| Bsoft 2.0.5 Bernard's software package

mol_bonds.h
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1
9 #include "rwmd.h"
10 #include "rwmolecule.h"
11 #include "mol_util.h"
12 #include "utilities.h"
13
14 // Function prototypes
15 Bbond* md_generate_bond_list(Bmolgroup* molgroup, Bmd* md);
16 Bbond* md_generate_molecular_bond_list(Bmolgroup* molgroup, Bmd* md);
17 Bbond* md_generate_bond_list_with_valence(Bmolgroup* molgroup, Bmd* md, int valence);
18 double md_bond_list_set_parameters(Bbond* bondlist, Bbondtype* bondtype);
19 int md_show_bonds(Bmolgroup* molgroup);
20 int md_show_angles(Bmolgroup* molgroup);
21 int md_show_bond_stats(Bmolgroup* molgroup);
22 Bangle* md_generate_angle_list(Bmolgroup* molgroup, Bmd* md);
23 int md_angle_list_set_parameters(Bangle* anglelist, Bangletype* angletype);
24 double md_find_bond_length(Batom* atom1, Batom* atom2, Bbondtype* bondtype);
25 Bbondtype* md_find_bond_type(Batom* atom1, Batom* atom2, Bbondtype* bondtype);
26 int md_show_bond_types(Bmolgroup* molgroup, Bbondtype* bondtype);
27 double md_angle(Batom* atom1, Batom* atom2, Batom* atom3);
28 Bangletype* md_find_angle_type(Batom* atom1, Batom* atom2, Batom* atom3, Bangletype* angletype);
29 double md_find_angle(Batom* atom1, Batom* atom2, Batom* atom3, Bangletype* angletype);
30 double md_calculate_deviations(Bmolgroup* molgroup, int wrap);
31 int md_calculate_radial_deviation(Bmolgroup* molgroup);
32
33
md_generate_molecular_bond_list
Bbond * md_generate_molecular_bond_list(Bmolgroup *molgroup, Bmd *md)
Generates an intramolecular distance-based bond list.
Definition: mol_bonds.cpp:105
md_calculate_deviations
double md_calculate_deviations(Bmolgroup *molgroup, int wrap)
Calculates deviations from the reference bond lengths and angles.
Definition: mol_bonds.cpp:742
md_show_bond_types
int md_show_bond_types(Bmolgroup *molgroup, Bbondtype *bondtype)
Shows the bond type composition.
Definition: mol_bonds.cpp:580
utilities.h
Header file for general utilities.
md_show_bonds
int md_show_bonds(Bmolgroup *molgroup)
Shows the bonds and bond lengths.
Definition: mol_bonds.cpp:329
md_show_angles
int md_show_angles(Bmolgroup *molgroup)
Shows the angles and angular sizes.
Definition: mol_bonds.cpp:350
md_angle
double md_angle(Batom *atom1, Batom *atom2, Batom *atom3)
Calculates the angle between three atoms.
Definition: mol_bonds.cpp:637
md_generate_bond_list
Bbond * md_generate_bond_list(Bmolgroup *molgroup, Bmd *md)
Generates a distance-based bond list.
Definition: mol_bonds.cpp:30
Bmd
Definition: rwmd.h:56
md_find_bond_type
Bbondtype * md_find_bond_type(Batom *atom1, Batom *atom2, Bbondtype *bondtype)
Finds the bond type.
Definition: mol_bonds.cpp:542
md_find_angle_type
Bangletype * md_find_angle_type(Batom *atom1, Batom *atom2, Batom *atom3, Bangletype *angletype)
Finds the reference angle type between three atoms.
Definition: mol_bonds.cpp:663
Bangle
Definition: rwmolecule.h:150
md_angle_list_set_parameters
int md_angle_list_set_parameters(Bangle *anglelist, Bangletype *angletype)
Assigns angles from angle types.
Definition: mol_bonds.cpp:485
mol_util.h
Library routines used for atomic coordinates.
rwmolecule.h
Header file for reading reflection files.
Bmolgroup
Definition: rwmolecule.h:170
md_find_bond_length
double md_find_bond_length(Batom *atom1, Batom *atom2, Bbondtype *bondtype)
Finds the reference covalent bond length.
Definition: mol_bonds.cpp:510
md_generate_angle_list
Bangle * md_generate_angle_list(Bmolgroup *molgroup, Bmd *md)
Generates an angle list.
Definition: mol_bonds.cpp:415
md_generate_bond_list_with_valence
Bbond * md_generate_bond_list_with_valence(Bmolgroup *molgroup, Bmd *md, int valence)
Generates a bond list based on a single valence and the shortest current bond lengths.
Definition: mol_bonds.cpp:208
md_bond_list_set_parameters
double md_bond_list_set_parameters(Bbond *bondlist, Bbondtype *bondtype)
Assigns covalent bond lengths to bonds.
Definition: mol_bonds.cpp:299
Batom
Definition: rwmolecule.h:24
Bangletype
Definition: rwmd.h:38
md_show_bond_stats
int md_show_bond_stats(Bmolgroup *molgroup)
Shows the number of bonds and the valency per atom.
Definition: mol_bonds.cpp:371
Bbond
Definition: rwmolecule.h:134
rwmd.h
Header to read and write molecular dynamics parameters in STAR format.
Bbondtype
Definition: rwmd.h:21
md_calculate_radial_deviation
int md_calculate_radial_deviation(Bmolgroup *molgroup)
Calculates the radial deviations from the center of the box.
Definition: mol_bonds.cpp:809
md_find_angle
double md_find_angle(Batom *atom1, Batom *atom2, Batom *atom3, Bangletype *angletype)
Finds the reference angle between three atoms.
Definition: mol_bonds.cpp:719