OEMapper¶
The mapper cube produces edges made of ligand pairs to run relative binding affinity calculations. In general given N ligands N(N-1)/2 edges can be used to run RBFE calculations. The mapper selects a reasonable subset of these edges with the goal to keep the computational demand low. The edges are selected based on set of heuristics like ligand mcs similarities, equal charges and OpenEye rocs score. The mapper output can be used with the NES floe to run RBFE calculations. In order to have successful RBFE results the ligands should be similar and do not attempt large mutations. The Mapper cube can accept a edge text input a text file as well. In this case the produced map is defined in the provide text file and no attempt to use internal heuristics is done. The text file has the following syntax:
ligAname >> ligBname
where “ligAname” and “ligBname” are the ligand name titles for the ligands to be transformed.
- Input
Data record Stream - Streamed-in of a set of similar ligands with 3D coordinates and correct Chemistry
OPTIONAL: Text file text file with the user defined edges based on the ligand titles
- Output
Data Record Stream - Streamed-out of records containing the edge ligand pairs
Mapper floe report - The Mapper floe report used in the Orion UI to visualize the generated edge map
Calculation Parameters¶
creation of edges between ligands of different charges. | Default: 0.5
Field parameters¶
Hardware Parameters¶
Machine hardware requirements
Metrics Parameters¶
Cube Metric Parameters