residue Struct Reference

#include <molecules.h>

Collaboration diagram for residue:

List of all members.

Public Attributes
int	n
	residue number given in input file
char *	cID
char *	IC
	insertion code
char *	N
	residue name
char *	T
	residue type
char *	D
	free-form description for residue
int	t
	type number
rtype *	typ
	pointer to rtype structure
molindex	moli
	the molecule index for this residue (address -- set .a to -1 or 0)
int	na
	number of atoms in residue
atom *	a
	atom structures (na of these)
atom_node *	aT
	na of these (one per atom)
double	m
	molecular weight
coord_3D	COM
	center of mass for residue
int	nrb
	number of bonds between residues
molbond *	rb
	nrb of these descriptions of bonds
int	mTi
	Index into the molecule's connection tree for this residue (m.rT)
int	nbs
	number of bond sets
molbondset *	bs
	(consecutive bonds, use these for plotting, etc.)
int	nring
	number of simple rings (no cage structures, etc.)
molindex_set *	ring
	molecule indices for the nring rings
int	nrc
coord_3D *	rc
	coordinates for ring/reference centers
int	nrp
	number of ring planes defined
plane *	rp
	equations for average/approximate/exact/etc. ring planes (where useful)
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 *	altname
	name of some other/original name for this residue
int	nOD
	number of other descriptors
char **	OD
	the nOD descriptors
int	nVP
	number of void structures
void *	VP
	nVP of these, whatever they may be

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Detailed Description

Definition at line 180 of file molecules.h.

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Member Data Documentation

atom* residue::a

atom structures (na of these)

Definition at line 191 of file molecules.h.

Referenced by add_assembly_to_ensemble(), find_residue_atoms_by_N(), follow_molecule_atom_molbonds_for_contree(), follow_molecule_atom_nodes_from_bonds(), follow_residue_atom_nodes_from_bonds(), get_assembly_molecule_COM(), get_assembly_PDB_ATOM_lines(), get_ensemble_COM(), get_ensemble_PDB_ATOM_lines(), get_moiety_selection_assembly(), get_molecule_COM(), get_molecule_PDB_ATOM_lines(), get_molecule_point_charge_dipole(), get_residue_COM(), get_residue_PDB_ATOM_lines(), initialize_residue(), load_dlg_mol(), normalize_molecule_vectors(), parse_amber_prmtop(), read_prepres(), rotate_vector_to_Z_M(), set_connection_tree_molecule_atoms(), set_molecule_atom_nodes_from_bonds(), set_molecule_residue_molbonds(), set_residue_atom_nodes_from_bonds(), set_residue_molindexes(), shift_molecule_atoms_by_vector_scale(), translate_ensemble_by_XYZ(), translate_molecule_by_XYZ(), translate_residue_by_XYZ(), and translate_zero_to_coord_M().

char* residue::altname

name of some other/original name for this residue

Definition at line 215 of file molecules.h.

Referenced by initialize_residue().

atom_node* residue::aT

na of these (one per atom)

Definition at line 192 of file molecules.h.

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

molbondset* residue::bs

(consecutive bonds, use these for plotting, etc.)

Definition at line 199 of file molecules.h.

Referenced by initialize_residue(), and read_prepres().

char* residue::cID

Chain identifier

Definition at line 182 of file molecules.h.

Referenced by getResInfo(), and initialize_residue().

coord_3D residue::COM

center of mass for residue

Definition at line 194 of file molecules.h.

Referenced by initialize_residue(), load_dlg_mol(), read_prepres(), set_molecule_COM(), and set_residue_COM().

char* residue::D

free-form description for residue

Definition at line 186 of file molecules.h.

Referenced by initialize_residue(), and read_prepres().

double* residue::d

other parameters, as needed (nd of these)

Definition at line 212 of file molecules.h.

Referenced by initialize_residue(), and read_prepres().

ensindex* residue::ensi

list of ensemble indices

Definition at line 214 of file molecules.h.

Referenced by parse_amber_prmtop().

int* residue::i

other indices, as needed (ni of these)

Definition at line 210 of file molecules.h.

Referenced by get_assembly_PDB_ATOM_lines(), get_ensemble_PDB_ATOM_lines(), get_residue_PDB_ATOM_lines(), initialize_residue(), and read_prepres().

char* residue::IC

insertion code

Definition at line 183 of file molecules.h.

Referenced by getMolecule(), getResInfo(), and initialize_residue().

double residue::m

molecular weight

Definition at line 193 of file molecules.h.

Referenced by follow_molecule_residue_nodes_from_bonds(), get_residue_COM(), initialize_residue(), load_dlg_mol(), read_prepres(), and set_molecule_COM().

molindex residue::moli

the molecule index for this residue (address -- set .a to -1 or 0)

Definition at line 189 of file molecules.h.

Referenced by add_assembly_to_ensemble(), parse_amber_prmtop(), and set_residue_molindexes().

int residue::mTi

Index into the molecule's connection tree for this residue (m.rT)

Definition at line 197 of file molecules.h.

Referenced by follow_molecule_residue_nodes_from_bonds(), initialize_residue(), and set_molecule_residue_nodes_from_bonds().

int residue::n

residue number given in input file

Definition at line 181 of file molecules.h.

Referenced by get_molecule_PDB_ATOM_lines(), get_PDB_line_for_ATOM(), get_residue_PDB_ATOM_lines(), initialize_residue(), parse_amber_prmtop(), and read_prepres().

char* residue::N

residue name

Definition at line 184 of file molecules.h.

Referenced by getResInfo(), initialize_residue(), parse_amber_prmtop(), and read_prepres().

int residue::na

number of atoms in residue

Definition at line 190 of file molecules.h.

Referenced by add_assembly_to_ensemble(), deallocateResidue(), find_residue_atoms_by_N(), follow_residue_atom_nodes_from_bonds(), get_alt_rms_mol(), get_alt_rms_res(), get_assembly_molecule_COM(), get_assembly_PDB_ATOM_lines(), get_ensemble_COM(), get_ensemble_PDB_ATOM_lines(), get_moiety_selection_assembly(), get_molecule_COM(), get_molecule_PDB_ATOM_lines(), get_molecule_point_charge_dipole(), get_residue_COM(), get_residue_PDB_ATOM_lines(), initialize_residue(), load_dlg_mol(), normalize_molecule_vectors(), parse_amber_prmtop(), read_prepres(), rotate_vector_to_Z_M(), set_connection_tree_molecule_atoms(), set_molecule_atom_nodes_from_bonds(), set_molecule_residue_molbonds(), set_residue_atom_nodes_from_bonds(), set_residue_molindexes(), shift_molecule_atoms_by_vector_scale(), translate_ensemble_by_XYZ(), translate_molecule_by_XYZ(), translate_residue_by_XYZ(), and translate_zero_to_coord_M().

int residue::nbs

number of bond sets

Definition at line 198 of file molecules.h.

Referenced by deallocateResidue(), initialize_residue(), and read_prepres().

int residue::nd

number of double-precision parameters

Definition at line 211 of file molecules.h.

Referenced by initialize_residue(), and read_prepres().

int residue::nensi

number of ensemble indices

Definition at line 213 of file molecules.h.

Referenced by parse_amber_prmtop().

int residue::ni

number of other indices

Definition at line 209 of file molecules.h.

Referenced by get_assembly_PDB_ATOM_lines(), get_ensemble_PDB_ATOM_lines(), initialize_residue(), and read_prepres().

int residue::nOD

number of other descriptors

Definition at line 216 of file molecules.h.

Referenced by deallocateResidue(), and initialize_residue().

int residue::nrb

number of bonds between residues

Definition at line 195 of file molecules.h.

Referenced by follow_molecule_residue_nodes_from_bonds(), initialize_residue(), and set_molecule_residue_molbonds().

int residue::nrc

Definition at line 204 of file molecules.h.

Referenced by initialize_residue(), and load_dlg_mol().

int residue::nring

number of simple rings (no cage structures, etc.)

Definition at line 200 of file molecules.h.

Referenced by initialize_residue().

int residue::nrp

number of ring planes defined

Definition at line 206 of file molecules.h.

Referenced by initialize_residue().

int residue::nVP

number of void structures

Definition at line 218 of file molecules.h.

Referenced by initialize_residue(), and read_prepres().

char** residue::OD

the nOD descriptors

Definition at line 217 of file molecules.h.

Referenced by initialize_residue().

molbond* residue::rb

nrb of these descriptions of bonds

Definition at line 196 of file molecules.h.

Referenced by follow_molecule_residue_nodes_from_bonds(), initialize_residue(), and set_molecule_residue_molbonds().

coord_3D* residue::rc

coordinates for ring/reference centers

Definition at line 205 of file molecules.h.

Referenced by initialize_residue(), and load_dlg_mol().

molindex_set* residue::ring

molecule indices for the nring rings

Definition at line 201 of file molecules.h.

plane* residue::rp

equations for average/approximate/exact/etc. ring planes (where useful)

Definition at line 207 of file molecules.h.

Referenced by initialize_residue().

char* residue::T

residue type

Definition at line 185 of file molecules.h.

Referenced by initialize_residue().

int residue::t

type number

Definition at line 187 of file molecules.h.

Referenced by initialize_residue().

rtype* residue::typ

pointer to rtype structure

Definition at line 188 of file molecules.h.

Referenced by deallocateResidue(), and initialize_residue().

void* residue::VP

nVP of these, whatever they may be

Definition at line 219 of file molecules.h.

Referenced by read_prepres().

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

• inc/molecules.h