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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_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 int fio_fd
 
typedef off_t fio_size_t
 
typedef void * fio_caddr_t
 
typedef struct
PLMD::molfile::molfile_timestep_metadata 		molfile_timestep_metadata_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 int(* vmdplugin_register_cb )(void *, vmdplugin_t *)
 Function pointer typedef for register callback functions. More...
 

Enumerations

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...
 
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_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  {
  PDB_HEADER, PDB_REMARK, PDB_ATOM, PDB_CONECT,
  PDB_UNKNOWN, PDB_END, PDB_EOF, PDB_CRYST1
}
 

Functions

static void swap2_unaligned (void *v, long ndata)
 
static void swap4_unaligned (void *v, long ndata)
 
static void swap8_unaligned (void *v, long ndata)
 
static void swap2_aligned (void *v, long ndata)
 
static void swap4_aligned (void *v, long ndata)
 
static void swap8_aligned (void *v, long ndata)
 
static int fio_open (const char *filename, int mode, fio_fd *fd)
 
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_readv (fio_fd fd, const fio_iovec *iov, int iovcnt)
 
static fio_size_t fio_fwrite (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 int fio_write_int32 (fio_fd fd, int i)
 
static int fio_read_int32 (fio_fd fd, int *i)
 
static int fio_write_str (fio_fd fd, const char *str)
 
static md_file * mdio_open (const char *, const int, const int=MDIO_READ)
 
static int mdio_close (md_file *)
 
static int mdio_header (md_file *, md_header *)
 
static int mdio_timestep (md_file *, md_ts *)
 
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 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 *)
 
static int g96_header (md_file *, char *, int, float *)
 
static int g96_timestep (md_file *, md_ts *)
 
static int g96_rec (md_file *, md_atom *)
 
static int g96_countatoms (md_file *)
 
static int xtc_int (md_file *, int *)
 
static int xtc_float (md_file *, float *)
 
static int xtc_timestep (md_file *, md_ts *)
 
static int xtc_3dfcoord (md_file *, float *, int *, float *)
 
static int mdio_errno (void)
 
static const char * mdio_errmsg (int)
 
static int mdio_seterror (int)
 
static int strip_white (char *)
 
static int mdio_readline (md_file *, char *, int, int=1)
 
static int mdio_tsfree (md_ts *, int=0)
 
static int mdio_readbox (md_box *, float *, float *, float *)
 
static int xtc_receivebits (int *, int)
 
static int host_is_little_endian (void)
 
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 xtc_data (md_file *mf, char *buf, int len)
 
static int xtc_sizeofint (int size)
 
static int xtc_sizeofints (int nints, unsigned int *sizes)
 
static void xtc_receiveints (int *buf, const int nints, int nbits, unsigned int *sizes, int *nums)
 
int molfile_dcdplugin_init (void)
 
int molfile_dcdplugin_register (void *, vmdplugin_register_cb)
 
int molfile_dcdplugin_fini (void)
 
int molfile_crdplugin_init (void)
 
int molfile_crdplugin_register (void *, vmdplugin_register_cb)
 
int molfile_crdplugin_fini (void)
 
int molfile_gromacsplugin_init (void)
 
int molfile_gromacsplugin_register (void *, vmdplugin_register_cb)
 
int molfile_gromacsplugin_fini (void)
 
int molfile_pdbplugin_init (void)
 
int molfile_pdbplugin_register (void *, vmdplugin_register_cb)
 
int molfile_pdbplugin_fini (void)
 
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 get_pte_idx (const char *label)
 
static int get_pte_idx_from_string (const char *label)
 
static int read_pdb_record (FILE *f, char *retStr)
 
static void get_pdb_cryst1 (const char *record, float *alpha, float *beta, float *gamma, float *a, float *b, float *c)
 
static void get_pdb_coordinates (const char *record, float *x, float *y, float *z, float *occup, float *beta)
 
static void adjust_pdb_field_string (char *field)
 
static void get_pdb_header (const char *record, char *pdbcode, char *date, char *classification)
 
static void get_pdb_conect (const char *record, int natoms, int *idxmap, int *maxbnum, int *nbonds, int **from, int **to)
 
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 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)
 
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...
 
VMDPLUGIN_EXTERN int VMDPLUGIN_fini (void)
 The Fini method is called when the application will no longer use any plugins in the library. More...
 

Variables

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

Typedef Documentation

typedef void* PLMD::molfile::fio_caddr_t
typedef int PLMD::molfile::fio_fd
typedef off_t PLMD::molfile::fio_size_t
typedef struct PLMD::molfile::molfile_qm_timestep_metadata PLMD::molfile::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.

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

Function pointer typedef for register callback functions.

Enumeration Type Documentation

anonymous enum
Enumerator
PDB_HEADER 
PDB_REMARK 
PDB_ATOM 
PDB_CONECT 
PDB_UNKNOWN 
PDB_END 
PDB_EOF 
PDB_CRYST1 
enum PLMD::molfile::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 
enum PLMD::molfile::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 
enum PLMD::molfile::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

static void PLMD::molfile::adjust_pdb_field_string ( char *  field)
static
static int PLMD::molfile::fio_fclose ( fio_fd  fd)
static
static fio_size_t PLMD::molfile::fio_fread ( void *  ptr,
fio_size_t  size,
fio_size_t  nitems,
fio_fd  fd 
)
static
static fio_size_t PLMD::molfile::fio_fseek ( fio_fd  fd,
fio_size_t  offset,
int  whence 
)
static
static fio_size_t PLMD::molfile::fio_ftell ( fio_fd  fd)
static
static fio_size_t PLMD::molfile::fio_fwrite ( void *  ptr,
fio_size_t  size,
fio_size_t  nitems,
fio_fd  fd 
)
static
static int PLMD::molfile::fio_open ( const char *  filename,
int  mode,
fio_fd *  fd 
)
static
static int PLMD::molfile::fio_read_int32 ( fio_fd  fd,
int *  i 
)
static
static fio_size_t PLMD::molfile::fio_readv ( fio_fd  fd,
const fio_iovec *  iov,
int  iovcnt 
)
static
static int PLMD::molfile::fio_write_int32 ( fio_fd  fd,
int  i 
)
static
static int PLMD::molfile::fio_write_str ( fio_fd  fd,
const char *  str 
)
static
static int PLMD::molfile::g96_countatoms ( md_file *  mf)
static
static int PLMD::molfile::g96_header ( md_file *  mf,
char *  title,
int  titlelen,
float *  timeval 
)
static
static int PLMD::molfile::g96_rec ( md_file *  mf,
md_atom *  ma 
)
static
static int PLMD::molfile::g96_timestep ( md_file *  mf,
md_ts *  ts 
)
static
static void PLMD::molfile::get_pdb_conect ( const char *  record,
int  natoms,
int *  idxmap,
int *  maxbnum,
int *  nbonds,
int **  from,
int **  to 
)
static
static void PLMD::molfile::get_pdb_coordinates ( const char *  record,
float *  x,
float *  y,
float *  z,
float *  occup,
float *  beta 
)
static
static void PLMD::molfile::get_pdb_cryst1 ( const char *  record,
float *  alpha,
float *  beta,
float *  gamma,
float *  a,
float *  b,
float *  c 
)
static
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
static void PLMD::molfile::get_pdb_header ( const char *  record,
char *  pdbcode,
char *  date,
char *  classification 
)
static
static int PLMD::molfile::get_pte_idx ( const char *  label)
static
static int PLMD::molfile::get_pte_idx_from_string ( const char *  label)
static
static const char* PLMD::molfile::get_pte_label ( const int  idx)
static
static float PLMD::molfile::get_pte_mass ( const int  idx)
static
static float PLMD::molfile::get_pte_vdw_radius ( const int  idx)
static
static int PLMD::molfile::gro_header ( md_file *  mf,
char *  title,
int  titlelen,
float *  timeval,
int *  natoms,
int  rewind = 1 
)
static
static int PLMD::molfile::gro_rec ( md_file *  mf,
md_atom *  ma 
)
static
static int PLMD::molfile::gro_timestep ( md_file *  mf,
md_ts *  ts 
)
static
static inline bool PLMD::molfile::host_is_little_endian ( void  )
inlinestatic

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

static int PLMD::molfile::mdio_close ( md_file *  mf)
static
static const char * PLMD::molfile::mdio_errmsg ( int  n)
static
static int PLMD::molfile::mdio_errno ( void  )
static
static int PLMD::molfile::mdio_header ( md_file *  mf,
md_header *  mdh 
)
static
md_file * PLMD::molfile::mdio_open ( const char *  fn,
const int  fmt,
const int  rw = MDIO_READ 
)
static
static int PLMD::molfile::mdio_readbox ( md_box *  box,
float *  x,
float *  y,
float *  z 
)
static
static int PLMD::molfile::mdio_readline ( md_file *  mf,
char *  buf,
int  n,
int  strip = 1 
)
static
static int PLMD::molfile::mdio_seterror ( int  code)
static
static int PLMD::molfile::mdio_timestep ( md_file *  mf,
md_ts *  ts 
)
static
static int PLMD::molfile::mdio_tsfree ( md_ts *  ts,
int  holderror = 0 
)
static
int PLMD::molfile::molfile_crdplugin_fini ( void  )
int PLMD::molfile::molfile_crdplugin_init ( void  )
int PLMD::molfile::molfile_crdplugin_register ( void *  ,
vmdplugin_register_cb   
)
int PLMD::molfile::molfile_dcdplugin_fini ( void  )
int PLMD::molfile::molfile_dcdplugin_init ( void  )
int PLMD::molfile::molfile_dcdplugin_register ( void *  ,
vmdplugin_register_cb   
)
int PLMD::molfile::molfile_gromacsplugin_fini ( void  )
int PLMD::molfile::molfile_gromacsplugin_init ( void  )
int PLMD::molfile::molfile_gromacsplugin_register ( void *  ,
vmdplugin_register_cb   
)
int PLMD::molfile::molfile_pdbplugin_fini ( void  )
int PLMD::molfile::molfile_pdbplugin_init ( void  )
int PLMD::molfile::molfile_pdbplugin_register ( void *  ,
vmdplugin_register_cb   
)
static int PLMD::molfile::put_trx_int ( md_file *  mf,
int  y 
)
static
static int PLMD::molfile::put_trx_real ( md_file *  mf,
float  y 
)
static
static int PLMD::molfile::put_trx_string ( md_file *  mf,
const char *  s 
)
static
static int PLMD::molfile::read_pdb_record ( FILE *  f,
char *  retStr 
)
static
static int PLMD::molfile::strip_white ( char *  buf)
static
static void PLMD::molfile::swap2_aligned ( void *  v,
long  ndata 
)
static
static void PLMD::molfile::swap2_unaligned ( void *  v,
long  ndata 
)
static
static void PLMD::molfile::swap4_aligned ( void *  v,
long  ndata 
)
static
static void PLMD::molfile::swap4_unaligned ( void *  v,
long  ndata 
)
static
static void PLMD::molfile::swap8_aligned ( void *  v,
long  ndata 
)
static
static void PLMD::molfile::swap8_unaligned ( void *  v,
long  ndata 
)
static
static int PLMD::molfile::trx_header ( md_file *  mf,
int  rewind = 0 
)
static
static int PLMD::molfile::trx_int ( md_file *  mf,
int *  y 
)
static
static int PLMD::molfile::trx_real ( md_file *  mf,
float *  y 
)
static
static int PLMD::molfile::trx_rvector ( md_file *  mf,
float *  vec 
)
static
static int PLMD::molfile::trx_string ( md_file *  mf,
char *  str,
int  max 
)
static
static int PLMD::molfile::trx_timestep ( md_file *  mf,
md_ts *  ts 
)
static
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_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_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_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.

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
static int PLMD::molfile::xtc_3dfcoord ( md_file *  mf,
float *  fp,
int *  size,
float *  precision 
)
static
static int PLMD::molfile::xtc_data ( md_file *  mf,
char *  buf,
int  len 
)
static
static int PLMD::molfile::xtc_float ( md_file *  mf,
float *  f 
)
static
static int PLMD::molfile::xtc_int ( md_file *  mf,
int *  i 
)
static
static int PLMD::molfile::xtc_receivebits ( int *  buf,
int  nbits 
)
static
static void PLMD::molfile::xtc_receiveints ( int *  buf,
const int  nints,
int  nbits,
unsigned int *  sizes,
int *  nums 
)
static
static int PLMD::molfile::xtc_sizeofint ( int  size)
static
static int PLMD::molfile::xtc_sizeofints ( int  nints,
unsigned int *  sizes 
)
static
static int PLMD::molfile::xtc_timestep ( md_file *  mf,
md_ts *  ts 
)
static

Variable Documentation

int PLMD::molfile::mdio_errcode
static
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
}
const char* PLMD::molfile::mdio_fmtexts[]
Initial value:
= {
"",
".gro",
".trr",
".g96",
".trj",
".xtc",
NULL
}
const int PLMD::molfile::nr_pte_entries = sizeof(pte_label) / sizeof(char *)
static
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"
}
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
}
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
}
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 }
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