molecule Struct Reference

#include <molecules.h>

Collaboration diagram for molecule:

List of all members.

Public Attributes
int	n
	molecule number given in an input file
int	i
	index
char *	Des
	Chain or other designation.
char *	N
	free-form name for molecule
char *	T
	free-form type for molecule
char *	D
	free-form description for residue
double	m
	molecular weight
char *	cID
int	mi
	number corresponding to the index in the parent ensemble
int	Ei
	number corresponding to parent ensemble
int	t
	type number
mtype *	typ
	pointer to atype structure
coord_3D	COM
	center of mass for molecule
int	na
	total number of atoms in molecule
atom **	a
	na of these, but should point into residues
atom_node *	aT
	nat of these
int	nr
	number of residues
residue *	r
	pointers to residues
residue_node *	rT
	nr of these residue-level connection trees
int	nrbs
	number of sets of bonds between residues (for example, linear chains)
molbondset *	rbs
	nrbs of these sets
int	nrc
	number of additional reference (ring centers, for example)
coord_3D *	rc
	nrc of these
int	nBOX
	Number of box_info structures defined.
boxinfo *	BOX
	The nBOX structures.
int	noi
	number of other indices
int *	oi
	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
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 223 of file molecules.h.

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Member Data Documentation

atom** molecule::a

na of these, but should point into residues

Definition at line 238 of file molecules.h.

Referenced by follow_molecule_atom_molbonds_for_contree(), and parse_amber_prmtop().

atom_node* molecule::aT

nat of these

Definition at line 239 of file molecules.h.

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

boxinfo* molecule::BOX

The nBOX structures.

Definition at line 248 of file molecules.h.

Referenced by load_dlg_mol().

char* molecule::cID

Chain identifier

Definition at line 231 of file molecules.h.

coord_3D molecule::COM

center of mass for molecule

Definition at line 236 of file molecules.h.

Referenced by initialize_molecule(), load_dlg_mol(), set_assembly_molecule_COM(), set_ensemble_COM(), and set_molecule_COM().

char* molecule::D

free-form description for residue

Definition at line 229 of file molecules.h.

Referenced by parse_amber_prmtop().

double* molecule::d

other parameters, as needed (nd of these)

Definition at line 253 of file molecules.h.

Referenced by initialize_molecule().

char* molecule::Des

Chain or other designation.

Definition at line 226 of file molecules.h.

Referenced by getAssembly().

int molecule::Ei

number corresponding to parent ensemble

Definition at line 233 of file molecules.h.

ensindex* molecule::ensi

list of ensemble indices

Definition at line 255 of file molecules.h.

Referenced by parse_amber_prmtop().

int molecule::i

index

Definition at line 225 of file molecules.h.

Referenced by initialize_molecule().

double molecule::m

molecular weight

Definition at line 230 of file molecules.h.

Referenced by get_molecule_COM(), initialize_molecule(), load_dlg_mol(), set_assembly_molecule_COM(), set_ensemble_COM(), and set_molecule_COM().

int molecule::mi

number corresponding to the index in the parent ensemble

Definition at line 232 of file molecules.h.

Referenced by set_molecule_molindexes().

int molecule::n

molecule number given in an input file

Definition at line 224 of file molecules.h.

char* molecule::N

free-form name for molecule

Definition at line 227 of file molecules.h.

Referenced by parse_amber_prmtop().

int molecule::na

total number of atoms in molecule

Definition at line 237 of file molecules.h.

Referenced by follow_molecule_atom_nodes_from_bonds(), initialize_molecule(), parse_amber_prmtop(), and set_molecule_atom_nodes_from_bonds().

int molecule::nBOX

Number of box_info structures defined.

Definition at line 247 of file molecules.h.

Referenced by deallocateMolecule(), initialize_molecule(), and load_dlg_mol().

int molecule::nd

number of double-precision parameters

Definition at line 252 of file molecules.h.

Referenced by initialize_molecule().

int molecule::nensi

number of ensemble indices

Definition at line 254 of file molecules.h.

Referenced by parse_amber_prmtop().

int molecule::nOD

number of other descriptors

Definition at line 256 of file molecules.h.

Referenced by deallocateMolecule().

int molecule::noi

number of other indices

Definition at line 250 of file molecules.h.

Referenced by initialize_molecule().

int molecule::nr

number of residues

Definition at line 240 of file molecules.h.

Referenced by add_assembly_to_ensemble(), deallocateMolecule(), follow_molecule_residue_nodes_from_bonds(), get_alt_rms_mol(), 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(), getAssembly(), initialize_molecule(), load_amber_prmtop(), load_dlg_mol(), normalize_molecule_vectors(), outputAsmblPDB(), parse_amber_prmtop(), read_prep(), rotate_vector_to_Z_M(), set_connection_tree_molecule_atoms(), set_molecule_atom_nodes_from_bonds(), set_molecule_COM(), set_molecule_molindexes(), set_molecule_residue_molbonds(), set_molecule_residue_nodes_from_bonds(), shift_molecule_atoms_by_vector_scale(), translate_ensemble_by_XYZ(), translate_molecule_by_XYZ(), and translate_zero_to_coord_M().

int molecule::nrbs

number of sets of bonds between residues (for example, linear chains)

Definition at line 243 of file molecules.h.

Referenced by deallocateMolecule(), and initialize_molecule().

int molecule::nrc

number of additional reference (ring centers, for example)

Definition at line 245 of file molecules.h.

Referenced by initialize_molecule(), and load_dlg_mol().

int molecule::nVP

number of void structures

Definition at line 258 of file molecules.h.

Referenced by initialize_molecule(), and read_prep().

char** molecule::OD

the nOD descriptors

Definition at line 257 of file molecules.h.

int* molecule::oi

other indices, as needed (ni of these)

Definition at line 251 of file molecules.h.

Referenced by initialize_molecule().

residue* molecule::r

pointers to residues

Definition at line 241 of file molecules.h.

Referenced by add_assembly_to_ensemble(), follow_molecule_atom_molbonds_for_contree(), follow_molecule_atom_nodes_from_bonds(), follow_molecule_residue_nodes_from_bonds(), get_alt_rms_mol(), 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(), getAssembly(), initialize_molecule(), load_amber_prmtop(), load_dlg_mol(), normalize_molecule_vectors(), parse_amber_prmtop(), read_prep(), rotate_vector_to_Z_M(), set_connection_tree_molecule_atoms(), set_molecule_atom_nodes_from_bonds(), set_molecule_COM(), set_molecule_residue_molbonds(), set_molecule_residue_nodes_from_bonds(), shift_molecule_atoms_by_vector_scale(), translate_ensemble_by_XYZ(), translate_molecule_by_XYZ(), and translate_zero_to_coord_M().

molbondset* molecule::rbs

nrbs of these sets

Definition at line 244 of file molecules.h.

Referenced by initialize_molecule().

coord_3D* molecule::rc

nrc of these

Definition at line 246 of file molecules.h.

Referenced by initialize_molecule(), and load_dlg_mol().

residue_node* molecule::rT

nr of these residue-level connection trees

Definition at line 242 of file molecules.h.

Referenced by follow_molecule_residue_nodes_from_bonds(), and set_molecule_residue_nodes_from_bonds().

char* molecule::T

free-form type for molecule

Definition at line 228 of file molecules.h.

int molecule::t

type number

Definition at line 234 of file molecules.h.

Referenced by initialize_molecule().

mtype* molecule::typ

pointer to atype structure

Definition at line 235 of file molecules.h.

Referenced by deallocateMolecule().

void* molecule::VP

nVP of these, whatever they may be

Definition at line 259 of file molecules.h.

Referenced by read_prep().

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

• inc/molecules.h