Apparatus and method for parsing a chemical string
AssigneeInternational Business Machines Corporation
InventorsSteven K. Boyer, Richard G. Casey, Alex M. Miller, Bernadette Oudot, Karl S. Zilles
Life of this patent
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Abstract
An apparatus and method for optical recognition of chemical graphics allows documents containing chemical structures to be optically scanned so that both the text and the chemical structures are recognized. The structures are converted directly into molecular structure files suitable for direct input into chemical databases, molecular modeling programs, image rendering programs and programs that perform real time manipulation of structures.
Claims19
In a data processing system including a digital processing unit, a data input, and a memory, a system for generating a list of atoms and bond connections therebetween from an input string of character identification codes corresponding to a chemical structure, comprising:
- separation means for receiving an input string of the character identification codes, parsing said input string to evaluate each character identification code thereof, and taking responsive action based on a value of each character identification code for separating the input character codes to generate a first output of character codes representing molecular front information and a second output of remaining character codes;
- treat string means for receiving as input the remaining character codes output by said separation means and dividing said remaining character codes into elementary substrings for separate processing;
- create stack means for receiving as input the elementary character substrings from said treat string means, parsing said elementary character substrings to evaluate each character identification code thereof, and taking responsive action based on a value of each character identification code for generating a stack of elementary substring character codes representing atoms and their associated valences;
- find group means for receiving as input the stack of elementary substring atoms and valences output by said create stack means, and the front information output by said separation means, and modifying said stack to order said elementary substring atoms in a connection sequence, adjusting said valences to reflect bond connections with other atoms, and adding a group structure identifier to each of said elementary substring atoms corresponding to the front information;
- and
- connect means for receiving as input said modified stack from said find group means and generating a connectivity table of said elementary substring atoms and their connectivity.
A chemical string processing method executable on a digital computer for generating a list of atoms and bond connections therebetween from an input string of character codes representing a chemical structure, comprising:
- reading successive character codes including chemical symbols;
- parsing said successive character codes to determine a value of each said character code;
- separating said character code values into a first output of molecular front information, if any, and a second output of remaining character code values;
- applying rules of chemistry based on said remaining character code values to generate a stack of atoms and bond connections corresponding to the input chemical structure;
- and
- modifying said stack of atoms and bond connections as necessary using said first output of molecular front information, if any, to generate a connectivity table of said atoms and bond connections corresponding to the input chemical structure.
Dependencies are inferred from the claim text.