Updated README for 2.0 (#97)

README.md

@@ -3,14 +3,13 @@
 This repository contains scripts and data files used in the creation of the SPICE dataset.  It does not contain the
 dataset itself.  That is available from Zenodo:
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8222043.svg)](https://doi.org/10.5281/zenodo.8222043)
-
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10835749.svg)](https://doi.org/10.5281/zenodo.10835749)
 
 SPICE (Small-Molecule/Protein Interaction Chemical Energies) is a collection of quantum mechanical data for
 training potential functions.  The emphasis is particularly on simulating drug-like small molecules interacting
 with proteins.  It is designed to achieve the following goals.
 
-- **Cover a wide range of chemical space**.  It includes 15 elements (H, Li, C, N, O, F, Na, Mg, P, S, Cl, K, Ca, Br, I)
+- **Cover a wide range of chemical space**.  It includes 17 elements (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, I)
   and a wide range of chemical groups.  It includes charged and polar molecules as well as neutral ones.  It is
   designed to sample a wide range of both covalent and non-covalent interactions.
 - **Cover a wide range of conformations**.  It includes both low and high energy conformations.  It is
@@ -29,27 +28,33 @@ with proteins.  It is designed to achieve the following goals.
   public domain equivalent [CC0 license](https://creativecommons.org/share-your-work/public-domain/cc0/).
 
 SPICE is made up of a collection of subsets.  Each one is designed to provide a particular type of information.
-They include the following.
+The subsets in the current version (2.0) include the following.
 
 - **Dipeptides**.  These provide comprehensive sampling of the covalent interactions found in proteins.
 - **Solvated amino acids**.  These provide sampling of protein-water and water-water interactions.
 - **PubChem molecules**.  These sample a very wide variety of drug-like small molecules.
+- **Solvated PubChem molecules**.  These provide sampling of ligand-water interactions.
 - **Monomer and dimer structures from [DES370K](https://www.nature.com/articles/s41597-021-00833-x)**.
   These provide sampling of a wide variety of non-covalent interactions.
+- **Amino acid, ligand pairs**.  These provide sampling of nonbonded protein-ligand interactions.
 - **Ion pairs**.  These provide further sampling of Coulomb interactions over a range of distances.
+- **Water clusters**.  These provide additional sampling of water-water interactions.
 
 This table summarizes the content of each subset: the number of molecules/clusters it contains, the total number of
 conformations, the range of sizes spanned by the molecules/clusters, and the list of elements that appear in the subset.
 
-|Subset|Molecules|Conformations|Atoms|Elements|
-|---|---|---|---|---|
-|Dipeptides|677|33850|26–60|H, C, N, O, S|
+|Subset|Molecules/Clusters|Conformations|Atoms|Elements|
+|------|------------------|-------------|-----|--------|
+|Dipeptides|677|33,850|26–60|H, C, N, O, S|
 |Solvated Amino Acids|26|1300|79–96|H, C, N, O, S|
-|DES370K Dimers|3490|345676|2–34|H, Li, C, N, O, F, Na, Mg, P, S, Cl, K, Ca, Br, I|
-|DES370K Monomers|374|18700|3–22|H, C, N, O, F, P, S, Cl, Br, I|
-|PubChem|14643|731856|3–50|H, C, N, O, F, P, S, Cl, Br, I|
+|DES370K Dimers|3490|345,676|2–34|H, Li, C, N, O, F, Na, Mg, P, S, Cl, K, Ca, Br, I|
+|DES370K Monomers|374|18,700|3–22|H, C, N, O, F, P, S, Cl, Br, I|
+|PubChem|28,039|1,398,566|3–50|H, B, C, N, O, F, Si, P, S, Cl, Br, I|
+|Solvated PubChem|1397|13,934|63–110|H, C, N, O, F, P, S, Cl, Br, I|
+|Amino Acid Ligand Pairs|79,967|194,174|24–72|H, C, N, O, F, P, S, Cl, Br, I|
 |Ion Pairs|28|1426|2|Li, F, Na, Cl, K, Br, I|
-|Total|19238|1132808|2–96|H, Li, C, N, O, F, Na, Mg, P, S, Cl, K, Ca, Br, I|
+|Water Clusters|1|1000|90|H, O|
+|Total|113,999|2,008,628|2–110|H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, I|
 
 ## Citing The Dataset