ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

Abstract

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher’s resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract. Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0175-x) contains supplementary material, which is available to authorized users.

Information Retrieval and Text Mining Technologies for Chemistry

“…Tools like ChemEngine have been implemented to automatically extract 3D molecular XYZ coordinates and atom information from articles with the aim to directly generate computable molecular structures. 434 This system used pattern recognition and regular expressions to detect molecular coordinates and distinguish it from surround-ing nonmolecular free text. After generating the atom coordinate matrix data from the previously detected molecular coordinates, tools like ChemEngine build molecules using the bond matrix and the atom connectivity.…”

“…Authors can also present chemical structural information in documents, especially in case of supporting/Supporting Information of scientific articles, in the form of plain text 3D X, Y, Z atom coordinate values. Tools like ChemEngine have been implemented to automatically extract 3D molecular XYZ coordinates and atom information from articles with the aim to directly generate computable molecular structures . This system used pattern recognition and regular expressions to detect molecular coordinates and distinguish it from surrounding nonmolecular free text.…”