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| cluster.sizestat | generate statistics on sizes of clusters |
| cluster.visualize | visualize clustering result using multi-dimensional scaling |
| cmp.cluster | cluster compounds using a descriptor database |
| cmp.duplicated | quickly detect compound duplication in a descriptor database |
| cmp.parse | Parse an SDF file and compute descriptors for all compounds |
| cmp.parse1 | Parsing an SDF file and calculate the descriptor for one compound |
| cmp.search | Search a descriptor database for compounds similar to query compound |
| cmp.similarity | Compute similarity between two compounds using their descriptors |
| db.explain | Explain an atom-pair descriptor or an array of atom-pair descriptors |
| db.subset | Subset a descriptor database and return a sub-database for the selected compounds |
| sdf.subset | Subset a SDF and return SDF segements for selected compounds |
| sdf.visualize | Subset a SDF and visualize selected compounds in a webpage |