Modular Chemical Descriptor Language (MCDL):  Composition, Connectivity, and Supplementary Modules

Abstract

The Modular Chemical Descriptor Language (MCDL) was developed to address the need for linear representation of structural and other chemical information for chemical databases, E-journals, and the Internet. The current paper describes in detail two major modules of the language: the composition and connectivity modules, which provide a representation of chemical structure. These modules are created using simple hierarchical principles based on ASCII codes and are unique except for stereoisomers and a few special cases (e.g., valence isomers, knot-type compounds). The MCDL also provides for additional information (such as atom coordinates, bond orders, spectra, and physical-chemical characteristics) to be included as a set of supplementary modules.

Extreme modulation properties of aromatic fluorine

“…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.)…”

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

“…It should be noted that in some rare cases the restoration of bond orders using only the MCDL connectivity module and the number of attached protons is not possible. These cases were examined in [19].…”

“…However, the absence of descriptors for fragment-centered properties can be considered as disadvantage. These shortcomings were taken into consideration during the development of the Modular Chemical Descriptor Language (MCDL), which is designed for linear representation of chemical structures and compound properties [19]. Composition and connectivity modules of the MCDL string are coded in canonical form and therefore can be used directly for structure comparison.…”

“…The MCDL class keeps the collection of methods for generation of MCDL code from connectivity matrix and reverse procedure-for generation of connectivity matrix from the MCDL string. The algorithms of the direct transformation were described previously [19]. The BondAlternate class is used to reconstruct bond order from the number of hydrogen atoms, attached to forming bond atoms.…”

Neural systems language: A formal modeling language for the systematic description, unambiguous communication, and automated digital curation of neural connectivity

“…Historically, these languages have been used to help solve problems and streamline operations and communication in engineering, chemistry, computer science, and electronics (Weiner, 1948; Boute, 1986; Weininger, 1988; Claessen and Sands, 1999; Gakh and Burnett, 2001). These new languages were methods to take advantage of newly available computational power, to systematically represent information, and to bridge the communication gap between human and machine.…”