struct t_symtab;
/* The particle type */
-enum {
- eptAtom, eptNucleus, eptShell, eptBond, eptVSite, eptNR
+enum
+{
+ eptAtom,
+ eptNucleus,
+ eptShell,
+ eptBond,
+ eptVSite,
+ eptNR
};
/* The particle type names */
-extern const char *ptype_str[eptNR+1];
+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
+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 */
+ 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) */
+ 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 */
+ 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;
//! Contains indices into group names for different groups.
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 */
+ 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 */
+ 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 */
- int *atomnumber; /* Atomic number, used for QM/MM */
+ int nr; /* number of atomtypes */
+ 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_and_delete_atoms(t_atoms *atoms);
-void done_atomtypes(t_atomtypes *at);
+void init_atom(t_atoms* at);
+void init_atomtypes(t_atomtypes* at);
+void done_atom(t_atoms* at);
+void done_and_delete_atoms(t_atoms* atoms);
+void done_atomtypes(t_atomtypes* at);
-void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
+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);
+void gmx_pdbinfo_init_default(t_pdbinfo* pdbinfo);
-t_atoms *copy_t_atoms(const t_atoms *src);
+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);
+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);
+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 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);
/*! \brief Compare information in the t_atoms data structure.
*
* \param[in] relativeTolerance Relative floating point comparison tolerance.
* \param[in] absoluteTolerance Absolute floating point comparison tolerance.
*/
-void compareAtoms(FILE *fp,
- const t_atoms *a1,
- const t_atoms *a2,
- real relativeTolerance,
- real absoluteTolerance);
+void compareAtoms(FILE* fp, const t_atoms* a1, const t_atoms* a2, real relativeTolerance, real absoluteTolerance);
/*! \brief Set mass for each atom using the atom and residue names using a database
*
* If printMissingMasss = TRUE, prints details for first 10 missing masses
* to stderr.
*/
-void atomsSetMassesBasedOnNames(t_atoms *atoms, gmx_bool printMissingMasses);
+void atomsSetMassesBasedOnNames(t_atoms* atoms, gmx_bool printMissingMasses);
//! Deleter for t_atoms, needed until it has a proper destructor.
using AtomsDataPtr = gmx::unique_cptr<t_atoms, done_and_delete_atoms>;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff