A method and system for harvesting molecular structures from non-editable documents is disclosed herein. A non-editable storage document is fed by a feeder which is received by a receiver. The molecular and non-molecular data contained in the non-editable storage document is recognized. The three-dimensional coordinates of the molecular data is separated using a pattern recognition. The molecular coordinates are encoded by a pattern sequence. A bond matrix data of the encoded data is generated. Subsequently the bond matrix data for accuracy is verified by comparing with a stored standardized data into a library.