#include <descriptors.h>
Data Fields | |
| float | hydrophobicity_score |
| float | volume_score |
| float | volume |
| float | prop_polar_atm |
| float | mean_asph_ray |
| float | masph_sacc |
| float | apolar_asphere_prop |
| float | mean_loc_hyd_dens |
| float | as_density |
| float | as_max_dst |
| float | flex |
| float | nas_norm |
| float | polarity_score_norm |
| float | mean_loc_hyd_dens_norm |
| float | prop_asapol_norm |
| float | as_density_norm |
| float | as_max_dst_norm |
| float | surf_vdw |
| float | surf_vdw14 |
| float | surf_vdw22 |
| float | surf_pol_vdw |
| float | surf_pol_vdw14 |
| float | surf_pol_vdw22 |
| float | surf_apol_vdw |
| float | surf_apol_vdw14 |
| float | surf_apol_vdw22 |
| int | aa_compo [20] |
| int | nb_asph |
| int | polarity_score |
| int | charge_score |
| float | as_max_r |
| float | drug_score |
| int | interChain |
| int | characterChain1 |
| int | characterChain2 |
| int | numResChain1 |
| int | numResChain2 |
| char | nameChain1 [2] |
| char | nameChain2 [2] |
| char | ligTag [8] |
| int | n_abpa |
Definition at line 56 of file descriptors.h.
Hydropathie score - for each aa
Definition at line 58 of file descriptors.h.
Referenced by drug_score_pocket(), print_pocket(), reset_desc(), set_aa_desc(), set_atom_based_descriptors(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
| float s_desc::volume_score |
Volume score - for each aa
Definition at line 58 of file descriptors.h.
Referenced by print_pocket(), reset_desc(), set_aa_desc(), set_atom_based_descriptors(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
| float s_desc::volume |
Pocket volume
Definition at line 58 of file descriptors.h.
Referenced by check_pockets(), compare_pockets_volume(), print_pocket(), reset_desc(), set_basic_overlap_volume(), set_descriptors(), set_mc_overlap_volume(), set_pocket_mtvolume(), set_pocket_volume(), write_pocket_pdb(), and write_pocket_pqr().
| float s_desc::prop_polar_atm |
Proportion of polar atoms
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), and set_atom_based_descriptors().
| float s_desc::mean_asph_ray |
Mean alpha sphere radius
Definition at line 58 of file descriptors.h.
Referenced by print_pocket(), reset_desc(), set_descriptors(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
| float s_desc::masph_sacc |
Mean alpha sphere solvent accessibility
Definition at line 58 of file descriptors.h.
Referenced by print_pocket(), reset_desc(), set_descriptors(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
Proportion of apolar alpha spheres
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), set_descriptors(), set_normalized_descriptors(), write_pocket_pdb(), and write_pocket_pqr().
Mean local hydrophobic density (from alpha spheres)
Definition at line 58 of file descriptors.h.
Referenced by print_pocket(), reset_desc(), set_descriptors(), set_normalized_descriptors(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
| float s_desc::as_density |
Pocket density, defined as mean distance between alpha spheres
Definition at line 58 of file descriptors.h.
Referenced by pck_final_clust(), reset_desc(), score_pocket(), set_descriptors(), and set_normalized_descriptors().
| float s_desc::as_max_dst |
Maximum distance between two alpha spheres The following descriptors are all normalized using observed values among all pocket found by the algorithm. These are not set in descriptor.c, but in pocket.c as we have to check all pocket first to store boundaries of the descriptor to normalize.
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), set_descriptors(), and set_normalized_descriptors().
| float s_desc::flex |
Normalized flexibility - based on B factors - ABUSIVE
Definition at line 58 of file descriptors.h.
Referenced by print_pocket(), reset_desc(), set_atom_based_descriptors(), set_normalized_descriptors(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
| float s_desc::nas_norm |
Normalized number of alpha sphere
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), score_pocket(), and set_normalized_descriptors().
Normalized polarity score
Definition at line 58 of file descriptors.h.
Referenced by drug_score_pocket(), reset_desc(), and set_normalized_descriptors().
Normalized mean local hydrophobic density
Definition at line 58 of file descriptors.h.
Referenced by drug_score_pocket(), reset_desc(), score_pocket(), and set_normalized_descriptors().
| float s_desc::prop_asapol_norm |
Normalized proportion of apolar alphasphere
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), score_pocket(), and set_normalized_descriptors().
| float s_desc::as_density_norm |
Normalized alpha sphere density
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), and set_normalized_descriptors().
| float s_desc::as_max_dst_norm |
normalized maximum distance between alpha sphere centers The following descriptors are various surface calculations
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), and set_normalized_descriptors().
| float s_desc::surf_vdw |
Van der Waals surface of the pocket
Definition at line 58 of file descriptors.h.
Referenced by reset_desc().
| float s_desc::surf_vdw14 |
Van der Waals surface + 1.4 A probe
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), and set_ASA().
| float s_desc::surf_vdw22 |
Van der Waals surface + 2.2 A probe
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), and set_ASA().
| float s_desc::surf_pol_vdw |
polar van der Waals surface of the pocket
Definition at line 58 of file descriptors.h.
Referenced by reset_desc().
| float s_desc::surf_pol_vdw14 |
polar van der Waals surface + 1.4 A probe
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), set_ASA(), and write_descriptors_DB().
| float s_desc::surf_pol_vdw22 |
polar an der Waals surface + 2.2 A probe
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), set_ASA(), and write_descriptors_DB().
| float s_desc::surf_apol_vdw |
polar van der Waals surface of the pocket
Definition at line 58 of file descriptors.h.
Referenced by reset_desc().
| float s_desc::surf_apol_vdw14 |
polar van der Waals surface + 1.4 A probe
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), set_ASA(), and write_descriptors_DB().
| float s_desc::surf_apol_vdw22 |
< polar van der Waals surface + 2.2 A probe
Definition at line 58 of file descriptors.h.
Referenced by reset_desc(), set_ASA(), and write_descriptors_DB().
| int s_desc::aa_compo[20] |
Absolute amino acid composition
Definition at line 94 of file descriptors.h.
Referenced by print_pocket(), reset_desc(), set_aa_desc(), write_descriptors_DB(), write_md_descriptors(), and write_pocket_desc().
| int s_desc::nb_asph |
Number of alpha spheres
Definition at line 95 of file descriptors.h.
Referenced by compare_pockets_nasph(), pck_final_clust(), print_pocket(), reset_desc(), set_descriptors(), set_normalized_descriptors(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
Polarity score (based on amino acids properties ; see aa.c & aa.h)
Definition at line 95 of file descriptors.h.
Referenced by print_pocket(), reset_desc(), score_pocket(), set_aa_desc(), set_normalized_descriptors(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
Sum of all net charges at pH = 7 (see aa.c & aa.h)
Definition at line 95 of file descriptors.h.
Referenced by print_pocket(), reset_desc(), set_aa_desc(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
| float s_desc::as_max_r |
Alpha sphere maximum radius
Definition at line 98 of file descriptors.h.
Referenced by set_descriptors().
| float s_desc::drug_score |
Drug score of the binding site
Definition at line 99 of file descriptors.h.
Referenced by calculate_md_dens_grid(), reset_desc(), set_pockets_descriptors(), update_md_grid(), write_descriptors_DB(), write_pocket_pdb(), and write_pocket_pqr().
0 if pocket in single chain, 1 if between 2 chains
Definition at line 100 of file descriptors.h.
Referenced by set_atom_based_descriptors(), and write_descriptors_DB().
0 if protein, 1 if nucl acid pocket, 2 if HETATM pocket
Definition at line 100 of file descriptors.h.
Referenced by reset_desc(), set_atom_based_descriptors(), and write_descriptors_DB().
0 if protein, 1 if nucl acid pocket, 2 if HETATM pocket
Definition at line 100 of file descriptors.h.
Referenced by reset_desc(), set_atom_based_descriptors(), and write_descriptors_DB().
number of resdiues on chain 1
Definition at line 100 of file descriptors.h.
Referenced by reset_desc(), set_atom_based_descriptors(), and write_descriptors_DB().
number of res on chain 2
Definition at line 100 of file descriptors.h.
Referenced by reset_desc(), set_atom_based_descriptors(), and write_descriptors_DB().
| char s_desc::nameChain1[2] |
name of the first chain in contact with the pocket
Definition at line 105 of file descriptors.h.
Referenced by set_atom_based_descriptors(), and write_descriptors_DB().
| char s_desc::nameChain2[2] |
name of the second chain in contact with the pocket, if there is
Definition at line 105 of file descriptors.h.
Referenced by set_atom_based_descriptors(), and write_descriptors_DB().
| char s_desc::ligTag[8] |
het atom tag of ligands situated in the pocket
Definition at line 107 of file descriptors.h.
Referenced by set_pocket_contacted_lig_name(), and write_descriptors_DB().
| int s_desc::n_abpa |
number of abpas in the binding site
Definition at line 108 of file descriptors.h.
Referenced by set_ASA(), and write_descriptors_DB().
1.5.6