cssr.h File Reference

Defines for CSSR handling. More...

#include "MathType.h"
#include "pdb.h"
#include "deprecated.h"

Go to the source code of this file.

Data Structures
struct	cssr_entry

Macros
#define	CLEAR_CSSR(p)
#define	_CSSR_H_DEPRECATED

Typedefs
typedef struct cssr_entry	CSSR

Functions
CSSR *	blReadCSSR (FILE *fp, int *natom, char *name, char *title)
PDB *	blReadCSSRasPDB (FILE *fp, int *natom)
void	blNormaliseCSSR (CSSR *cssr, REAL cell[3], REAL alpha, REAL beta, REAL gamma)
void	blNormalisePDB (PDB *pdb, REAL cell[3], REAL alpha, REAL beta, REAL gamma)
void	blOrtho (REAL cell[3], REAL alpha, REAL beta, REAL gamma, REAL amatrx[3][3], int isw, int ncode)
void	blWriteCSSR (FILE *fp, CSSR *cssr, char *name, char *title)

Detailed Description

Defines for CSSR handling.

Version

V1.3

Date

14.08.14

Copyright

SciTech Software 1991-2014

Author

Andrew C. R. Martin

Institute of Structural & Molecular Biology, University College London, Gower Street, London. WC1E 6BT.

andre.nosp@m.w@bi.nosp@m.oinf..nosp@m.org..nosp@m.uk andre.nosp@m.w.ma.nosp@m.rtin@.nosp@m.ucl..nosp@m.ac.uk

This code is NOT IN THE PUBLIC DOMAIN, but it may be copied according to the conditions laid out in the accompanying file COPYING.DOC.

The code may be modified as required, but any modifications must be documented so that the person responsible can be identified.

The code may not be sold commercially or included as part of a commercial product except as described in the file COPYING.DOC.

Description:

Structure definitions for ReadCSSR()

Usage:

Revision History:

• V1.1 07.07.14 Use bl prefix for functions By: CTP
• V1.2 31.07.14 Updated deprecation: Removed deprecated.h and added prototypes for renamed functions. By: CTP
• V1.3 14.08.14 Moved deprecated function prototypes to deprecated.h By: CTP

Definition in file cssr.h.

Macro Definition Documentation

#define _CSSR_H_DEPRECATED

Definition at line 101 of file cssr.h.

#define CLEAR_CSSR

(

p

)

Value:

p->atnum=0; \
                      strcpy(p->atnam,"    "); \
                      p->group=0; \
                      p->x = 0.0; p->y = 0.0; p->z = 0.0; \
                      p->charge = 0.0; \
                      p->link[0] = p->link[1] = p->link[2] = p->link[3] = 0; \
                      p->link[4] = p->link[5] = p->link[6] = p->link[7] = 0; \
                      p->next = NULL

Definition at line 76 of file cssr.h.

Typedef Documentation

typedef struct cssr_entry CSSR

Definition at line 74 of file cssr.h.

Function Documentation

void blNormaliseCSSR	(	CSSR *	cssr,
		REAL	cell[3],
		REAL	alpha,
		REAL	beta,
		REAL	gamma
	)

Parameters

[in,out]	*cssr	Pointer to CSSR linked list
[in]	cell	Unit cell dimensions
[in]	alpha	Unit cell angles
[in]	beta
[in]	gamma	Convert a CSSR linked list in fractional coordinates to orthonormal

• 06.09.91 Original
• 01.06.92 Documented
• 10.06.93 void return
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 513 of file ReadCSSR.c.

void blNormalisePDB	(	PDB *	pdb,
		REAL	cell[3],
		REAL	alpha,
		REAL	beta,
		REAL	gamma
	)

Parameters

[in,out]	*pdb	Pointer to PDB linked list
[in]	cell	Unit cell dimensions
[in]	alpha	Unit cell angles
[in]	beta
[in]	gamma	Convert a PDB linked list in fractional cooridinates to orthonormal

• 06.09.91 Original
• 01.06.92 Documented
• 10.06.93 void return
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 574 of file ReadCSSR.c.

void blOrtho	(	REAL	cell[3],
		REAL	alpha,
		REAL	beta,
		REAL	gamma,
		REAL	amatrx[3][3],
		int	isw,
		int	ncode
	)

Parameters

[in]	cell	Unit cell dimensions
[in]	alpha	Unit cell angles
[in]	beta
[in]	gamma
[out]	amatrx	Returned conversion matrix
[in]	isw	0: Frac–>Ortho, 1: Ortho–>Frac
[in]	ncode	Orientation of reciprocal axes wrt true axes.

   ncode    Orientation of reciprocal axes wrt true axes.

                              1: a || xo,          c* || zo
                              2: b || xo,          a* || zo
                              3: c || xo,          b* || zo
                              4: hex a & b || xo,  c* || zo
                              5: a* || xo,         c  || zo

Function to calculate a matrix which will convert between fractional and orthonormal coordinates given unit cell dimensions and angles. ncode defines the orientation of the reciprocal axes wrt the real axes.

See Rollett `Computing Methods in Crystallography' p.23

• 06.09.91 Original
• 01.06.92 Documented
• 10.06.93 void return
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 643 of file ReadCSSR.c.

CSSR* blReadCSSR	(	FILE *	fp,
		int *	natom,
		char *	name,
		char *	title
	)

Parameters

[in]	*fp	A pointer to type FILE in which the CSSR file is stored.
[out]	*natom	Number of atoms read.
[out]	*name	The molecule's name.
[out]	*title	Title on the molecule.

Read a CSSR file into a CSSR linked list

• 06.09.91 Original
• 24.01.92 Fixed for blank link columns (V1.1)
• 01.06.92 Documented
• 10.06.93 Returns TRUE or FALSE to indicate success
• 09.07.93 Changed allocation scheme. Now returns pointer to start of list. No need to call init_cssr
• 13.07.93 Returns NULL if allocation failed
• 27.07.93 Changed I/O to double precision
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 224 of file ReadCSSR.c.

PDB* blReadCSSRasPDB	(	FILE *	fp,
		int *	natom
	)

Parameters

[in]	*fp	A pointer to type FILE in which the CSSR file is stored.
[out]	*natom	Number of atoms read.

Returns

A pointer to the first allocated item of the PDB linked list

Read a CSSR file into a PDB linked list

• 06.09.91 Original
• 01.06.92 Documented
• 10.06.93 Returns TRUE or FALSE to indicate success
• 09.07.93 Changed allocation scheme. Now returns pointer to start of list. No need to call init_pdb
• 13.07.93 Returns NULL if allocation failed
• 27.07.93 Changed I/O to double precision
• 07.07.14 Use bl prefix for functions By: CTP
• 15.08.14 Use CLEAR_PDB() By: CTP

Definition at line 368 of file ReadCSSR.c.

void blWriteCSSR	(	FILE *	fp,
		CSSR *	cssr,
		char *	name,
		char *	title
	)

Parameters

[in]	*fp	A pointer to type FILE in which the CSSR file is stored.
[in]	*cssr	A pointer to the first allocated item of the CSSR linked list
[in]	*name	The molecule's name.
[in]	*title	Title on the molecule.

Write a CSSR file from a CSSR linked list.

• 22.09.91 Original
• 01.06.92 Autodoc'd
• 10.06.93 void return; float->REAL
• 27.07.93 f -> lf
• 01.03.94 lf -> f (!)
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 130 of file WrtCSSR.c.