Faster reaction mapping through improved naming techniques

Int. J. Found. Comput. Sci.

Pascua

Mehta

2015

Self Cite

This paper describes a random model for chemical graphs that captures the notion of valence along with algorithms to generate chemical graphs using this model. An approach for computing the probability that a particular chemical graph is generated under this model is provided. The model is also used to provide theoretical bounds on the accuracy of a class of canonical labeling algorithms for a class of hydrocarbons.

Section: Practical Canonical Naming Algorithms For Chemical Graphsmentioning

confidence: 99%

Section: Practical Canonical Naming Algorithms For Chemical Graphsmentioning

confidence: 99%

Random Models and Analyses for Chemical Graphs

Int. J. Found. Comput. Sci.

Pascua

Mehta

2015

Self Cite

“…The algorithms differ in the way candidate equations are generated, searched, and how canonical names are generated and stored. We refer the reader to 16,18,44 for a detailed treatment and comparison of the algorithms.…”

Section: Automated Reaction Mappingmentioning

confidence: 99%

“…The system allows one to configure the algorithms to use a variety of canonical naming algorithms and change classification rules as needed without making code changes 17. We were usually able to map and classify the reactions in a reasonable amount of time 16,18,44. A summary of the time required to find all minimum cost mappings using our two fastest algorithms (2‐CCV NR FDN and 2‐CCV FDN MS) is provided in Table VI.…”

Section: Examplesmentioning

confidence: 99%

RCARM: Reaction classification using automated reaction mapping

Int J of Chemical Kinetics

Crabtree

Huynh

et al. 2012

Self Cite

Detailed chemical kinetic modeling of gas-phase reactions can result in automatically generated mechanisms that contain thousands of reactions. In this paper, we describe the development of a rule-based expert system tool that organizes these reactions into classes such as hydrogen abstraction and beta scission. We have developed 29 simple classification rules, 20 complex (well-skipping) classification rules, and four second-stage classification rules. This greatly simplifies the task of the chemical kineticist who wishes to verify, analyze, and gain insights into the reactions comprising the mechanism. This system, which is based on the automated identification of the bonds that break and form in a chemical reaction (the reaction mapping problem), is used to classify reactions in three different mechanisms. C 2012 Wiley Periodicals, Inc. Int J Chem Kinet 45: 125-

“…The algorithm presented is inspired by the random graph canonical labeling algorithms presented in refs 27 and 28 and the primitive refinement step used in Nauty 19 and was used to speed up ARM computations. 6,7 The main idea of the degree neighborhood (DN) algorithm is to assign each atom a name based on its symbol and degree and the symbol and degree of each of its neighbors. The names of each atom are then used to assign a name to the molecule.…”

Section: ■ Introductionmentioning

confidence: 99%

“Social” Network of Isomers Based on Bond Count Distance: Algorithms

Awale

Slyby

et al. 2014

J. Chem. Inf. Model.

Self Cite

This paper introduces the concept of an isomer network based on the reaction step counts between pairs of isomers as an alternative means to view and analyze isomer space. The computation of isomer networks is computationally expensive with respect to both run time and memory. Accordingly, this paper focuses on the design of algorithms to compute isomer networks and their analysis on structurally diverse subsets of isomers of nicotine, tyrosine, and phenmetrazine generated using molecular quantum number nearest neighbors. An analysis correlating isomer networks to extended connectivity fingerprints is also provided.