molecules.h File Reference

Header file for molecule structures. More...

#include <geometries.h>
#include <parameter_sets.h>

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Classes
struct	molindex
struct	ensindex
struct	molindex_set
struct	residue_tree_index
struct	molecule_tree_index
struct	ensemble_tree_index
struct	moiety_selection
struct	bond
struct	bondset
struct	molbond
struct	molbondset
struct	position_set
struct	residue_node
struct	atom_node
struct	angle_index
struct	torsion_index
struct	atom
struct	residue
struct	molecule
struct	dockinfo
struct	assembly
struct	ensemble
Functions
void	print_molecule (molecule *, int)
void	print_residue (residue *, int)
void	print_bondset (bondset *, int)
void	print_atom (atom *, int)
void	print_bond (bond *)
void	print_atype (atype *, int)
void	print_plane (plane *)
void	print_vectormag_3D (vectormag_3D *)
void	print_coord_3D (coord_3D *)
void	dprint_molecule (molecule *, int)
void	dprint_residue (residue *, int)
void	dprint_bondset (bondset *, int)
void	dprint_molbondset (molbondset *, int)
void	dprint_atom (atom *, int)
void	dprint_bond (bond *)
void	dprint_molbond (molbond *mb)
void	dprint_atype (atype *, int)
void	dprint_plane (plane *)
void	dprint_vectormag_3D (vectormag_3D *)
void	dprint_coord_3D (coord_3D *)
void	dXprint_molecule (molecule *, int)
void	dXprint_residue (residue *, int)
void	dXprint_bondset (bondset *, int)
void	dXprint_atom (atom *, int)
void	dXprint_bond (bond *)
void	dXprint_molbondset (molbondset *, int)
void	dXprint_molbond (molbond *mb)
void	dXprint_atype (atype *, int)
void	dXprint_plane (plane *)
void	dXprint_vectormag_3D (vectormag_3D *)
void	dXprint_coord_3D (coord_3D *)
void	translate_residue_by_XYZ (residue *r, int xs, int xd, coord_3D)
void	translate_molecule_by_XYZ (molecule *m, int xs, int xd, coord_3D)
void	translate_ensemble_by_XYZ (ensemble *e, int xs, int xd, coord_3D)
void	translate_zero_to_coord_M (molecule *m, int xs, int xd, coord_3D)
coord_3D **	atoms_to_coord_list (atom **atoms, int num_atoms)
void	rotate_vector_to_Z_M (molecule *m, int xs, int xd, int vs, int vd, vectormag_3D vec)
void	normalize_molecule_vectors (molecule *m, int vs, int vd)
void	normalize_ensemble_vectors (ensemble *e, int vs, int vd)
void	shift_molecule_atoms_by_vector_scale (molecule *m, int xs, int xd, int vr, double scale)
vectormag_3D	get_molecule_point_charge_dipole (molecule *m, int xs, int chgsrc, atype *AT)
void	rollMolecule (molecule *m, double rad)
void	pitchMolecule (molecule *m, double rad)
void	yawMolecule (molecule *m, double rad)
void	rollAssembly (assembly *a, double rad)
void	pitchAssembly (assembly *a, double rad)
void	yawAssembly (assembly *a, double rad)
double	get_distance_from_point_to_plane (plane p, coord_3D pt, int absl)
double	get_angle_between_plane_and_vector (plane p, coord_3D pt1, coord_3D pt2)
void	set_residue_COM (residue *r, atype *ATYPE, int xs)
void	set_molecule_COM (molecule *m, atype *ATYPE, int xs)
void	set_assembly_molecule_COM (assembly *a, atype *ATYPE, int xs)
void	set_ensemble_COM (ensemble *e, atype *ATYPE, int xs)
coord_3D	get_residue_COM (residue *r, atype *ATYPE, int xs)
coord_3D	get_molecule_COM (molecule *m, atype *ATYPE, int xs)
coord_3D	get_assembly_molecule_COM (assembly *a, atype *ATYPE, int xs)
coord_3D	get_ensemble_COM (ensemble *e, atype *ATYPE, int xs)
double	get_alt_rms_res (residue *r, int xs, int xt)
double	get_alt_rms_mol (molecule *m, int xs, int xt)
void	find_vdw_clashes_pairwize_between_Assemblies (assembly *A, int xsA, assembly *B, int xsB)
ensindex	copy_moli_to_ensi (molindex moli)
char	is_consistent_ensi_moli (ensindex ensi, molindex moli)
char	is_consistent_moli_moli (molindex mone, molindex mtwo)
char	is_consistent_molbond_molbond (molbond mb1, molbond mb2)
char	is_consistent_molbond_molbond_inverse (molbond mb1, molbond mb2)
char	is_consistent_ensi_ensi (ensindex eone, ensindex etwo)
void	set_ensemble_molindexes (ensemble *E)
void	set_assembly_molindexes (assembly *A)
void	set_molecule_molindexes (molecule *m, int mi)
void	set_residue_molindexes (residue *r, int mi, int ri)
molindex_set	find_residue_atoms_by_N (residue *r, const char *name)
molindex_set	find_molecule_atoms_by_N (molecule *m, const char *name)
molindex_set	find_molecule_residues_by_N (molecule *m, const char *name)
molindex_set	find_assembly_top_level_atoms_by_N (assembly *a, const char *name)
molindex_set	find_residue_atoms_by_n (residue *r, int number)
molindex_set	find_molecule_atoms_by_n (molecule *m, int number)
molindex_set	find_molecule_residues_by_n (molecule *m, int number)
molindex_set	find_assembly_top_level_atoms_by_n (assembly *a, int number)
void	set_molecule_atom_nodes_from_bonds (molecule *m)
int	follow_molecule_atom_nodes_from_bonds (molecule *m, int iTree, atom *a)
void	set_molecule_residue_molbonds (molecule *m)
void	set_residue_atom_nodes_from_bonds (residue *r)
int	follow_residue_atom_nodes_from_bonds (residue *r, int iTree, atom *a)
void	set_molecule_residue_nodes_from_bonds (molecule *m)
int	follow_molecule_residue_nodes_from_bonds (molecule *m, int iTree, residue *r)
void	set_nbonds_for_atoms_in_assembly (assembly *A)
atype *	ATYPE_init ()
void	initialize_atype (atype *at)
void	initialize_rtype (rtype *rt)
void	initialize_mtype (mtype *mt)
void	initialize_types (types *t)
void	initialize_molindex (molindex *mi)
void	initialize_ensindex (ensindex *ei)
void	initialize_bond (bond *b)
void	initialize_bondset (bondset *bs)
void	initialize_molbond (molbond *mb)
void	initialize_molbondset (molbondset *mbs)
void	initialize_atom (atom *a)
void	initialize_residue (residue *r)
void	initialize_molecule (molecule *m)
void	initialize_dockinfo (dockinfo *di)
void	initialize_assembly (assembly *A)
void	initialize_ensemble (ensemble *E)
void	deallocateBondType (bond_type *btp)
void	deallocateMolbond (molbond *mlb)
void	deallocateBond (bond *bnd)
void	deallocateBondset (bondset *bst)
void	deallocateAtom (atom *atm)
void	deallocateResidue (residue *res)
void	deallocateMolecule (molecule *mol)
void	set_atom_element_best_guess (atom *a)
void	add_assembly_to_ensemble (assembly *A, ensemble *E)
Variables
char *	ATYPESFILE
char *	RTYPESFILE
char *	MTYPESFILE

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Detailed Description

Header file for molecule structures.

File begun May 2007 by Lachele Foley and modified continually ever since by Lachele Foley and others, including Mike Tessier.

Definition in file molecules.h.