3/18/2023 0 Comments Fminer run code action![]() ![]() ![]() nothing inside the $(.) is identified with the outside, we need (~*) to enforce that at least one additional branch is actually attached. Since the standard is “truly recursive”, i.e. It consists of back and forward links, but additionally specifies either a nitrogen or a nitrogen/carbon branch. The middle carbon’s local environment is recursively described. This denotes a nitrogen connected to a carbon double-connected to a carbon. The pattern bi is itself a LAST-SMARTS, and the local neighborhoods are combined via disjunction (there must be at least two due to (*)).įormally, LAST-SMARTS are defined as follows (EBNF):ĪN := ’17’ | ’35’ | ’5’ | ’6’ | ’7’ | ’8’ | ’15’ | ’16’ | ’9’ | ’53’ In case of (*), for each branch bi, i in, we describe the 1-step ('local') neighborhood of the node by a recursive SMARTS pattern, including the node itself, predecessor,bi, and successor. Bonds are represented by their order (1-3).įor an introduction to SMARTS, see e.g.įor every node visited, we demand an explicit but arbitrary branch with '(~*)' IF AND ONLY IF there are n optional branches with n>1 (*). Atoms are represented by their number, e.g. The implementation used here, (LAST-SMARTS), is recursively generated by a depth-first traversal of each LAST graph, starting at node 0. SMARTS are regular expressions for chemical fragments. path/to/last-utils/last-utils.rb 2 /path/to/cpdbdata/salmonella_mutagenicity/salmonella_mutagenicity_alt.smi salm-last.instįor precise synopsis and information run last-utils.rb without arguments. ![]() smi file using the last descriptors we just mined: Note: Variants 'msa' and 'nls' produce LAST-SMARTS with optional parts of the structures (with recursive SMARTS), while 'nop' disallows optional parts of the structures (ambiguities only on the atom / edge level).Ģ) Find instantiations of molecules in a. Note: This should be called from the current directory. last-utils.rb 1 "nls" > salm-last.smarts path/to/fminer -f14 /path/to/cpdbdata/salmonella_mutagenicity/salmonella_mutagenicity_alt.smi /path/to/cpdbdata/salmonella_mutagenicity/salmonella_mutagenicity_alt.class |. Its an easy to use web data extraction tool that combines best-of-class features with an intuitive visual project design tool to make your next data mining project a breeze. Two modi are available: conversion LAST->SMARTS and instantiation SMARTS/SMILES.ġ) Mine LAST descriptors and convert output to SMARTS (see LAST README file how to use the fminer frontend binary for LAST) using cpdbdata (see ): FMiner is a software for web scraping, web data extraction, screen scraping, web harvesting, web crawling and web macro support windows and Mac OS X. Requirements: ruby 1.8 with OpenBabel bindings (see ). These are LAST utilities, available from. ![]()
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