A program that perceives the [Bemis-1996] regions of the input structures and outputs role information and annotations as SD data in the output. Uncoloring of the fragment regions to remove atom types and properties can optionally be requested for the output SMILES string annotations. An example command would be:
BemisMurckoPerception [ -uncolor ] input.sdf output.sdf
A program that performs a matched pair analysis of a set of structures for indexing, then reads an input set of structures and outputs transformed structures based on the matched pairs discovered during indexing.
The command is:
MatchedPairTransform index.sdf input.sdf output.sdf
A program that performs a matched pair analysis of a set of structures for indexing, then prints the transformations and matched pairs found from the analysis. If an (optional, numeric) data field is provided, the returned transformations can also be ranked by the largest increase in the delta property found from the matched pairs that define it. The command is:
MatchedPairTransformList [ -datafield sdDataField ] index.sdf
A utility that reads an input set of structures and outputs transformed structures along with annotations containing of the original data based on the matched pairs discovered from indexing solubility data from the [ChEMBL18-2014] data set. The command is:
ChEMBLsolubility input.sdf output.sdf
A program that indexes a set of input structures or loads an index from a prior indexing run, and then returns the highest Maximum Common Substructure (Tanimoto) scores from the provided input query structures.
The command is:
MCSFragDatabase -inmols index.sdf -query input.sdf
A program that indexes a set of input structures, and then reports the most common fragments identified by fragmentation from the input structures. The command is:
MCSFragOccurrence -inmols index.sdf