| Bsoft 2.0.5 Bernard's software package

mol_util.h
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1
9 #include "Vector3.h"
10 #include "rwmolecule.h"
11
12 #ifndef _Latom_
13 #define _Latom_
14 /************************************************************************
15 @Object: struct Latom
16 @Description:
17 A structure for use in a linked list of atoms.
18 @Features:
19 This is used to group an arbitrary set of atoms.
20 *************************************************************************/
21 struct Latom {
22 Latom* next; // Next atom
23 Batom* atom;
24 } ;
25 #endif
26
27 // Function prototypes
28 int molgroup_Bfactors(Bmolgroup* molgroup);
29 int molgroup_print_sequence(Bmolgroup* molgroup);
30 int molgroup_set_radius(Bmolgroup* molgroup, double radius);
31 int molgroup_rename(Bmolgroup* molgroup, char first_name);
32 int molgroup_residue_renumber(Bmolgroup* molgroup, int first);
33 int molgroup_atom_renumber(Bmolgroup* molgroup, int first);
34 int molgroup_coor_reset_occupancy(Bmolgroup* molgroup, int range_first,
35 int range_last, double occupancy);
36 double molgroup_calculate_weight(Bmolgroup* molgroup);
37 Vector3<double> molgroup_center_of_mass(Bmolgroup* molgroup);
38 Vector3<double> molgroup_selected_center_of_mass(Bmolgroup* molgroup);
39 Vector3<double> molgroup_show_center_of_mass(Bmolgroup* molgroup);
40 Vector3<double> mol_center_of_mass(Bmolecule* mol);
41 Vector3<double> mol_show_center_of_mass(Bmolecule* mol);
42 Vector3<double> molgroup_principal_axes(Bmolgroup* molgroup, Vector3<double>* eigenvec);
43 Vector3<double> mol_principal_axes(Bmolecule* mol, Vector3<double>* eigenvec);
44 double molgroup_density(Bmolgroup* molgroup);
45 double molgroup_volume(Bmolgroup* molgroup, Bstring& paramfile, int wrap);
46 int molgroup_composition(Bmolgroup* molgroup, Bstring& paramfile);
47 int molgroup_radial_density(Bmolgroup* molgroup, double interval, double cutoff, int wrap);
48 Latom** molgroup_atom_mesh_lists(Bmolgroup* molgroup, Vector3<int> size, Vector3<double> sampling);
49 Batom** atom_get_array(Bmolgroup* molgroup, long* natom);
50
Latom::next
Latom * next
Definition: mol_util.h:22
molgroup_atom_mesh_lists
Latom ** molgroup_atom_mesh_lists(Bmolgroup *molgroup, Vector3< int > size, Vector3< double > sampling)
Generates lists of atoms based on a grid.
Definition: mol_util.cpp:882
Latom
Definition: mol_util.h:21
Latom::atom
Batom * atom
Definition: mol_util.h:23
molgroup_composition
int molgroup_composition(Bmolgroup *molgroup, Bstring &paramfile)
Calculates the elemental composition of a molecular system.
Definition: mol_util.cpp:699
molgroup_selected_center_of_mass
Vector3< double > molgroup_selected_center_of_mass(Bmolgroup *molgroup)
Calculates the center of mass of a molecule group.
Definition: mol_util.cpp:347
molgroup_show_center_of_mass
Vector3< double > molgroup_show_center_of_mass(Bmolgroup *molgroup)
Calculates the center of mass of a molecule group.
Definition: mol_util.cpp:387
molgroup_rename
int molgroup_rename(Bmolgroup *molgroup, char first_name)
Renames molecules.
Definition: mol_util.cpp:161
molgroup_coor_reset_occupancy
int molgroup_coor_reset_occupancy(Bmolgroup *molgroup, int range_first, int range_last, double occupancy)
Sets occupancies to new values..
Definition: mol_util.cpp:243
molgroup_center_of_mass
Vector3< double > molgroup_center_of_mass(Bmolgroup *molgroup)
Calculates the center of mass of a molecule group.
Definition: mol_util.cpp:307
mol_principal_axes
Vector3< double > mol_principal_axes(Bmolecule *mol, Vector3< double > *eigenvec)
Calculates the principal axes of a molecule.
Definition: mol_util.cpp:500
rwmolecule.h
Header file for reading reflection files.
Bmolgroup
Definition: rwmolecule.h:170
molgroup_calculate_weight
double molgroup_calculate_weight(Bmolgroup *molgroup)
Calculates the weight of each molecule.
Definition: mol_util.cpp:270
molgroup_set_radius
int molgroup_set_radius(Bmolgroup *molgroup, double radius)
Shifts all coordinates to a given radius.
Definition: mol_util.cpp:114
molgroup_density
double molgroup_density(Bmolgroup *molgroup)
Calculates the number and mass density of a molecular system.
Definition: mol_util.cpp:548
molgroup_radial_density
int molgroup_radial_density(Bmolgroup *molgroup, double interval, double cutoff, int wrap)
Calculates a radial distribution function.
Definition: mol_util.cpp:780
Bmolecule
Definition: rwmolecule.h:107
molgroup_Bfactors
int molgroup_Bfactors(Bmolgroup *molgroup)
Calculates the average Bfactors for residues in molecules.
Definition: mol_util.cpp:28
Bstring
Definition: Bstring.h:29
Batom
Definition: rwmolecule.h:24
atom_get_array
Batom ** atom_get_array(Bmolgroup *molgroup, long *natom)
Generates an array of pointers to atom structures.
Definition: mol_util.cpp:931
molgroup_print_sequence
int molgroup_print_sequence(Bmolgroup *molgroup)
Prints the sequence of a molecule as a single letter code string.
Definition: mol_util.cpp:92
Vector3< double >
Vector3.h
Class for 3-value vectors.
molgroup_principal_axes
Vector3< double > molgroup_principal_axes(Bmolgroup *molgroup, Vector3< double > *eigenvec)
Calculates the principal axes of a molecule group.
Definition: mol_util.cpp:455
molgroup_volume
double molgroup_volume(Bmolgroup *molgroup, Bstring &paramfile, int wrap)
Calculates the volume of a molecular system.
Definition: mol_util.cpp:586
molgroup_residue_renumber
int molgroup_residue_renumber(Bmolgroup *molgroup, int first)
Renumbers residues.
Definition: mol_util.cpp:182
mol_center_of_mass
Vector3< double > mol_center_of_mass(Bmolecule *mol)
Calculates the center of mass of a molecule.
Definition: mol_util.cpp:401
mol_show_center_of_mass
Vector3< double > mol_show_center_of_mass(Bmolecule *mol)
Calculates the center of mass of a molecule.
Definition: mol_util.cpp:439
molgroup_atom_renumber
int molgroup_atom_renumber(Bmolgroup *molgroup, int first)
Renumbers all atoms, disregarding molecule distinction.
Definition: mol_util.cpp:211