s_fparams Struct Reference

#include <fparams.h>

Data Fields
char	pdb_path [M_MAX_PDB_NAME_LEN]
char **	pdb_lst
int	npdb
int	flag_do_asa_and_volume_calculations
int	min_apol_neigh
int	sl_clust_min_nneigh
int	nb_mcv_iter
int	basic_volume_div
int	min_pock_nb_asph
int	db_run
float	clust_max_dist
float	refine_min_apolar_asphere_prop
float	sl_clust_max_dist
float	refine_clust_dist
float	asph_min_size
float	asph_max_size

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Detailed Description

Structure containing all necessary parameters that can be changed by the user. This structure is commun to both programs (validation and pocket finding), even if the pocked finding programm doesn't need some parameters.

Definition at line 134 of file fparams.h.

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Field Documentation

char s_fparams::pdb_path[M_MAX_PDB_NAME_LEN]

The pdb file

Definition at line 136 of file fparams.h.

Referenced by check_fparams(), check_fpocket(), get_fpocket_args(), init_def_fparams(), main(), print_fparams(), and test_fpocket().

char** s_fparams::pdb_lst

Definition at line 137 of file fparams.h.

Referenced by free_fparams(), get_fpocket_args(), init_def_fparams(), and main().

int s_fparams::npdb

number of pdb files

Definition at line 138 of file fparams.h.

Referenced by free_fparams(), get_fpocket_args(), init_def_fparams(), and main().

int s_fparams::flag_do_asa_and_volume_calculations

if 1, asa and volume calculations are performed(slower), if 0, not

Definition at line 139 of file fparams.h.

Referenced by get_explicit_desc(), init_def_fparams(), mdpocket_characterize(), mdpocket_detect(), and set_pockets_descriptors().

int s_fparams::min_apol_neigh

Min number of apolar neighbours for an a-sphere to be an apolar a-sphere

Definition at line 141 of file fparams.h.

Referenced by check_fparams(), init_def_fparams(), parse_min_apol_neigh(), print_fparams(), print_params(), and search_pocket().

int s_fparams::sl_clust_min_nneigh

Min number of neighbours for single linkage clustering

Definition at line 141 of file fparams.h.

Referenced by check_fparams(), init_def_fparams(), parse_sclust_min_nneigh(), pck_ml_clust(), pck_ml_clust_test(), print_fparams(), print_params(), and write_md_grid().

int s_fparams::nb_mcv_iter

Number of iteration for the Monte Carlo volume calculation

Definition at line 141 of file fparams.h.

Referenced by desc_pocket(), get_explicit_desc(), init_def_fparams(), mdpocket_characterize(), parse_mc_niter(), print_fparams(), print_params(), set_overlap_volumes(), set_pockets_descriptors(), and test_set().

int s_fparams::basic_volume_div

Box division factor for basic volume calculation

Definition at line 141 of file fparams.h.

Referenced by init_def_fparams(), parse_basic_vol_div(), print_fparams(), print_params(), and set_overlap_volumes().

int s_fparams::min_pock_nb_asph

Minimump number of alpha spheres per pocket

Definition at line 141 of file fparams.h.

Referenced by check_fparams(), dropSmallNpolarPockets(), init_def_fparams(), parse_min_pock_nb_asph(), and write_md_grid().

int s_fparams::db_run

flag for running fpocket for db population

Definition at line 141 of file fparams.h.

Referenced by get_fpocket_args(), init_def_fparams(), main(), and process_pdb().

float s_fparams::clust_max_dist

First clustering distance criteria

Definition at line 150 of file fparams.h.

Referenced by check_fparams(), init_def_fparams(), parse_clust_max_dist(), print_fparams(), print_params(), updateIds(), and write_md_grid().

float s_fparams::refine_min_apolar_asphere_prop

Min proportion of apolar alpha spheres for each pocket

Definition at line 150 of file fparams.h.

Referenced by check_fparams(), dropSmallNpolarPockets(), init_def_fparams(), parse_refine_minaap(), print_fparams(), and print_params().

float s_fparams::sl_clust_max_dist

Single linkage clusturing distance criteria

Definition at line 150 of file fparams.h.

Referenced by check_fparams(), init_def_fparams(), parse_sclust_max_dist(), pck_final_clust(), pck_ml_clust(), pck_ml_clust_test(), print_fparams(), print_params(), and write_md_grid().

float s_fparams::refine_clust_dist

Refine clustering distance criteria

Definition at line 150 of file fparams.h.

Referenced by check_fparams(), init_def_fparams(), parse_refine_dist(), print_fparams(), print_params(), and write_md_grid().

float s_fparams::asph_min_size

Minimum size of alpha spheres to keep

Definition at line 150 of file fparams.h.

Referenced by check_fparams(), init_def_fparams(), parse_asph_min_size(), print_fparams(), print_params(), search_pocket(), and write_md_grid().

float s_fparams::asph_max_size

Maximum size of alpha spheres to keep

Definition at line 150 of file fparams.h.

Referenced by check_fparams(), init_def_fparams(), parse_asph_max_size(), print_fparams(), print_params(), search_pocket(), and write_md_grid().

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The documentation for this struct was generated from the following file:

• fparams.h