/usr/include/gromacs/topology/atoms.h is in libgromacs-dev 2018.1-1.
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* This file is part of the GROMACS molecular simulation package.
*
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* Copyright (c) 2001-2004, The GROMACS development team.
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#ifndef GMX_TOPOLOGY_ATOMS_H
#define GMX_TOPOLOGY_ATOMS_H
#include <stdio.h>
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct t_symtab;
/* The particle type */
enum {
eptAtom, eptNucleus, eptShell, eptBond, eptVSite, eptNR
};
/* The particle type names */
extern const char *ptype_str[eptNR+1];
/* Enumerated type for pdb records. The other entries are ignored
* when reading a pdb file
*/
enum PDB_record {
epdbATOM, epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
epdbMODEL, epdbENDMDL, epdbTER, epdbHEADER, epdbTITLE, epdbREMARK,
epdbCONECT, epdbNR
};
typedef struct t_atom
{
real m, q; /* Mass and charge */
real mB, qB; /* Mass and charge for Free Energy calc */
unsigned short type; /* Atom type */
unsigned short typeB; /* Atom type for Free Energy calc */
int ptype; /* Particle type */
int resind; /* Index into resinfo (in t_atoms) */
int atomnumber; /* Atomic Number or 0 */
char elem[4]; /* Element name */
} t_atom;
typedef struct t_resinfo
{
char **name; /* Pointer to the residue name */
int nr; /* Residue number */
unsigned char ic; /* Code for insertion of residues */
int chainnum; /* Iincremented at TER or new chain id */
char chainid; /* Chain identifier written/read to pdb */
char **rtp; /* rtp building block name (optional) */
} t_resinfo;
typedef struct t_pdbinfo
{
int type; /* PDB record name */
int atomnr; /* PDB atom number */
char altloc; /* Alternate location indicator */
char atomnm[6]; /* True atom name including leading spaces */
real occup; /* Occupancy */
real bfac; /* B-factor */
gmx_bool bAnisotropic; /* (an)isotropic switch */
int uij[6]; /* Anisotropic B-factor */
} t_pdbinfo;
typedef struct t_grps
{
int nr; /* Number of different groups */
int *nm_ind; /* Index in the group names */
} t_grps;
typedef struct t_atoms
{
int nr; /* Nr of atoms */
t_atom *atom; /* Array of atoms (dim: nr) */
/* The following entries will not */
/* always be used (nres==0) */
char ***atomname; /* Array of pointers to atom name */
/* use: (*(atomname[i])) */
char ***atomtype; /* Array of pointers to atom types */
/* use: (*(atomtype[i])) */
char ***atomtypeB; /* Array of pointers to B atom types */
/* use: (*(atomtypeB[i])) */
int nres; /* The number of resinfo entries */
t_resinfo *resinfo; /* Array of residue names and numbers */
t_pdbinfo *pdbinfo; /* PDB Information, such as aniso. Bfac */
/* Flags that tell if properties are set for all nr atoms.
* For B-state parameters, both haveBState and the mass/charge/type
* flag should be TRUE.
*/
gmx_bool haveMass; /* Mass available */
gmx_bool haveCharge; /* Charge available */
gmx_bool haveType; /* Atom type available */
gmx_bool haveBState; /* B-state parameters available */
gmx_bool havePdbInfo; /* pdbinfo available */
} t_atoms;
typedef struct t_atomtypes
{
int nr; /* number of atomtypes */
real *radius; /* GBSA radius for each atomtype */
real *vol; /* GBSA efective volume for each atomtype */
real *surftens; /* implicit solvent surftens for each atomtype */
real *gb_radius; /* GB radius for each atom type */
real *S_hct; /* Overlap factors for HCT/OBC GB models */
int *atomnumber; /* Atomic number, used for QM/MM */
} t_atomtypes;
#define PERTURBED(a) (((a).mB != (a).m) || ((a).qB != (a).q) || ((a).typeB != (a).type))
void init_atom(t_atoms *at);
void init_atomtypes(t_atomtypes *at);
void done_atom(t_atoms *at);
void done_atomtypes(t_atomtypes *at);
void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
/* allocate memory for the arrays, set nr to natoms and nres to 0
* set pdbinfo to NULL or allocate memory for it */
void gmx_pdbinfo_init_default(t_pdbinfo *pdbinfo);
t_atoms *copy_t_atoms(const t_atoms *src);
/* copy an atoms struct from src to a new one */
void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra);
/* allocate extra space for more atoms and or residues */
void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, struct t_symtab *symtab,
const char *resname, int resnr, unsigned char ic,
int chainnum, char chainid);
/* Set the residue name, number, insertion code and chain identifier
* of atom index atom_ind.
*/
void pr_atoms(FILE *fp, int indent, const char *title, const t_atoms *atoms,
gmx_bool bShownumbers);
void pr_atomtypes(FILE *fp, int indent, const char *title,
const t_atomtypes *atomtypes, gmx_bool bShowNumbers);
void cmp_atoms(FILE *fp, const t_atoms *a1, const t_atoms *a2, real ftol, real abstol);
/*! \brief Set mass for each atom using the atom and residue names using a database
*
* If atoms->haveMass = TRUE does nothing.
* If printMissingMasss = TRUE, prints details for first 10 missing masses
* to stderr.
*/
void atomsSetMassesBasedOnNames(t_atoms *atoms, gmx_bool printMissingMasses);
#endif
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