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ChemEngine ACS

Muthukumarasamy Karthikeyan
Muthukumarasamy Karthikeyan

This document describes ChemEngine, a program that can extract 3D molecular data from PDF files. ChemEngine uses pattern recognition to identify molecular coordinates in supplementary scientific articles. It generates standard molecular data like bond matrices and atomic coordinates that can then be used for computational analysis. The methodology was demonstrated on three case studies involving different coordinate data formats. ChemEngine accurately extracted coordinates and produced computational results like energies that agreed with original literature values. The tool aims to automate the conversion of molecular data from PDFs into a format suitable for computational workflows.

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ChemEngine: Harvest Chemical Data from PDF Files M. Karthikeyan, Ph.D CSIR-National Chemical Laboratory http://moltable.ncl.res.in/ Pune, India
ChemEngine
ChemEngine ACS
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 publishers 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, 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.
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 in the form of jar file is available for downloading at the Sourceforge site.
General Workflow
General Workflow Input Data Format Pattern Recognition Regular Expression Generate Coordinates
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,}") Pattern Recognition
Harvesting Molecular Data Bond matrix data (Computed) Coordinates Data (From PDF) (To be Processed) Non- Molecular Data (From PDF) (To be Excluded) 0:---- Mol_0 1 C1 H2 1.09011 1.200 -0.109889 Mol_0 2 C1 H3 1.08923 1.200 -0.110769 Mol_0 3 C1 H4 1.08923 1.200 -0.110769 Mol_0 4 C1 S5 1.831868 1.55 0.281868 Mol_0 5 S5 H6 1.34383 1.410 -0.066162 C -0.04781100 1.16216400 0.00000000 H -1.09556300 1.46309200 0.00000000 H 0.43082600 1.55738100 0.89506100 H 0.43082600 1.55738100 -0.89506100 S -0.04781100 -0.66970400 0.00000000 H 1.28575000 -0.83557700 0.00000000 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 06459.
AS C -1.1744 0.5417 -0.9605 S -0.0501 -0.0786 0.1566 C 1.0931 -1.1415 -0.7978 C 1.1877 1.1781 0.7204 H -2.1028 0.8352 -0.4693 H -0.7923 1.2464 -1.7030 6 -1.587291 -1.111365 4.067000 6 -0.971341 0.146218 4.067000 6 0.409526 0.261943 4.067000 7 1.580845 0.365064 4.067000 1 -2.671280 -1.185650 4.067000 1 -1.001643 -2.026790 4.067000 AS Delimiter (Space) AN Delimiter (Space) Delimiter (Comma) C,0,0.2760228632,-1.0699067694,1.2573191608 C,0,0.1782250457,1.2145223184,1.2478315394 C,0,0.178225046,1.2145223184,-1.2478315394 C,0,0.2760228634,-1.0699067694,-1.2573191608 C,0,-1.15402211,-0.680015634,-1.5218932206 C,0,-1.2153634407,0.7116626186,-1.5239653892 ChemEngine Pattern Recognition C -1.1744 0.5417 -0.9605 S -0.0501 -0.0786 0.1566 C 1.0931 -1.1415 -0.7978 C 1.1877 1.1781 0.7204 H -2.1028 0.8352 -0.4693 H -0.7923 1.2464 -1.7030 C1 S2 1.7019797266712668 1.55 0.1519797266712668 C1 H5 1.0905715244769594 1.2000000000000002 -0.1094284755230408 C1 H6 1.0926613153214495 1.2000000000000002 -0.10733868467855068 X Y ZAS X Y ZAN AS X Y Z AN X Y Z Optional CT Coordinate matrix 3D MOLECULE
Bond Recognition A1 A2 r1 r2 l1 l1 Bond Recognition A1 A2 l1 r1 r2 l1 A1 A2 r1 r2 d1 0.35 A1 A2 r'1 r2 (a) (b) (c)
Compare the Bond distance ChemEngine Gaussian 09
Computed Conformational Energy R族 = 0.9979 -1200 -1000 -800 -600 -400 -200 0 -1200 -1000 -800 -600 -400 -200 0 Energy(RHF) Energy (CBS-QB3)
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 ^[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,} Text Space 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,} PDF Comma
ChemEngine
Harvesting Molecular Data
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ChemEngine ACS

  • 1. ChemEngine: Harvest Chemical Data from PDF Files M. Karthikeyan, Ph.D CSIR-National Chemical Laboratory http://moltable.ncl.res.in/ Pune, India
  • 4. 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 publishers 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, 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.
  • 5. 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 in the form of jar file is available for downloading at the Sourceforge site.
  • 7. General Workflow Input Data Format Pattern Recognition Regular Expression Generate Coordinates
  • 8. 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,}") Pattern Recognition
  • 9. Harvesting Molecular Data Bond matrix data (Computed) Coordinates Data (From PDF) (To be Processed) Non- Molecular Data (From PDF) (To be Excluded) 0:---- Mol_0 1 C1 H2 1.09011 1.200 -0.109889 Mol_0 2 C1 H3 1.08923 1.200 -0.110769 Mol_0 3 C1 H4 1.08923 1.200 -0.110769 Mol_0 4 C1 S5 1.831868 1.55 0.281868 Mol_0 5 S5 H6 1.34383 1.410 -0.066162 C -0.04781100 1.16216400 0.00000000 H -1.09556300 1.46309200 0.00000000 H 0.43082600 1.55738100 0.89506100 H 0.43082600 1.55738100 -0.89506100 S -0.04781100 -0.66970400 0.00000000 H 1.28575000 -0.83557700 0.00000000 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 06459.
  • 10. AS C -1.1744 0.5417 -0.9605 S -0.0501 -0.0786 0.1566 C 1.0931 -1.1415 -0.7978 C 1.1877 1.1781 0.7204 H -2.1028 0.8352 -0.4693 H -0.7923 1.2464 -1.7030 6 -1.587291 -1.111365 4.067000 6 -0.971341 0.146218 4.067000 6 0.409526 0.261943 4.067000 7 1.580845 0.365064 4.067000 1 -2.671280 -1.185650 4.067000 1 -1.001643 -2.026790 4.067000 AS Delimiter (Space) AN Delimiter (Space) Delimiter (Comma) C,0,0.2760228632,-1.0699067694,1.2573191608 C,0,0.1782250457,1.2145223184,1.2478315394 C,0,0.178225046,1.2145223184,-1.2478315394 C,0,0.2760228634,-1.0699067694,-1.2573191608 C,0,-1.15402211,-0.680015634,-1.5218932206 C,0,-1.2153634407,0.7116626186,-1.5239653892 ChemEngine Pattern Recognition C -1.1744 0.5417 -0.9605 S -0.0501 -0.0786 0.1566 C 1.0931 -1.1415 -0.7978 C 1.1877 1.1781 0.7204 H -2.1028 0.8352 -0.4693 H -0.7923 1.2464 -1.7030 C1 S2 1.7019797266712668 1.55 0.1519797266712668 C1 H5 1.0905715244769594 1.2000000000000002 -0.1094284755230408 C1 H6 1.0926613153214495 1.2000000000000002 -0.10733868467855068 X Y ZAS X Y ZAN AS X Y Z AN X Y Z Optional CT Coordinate matrix 3D MOLECULE
  • 11. Bond Recognition A1 A2 r1 r2 l1 l1 Bond Recognition A1 A2 l1 r1 r2 l1 A1 A2 r1 r2 d1 0.35 A1 A2 r'1 r2 (a) (b) (c)
  • 12. Compare the Bond distance ChemEngine Gaussian 09
  • 13. Computed Conformational Energy R族 = 0.9979 -1200 -1000 -800 -600 -400 -200 0 -1200 -1000 -800 -600 -400 -200 0 Energy(RHF) Energy (CBS-QB3)
  • 14. 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 ^[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,} Text Space 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,} PDF Comma