Descriptors
Use the -d flag to save pocket descriptors in a CSV file (descriptors.csv). The file contains one row per pocket with the following columns, in order:
Column |
Description |
|---|---|
|
Index of the frame in the output trajectory. Equal to the input frame index when no extraction or sorting is performed. |
|
Index of the frame in the input trajectory. When multiple trajectories are concatenated this is the index in the concatenated trajectory (the reference frame is not counted). |
|
Residue ID assigned to the pocket in the volume PDB file (starting at 800). |
|
Druggability score assigned by the neural network model. |
|
Low-energy space available to the ligand, in ų. Proportional to the number of grid points and the grid spacing. |
|
Surface area of the pocket, in Ų. A point is considered superficial when it has fewer than 5 adjacent points. The surface-to-volume ratio provides insight into pocket shape. |
|
Low-energy space surrounding the pocket core, in ų. Counted on the low-resolution grid within the distance set by |
|
First principal length of the pocket: the square root of the largest eigenvalue of the covariance matrix of the pocket surface points, in units of the grid spacing (0.5 Å). |
|
Second principal length, in the same units. |
|
Third principal length (smallest), in the same units. |
|
Fraction of pocket atoms with an absolute partial charge less than 0.3e. |
|
Enclosure indicator between 0 and 1, computed from the vectors joining each surface point to its nearest atoms. In a buried pocket the atoms surround the points and the vectors cancel out, giving a value close to 1; in an open pocket they point one way and the value is close to 0. |
|
Number of pocket atoms with an absolute partial charge between 0.3e and 0.7e. |
|
Number of pocket atoms with an absolute partial charge greater than 0.7e. |
|
Space-separated list of residue IDs that form the pocket. |
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(Optional) Space-separated list of atom indices belonging to the pocket. Only included when the |