1. from scientific literature Principal Scientist (Chemoinformatics)
ChemEngine
An automated chemical data harvesting tool for molecular inventory and chemical computing
from scientific literature
M. Karthikeyan Ph.D
Principal Scientist (Chemoinformatics)
CSIR-National Chemical Laboratory
Pune, India

2. Open Source in Chemoinformatics
ChemXtreme (JCIM 2005) GoogleAPI (MSDS)
ChemStar (JCIM2008) (Pubchem 18m)
ChemRobot (2011 * Denver) (Img2Str)
ChemInfoCloud (2014 * San Fransisco)
ChemScreener (CCHTS 2015) Virtual Screening
ChemEngine (2016 * San Diego) Poster CINF
Why Open Source?

3. ChemEngine
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 an application, 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.

4. ChemEngine
The methodology has been demonstrated via three 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 (SPEs) 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 PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes.
Software Source code Project file is available for downloading at the Sourceforge site. FREE !

5. Re-usable Chemical Structures
When chemical structures are stored in truly computable format with atoms and bond matrices (vector format-Cartesian co-ordinates), they can be processed electronically for computational and informatics purposes.
However while transforming/storing the files in PDF (Printable/Portable Document/Data Format) that are usually used for the convenience of printing and reading, the valuable and re-usable molecular data is totally lost and buried in scientific literature as documents and seldom used for further computational studies.

6. Image to Structure
Transforming the raster images into vector graphics followed by identification of relevant pixel information associated with atoms and bonds of a molecule is a cumbersome job.
Tools have also been developed to harvest molecular data from images using web camera, scanned images wherein the raster graphics data was transformed into vector graphics to eventually retrieve the atoms and bonds information for the generation of truly computable and re-usable chemical structures.
Several attempts have been made to convert molecular images into truly computable format such as ChemRobot, OSRA, ChemReader, CLiDE, but only partial success has been achieved.

7. ChemEngine
FREE !

8. Chem Engine
We have developed an application, ChemEngine that reads all the files stored in the pdf format to generate computable molecular structures.
To demonstrate the efficiency of the program, supporting material data files of three different formats available freely from the publishers were selected and data was parsed using PDF readers to extract the textual information.

9. The Challenge
Supporting materials of molecular data files also include brief description of molecules, computed data, plots, page numbers, document information, manuscript bibliographic details etc. as a single document in pdf format that makes harvesting the molecular data extremely difficult as these have to be excluded while parsing the PDF file.

10. General Workflow

11. General Workflow Input Data Format Pattern Recognition
Regular Expression
Generate Coordinates

12. Pattern Recognition Pseudo code:
(Co-ordinate Text).matches(“Regular Expression Pattern with Delimiter Definition”);
For Example: Delimiter: Comma
String_Data.matches("^[A-Za-z0-9]{1,2}\\,[0]{0,1}[\\,]{0,1}-{0,1}.{1,2}[0-9]{1,10}\\,-{0,1}.{1,2}[0-9]{1,10}.{1,}")
Delimiter: Space
String_Data.matches("^[A-Za-z0-9]{1,2}\\s+[0]{0,1}[\\s+]{0,1}-{0,1}.{1,2}[0-9]{0,10}\\s+-{0,1}.{1,2}[0-9]{0,10}.{1,}")

13. Harvesting Molecular Data
Bond matrix data
(Computed) 
Coordinates Data
(From PDF)
(To be Processed)
Non- Molecular Data
(To be Excluded)
0:----
Mol_0 1 C1 H
Mol_0 2 C1 H
Mol_0 3 C1 H
Mol_0 4 C1 S
Mol_0 5 S5 H   C H H H S H    S1
SUPPORTING INFORMATION
Thiol-Ene Click Chemistry: Computational and Kinetic
Analysis of the Influence of Alkene Functionality.
Brian H. Northrop* and Roderick N. Coffey
Department of Chemistry
Wesleyan University, Middletown, Connecticut

14. AS X Y Z AN X Y Z AS X Y Z AS Delimiter (Space) Delimiter (Comma) ANH H
C,0, , ,
C,0, , ,
C,0, , ,
C,0, , ,
C,0, , ,
C,0, , , AS
Delimiter
(Space)
Delimiter
(Comma) AN
Delimiter
(Space) AS
ChemEngine
Pattern Recognition AN X Y Z C S C C H H
Coordinate matrix
C1 S
C1 H
C1 H
Optional CT
3D MOLECULE

15. Bond Recognition (a) A2 A1 (b) (c) Bond Recognition r1 r2 l1 r1’ r2’
0.35 Å
r'1
r‘2
(a)
(b)
(c)

16. Compare the Bond distance
ChemEngine
Gaussian 09

17. Computed Conformational Energy

18. Case Studies Entry Case Study N= molecules Regular Expression pattern
Format & Delimit er 1
Epoxide formation
from sulfur ylides and aldehydes 29
^[A-Za-z0-9]{1,2}\\s+- {0,1}.{1,2}[0-9]{1,8}\\s+- {0,1}.{1,2}[0-9]{1,8}.{1,}
PDF
Space 2
Thiol ene click chemistry
115
Text 3
Design of tetra(arenediyl)bis(allyl) derivatives for cope rearrangement transition states 55
^[A-Za-z0- 9]{1,2}\\,[0]{0,1}[\\,]{0,1}- {0,1}.{1,2}[0-9]{1,10}\\,- {0,1}.{1,2}[0-9]{1,10}.{1,}
Comma

19. ChemEngine

20. Harvesting Molecular Data

21. Graphical User
Interface

23. Acknowledgement The Director, CSIR-National Chemical Laboratory, Pune
Department of Science and Technology for International Travel Grant
ACS-CINF Division
SourceForge

24. Thank You