atom Struct Reference

#include <molecules.h>

Collaboration diagram for atom:

List of all members.

Public Attributes
int	n
	atom number or other identifying index
char *	N
	atom name
char *	T
	atom type name
char *	D
	free-form description
char *	E
	atom element
double	m
	atom mass -- units defined per program needs
int	t
	type number -- must correspond to assignments of "atype" (see)
atype *	typ
	pointer to atype structure
molindex	moli
	the molecule index for this atom (address)
int	nb
	number of bonds within this residue (deprecated, soon to go away)
bond *	b
	bond structures (nb of these)
int	nmb
	number of bonds to other residues or molecules
molbond *	mb
	nmb of these (pointers to the structures)
int	mTi
	Index into the molecule's connection tree for this atom (m.aT)
int	rTi
	Index into the residue's connection tree for this atom (r.aT)
coord_3D	x
	atom's main coordinates
coord_3D	xv
	atom's main velocity
int	nalt
	number of alternate coordinate sets
coord_3D *	xa
	nalt of alternate coords
int	nxva
	number of alternate velocities defined
coord_3D *	xva
	nxva alternate velocities
int	nvec
	number of vector sets
vectormag_3D *	v
	vector sets
int	nch
	number of charges
double *	ch
	nch charges for this atom
int	ni
	number of other indices
int *	i
	other indices, as needed (ni of these)
int	nd
	number of double-precision parameters
double *	d
	other parameters, as needed (nd of these)
int	nensi
	number of ensemble indices
ensindex *	ensi
	list of ensemble indices
char *	sres
	name of some other/original residue to which this atom belongs
int	nOD
	number of other descriptors
char **	OD
	the nOD descriptors
int	nVP
	number of void structures
char *	cID
	chain identifier
void *	VP
	nVP of these, whatever they may be

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Detailed Description

Definition at line 139 of file molecules.h.

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Member Data Documentation

bond* atom::b

bond structures (nb of these)

Definition at line 150 of file molecules.h.

Referenced by initialize_atom().

double* atom::ch

nch charges for this atom

Definition at line 164 of file molecules.h.

Referenced by get_molecule_point_charge_dipole(), initialize_atom(), and parse_amber_prmtop().

char* atom::cID

chain identifier

Definition at line 175 of file molecules.h.

Referenced by initialize_atom().

char* atom::D

free-form description

Definition at line 143 of file molecules.h.

Referenced by initialize_atom().

double* atom::d

other parameters, as needed (nd of these)

Definition at line 168 of file molecules.h.

Referenced by initialize_atom().

char* atom::E

atom element

Definition at line 144 of file molecules.h.

Referenced by initialize_atom().

ensindex* atom::ensi

list of ensemble indices

Definition at line 170 of file molecules.h.

Referenced by initialize_atom(), and parse_amber_prmtop().

int* atom::i

other indices, as needed (ni of these)

Definition at line 166 of file molecules.h.

Referenced by dprint_atom(), dXprint_atom(), get_assembly_PDB_ATOM_lines(), get_ensemble_PDB_ATOM_lines(), get_PDB_line_for_ATOM(), and initialize_atom().

double atom::m

atom mass -- units defined per program needs

Definition at line 145 of file molecules.h.

Referenced by follow_molecule_atom_nodes_from_bonds(), get_assembly_molecule_COM(), get_ensemble_COM(), get_molecule_COM(), get_residue_COM(), getAssembly(), initialize_atom(), and parse_amber_prmtop().

molbond* atom::mb

nmb of these (pointers to the structures)

Definition at line 152 of file molecules.h.

Referenced by follow_molecule_atom_molbonds_for_contree(), follow_molecule_atom_nodes_from_bonds(), follow_residue_atom_nodes_from_bonds(), get_molecule_PDB_ATOM_lines(), initialize_atom(), parse_amber_prmtop(), set_assembly_atom_molbonds_from_PDB_CONECT(), and set_molecule_residue_molbonds().

molindex atom::moli

the molecule index for this atom (address)

Definition at line 148 of file molecules.h.

Referenced by add_assembly_to_ensemble(), find_assembly_top_level_atoms_by_n(), find_residue_atoms_by_N(), follow_molecule_atom_molbonds_for_contree(), parse_amber_prmtop(), set_assembly_atom_molbonds_from_PDB_CONECT(), set_connection_tree_molecule_atoms(), and set_residue_molindexes().

int atom::mTi

Index into the molecule's connection tree for this atom (m.aT)

Definition at line 153 of file molecules.h.

Referenced by follow_molecule_atom_molbonds_for_contree(), follow_molecule_atom_nodes_from_bonds(), initialize_atom(), set_connection_tree_molecule_atoms(), and set_molecule_atom_nodes_from_bonds().

int atom::n

atom number or other identifying index

Definition at line 140 of file molecules.h.

Referenced by get_PDB_line_for_ATOM(), get_residue_PDB_ATOM_lines(), initialize_atom(), load_dlg_mol(), outputAsmblPDB(), outputMolPDB(), parse_amber_prmtop(), read_prepatom(), and set_assembly_atom_molbonds_from_PDB_CONECT().

char* atom::N

atom name

Definition at line 141 of file molecules.h.

Referenced by initialize_atom(), outputAsmblPDB(), outputMolPDB(), parse_amber_prmtop(), and read_prepatom().

int atom::nalt

number of alternate coordinate sets

Definition at line 157 of file molecules.h.

Referenced by add_trajcrds_to_prmtop_assembly(), get_assembly_PDB_ATOM_lines(), get_ensemble_PDB_ATOM_lines(), initialize_atom(), and load_dlg_mol().

int atom::nb

number of bonds within this residue (deprecated, soon to go away)

Definition at line 149 of file molecules.h.

Referenced by deallocateAtom(), and initialize_atom().

int atom::nch

number of charges

Definition at line 163 of file molecules.h.

Referenced by initialize_atom(), and parse_amber_prmtop().

int atom::nd

number of double-precision parameters

Definition at line 167 of file molecules.h.

Referenced by initialize_atom().

int atom::nensi

number of ensemble indices

Definition at line 169 of file molecules.h.

Referenced by initialize_atom(), and parse_amber_prmtop().

int atom::ni

number of other indices

Definition at line 165 of file molecules.h.

Referenced by get_assembly_PDB_ATOM_lines(), get_ensemble_PDB_ATOM_lines(), getAssembly(), and initialize_atom().

int atom::nmb

number of bonds to other residues or molecules

Definition at line 151 of file molecules.h.

Referenced by deallocateAtom(), follow_molecule_atom_molbonds_for_contree(), follow_molecule_atom_nodes_from_bonds(), follow_residue_atom_nodes_from_bonds(), get_molecule_PDB_ATOM_lines(), initialize_atom(), parse_amber_prmtop(), set_assembly_atom_molbonds_from_PDB_CONECT(), and set_molecule_residue_molbonds().

int atom::nOD

number of other descriptors

Definition at line 172 of file molecules.h.

Referenced by deallocateAtom(), and initialize_atom().

int atom::nvec

number of vector sets

Definition at line 161 of file molecules.h.

Referenced by add_trajcrds_to_prmtop_assembly(), and initialize_atom().

int atom::nVP

number of void structures

Definition at line 174 of file molecules.h.

Referenced by initialize_atom(), and read_prepatom().

int atom::nxva

number of alternate velocities defined

Definition at line 159 of file molecules.h.

Referenced by initialize_atom().

char** atom::OD

the nOD descriptors

Definition at line 173 of file molecules.h.

Referenced by initialize_atom().

int atom::rTi

Index into the residue's connection tree for this atom (r.aT)

Definition at line 154 of file molecules.h.

Referenced by follow_residue_atom_nodes_from_bonds(), initialize_atom(), and set_residue_atom_nodes_from_bonds().

char* atom::sres

name of some other/original residue to which this atom belongs

Definition at line 171 of file molecules.h.

char* atom::T

atom type name

Definition at line 142 of file molecules.h.

Referenced by initialize_atom(), parse_amber_prmtop(), and read_prepatom().

int atom::t

type number -- must correspond to assignments of "atype" (see)

Definition at line 146 of file molecules.h.

Referenced by get_assembly_molecule_COM(), get_ensemble_COM(), get_molecule_COM(), get_residue_COM(), initialize_atom(), load_dlg_mol(), parse_amber_prmtop(), read_prepatom(), and read_prepres().

atype* atom::typ

pointer to atype structure

Definition at line 147 of file molecules.h.

Referenced by deallocateAtom(), and initialize_atom().

vectormag_3D* atom::v

vector sets

Definition at line 162 of file molecules.h.

Referenced by add_trajcrds_to_prmtop_assembly(), initialize_atom(), normalize_molecule_vectors(), and rotate_vector_to_Z_M().

void* atom::VP

nVP of these, whatever they may be

Definition at line 176 of file molecules.h.

Referenced by read_prepatom().

coord_3D atom::x

atom's main coordinates

Definition at line 155 of file molecules.h.

Referenced by dprint_atom(), dXprint_atom(), get_assembly_molecule_COM(), get_ensemble_COM(), get_molecule_COM(), get_molecule_point_charge_dipole(), get_residue_COM(), initialize_atom(), load_dlg_mol(), outputAsmblPDB(), outputMolPDB(), rollAssembly(), rollMolecule(), rotate_vector_to_Z_M(), shift_molecule_atoms_by_vector_scale(), translate_ensemble_by_XYZ(), translate_molecule_by_XYZ(), translate_residue_by_XYZ(), and translate_zero_to_coord_M().

coord_3D* atom::xa

nalt of alternate coords

Definition at line 158 of file molecules.h.

Referenced by add_trajcrds_to_prmtop_assembly(), get_assembly_molecule_COM(), get_ensemble_COM(), get_molecule_COM(), get_molecule_point_charge_dipole(), get_residue_COM(), initialize_atom(), load_dlg_mol(), rotate_vector_to_Z_M(), shift_molecule_atoms_by_vector_scale(), translate_ensemble_by_XYZ(), translate_molecule_by_XYZ(), translate_residue_by_XYZ(), and translate_zero_to_coord_M().

coord_3D atom::xv

atom's main velocity

Definition at line 156 of file molecules.h.

Referenced by initialize_atom().

coord_3D* atom::xva

nxva alternate velocities

Definition at line 160 of file molecules.h.

Referenced by initialize_atom().

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The documentation for this struct was generated from the following file:

• inc/molecules.h