assembly Struct Reference

#include <molecules.h>

Collaboration diagram for assembly:

List of all members.

Public Attributes
int	i
	index
char *	N
	name
char *	T
	type
char *	D
	description (free-form) (was *desc)
double	mass
	mass of assembly
double	TIME
	current/initial/reference time in the simulation
coord_3D	COM
	center of mass
int	nm
	number of molecule structures
molecule **	m
	nm of these
atom_node *	mT
	nm of these
int	nr
	number of residues
residue **	r
	nr of these -- probably best to point into molecules...
residue_node *	rT
	nr of these
int	na
	number of atoms
atom **	a
	na of these -- probably best to point into mol/res combos
atom_node *	aT
	na of these
int	nb
	total number of bonds
molbond *	b
	the bonds
int	nANG
	# of angles
angle_index *	ANG
	nANG of these
int	nTOR
	# of torsions
torsion_index *	TOR
	nTOR of these
int	nPRM
	number of parameter sets
parameter_set **	PRM
	pointers to parameter sets
int	nmbs
	number of sets of connections between molecules
molbondset *	mbs
	nmbs of these sets
int	nBOX
	Number of box_info structures defined.
boxinfo *	BOX
	The nBOX structures.
int	nOD
	number of other descriptors
char **	OD
	the nOD descriptors
int	nensi
	number of ensemble indices
ensindex *	ensi
	list of ensemble indices
int	nVP
	number of void pointers
void *	VP
	void pointers

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Detailed Description

Definition at line 289 of file molecules.h.

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Member Data Documentation

atom** assembly::a

na of these -- probably best to point into mol/res combos

Definition at line 306 of file molecules.h.

Referenced by add_assembly_to_ensemble(), add_trajcrds_to_prmtop_assembly(), find_assembly_top_level_atoms_by_n(), get_moiety_selection_assembly(), getAssembly(), parse_amber_prmtop(), and set_assembly_atom_molbonds_from_PDB_CONECT().

angle_index* assembly::ANG

nANG of these

Definition at line 312 of file molecules.h.

Referenced by parse_amber_prmtop().

atom_node* assembly::aT

na of these

Definition at line 308 of file molecules.h.

molbond* assembly::b

the bonds

Definition at line 310 of file molecules.h.

Referenced by initialize_assembly(), and parse_amber_prmtop().

boxinfo* assembly::BOX

The nBOX structures.

Definition at line 320 of file molecules.h.

Referenced by add_trajcrds_to_prmtop_assembly(), and parse_amber_prmtop().

coord_3D assembly::COM

center of mass

Definition at line 296 of file molecules.h.

Referenced by initialize_assembly(), and set_assembly_molecule_COM().

char* assembly::D

description (free-form) (was *desc)

Definition at line 293 of file molecules.h.

Referenced by parse_amber_prmtop().

ensindex* assembly::ensi

list of ensemble indices

Definition at line 327 of file molecules.h.

int assembly::i

index

Definition at line 290 of file molecules.h.

Referenced by initialize_assembly().

molecule** assembly::m

nm of these

Definition at line 298 of file molecules.h.

Referenced by add_assembly_to_ensemble(), get_assembly_molecule_COM(), get_assembly_PDB_ATOM_lines(), get_moiety_selection_assembly(), getAssembly(), initialize_assembly(), load_amber_prmtop(), parse_amber_prmtop(), and set_assembly_molecule_COM().

double assembly::mass

mass of assembly

Definition at line 294 of file molecules.h.

Referenced by get_assembly_molecule_COM(), initialize_assembly(), and set_assembly_molecule_COM().

molbondset* assembly::mbs

nmbs of these sets

Definition at line 318 of file molecules.h.

Referenced by initialize_assembly().

atom_node* assembly::mT

nm of these

Definition at line 299 of file molecules.h.

char* assembly::N

name

Definition at line 291 of file molecules.h.

int assembly::na

number of atoms

Definition at line 305 of file molecules.h.

Referenced by add_assembly_to_ensemble(), add_trajcrds_to_prmtop_assembly(), find_assembly_top_level_atoms_by_n(), get_moiety_selection_assembly(), parse_amber_prmtop(), and set_assembly_atom_molbonds_from_PDB_CONECT().

int assembly::nANG

# of angles

Definition at line 311 of file molecules.h.

Referenced by deallocateAssembly(), and parse_amber_prmtop().

int assembly::nb

total number of bonds

Definition at line 309 of file molecules.h.

Referenced by deallocateAssembly(), initialize_assembly(), and parse_amber_prmtop().

int assembly::nBOX

Number of box_info structures defined.

Definition at line 319 of file molecules.h.

Referenced by add_trajcrds_to_prmtop_assembly(), deallocateAssembly(), initialize_assembly(), and parse_amber_prmtop().

int assembly::nensi

number of ensemble indices

Definition at line 326 of file molecules.h.

int assembly::nm

number of molecule structures

Definition at line 297 of file molecules.h.

Referenced by add_assembly_to_ensemble(), deallocateFullAssembly(), get_assembly_molecule_COM(), get_assembly_PDB_ATOM_lines(), get_moiety_selection_assembly(), getAssembly(), initialize_assembly(), load_amber_prmtop(), outputAsmblPDB(), parse_amber_prmtop(), set_assembly_molecule_COM(), and set_assembly_molindexes().

int assembly::nmbs

number of sets of connections between molecules

Definition at line 317 of file molecules.h.

Referenced by deallocateAssembly(), and initialize_assembly().

int assembly::nOD

number of other descriptors

Definition at line 324 of file molecules.h.

Referenced by deallocateAssembly().

int assembly::nPRM

number of parameter sets

Definition at line 315 of file molecules.h.

Referenced by deallocateAssembly(), and parse_amber_prmtop().

int assembly::nr

number of residues

Definition at line 302 of file molecules.h.

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

int assembly::nTOR

# of torsions

Definition at line 313 of file molecules.h.

Referenced by deallocateAssembly(), and parse_amber_prmtop().

int assembly::nVP

number of void pointers

Definition at line 328 of file molecules.h.

Referenced by initialize_assembly(), and parse_amber_prmtop().

char** assembly::OD

the nOD descriptors

Definition at line 325 of file molecules.h.

parameter_set** assembly::PRM

pointers to parameter sets

Definition at line 316 of file molecules.h.

Referenced by parse_amber_prmtop().

residue** assembly::r

nr of these -- probably best to point into molecules...

Definition at line 303 of file molecules.h.

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

residue_node* assembly::rT

nr of these

Definition at line 304 of file molecules.h.

char* assembly::T

type

Definition at line 292 of file molecules.h.

double assembly::TIME

current/initial/reference time in the simulation

Definition at line 295 of file molecules.h.

torsion_index* assembly::TOR

nTOR of these

Definition at line 314 of file molecules.h.

Referenced by parse_amber_prmtop().

void* assembly::VP

void pointers

Definition at line 329 of file molecules.h.

Referenced by parse_amber_prmtop().

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

• inc/molecules.h