc(Cl)cc2)C(Cl)(Cl)Cl + +A SMARTS is an expression that looks for a match of a particular arrangement +of atoms/bonds in that compound, here di-aryl ethane with any 3 halogens: + +* C(c)(c)C([Br,Cl,F])([Br,Cl,F])([Br,Cl,F]) + +Inspired by UNIX implementation of the mathematical idea of regular expressions, o -Inspired by xxx +[SMARTS syntax summary] (cheat-sheet.txt) -## Scaffold screens +### Scaffold screens A good example of the utility of SMARTS is shown by the scaffold screening code in this project ('screen.for')