Lignin Structure(LGS) Generator Tool

Molecular structure simulation tool for lignin macromolecule. Lignin structure generator uses sequence-controlled structure generation approach for generating polymer chains of length 3 to 25. Workflow includes following functionalities

a) Sequencing of lignin monomers and conditional linkage generation
b) Generating the topological matrices and directed graph representation
c) Converting the directed graphs into molecular structures
d) Validation the dataset against the experimental observations and simulated structures from previous studies
e) Storing the valid structures forming a dataset

Dependencies (to run the tool)

1. Lignin generator requires JDK 8 or newer version.
2. CDK Toolkit (https://cdk.github.io/) (Integrated in Jar)

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Executable jar and config file for download

Lignin structure (LGS) generator

Configuration file : Configure the structural composition for generating the structure

project-config.yaml

Properties	Values	Comments
Degree of polymerization(dp)	dp: 0 (or) min_dp: 3 max_dp: 25.	Configure either single DP (or min & max dp for generating structures in a range of DP)
Bond proportion	# percentage(%) values BO4: 61 BB: 12 B5: 3 4O5: 2 55: 1 DBDO: 1.	Experimental observation from NMR or other analysis results (Add in the percentage (%) values)
Monomer proportion	s_g_ratio: 1.8 (or) percentage(%) values G: 32 S: 68 H: 0.	Use either S/G ratio or Monomer percentages. If both the values are given S/G ratio takes precedence. - set s_g_ratio to -1 to use S/G/H percentage values - set s_g_ratio to 0 to generate G Type structures - set s_g_ratio as S/G ratio to generate SG type structures. Example : 1.8
Output formats	# true/false value _png: false matrices: false sdf: true	Enabling to store individual structurual definition in any of the formats # 2D structure # Adjacency and Connectivity Matrix # mol file
Comprehensive dataset	# true/false value json: true.	Comprehensive dataset (SMILES and evaluatied properties of the stuctures generated) #To write json file

Instruction to run the executable version

1. Download Executable_Jar_and_Config_file.zip file to local path

2. Unzip the file

   project-config.yaml will be available within "resource" folder as downloaded from Executable jar and config file.

   

3. Edit the lignin structural configurations in project-config.yaml

4. Set JAVA_HOME in Environment variables

5. In Windows, execute "lgs-run.bat"

   In Linux/Unix and Mac OS, execute "./lgs-run.sh"

   Example: Executing from Window's command prompt

   

Generated structural data are stored as JSON / Matrices(.csv) / MOL V3000(.mol) files with respective folder names in 'output' folder

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Illustrations

G Type - Model-1

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SG Type - Model-1

Related resources

Eswaran, S. c. d., Subramaniam, S., Sanyal, U., Rallo, R. & Zhang, X. Molecular structural dataset of lignin macromolecule elucidating experimental structural compositions. Scientific Data 9, 647, doi:10.1038/s41597-022-01709-4 (2022)