Ring Perception Using Breadth-First Search

Figueras, John

doi:10.1021/ci960013p

Cited by 48 publications

(51 citation statements)

References 9 publications

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“…John Figueras' fast algorithm for finding the Smallest Set of Smallest Rings (SSSR) has been implemented and is used for example by the structure diagram generation package. 37 Especially large condensed ring systems, for which the process of coordinate generation could take up to a minute due to a slow depth first ring perception algorithm in older systems, 38 can now be layed out within fractions of a second as shown in Figure 4. Further this package contains a class for partioning a given ring systems into AtomContainers, one for each ring.…”

Section: D Structure Graphicalmentioning

confidence: 99%

The Chemistry Development Kit (CDK): An Open‐Source Java Library for Chemo‐ and Bioinformatics.

et al. 2003

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The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemoand Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given.

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Section: D Structure Graphicalmentioning

confidence: 99%

The Chemistry Development Kit (CDK): An Open‐Source Java Library for Chemo‐ and Bioinformatics.

et al. 2003

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“…The set of the minimum number of cycles in the compound is calculated using an algorithm [41] and stored in the LIST. 2.…”

Section: Structure Diagram Generation Of Polycyclic Compoundsmentioning

confidence: 99%

A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL)

et al. 2006

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Abstract:A compact Modular Chemical Descriptor Language (MCDL) chemical structure editor (Java applet) is described. The small size (approximately 200 KB) of the applet allows its use to display and edit chemical structures in various Internet applications. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI).

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“…Figueras' algorithm [20] for computing an SSSR has been celebrated as significant advance because of its computational speed. It is implemented e.g.…”

Section: Sssr: Smallest Set Of Smallest Ringsmentioning

confidence: 99%

“…Figueras' method, however, may fail also for simple planar graphs: (i) In the first step of the algorithm the set of vertices of degree two (the N2 nodes in [20]) is investigated. For each vertex of this type, the algorithm generates a shortest cycle (note that this cycle need not be unique) and adds it to a cycle set.…”

Section: Sssr: Smallest Set Of Smallest Ringsmentioning

confidence: 99%

Counterexamples in Chemical Ring Perception

Berger

Flamm

Gleiss

et al. 2004

J. Chem. Inf. Comput. Sci.

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Abstract. Ring information is a large part of the structural topology used to identify and characterize molecular structures. It is hence of crucial importance to obtain this information for a variety of tasks in computational chemistry. Many different approaches for "ring perception", i.e., the extraction of cycles from a molecular graph, have been described. The chemistry literature on this topic, however, reports a surprisingly large number of incorrect statements about the properties of chemically relevant ring sets and, in particular, about the mutual relationships of different sets of cycles in a graph. In part these problems seem to have arisen from a sometimes rather idiosyncratic terminology for notions that are fairly standard in graph theory. In this contribution we translate the definitions of concepts such as the Smallest Set of Smallest Rings, Essential Set of Essential Rings, Extended Set of Smallest Rings, Set of Smallest Cycles at Edges, Set of Elementary Rings, K-rings, and β-rings into a more widely-used mathematical language. We then outline the basic properties of different cycle sets and provide numerous counterexamples to incorrect claims in the published literature. These counterexamples may have a serious practical impact because at least some of them are molecular graphs of well-known molecules. As a consequence, we propose a catalogue of desirable properties for chemically useful sets of rings.

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Ring Perception Using Breadth-First Search

Cited by 48 publications

References 9 publications

The Chemistry Development Kit (CDK): An Open‐Source Java Library for Chemo‐ and Bioinformatics.

The Chemistry Development Kit (CDK): An Open‐Source Java Library for Chemo‐ and Bioinformatics.

A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL)

Counterexamples in Chemical Ring Perception

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