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
	Per-timestep atom coordinates, velocities, time, energies and periodic cell info. More...

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_file *	mdio_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, ptrdiff_t ndata)

static void	swap2_unaligned (void *v, ptrdiff_t ndata)

static void	swap4_aligned (void *v, ptrdiff_t ndata)

static void	swap4_unaligned (void *v, ptrdiff_t ndata)

static void	swap8_aligned (void *v, ptrdiff_t ndata)

static void	swap8_unaligned (void *v, ptrdiff_t 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

typedef void* PLMD::molfile::fio_caddr_t

◆ fio_fd

typedef int PLMD::molfile::fio_fd

◆ fio_size_t

typedef off_t PLMD::molfile::fio_size_t

◆ molfile_qm_timestep_metadata_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.

◆ molfile_timestep_metadata_t

typedef struct PLMD::molfile::molfile_timestep_metadata PLMD::molfile::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

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

◆ molfile_qm_charge_type

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

◆ molfile_qm_wavefunc_type

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

◆ 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,
		ptrdiff_t	ndata
	)

static

◆ swap2_unaligned()

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

static

◆ swap4_aligned()

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

static

◆ swap4_unaligned()

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

static

◆ swap8_aligned()

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

static

◆ swap8_unaligned()

static void PLMD::molfile::swap8_unaligned	(	void *	v,
		ptrdiff_t	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:

= { 
00000, 1.00794, 4.00260, 6.941, 9.012182, 10.811,  
0107, 14.0067, 15.9994, 18.9984032, 20.1797, 
989770, 24.3050, 26.981538, 28.0855, 30.973761,
065, 35.453, 39.948, 39.0983, 40.078, 44.955910,
867, 50.9415, 51.9961, 54.938049, 55.845, 58.9332,
6934, 63.546, 65.409, 69.723, 72.64, 74.92160, 
96, 79.904, 83.798, 85.4678, 87.62, 88.90585, 
224, 92.90638, 95.94, 98.0, 101.07, 102.90550,
42, 107.8682, 112.411, 114.818, 118.710, 121.760, 
60, 126.90447, 131.293, 132.90545, 137.327, 
9055, 140.116, 140.90765, 144.24, 145.0, 150.36,
964, 157.25, 158.92534, 162.500, 164.93032, 
259, 168.93421, 173.04, 174.967, 178.49, 180.9479,
84, 186.207, 190.23, 192.217, 195.078, 196.96655, 
59, 204.3833, 207.2, 208.98038, 209.0, 210.0, 222.0, 
0, 226.0, 227.0, 232.0381, 231.03588, 238.02891,
0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0,
0, 259.0, 262.0, 261.0, 262.0, 266.0, 264.0, 269.0,
0, 271.0, 272.0
}

◆ pte_vdw_radius

const float PLMD::molfile::pte_vdw_radius[]

static

Initial value:

= { 
5, 1.2, 1.4, 1.82, 2.0, 2.0,  
7, 1.55, 1.52, 1.47, 1.54, 
36, 1.18, 2.0, 2.1, 1.8,
8, 2.27, 1.88, 1.76, 1.37, 2.0,
0, 2.0, 2.0, 2.0, 2.0, 2.0,
63, 1.4, 1.39, 1.07, 2.0, 1.85,
9, 1.85, 2.02, 2.0, 2.0, 2.0, 
0, 2.0, 2.0, 2.0, 2.0, 2.0,
63, 1.72, 1.58, 1.93, 2.17, 2.0, 
06, 1.98, 2.16, 2.1, 2.0,
0, 2.0, 2.0, 2.0, 2.0, 2.0,
0, 2.0, 2.0, 2.0, 2.0,
0, 2.0, 2.0, 2.0, 2.0, 2.0,
0, 2.0, 2.0, 2.0, 1.72, 1.66,
55, 1.96, 2.02, 2.0, 2.0, 2.0, 2.0,
0, 2.0, 2.0, 2.0, 2.0, 1.86,
0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
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 }

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ fio_caddr_t

◆ fio_fd

◆ fio_size_t

◆ molfile_qm_timestep_metadata_t

◆ molfile_timestep_metadata_t

◆ vmdplugin_register_cb

Enumeration Type Documentation

◆ anonymous enum

◆ molfile_graphics_type

◆ molfile_qm_charge_type

◆ molfile_qm_wavefunc_type

NBO related localizations:

Function Documentation

◆ adjust_pdb_field_string()

◆ fio_fclose()

◆ fio_fread()

◆ fio_fseek()

◆ fio_ftell()

◆ fio_fwrite()

◆ fio_open()

◆ fio_read_int32()

◆ fio_readv()

◆ fio_write_int32()

◆ fio_write_str()

◆ g96_countatoms()

◆ g96_header()

◆ g96_rec()

◆ g96_timestep()

◆ get_pdb_conect()

◆ get_pdb_coordinates()

◆ get_pdb_cryst1()

◆ get_pdb_fields()

◆ get_pdb_header()

◆ get_pte_idx()

◆ get_pte_idx_from_string()

◆ get_pte_label()

◆ get_pte_mass()

◆ get_pte_vdw_radius()

◆ gro_header()

◆ gro_rec()

◆ gro_timestep()

◆ host_is_little_endian()

◆ mdio_close()

◆ mdio_errmsg()

◆ mdio_errno()

◆ mdio_header()

◆ mdio_open()

◆ mdio_readbox()

◆ mdio_readline()

◆ mdio_seterror()

◆ mdio_timestep()

◆ mdio_tsfree()

◆ molfile_crdplugin_fini()

◆ molfile_crdplugin_init()

◆ molfile_crdplugin_register()

◆ molfile_dcdplugin_fini()

◆ molfile_dcdplugin_init()

◆ molfile_dcdplugin_register()

◆ molfile_gromacsplugin_fini()

◆ molfile_gromacsplugin_init()

◆ molfile_gromacsplugin_register()

◆ molfile_pdbplugin_fini()

◆ molfile_pdbplugin_init()

◆ molfile_pdbplugin_register()

◆ put_trx_int()

◆ put_trx_real()

◆ put_trx_string()

◆ read_pdb_record()

◆ strip_white()

◆ swap2_aligned()

◆ swap2_unaligned()

◆ swap4_aligned()

◆ swap4_unaligned()

◆ swap8_aligned()