Classes | Typedefs | Enumerations | Functions | Variables
PLMD::molfile Namespace Reference

Classes

struct  fio_iovec
 
struct  md_atom
 
struct  md_box
 
struct  md_file
 
struct  md_header
 
struct  md_ts
 
struct  molfile_atom_t
 Per-atom attributes and information. More...
 
struct  molfile_graphics_t
 Individual graphics object/element data. More...
 
struct  molfile_metadata_t
 File level comments, origin information, and annotations. More...
 
struct  molfile_plugin_t
 Main file reader API. More...
 
struct  molfile_qm_basis_t
 Data for QM basis set. More...
 
struct  molfile_qm_hessian_t
 Data from QM Hessian/normal mode runs. More...
 
struct  molfile_qm_metadata_t
 Sizes of various QM-related, timestep independent data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data. More...
 
struct  molfile_qm_sysinfo_t
 QM run info. More...
 
struct  molfile_qm_t
 QM related information that is timestep independent. More...
 
struct  molfile_qm_timestep_metadata
 Sizes of various QM-related, per-timestep data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data. More...
 
struct  molfile_qm_timestep_t
 QM per trajectory timestep info Note that each timestep can contain multiple wavefunctions. More...
 
struct  molfile_qm_wavefunction_t
 QM wavefunction. More...
 
struct  molfile_timestep_metadata
 
struct  molfile_timestep_t
 
struct  molfile_volumetric_readwrite_t
 Volumetric dataset read/write structure with both flag/parameter sets and VMD-allocated pointers for fields to be used by the plugin. More...
 
struct  molfile_volumetric_t
 Metadata for volumetric datasets, read initially and used for subsequent memory allocations and file loading. More...
 
struct  trx_hdr
 
struct  vmdplugin_t
 Typedef for generic plugin header, individual plugins can make their own structures as long as the header info remains the same as the generic plugin header, most easily done by using the vmdplugin_HEAD macro. More...
 

Typedefs

typedef void * fio_caddr_t
 
typedef int fio_fd
 
typedef off_t fio_size_t
 
typedef struct PLMD::molfile::molfile_qm_timestep_metadata molfile_qm_timestep_metadata_t
 Sizes of various QM-related, per-timestep data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data. More...
 
typedef struct PLMD::molfile::molfile_timestep_metadata molfile_timestep_metadata_t
 
typedef int(* vmdplugin_register_cb) (void *, vmdplugin_t *)
 Function pointer typedef for register callback functions. More...
 

Enumerations

enum  {
  PDB_HEADER, PDB_REMARK, PDB_ATOM, PDB_CONECT,
  PDB_UNKNOWN, PDB_END, PDB_EOF, PDB_CRYST1
}
 
enum  molfile_graphics_type {
  MOLFILE_POINT, MOLFILE_TRIANGLE, MOLFILE_TRINORM, MOLFILE_NORMS,
  MOLFILE_LINE, MOLFILE_CYLINDER, MOLFILE_CAPCYL, MOLFILE_CONE,
  MOLFILE_SPHERE, MOLFILE_TEXT, MOLFILE_COLOR, MOLFILE_TRICOLOR
}
 Enumeration of all of the supported graphics objects that can be read from graphics file reader plugins. More...
 
enum  molfile_qm_charge_type {
  MOLFILE_QMCHARGE_UNKNOWN, MOLFILE_QMCHARGE_MULLIKEN, MOLFILE_QMCHARGE_LOWDIN, MOLFILE_QMCHARGE_ESP,
  MOLFILE_QMCHARGE_NPA
}
 Enumeration of all of the supported QM related charge types. More...
 
enum  molfile_qm_wavefunc_type {
  MOLFILE_WAVE_CANON, MOLFILE_WAVE_GEMINAL, MOLFILE_WAVE_MCSCFNAT, MOLFILE_WAVE_MCSCFOPT,
  MOLFILE_WAVE_CINATUR, MOLFILE_WAVE_PIPEK, MOLFILE_WAVE_BOYS, MOLFILE_WAVE_RUEDEN,
  MOLFILE_WAVE_NAO, MOLFILE_WAVE_PNAO, MOLFILE_WAVE_NHO, MOLFILE_WAVE_PNHO,
  MOLFILE_WAVE_NBO, MOLFILE_WAVE_PNBO, MOLFILE_WAVE_PNLMO, MOLFILE_WAVE_NLMO,
  MOLFILE_WAVE_MOAO, MOLFILE_WAVE_NATO, MOLFILE_WAVE_UNKNOWN
}
 Enumeration of all of the wavefunction types that can be read from QM file reader plugins. More...
 

Functions

static void adjust_pdb_field_string (char *field)
 
static int fio_fclose (fio_fd fd)
 
static fio_size_t fio_fread (void *ptr, fio_size_t size, fio_size_t nitems, fio_fd fd)
 
static fio_size_t fio_fseek (fio_fd fd, fio_size_t offset, int whence)
 
static fio_size_t fio_ftell (fio_fd fd)
 
static fio_size_t fio_fwrite (void *ptr, fio_size_t size, fio_size_t nitems, fio_fd fd)
 
static int fio_open (const char *filename, int mode, fio_fd *fd)
 
static int fio_read_int32 (fio_fd fd, int *i)
 
static fio_size_t fio_readv (fio_fd fd, const fio_iovec *iov, int iovcnt)
 
static int fio_write_int32 (fio_fd fd, int i)
 
static int fio_write_str (fio_fd fd, const char *str)
 
static int g96_countatoms (md_file *)
 
static int g96_header (md_file *, char *, int, float *)
 
static int g96_rec (md_file *, md_atom *)
 
static int g96_timestep (md_file *, md_ts *)
 
static void get_pdb_conect (const char *record, int natoms, int *idxmap, int *maxbnum, int *nbonds, int **from, int **to)
 
static void get_pdb_coordinates (const char *record, float *x, float *y, float *z, float *occup, float *beta)
 
static void get_pdb_cryst1 (const char *record, float *alpha, float *beta, float *gamma, float *a, float *b, float *c)
 
static void get_pdb_fields (const char *record, int reclength, int *serial, char *name, char *resname, char *chain, char *segname, char *resid, char *insertion, char *altloc, char *elementsymbol, float *x, float *y, float *z, float *occup, float *beta)
 
static void get_pdb_header (const char *record, char *pdbcode, char *date, char *classification)
 
static int get_pte_idx (const char *label)
 
static int get_pte_idx_from_string (const char *label)
 
static const char * get_pte_label (const int idx)
 
static float get_pte_mass (const int idx)
 
static float get_pte_vdw_radius (const int idx)
 
static int gro_header (md_file *, char *, int, float *, int *, int=1)
 
static int gro_rec (md_file *, md_atom *)
 
static int gro_timestep (md_file *, md_ts *)
 
static int host_is_little_endian (void)
 
static int mdio_close (md_file *)
 
static const char * mdio_errmsg (int)
 
static int mdio_errno (void)
 
static int mdio_header (md_file *, md_header *)
 
static md_filemdio_open (const char *, const int, const int=MDIO_READ)
 
static int mdio_readbox (md_box *, float *, float *, float *)
 
static int mdio_readline (md_file *, char *, int, int=1)
 
static int mdio_seterror (int)
 
static int mdio_timestep (md_file *, md_ts *)
 
static int mdio_tsfree (md_ts *, int=0)
 
int molfile_crdplugin_fini (void)
 
int molfile_crdplugin_init (void)
 
int molfile_crdplugin_register (void *, vmdplugin_register_cb)
 
int molfile_dcdplugin_fini (void)
 
int molfile_dcdplugin_init (void)
 
int molfile_dcdplugin_register (void *, vmdplugin_register_cb)
 
int molfile_gromacsplugin_fini (void)
 
int molfile_gromacsplugin_init (void)
 
int molfile_gromacsplugin_register (void *, vmdplugin_register_cb)
 
int molfile_pdbplugin_fini (void)
 
int molfile_pdbplugin_init (void)
 
int molfile_pdbplugin_register (void *, vmdplugin_register_cb)
 
static int put_trx_int (md_file *mf, int y)
 
static int put_trx_real (md_file *mf, float y)
 
static int put_trx_string (md_file *mf, const char *s)
 
static int read_pdb_record (FILE *f, char *retStr)
 
static int strip_white (char *)
 
static void swap2_aligned (void *v, long ndata)
 
static void swap2_unaligned (void *v, long ndata)
 
static void swap4_aligned (void *v, long ndata)
 
static void swap4_unaligned (void *v, long ndata)
 
static void swap8_aligned (void *v, long ndata)
 
static void swap8_unaligned (void *v, long ndata)
 
static int trx_header (md_file *, int=0)
 
static int trx_int (md_file *, int *)
 
static int trx_real (md_file *, float *)
 
static int trx_rvector (md_file *, float *)
 
static int trx_string (md_file *, char *, int)
 
static int trx_timestep (md_file *, md_ts *)
 
VMDPLUGIN_EXTERN int VMDPLUGIN_fini (void)
 The Fini method is called when the application will no longer use any plugins in the library. More...
 
VMDPLUGIN_EXTERN int VMDPLUGIN_init (void)
 Init routine: called the first time the library is loaded by the application and before any other API functions are referenced. More...
 
VMDPLUGIN_EXTERN int VMDPLUGIN_register (void *, vmdplugin_register_cb)
 Allow the library to register plugins with the application. More...
 
VMDPLUGIN_EXTERN int VMDPLUGIN_register_tcl (void *, void *tcl_interp, vmdplugin_register_cb)
 Allow the library to register Tcl extensions. More...
 
static int write_raw_pdb_record (FILE *fd, const char *recordname, int index, const char *atomname, const char *resname, int resid, const char *insertion, const char *altloc, const char *elementsymbol, float x, float y, float z, float occ, float beta, const char *chain, const char *segname)
 
static int xtc_3dfcoord (md_file *, float *, int *, float *)
 
static int xtc_data (md_file *mf, char *buf, int len)
 
static int xtc_float (md_file *, float *)
 
static int xtc_int (md_file *, int *)
 
static int xtc_receivebits (int *, int)
 
static void xtc_receiveints (int *buf, const int nints, int nbits, unsigned int *sizes, int *nums)
 
static int xtc_sizeofint (int size)
 
static int xtc_sizeofints (int nints, unsigned int *sizes)
 
static int xtc_timestep (md_file *, md_ts *)
 

Variables

static int mdio_errcode
 
static const char * mdio_errdescs []
 
const char * mdio_fmtexts []
 
static const int nr_pte_entries = sizeof(pte_label) / sizeof(char *)
 
static const char * pte_label []
 
static const float pte_mass []
 
static const float pte_vdw_radius []
 
static int xtc_magicints []
 

Typedef Documentation

◆ fio_caddr_t

◆ fio_fd

typedef int PLMD::molfile::fio_fd

◆ fio_size_t

◆ molfile_qm_timestep_metadata_t

Sizes of various QM-related, per-timestep data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data.

◆ molfile_timestep_metadata_t

◆ vmdplugin_register_cb

typedef int(* PLMD::molfile::vmdplugin_register_cb) (void *, vmdplugin_t *)

Function pointer typedef for register callback functions.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum
Enumerator
PDB_HEADER 
PDB_REMARK 
PDB_ATOM 
PDB_CONECT 
PDB_UNKNOWN 
PDB_END 
PDB_EOF 
PDB_CRYST1 

◆ molfile_graphics_type

Enumeration of all of the supported graphics objects that can be read from graphics file reader plugins.

Enumerator
MOLFILE_POINT 
MOLFILE_TRIANGLE 
MOLFILE_TRINORM 
MOLFILE_NORMS 
MOLFILE_LINE 
MOLFILE_CYLINDER 
MOLFILE_CAPCYL 
MOLFILE_CONE 
MOLFILE_SPHERE 
MOLFILE_TEXT 
MOLFILE_COLOR 
MOLFILE_TRICOLOR 

◆ molfile_qm_charge_type

Enumeration of all of the supported QM related charge types.

Enumerator
MOLFILE_QMCHARGE_UNKNOWN 
MOLFILE_QMCHARGE_MULLIKEN 
MOLFILE_QMCHARGE_LOWDIN 
MOLFILE_QMCHARGE_ESP 
MOLFILE_QMCHARGE_NPA 

◆ molfile_qm_wavefunc_type

Enumeration of all of the wavefunction types that can be read from QM file reader plugins.

CANON = canonical (i.e diagonalized) wavefunction GEMINAL = GVB-ROHF geminal pairs MCSCFNAT = Multi-Configuration SCF natural orbitals MCSCFOPT = Multi-Configuration SCF optimized orbitals CINATUR = Configuration-Interaction natural orbitals BOYS = Boys localization RUEDEN = Ruedenberg localization PIPEK = Pipek-Mezey population localization

NBO related localizations:

NAO = Natural Atomic Orbitals PNAO = pre-orthogonal NAOs NBO = Natural Bond Orbitals PNBO = pre-orthogonal NBOs NHO = Natural Hybrid Orbitals PNHO = pre-orthogonal NHOs NLMO = Natural Localized Molecular Orbitals PNLMO = pre-orthogonal NLMOs

UNKNOWN = Use this for any type not listed here You can use the string field for description

Enumerator
MOLFILE_WAVE_CANON 
MOLFILE_WAVE_GEMINAL 
MOLFILE_WAVE_MCSCFNAT 
MOLFILE_WAVE_MCSCFOPT 
MOLFILE_WAVE_CINATUR 
MOLFILE_WAVE_PIPEK 
MOLFILE_WAVE_BOYS 
MOLFILE_WAVE_RUEDEN 
MOLFILE_WAVE_NAO 
MOLFILE_WAVE_PNAO 
MOLFILE_WAVE_NHO 
MOLFILE_WAVE_PNHO 
MOLFILE_WAVE_NBO 
MOLFILE_WAVE_PNBO 
MOLFILE_WAVE_PNLMO 
MOLFILE_WAVE_NLMO 
MOLFILE_WAVE_MOAO 
MOLFILE_WAVE_NATO 
MOLFILE_WAVE_UNKNOWN 

Function Documentation

◆ adjust_pdb_field_string()

static void PLMD::molfile::adjust_pdb_field_string ( char *  field)
static

◆ fio_fclose()

static int PLMD::molfile::fio_fclose ( fio_fd  fd)
static

◆ fio_fread()

static fio_size_t PLMD::molfile::fio_fread ( void *  ptr,
fio_size_t  size,
fio_size_t  nitems,
fio_fd  fd 
)
static

◆ fio_fseek()

static fio_size_t PLMD::molfile::fio_fseek ( fio_fd  fd,
fio_size_t  offset,
int  whence 
)
static

◆ fio_ftell()

static fio_size_t PLMD::molfile::fio_ftell ( fio_fd  fd)
static

◆ fio_fwrite()

static fio_size_t PLMD::molfile::fio_fwrite ( void *  ptr,
fio_size_t  size,
fio_size_t  nitems,
fio_fd  fd 
)
static

◆ fio_open()

static int PLMD::molfile::fio_open ( const char *  filename,
int  mode,
fio_fd fd 
)
static

◆ fio_read_int32()

static int PLMD::molfile::fio_read_int32 ( fio_fd  fd,
int *  i 
)
static

◆ fio_readv()

static fio_size_t PLMD::molfile::fio_readv ( fio_fd  fd,
const fio_iovec iov,
int  iovcnt 
)
static

◆ fio_write_int32()

static int PLMD::molfile::fio_write_int32 ( fio_fd  fd,
int  i 
)
static

◆ fio_write_str()

static int PLMD::molfile::fio_write_str ( fio_fd  fd,
const char *  str 
)
static

◆ g96_countatoms()

static int PLMD::molfile::g96_countatoms ( md_file mf)
static

◆ g96_header()

static int PLMD::molfile::g96_header ( md_file mf,
char *  title,
int  titlelen,
float *  timeval 
)
static

◆ g96_rec()

static int PLMD::molfile::g96_rec ( md_file mf,
md_atom ma 
)
static

◆ g96_timestep()

static int PLMD::molfile::g96_timestep ( md_file mf,
md_ts ts 
)
static

◆ get_pdb_conect()

static void PLMD::molfile::get_pdb_conect ( const char *  record,
int  natoms,
int *  idxmap,
int *  maxbnum,
int *  nbonds,
int **  from,
int **  to 
)
static

◆ get_pdb_coordinates()

static void PLMD::molfile::get_pdb_coordinates ( const char *  record,
float *  x,
float *  y,
float *  z,
float *  occup,
float *  beta 
)
static

◆ get_pdb_cryst1()

static void PLMD::molfile::get_pdb_cryst1 ( const char *  record,
float *  alpha,
float *  beta,
float *  gamma,
float *  a,
float *  b,
float *  c 
)
static

◆ get_pdb_fields()

static void PLMD::molfile::get_pdb_fields ( const char *  record,
int  reclength,
int *  serial,
char *  name,
char *  resname,
char *  chain,
char *  segname,
char *  resid,
char *  insertion,
char *  altloc,
char *  elementsymbol,
float *  x,
float *  y,
float *  z,
float *  occup,
float *  beta 
)
static

◆ get_pdb_header()

static void PLMD::molfile::get_pdb_header ( const char *  record,
char *  pdbcode,
char *  date,
char *  classification 
)
static

◆ get_pte_idx()

static int PLMD::molfile::get_pte_idx ( const char *  label)
static

◆ get_pte_idx_from_string()

static int PLMD::molfile::get_pte_idx_from_string ( const char *  label)
static

◆ get_pte_label()

static const char* PLMD::molfile::get_pte_label ( const int  idx)
static

◆ get_pte_mass()

static float PLMD::molfile::get_pte_mass ( const int  idx)
static

◆ get_pte_vdw_radius()

static float PLMD::molfile::get_pte_vdw_radius ( const int  idx)
static

◆ gro_header()

static int PLMD::molfile::gro_header ( md_file mf,
char *  title,
int  titlelen,
float *  timeval,
int *  natoms,
int  rewind = 1 
)
static

◆ gro_rec()

static int PLMD::molfile::gro_rec ( md_file mf,
md_atom ma 
)
static

◆ gro_timestep()

static int PLMD::molfile::gro_timestep ( md_file mf,
md_ts ts 
)
static

◆ host_is_little_endian()

static inline bool PLMD::molfile::host_is_little_endian ( void  )
inlinestatic

detect endiannes of host machine. returns true on little endian machines.

◆ mdio_close()

static int PLMD::molfile::mdio_close ( md_file mf)
static

◆ mdio_errmsg()

static const char * PLMD::molfile::mdio_errmsg ( int  n)
static

◆ mdio_errno()

static int PLMD::molfile::mdio_errno ( void  )
static

◆ mdio_header()

static int PLMD::molfile::mdio_header ( md_file mf,
md_header mdh 
)
static

◆ mdio_open()

md_file * PLMD::molfile::mdio_open ( const char *  fn,
const int  fmt,
const int  rw = MDIO_READ 
)
static

◆ mdio_readbox()

static int PLMD::molfile::mdio_readbox ( md_box box,
float *  x,
float *  y,
float *  z 
)
static

◆ mdio_readline()

static int PLMD::molfile::mdio_readline ( md_file mf,
char *  buf,
int  n,
int  strip = 1 
)
static

◆ mdio_seterror()

static int PLMD::molfile::mdio_seterror ( int  code)
static

◆ mdio_timestep()

static int PLMD::molfile::mdio_timestep ( md_file mf,
md_ts ts 
)
static

◆ mdio_tsfree()

static int PLMD::molfile::mdio_tsfree ( md_ts ts,
int  holderror = 0 
)
static

◆ molfile_crdplugin_fini()

int PLMD::molfile::molfile_crdplugin_fini ( void  )

◆ molfile_crdplugin_init()

int PLMD::molfile::molfile_crdplugin_init ( void  )

◆ molfile_crdplugin_register()

int PLMD::molfile::molfile_crdplugin_register ( void *  ,
vmdplugin_register_cb   
)

◆ molfile_dcdplugin_fini()

int PLMD::molfile::molfile_dcdplugin_fini ( void  )

◆ molfile_dcdplugin_init()

int PLMD::molfile::molfile_dcdplugin_init ( void  )

◆ molfile_dcdplugin_register()

int PLMD::molfile::molfile_dcdplugin_register ( void *  ,
vmdplugin_register_cb   
)

◆ molfile_gromacsplugin_fini()

int PLMD::molfile::molfile_gromacsplugin_fini ( void  )

◆ molfile_gromacsplugin_init()

int PLMD::molfile::molfile_gromacsplugin_init ( void  )

◆ molfile_gromacsplugin_register()

int PLMD::molfile::molfile_gromacsplugin_register ( void *  ,
vmdplugin_register_cb   
)

◆ molfile_pdbplugin_fini()

int PLMD::molfile::molfile_pdbplugin_fini ( void  )

◆ molfile_pdbplugin_init()

int PLMD::molfile::molfile_pdbplugin_init ( void  )

◆ molfile_pdbplugin_register()

int PLMD::molfile::molfile_pdbplugin_register ( void *  ,
vmdplugin_register_cb   
)

◆ put_trx_int()

static int PLMD::molfile::put_trx_int ( md_file mf,
int  y 
)
static

◆ put_trx_real()

static int PLMD::molfile::put_trx_real ( md_file mf,
float  y 
)
static

◆ put_trx_string()

static int PLMD::molfile::put_trx_string ( md_file mf,
const char *  s 
)
static

◆ read_pdb_record()

static int PLMD::molfile::read_pdb_record ( FILE *  f,
char *  retStr 
)
static

◆ strip_white()

static int PLMD::molfile::strip_white ( char *  buf)
static

◆ swap2_aligned()

static void PLMD::molfile::swap2_aligned ( void *  v,
long  ndata 
)
static

◆ swap2_unaligned()

static void PLMD::molfile::swap2_unaligned ( void *  v,
long  ndata 
)
static

◆ swap4_aligned()

static void PLMD::molfile::swap4_aligned ( void *  v,
long  ndata 
)
static

◆ swap4_unaligned()

static void PLMD::molfile::swap4_unaligned ( void *  v,
long  ndata 
)
static

◆ swap8_aligned()

static void PLMD::molfile::swap8_aligned ( void *  v,
long  ndata 
)
static

◆ swap8_unaligned()

static void PLMD::molfile::swap8_unaligned ( void *  v,
long  ndata 
)
static

◆ trx_header()

static int PLMD::molfile::trx_header ( md_file mf,
int  rewind = 0 
)
static

◆ trx_int()

static int PLMD::molfile::trx_int ( md_file mf,
int *  y 
)
static

◆ trx_real()

static int PLMD::molfile::trx_real ( md_file mf,
float *  y 
)
static

◆ trx_rvector()

static int PLMD::molfile::trx_rvector ( md_file mf,
float *  vec 
)
static

◆ trx_string()

static int PLMD::molfile::trx_string ( md_file mf,
char *  str,
int  max 
)
static

◆ trx_timestep()

static int PLMD::molfile::trx_timestep ( md_file mf,
md_ts ts 
)
static

◆ VMDPLUGIN_fini()

VMDPLUGIN_EXTERN int PLMD::molfile::VMDPLUGIN_fini ( void  )

The Fini method is called when the application will no longer use any plugins in the library.


◆ VMDPLUGIN_init()

VMDPLUGIN_EXTERN int PLMD::molfile::VMDPLUGIN_init ( void  )

Init routine: called the first time the library is loaded by the application and before any other API functions are referenced.

Return 0 on success.

◆ VMDPLUGIN_register()

VMDPLUGIN_EXTERN int PLMD::molfile::VMDPLUGIN_register ( void *  ,
vmdplugin_register_cb   
)

Allow the library to register plugins with the application.

The callback should be called using the passed-in void pointer, which should not be interpreted in any way by the library. Each vmdplugin_t pointer passed to the application should point to statically-allocated or heap-allocated memory and should never be later modified by the plugin. Applications must be permitted to retain only a copy of the the plugin pointer, without making any deep copy of the items in the struct.

◆ VMDPLUGIN_register_tcl()

VMDPLUGIN_EXTERN int PLMD::molfile::VMDPLUGIN_register_tcl ( void *  ,
void *  tcl_interp,
vmdplugin_register_cb   
)

Allow the library to register Tcl extensions.


This API is optional; if found by dlopen, it will be called after first calling init and register.

◆ write_raw_pdb_record()

static int PLMD::molfile::write_raw_pdb_record ( FILE *  fd,
const char *  recordname,
int  index,
const char *  atomname,
const char *  resname,
int  resid,
const char *  insertion,
const char *  altloc,
const char *  elementsymbol,
float  x,
float  y,
float  z,
float  occ,
float  beta,
const char *  chain,
const char *  segname 
)
static

◆ xtc_3dfcoord()

static int PLMD::molfile::xtc_3dfcoord ( md_file mf,
float *  fp,
int *  size,
float *  precision 
)
static

◆ xtc_data()

static int PLMD::molfile::xtc_data ( md_file mf,
char *  buf,
int  len 
)
static

◆ xtc_float()

static int PLMD::molfile::xtc_float ( md_file mf,
float *  f 
)
static

◆ xtc_int()

static int PLMD::molfile::xtc_int ( md_file mf,
int *  i 
)
static

◆ xtc_receivebits()

static int PLMD::molfile::xtc_receivebits ( int *  buf,
int  nbits 
)
static

◆ xtc_receiveints()

static void PLMD::molfile::xtc_receiveints ( int *  buf,
const int  nints,
int  nbits,
unsigned int *  sizes,
int *  nums 
)
static

◆ xtc_sizeofint()

static int PLMD::molfile::xtc_sizeofint ( int  size)
static

◆ xtc_sizeofints()

static int PLMD::molfile::xtc_sizeofints ( int  nints,
unsigned int *  sizes 
)
static

◆ xtc_timestep()

static int PLMD::molfile::xtc_timestep ( md_file mf,
md_ts ts 
)
static

Variable Documentation

◆ mdio_errcode

int PLMD::molfile::mdio_errcode
static

◆ mdio_errdescs

const char* PLMD::molfile::mdio_errdescs[]
static
Initial value:
= {
"no error",
"file does not match format",
"unexpected end-of-file reached",
"function called with bad parameters",
"file i/o error",
"unsupported precision",
"out of memory",
"cannot open file",
"bad file extension",
"unknown file format",
"cannot close file",
"wrong file format for this function",
"binary i/o error: sizeof(int) != 4",
NULL
}

◆ mdio_fmtexts

const char* PLMD::molfile::mdio_fmtexts[]
Initial value:
= {
"",
".gro",
".trr",
".g96",
".trj",
".xtc",
NULL
}

◆ nr_pte_entries

const int PLMD::molfile::nr_pte_entries = sizeof(pte_label) / sizeof(char *)
static

◆ pte_label

const char* PLMD::molfile::pte_label[]
static
Initial value:
= {
"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne",
"Na", "Mg", "Al", "Si", "P" , "S", "Cl", "Ar", "K", "Ca", "Sc",
"Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge",
"As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc",
"Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe",
"Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb",
"Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os",
"Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr",
"Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf",
"Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt",
"Ds", "Rg"
}

◆ pte_mass

const float PLMD::molfile::pte_mass[]
static
Initial value:
= {
0.00000, 1.00794, 4.00260, 6.941, 9.012182, 10.811,
12.0107, 14.0067, 15.9994, 18.9984032, 20.1797,
22.989770, 24.3050, 26.981538, 28.0855, 30.973761,
32.065, 35.453, 39.948, 39.0983, 40.078, 44.955910,
47.867, 50.9415, 51.9961, 54.938049, 55.845, 58.9332,
58.6934, 63.546, 65.409, 69.723, 72.64, 74.92160,
78.96, 79.904, 83.798, 85.4678, 87.62, 88.90585,
91.224, 92.90638, 95.94, 98.0, 101.07, 102.90550,
106.42, 107.8682, 112.411, 114.818, 118.710, 121.760,
127.60, 126.90447, 131.293, 132.90545, 137.327,
138.9055, 140.116, 140.90765, 144.24, 145.0, 150.36,
151.964, 157.25, 158.92534, 162.500, 164.93032,
167.259, 168.93421, 173.04, 174.967, 178.49, 180.9479,
183.84, 186.207, 190.23, 192.217, 195.078, 196.96655,
200.59, 204.3833, 207.2, 208.98038, 209.0, 210.0, 222.0,
223.0, 226.0, 227.0, 232.0381, 231.03588, 238.02891,
237.0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0,
258.0, 259.0, 262.0, 261.0, 262.0, 266.0, 264.0, 269.0,
268.0, 271.0, 272.0
}

◆ pte_vdw_radius

const float PLMD::molfile::pte_vdw_radius[]
static
Initial value:
= {
1.5, 1.2, 1.4, 1.82, 2.0, 2.0,
1.7, 1.55, 1.52, 1.47, 1.54,
1.36, 1.18, 2.0, 2.1, 1.8,
1.8, 2.27, 1.88, 1.76, 1.37, 2.0,
2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
1.63, 1.4, 1.39, 1.07, 2.0, 1.85,
1.9, 1.85, 2.02, 2.0, 2.0, 2.0,
2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
1.63, 1.72, 1.58, 1.93, 2.17, 2.0,
2.06, 1.98, 2.16, 2.1, 2.0,
2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
2.0, 2.0, 2.0, 2.0, 2.0,
2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
2.0, 2.0, 2.0, 2.0, 1.72, 1.66,
1.55, 1.96, 2.02, 2.0, 2.0, 2.0, 2.0,
2.0, 2.0, 2.0, 2.0, 2.0, 1.86,
2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
2.0, 2.0, 2.0
}

◆ xtc_magicints

int PLMD::molfile::xtc_magicints[]
static
Initial value:
= {
0, 0, 0, 0, 0, 0, 0, 0, 0,8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
80, 101, 128, 161, 203, 256, 322, 406, 512, 645, 812, 1024, 1290,
1625, 2048, 2580, 3250, 4096, 5060, 6501, 8192, 10321, 13003, 16384,
20642, 26007, 32768, 41285, 52015, 65536, 82570, 104031, 131072,
165140, 208063, 262144, 330280, 416127, 524287, 660561, 832255,
1048576, 1321122, 1664510, 2097152, 2642245, 3329021, 4194304,
5284491, 6658042, 8388607, 10568983, 13316085, 16777216 }