#include "common.h"

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Classes
struct	atom_kind

struct	atom_equivalence

struct	acceptor_kind

Functions
bool	ad_is_hydrogen (sz ad)

bool	ad_is_heteroatom (sz ad)

sz	ad_type_to_el_type (sz t)

fl	xs_radius (sz t)

bool	is_non_ad_metal_name (const std::string &name)

bool	xs_is_hydrophobic (sz xs)

bool	xs_is_acceptor (sz xs)

bool	xs_is_donor (sz xs)

bool	xs_donor_acceptor (sz t1, sz t2)

bool	xs_h_bond_possible (sz t1, sz t2)

const atom_kind &	ad_type_property (sz i)

sz	string_to_ad_type (const std::string &name)

fl	max_covalent_radius ()

Variables
const sz	EL_TYPE_H = 0

const sz	EL_TYPE_C = 1

const sz	EL_TYPE_N = 2

const sz	EL_TYPE_O = 3

const sz	EL_TYPE_S = 4

const sz	EL_TYPE_P = 5

const sz	EL_TYPE_F = 6

const sz	EL_TYPE_Cl = 7

const sz	EL_TYPE_Br = 8

const sz	EL_TYPE_I = 9

const sz	EL_TYPE_Met = 10

const sz	EL_TYPE_SIZE = 11

const sz	AD_TYPE_C = 0

const sz	AD_TYPE_A = 1

const sz	AD_TYPE_N = 2

const sz	AD_TYPE_O = 3

const sz	AD_TYPE_P = 4

const sz	AD_TYPE_S = 5

const sz	AD_TYPE_H = 6

const sz	AD_TYPE_F = 7

const sz	AD_TYPE_I = 8

const sz	AD_TYPE_NA = 9

const sz	AD_TYPE_OA = 10

const sz	AD_TYPE_SA = 11

const sz	AD_TYPE_HD = 12

const sz	AD_TYPE_Mg = 13

const sz	AD_TYPE_Mn = 14

const sz	AD_TYPE_Zn = 15

const sz	AD_TYPE_Ca = 16

const sz	AD_TYPE_Fe = 17

const sz	AD_TYPE_Cl = 18

const sz	AD_TYPE_Br = 19

const sz	AD_TYPE_SIZE = 20

const sz	XS_TYPE_C_H = 0

const sz	XS_TYPE_C_P = 1

const sz	XS_TYPE_N_P = 2

const sz	XS_TYPE_N_D = 3

const sz	XS_TYPE_N_A = 4

const sz	XS_TYPE_N_DA = 5

const sz	XS_TYPE_O_P = 6

const sz	XS_TYPE_O_D = 7

const sz	XS_TYPE_O_A = 8

const sz	XS_TYPE_O_DA = 9

const sz	XS_TYPE_S_P = 10

const sz	XS_TYPE_P_P = 11

const sz	XS_TYPE_F_H = 12

const sz	XS_TYPE_Cl_H = 13

const sz	XS_TYPE_Br_H = 14

const sz	XS_TYPE_I_H = 15

const sz	XS_TYPE_Met_D = 16

const sz	XS_TYPE_SIZE = 17

const sz	SY_TYPE_C_3 = 0

const sz	SY_TYPE_C_2 = 1

const sz	SY_TYPE_C_ar = 2

const sz	SY_TYPE_C_cat = 3

const sz	SY_TYPE_N_3 = 4

const sz	SY_TYPE_N_ar = 5

const sz	SY_TYPE_N_am = 6

const sz	SY_TYPE_N_pl3 = 7

const sz	SY_TYPE_O_3 = 8

const sz	SY_TYPE_O_2 = 9

const sz	SY_TYPE_O_co2 = 10

const sz	SY_TYPE_S = 11

const sz	SY_TYPE_P = 12

const sz	SY_TYPE_F = 13

const sz	SY_TYPE_Cl = 14

const sz	SY_TYPE_Br = 15

const sz	SY_TYPE_I = 16

const sz	SY_TYPE_Met = 17

const sz	SY_TYPE_SIZE = 18

const atom_kind	atom_kind_data []

const fl	metal_solvation_parameter = -0.00110

const fl	metal_covalent_radius = 1.75

const sz	atom_kinds_size = sizeof(atom_kind_data) / sizeof(const atom_kind)

const atom_equivalence	atom_equivalence_data []

const sz	atom_equivalences_size = sizeof(atom_equivalence_data) / sizeof(const atom_equivalence)

const acceptor_kind	acceptor_kind_data []

const sz	acceptor_kinds_size = sizeof(acceptor_kind_data) / sizeof(acceptor_kind)

const fl	xs_vdw_radii []

const std::string	non_ad_metal_names []

Function Documentation

bool ad_is_hydrogen ( sz ad )

inline

References AD_TYPE_H, and AD_TYPE_HD.

Referenced by atom_type::is_hydrogen().

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bool ad_is_heteroatom ( sz ad )

inline

References AD_TYPE_A, AD_TYPE_C, AD_TYPE_H, AD_TYPE_HD, and AD_TYPE_SIZE.

Referenced by atom_type::is_heteroatom().

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sz ad_type_to_el_type ( sz t )

inline

References AD_TYPE_A, AD_TYPE_Br, AD_TYPE_C, AD_TYPE_Ca, AD_TYPE_Cl, AD_TYPE_F, AD_TYPE_Fe, AD_TYPE_H, AD_TYPE_HD, AD_TYPE_I, AD_TYPE_Mg, AD_TYPE_Mn, AD_TYPE_N, AD_TYPE_NA, AD_TYPE_O, AD_TYPE_OA, AD_TYPE_P, AD_TYPE_S, AD_TYPE_SA, AD_TYPE_SIZE, AD_TYPE_Zn, EL_TYPE_Br, EL_TYPE_C, EL_TYPE_Cl, EL_TYPE_F, EL_TYPE_H, EL_TYPE_I, EL_TYPE_Met, EL_TYPE_N, EL_TYPE_O, EL_TYPE_P, EL_TYPE_S, EL_TYPE_SIZE, and VINA_CHECK.

Referenced by atom_type::assign_el().

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fl xs_radius ( sz t )

inline

References XS_TYPE_SIZE, and xs_vdw_radii.

Referenced by optimal_distance(), and volume().

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bool is_non_ad_metal_name ( const std::string & name )

inline

References non_ad_metal_names, and VINA_FOR.

Referenced by parse_pdbqt_atom_string().

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bool xs_is_hydrophobic ( sz xs )

inline

References XS_TYPE_Br_H, XS_TYPE_C_H, XS_TYPE_Cl_H, XS_TYPE_F_H, and XS_TYPE_I_H.

Referenced by conf_independent_inputs::conf_independent_inputs(), hydrophobic::eval(), and non_hydrophobic::eval().

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bool xs_is_acceptor ( sz xs )

inline

References XS_TYPE_N_A, XS_TYPE_N_DA, XS_TYPE_O_A, and XS_TYPE_O_DA.

Referenced by conf_independent_inputs::conf_independent_inputs(), and xs_donor_acceptor().

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bool xs_is_donor ( sz xs )

inline

References XS_TYPE_Met_D, XS_TYPE_N_D, XS_TYPE_N_DA, XS_TYPE_O_D, and XS_TYPE_O_DA.

Referenced by conf_independent_inputs::conf_independent_inputs(), and xs_donor_acceptor().

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bool xs_donor_acceptor	(	sz	t1,
		sz	t2
	)

inline

References xs_is_acceptor(), and xs_is_donor().

Referenced by xs_h_bond_possible().

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bool xs_h_bond_possible	(	sz	t1,
		sz	t2
	)

inline

References xs_donor_acceptor().

Referenced by non_dir_h_bond::eval().

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const atom_kind& ad_type_property ( sz i )

inline

References AD_TYPE_SIZE, and atom_kinds_size.

Referenced by model::assign_bonds(), atom_type::covalent_radius(), solvation_parameter(), and volume().

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sz string_to_ad_type ( const std::string & name )

inline

References AD_TYPE_SIZE, atom_kinds_size, and VINA_FOR.

Referenced by parse_pdbqt_atom_string().

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fl max_covalent_radius ( )

inline

References atom_kinds_size, atom_kind::covalent_radius, and VINA_FOR.

Referenced by model::assign_bonds().

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Variable Documentation

const sz EL_TYPE_H = 0

Referenced by ad_type_to_el_type(), model::assign_types(), conf_independent_inputs::conf_independent_inputs(), model::get_heavy_atom_movable_coords(), model::gyration_radius(), model::rmsd_ligands_upper_bound(), model::rmsd_lower_bound_asymmetric(), and model::rmsd_upper_bound().

const sz EL_TYPE_C = 1

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz EL_TYPE_N = 2

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz EL_TYPE_O = 3

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz EL_TYPE_S = 4

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz EL_TYPE_P = 5

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz EL_TYPE_F = 6

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz EL_TYPE_Cl = 7

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz EL_TYPE_Br = 8

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz EL_TYPE_I = 9

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz EL_TYPE_Met = 10

Referenced by ad_type_to_el_type(), atom_type::assign_el(), and model::assign_types().

const sz EL_TYPE_SIZE = 11

Referenced by ad_type_to_el_type(), model::assign_types(), and num_atom_types().

const sz AD_TYPE_C = 0

Referenced by ad_is_heteroatom(), and ad_type_to_el_type().

const sz AD_TYPE_A = 1

Referenced by ad_is_heteroatom(), and ad_type_to_el_type().

const sz AD_TYPE_N = 2

Referenced by ad_type_to_el_type().

const sz AD_TYPE_O = 3

Referenced by ad_type_to_el_type().

const sz AD_TYPE_P = 4

Referenced by ad_type_to_el_type().

const sz AD_TYPE_S = 5

Referenced by ad_type_to_el_type().

const sz AD_TYPE_H = 6

Referenced by ad_is_heteroatom(), ad_is_hydrogen(), and ad_type_to_el_type().

const sz AD_TYPE_F = 7

Referenced by ad_type_to_el_type().

const sz AD_TYPE_I = 8

Referenced by ad_type_to_el_type().

const sz AD_TYPE_NA = 9

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz AD_TYPE_OA = 10

Referenced by ad_type_to_el_type(), and model::assign_types().

const sz AD_TYPE_SA = 11

Referenced by ad_type_to_el_type().

const sz AD_TYPE_HD = 12

Referenced by ad_is_heteroatom(), ad_is_hydrogen(), ad_type_to_el_type(), and model::bonded_to_HD().

const sz AD_TYPE_Mg = 13

Referenced by ad_type_to_el_type().

const sz AD_TYPE_Mn = 14

Referenced by ad_type_to_el_type().

const sz AD_TYPE_Zn = 15

Referenced by ad_type_to_el_type().

const sz AD_TYPE_Ca = 16

Referenced by ad_type_to_el_type().

const sz AD_TYPE_Fe = 17

Referenced by ad_type_to_el_type().

const sz AD_TYPE_Cl = 18

Referenced by ad_type_to_el_type().

const sz AD_TYPE_Br = 19

Referenced by ad_type_to_el_type().

const sz AD_TYPE_SIZE = 20

Referenced by atom_type::acceptable_type(), ad_is_heteroatom(), ad_type_property(), ad_type_to_el_type(), model::assign_bonds(), atom_type::assign_el(), atom_type::covalent_radius(), num_atom_types(), solvation_parameter(), string_to_ad_type(), and volume().

const sz XS_TYPE_C_H = 0

Referenced by model::assign_types(), and xs_is_hydrophobic().

const sz XS_TYPE_C_P = 1

Referenced by model::assign_types().

const sz XS_TYPE_N_P = 2

Referenced by model::assign_types().

const sz XS_TYPE_N_D = 3

Referenced by model::assign_types(), and xs_is_donor().

const sz XS_TYPE_N_A = 4

Referenced by model::assign_types(), and xs_is_acceptor().

const sz XS_TYPE_N_DA = 5

Referenced by model::assign_types(), xs_is_acceptor(), and xs_is_donor().

const sz XS_TYPE_O_P = 6

Referenced by model::assign_types().

const sz XS_TYPE_O_D = 7

Referenced by model::assign_types(), and xs_is_donor().

const sz XS_TYPE_O_A = 8

Referenced by model::assign_types(), and xs_is_acceptor().

const sz XS_TYPE_O_DA = 9

Referenced by model::assign_types(), xs_is_acceptor(), and xs_is_donor().

const sz XS_TYPE_S_P = 10

Referenced by model::assign_types().

const sz XS_TYPE_P_P = 11

Referenced by model::assign_types().

const sz XS_TYPE_F_H = 12

Referenced by model::assign_types(), and xs_is_hydrophobic().

const sz XS_TYPE_Cl_H = 13

Referenced by model::assign_types(), and xs_is_hydrophobic().

const sz XS_TYPE_Br_H = 14

Referenced by model::assign_types(), and xs_is_hydrophobic().

const sz XS_TYPE_I_H = 15

Referenced by model::assign_types(), and xs_is_hydrophobic().

const sz XS_TYPE_Met_D = 16

Referenced by atom_type::acceptable_type(), atom_type::assign_el(), model::assign_types(), atom_type::covalent_radius(), atom_type::is_heteroatom(), parse_pdbqt_atom_string(), solvation_parameter(), and xs_is_donor().

const sz XS_TYPE_SIZE = 17

Referenced by num_atom_types(), volume(), and xs_radius().

const sz SY_TYPE_C_3 = 0

const sz SY_TYPE_C_2 = 1

const sz SY_TYPE_C_ar = 2

const sz SY_TYPE_C_cat = 3

const sz SY_TYPE_N_3 = 4

const sz SY_TYPE_N_ar = 5

const sz SY_TYPE_N_am = 6

const sz SY_TYPE_N_pl3 = 7

const sz SY_TYPE_O_3 = 8

const sz SY_TYPE_O_2 = 9

const sz SY_TYPE_O_co2 = 10

const sz SY_TYPE_S = 11

const sz SY_TYPE_P = 12

const sz SY_TYPE_F = 13

const sz SY_TYPE_Cl = 14

const sz SY_TYPE_Br = 15

const sz SY_TYPE_I = 16

const sz SY_TYPE_Met = 17

const sz SY_TYPE_SIZE = 18

Referenced by num_atom_types().

const atom_kind atom_kind_data[]

Initial value:

= { 
        { "C",    2.00000,    0.15000,   -0.00143,   33.51030,   0.77}, 
        { "A",    2.00000,    0.15000,   -0.00052,   33.51030,   0.77}, 
        { "N",    1.75000,    0.16000,   -0.00162,   22.44930,   0.75}, 
        { "O",    1.60000,    0.20000,   -0.00251,   17.15730,   0.73}, 
        { "P",    2.10000,    0.20000,   -0.00110,   38.79240,   1.06}, 
        { "S",    2.00000,    0.20000,   -0.00214,   33.51030,   1.02}, 
        { "H",    1.00000,    0.02000,    0.00051,    0.00000,   0.37}, 
        { "F",    1.54500,    0.08000,   -0.00110,   15.44800,   0.71}, 
        { "I",    2.36000,    0.55000,   -0.00110,   55.05850,   1.33}, 
        {"NA",    1.75000,    0.16000,   -0.00162,   22.44930,   0.75}, 
        {"OA",    1.60000,    0.20000,   -0.00251,   17.15730,   0.73}, 
        {"SA",    2.00000,    0.20000,   -0.00214,   33.51030,   1.02}, 
        {"HD",    1.00000,    0.02000,    0.00051,    0.00000,   0.37}, 
        {"Mg",    0.65000,    0.87500,   -0.00110,    1.56000,   1.30}, 
        {"Mn",    0.65000,    0.87500,   -0.00110,    2.14000,   1.39}, 
        {"Zn",    0.74000,    0.55000,   -0.00110,    1.70000,   1.31}, 
        {"Ca",    0.99000,    0.55000,   -0.00110,    2.77000,   1.74}, 
        {"Fe",    0.65000,    0.01000,   -0.00110,    1.84000,   1.25}, 
        {"Cl",    2.04500,    0.27600,   -0.00110,   35.82350,   0.99}, 
        {"Br",    2.16500,    0.38900,   -0.00110,   42.56610,   1.14}  
}

const fl metal_solvation_parameter = -0.00110

Referenced by solvation_parameter().

const fl metal_covalent_radius = 1.75

Referenced by atom_type::covalent_radius().

const sz atom_kinds_size = sizeof(atom_kind_data) / sizeof(const atom_kind)

Referenced by ad_type_property(), max_covalent_radius(), and string_to_ad_type().

const atom_equivalence atom_equivalence_data[]

Initial value:

= {
        {"Se",  "S"}
}

const sz atom_equivalences_size = sizeof(atom_equivalence_data) / sizeof(const atom_equivalence)

const acceptor_kind acceptor_kind_data[]

Initial value:

= { 
        {AD_TYPE_NA, 1.9, 5.0},
        {AD_TYPE_OA, 1.9, 5.0},
        {AD_TYPE_SA, 2.5, 1.0}
}

const sz acceptor_kinds_size = sizeof(acceptor_kind_data) / sizeof(acceptor_kind)

const fl xs_vdw_radii[]

Initial value:

Referenced by xs_radius().

const std::string non_ad_metal_names[]

Initial value:

= { 
        "Cu", "Fe", "Na", "K", "Hg", "Co", "U", "Cd", "Ni"
}

Referenced by is_non_ad_metal_name().

Classes

Functions

Variables

Function Documentation

Variable Documentation