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

Abstract

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).

Extreme modulation properties of aromatic fluorine

“…(Free-Wilson analysis is a variant of QSAR which assumes that in the parent structure each variable fragment contributes additively to the logarithm of biological activity, and there is no interaction between the fragments.) Initially, the 35,645 compound set was converted to MCDL strings using the MCDL Java Editor [19]. Only the composition MCDL modules (bold, Fig.…”

“…Further evaluation of the available NCI data was made using Free-Wilson [17] analysis based on the MCDL fragment approach [18,19]. (Free-Wilson analysis is a variant of QSAR which assumes that in the parent structure each variable fragment contributes additively to the logarithm of biological activity, and there is no interaction between the fragments.)…”

Modular Chemical Descriptor Language (MCDL): Stereochemical modules

“…In the original algorithm for structure diagram generation [2], after generation of the initial 2D atomic coordinates, bond rotations were performed to remove overlapping. In the new algorithm, prior to any bond rotation, the 2D coordinates are used to calculate MCDL double bonds stereodescriptors, which are compared with the initial ones.…”

“…To improve the graphic performance of the Java applet, we expanded the database of pre-defined templates [2] from 105 to 145. There was no overlapping in any of the structure diagrams.…”

Universal Structure Conversion Method for Organic Molecules: From Atomic Connectivity to Three‐Dimensional Geometry

“…However, those methods demand knowledge of the 3D geometry of the molecules. Although the BOs can be assigned using valence rules without 3D coordinates, such rules have many exceptions and thus often demand careful post‐processing. Wang et al .…”