add zenodo doi to readme

Author: LindeSchoenmaker

README.md

@@ -1,24 +1,6 @@
 # IMERGE-FEP
 This repository contains the code and files that form the basis of the manuscript "IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates"
 
-## Contents
-Folders
-
-* rgroupinterm - a tool for pairwise R-group enumeration and pruning for the automatic creation of intermediate molecules
-* rhfe_gromacs - the code, input files and md files to run the free energy perturbations described in the manuscript
-* rhfe_analysis - code for analysing FEP output
-* data - raw data used as input
-* supplemental information - sdf files & visualization of molecules from the perturbations that were run
-* figures - code for manuscript figures
-
-Files
-
-* rgroup_enumeration.ipynb - documentation basic functionality enumerator
-* eg5_case_study.ipynb - application of enumerator on cogeneric series
-* perserving_chirality.ipynb - background on chiral information in RDkit
-* jacs_intermediates.py - script to enumerate all intermediates of the jacs files (takes a while)
-* calc_scores.py - calculates similarity scores of intermediates using the pruners (takes two days to run this for all intermediates in the jacs set)
-
 ## Installation
 Use setup.py for creating the environment for the intermediate generation
 
@@ -41,4 +23,25 @@ download the benchmark ligands from: https://github.com/JenkeScheen/fep_intermed
 gromacs version: gromacs/2022.1/gcc.8.4.0-cuda.11.7.1
 
 ## Generating intermediates for a molecular pair
-The functionality and use of the intermediate generator is shown the jupyter notebook rgroup_enumeration.ipynb
+The functionality and use of the intermediate generator is shown the jupyter notebook rgroup_enumeration.ipynb
+
+## Contents
+Folders
+
+* rgroupinterm - a tool for pairwise R-group enumeration and pruning for the automatic creation of intermediate molecules
+* rhfe_gromacs - the code, input files and md files to run the free energy perturbations described in the manuscript
+* rhfe_analysis - code for analysing FEP output
+* data - raw data used as input
+* supplemental information - sdf files & visualization of molecules from the perturbations that were run
+* figures - code for manuscript figures
+
+Files
+
+* rgroup_enumeration.ipynb - documentation basic functionality enumerator
+* eg5_case_study.ipynb - application of enumerator on cogeneric series
+* perserving_chirality.ipynb - background on chiral information in RDkit
+* jacs_intermediates.py - script to enumerate all intermediates of the jacs files (takes a while)
+* calc_scores.py - calculates similarity scores of intermediates using the pruners (takes two days to run this for all intermediates in the jacs set)
+
+## Related documents
+For the tpr files used for running of the RHFE simulations in gromacs can be found in [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13939493.svg)](https://doi.org/10.5281/zenodo.13939493)