# OEMedChem Examples Summary¶

## Molecule perception¶

### Bemis Murcko perception¶

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.py [ -uncolor ] input.sdf output.sdf


## Matched Pair Analysis¶

### Matched Pair analysis and transformations¶

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.

Schematic representation of the Matched Pair Analysis process

The command is:

MatchedPairTransform.py index.sdf input.sdf output.sdf


### Matched Pair analysis and listing of transformations¶

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.py [ -datafield sdDataField ] index.sdf


### Apply ChEMBL solubility transformations¶

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.py input.sdf output.sdf


## Maximum Common Substructure (MCS) Similarity¶

### MCS Similarity score reporting¶

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.

Schematic representation of the MCS fragment search process

The command is:

MCSFragDatabase.py -inmols index.sdf -query input.sdf


### Reporting the most common substructures from an input set of structures¶

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.py -inmols index.sdf