Automated Drawing of Structural Molecular Formulas under Constraints

Abstract

In this paper, we present a new algorithm for automated drawing of 2D structural formulas of molecules. The algorithm is based on the classical scheme of a drawing queue placing the molecular fragments in a sequential way. We extend the concept of so-called prefabricated units developed for complex ring systems to automatically created drawing units for chains and rings which will then be assembled in a sequential fashion. The approach is fast and can be naturally extended to the problem of drawing molecules with common core structures. Further on, we present an algorithm that allows the drawing of 2D structural formulas under directional constraints assigned to a subset of bonds. Since no numerical optimization is necessary, the algorithm creates drawings of small organic molecules on the order of 500 structures per second. The new algorithm is relevant for all kinds of prediction and analysis software presenting a large number of probably similar molecular structures to the user of the software.

Exploring fragment spaces under multiple physicochemical constraints

“…For example, Fig.7 contains the images of different pairs of inhibitors and molecules that we selected from the results of the calculations described above. The individual figures were created using the method from Fricker et al [27] In all cases, the structural similarity of the compound pairs becomes apparent and reasonable functional variations can be observed.…”

Basic primitives for molecular diagram sketching

“…There is now an abundance of software packages which allow the user to sketch a molecular diagram on a desktop or laptop computer, using the mouse and keyboard to specify the content and geometry of the molecule [5,6]. There are also a number of algorithms in general use which allow molecular structure diagrams to be produced automatically using only the molecular topology [7-10]. The availability of information relating molecular connection tables to important properties has made possible the rise of the subfield of computational chemistry commonly known as cheminformatics [11,12], and the usual data entry method for chemical structures is via software designed for sketching 2 D diagrams of molecules.…”

XFb – a combined approach for 2D ring drawing

“…In this case, extensions like a ring template database (RDB) or force field (FF) based drawing methods are required [1]. We introduced an algorithm (XFb) that combines both methods -the RDB as well as the FF as extension for the structure diagram drawing tool 2D draw [2].The order of methods in the computation of the ring system layout is chosen accordingly to the quality of the resulting coordinates. At first the RDB containing hand generated coordinates is scanned for a template of the given ring system.…”

“…In this case, extensions like a ring template database (RDB) or force field (FF) based drawing methods are required [1]. We introduced an algorithm (XFb) that combines both methods -the RDB as well as the FF as extension for the structure diagram drawing tool 2D draw [2].…”