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--score_coefficients=c0,...,c8 replaces the pocket score by a linear score over nine terms: intercept, nas_norm, prop_asapol_norm, mean_loc_hyd_dens_norm, polarity_score, as_density, convex_hull_volume, surf_pol_vdw14 and surf_apol_vdw14. fpocket 4's built-in score is this form with coefficients -0.03783394,0.48461469,0,0,0,0.09093926,0.0004155899, -0.003995233,-0.004072336, which reproduces it exactly. --write_score_descriptors writes those descriptors for every pocket to <name>_out/<name>_score_desc.txt, so a score can be refitted without re-running fpocket. Without either option fpocket's behaviour and output are unchanged.
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Adds two opt-in options to fpocket. Without them, behaviour and output are unchanged.
--score_coefficients c0,...,c8replaces the pocket score by a linear score over nine terms:fpocket 4's built-in score (the last assignment in
score_pocket) has exactly this form. Passing its coefficients,-0.03783394,0.48461469,0,0,0,0.09093926,0.0004155899,-0.003995233,-0.004072336, reproduces the default scores and ranking exactly. The option exists so the ranking can be refitted for structures that differ from the all-atom training data, without recompiling. We use it for coarse-grained proteins (Martini 2, Martini 3, SIRAH), where the default score ranks pockets poorly. We refitted the score on fpocket's own training set (fpocket-data-1.0, 263 complexes) and retuned the detection flags. Together they raise Top-1 on fpocket's 48 apo test structures from about 0.1 to about 0.6.--write_score_descriptorswrites those eight descriptors for every pocket to<name>_out/<name>_score_desc.txt, so a score can be refitted from one fpocket run per structure.Changes:
fparams.h/fparams.c: the two long options, parsing (exits with a message unless exactly 9 numbers are given), and-htext.pscoring.c:score_pocket_custom().pocket.c: use it when the option is set.fpout.c/fpmain.c: the descriptor file.Testing: