A rule-based algorithm for automatic bond type perception.

ABSTRACT: Assigning bond orders is a necessary and essential step for characterizing a chemical structure correctly in force field based simulations. Several methods have been developed to do this. They all have advantages but with limitations too. Here, an automatic algorithm for assigning chemical connectivity and bond order regardless of hydrogen for organic molecules is provided, and only three dimensional coordinates and element identities are needed for our algorithm. The algorithm uses hard rules, length rules and conjugation rules to fix the structures. The hard rules determine bond orders based on the basic chemical rules; the length rules determine bond order by the length between two atoms based on a set of predefined values for different bond types; the conjugation rules determine bond o

SUBMITTER: Zhang Q 

PROVIDER: S-EPMC3557220 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature