Read a CSSR file. More...

#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
#include "SysDefs.h"
#include "MathType.h"
#include "cssr.h"
#include "matrix.h"
#include "general.h"
#include "macros.h"

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)

Detailed Description

Read a CSSR file.

Version: V1.7

Date: 15.08.14

Copyright: (c) UCL / Dr. Andrew C. R. Martin 1991-2014

Author: Dr. 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:

ReadCSSR(fp,cssr,natom,name,title)

This subroutine will read a CSSR file of any size and form a linked list of the structure. This list is contained in a linked set of structures of type cssr_entry. The strucure is set up by including the file "cssr.h". For details of the structure, see this file.

To define a structure list in which to store the protein, the user need only include the file "cssr.h", declare a pointer to a structure of type CSSR using the statement: CSSR *mycssr;

ReadCSSRasPDB(fp,cssr,natom)

As ReadCSSR(), but reads the structure into a PDB type linked list. Atom connection information is ignored, and charges are placed into the B-val column.

NormaliseCSSR(cssr,cell,alpha,beta,gamma)

Given the unit cell dimensions, converts CSSR to orthonormal coordinates.

NormalisePDB(pdb,cell,alpha,beta,gamma)

Given the unit cell dimensions, converts PDB to orthonormal coordinates.

ortho(cell,alpha,beta,gamma,amatrx,isw,ncode)

Calculates the 3x3 matrix required to convert between fractional and orthonormal coordinates given the unit cell dimensions.

Usage:

   ReadCSSR(fp,cssr,natom,name,title)
   Input:   FILE     *fp      A pointer to type FILE in which the
                              CSSR file is stored.
            CSSR     *cssr    A pointer to the first allocated item of
                              the CSSR linked list
   Output:  int      *natom   Number of atoms read.
            char     *name    The molecule's name.
            char     *title   Title on the molecule.

   ReadCSSRasPDB(fp,pdb,natom)
                              into a PDB linked list
   Input:   FILE     *fp      A pointer to type FILE in which the
                              CSSR file is stored.
            PDB      *pdb     A pointer to the first allocated item of
                              the PDB linked list
   Output:  int      *natom   Number of atoms read.

   NormaliseCSSR(cssr,cell,alpha,beta,gamma)
   I/O:     CSSR     *cssr    Pointer to CSSR linked list
   Input:   REAL     cell[3]  Unit cell dimensions
                     alpha    Unit cell angles
                     beta
                     gamma

   NormalisePDB(pdb,cell,alpha,beta,gamma)
   I/O:     PDB      *pdb     Pointer to PDB linked list
   Input:   REAL     cell[3]  Unit cell dimensions
                     alpha    Unit cell angles
                     beta
                     gamma

   ortho(cell,alpha,beta,gamma,amatrx,isw,ncode)
   Input:   REAL     cell[3]  Unit cell dimensions
                     alpha    Unit cell angles
                     beta
                     gamma
   Output:  REAL     amatrx[3][3]   Returned conversion matrix
   Input:   int      isw      0: Frac-->Ortho,  1: Ortho-->Frac
            int      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

Revision History:

V1.0 06.09.91 Original
V1.1 24.01.92 Fixed for reading files with blank link numbers.
V1.2 01.06.92 Documented and added FPU check
V1.3 10.06.93 Tidied for book
V1.4 27.07.93 Changed I/O to double precision
V1.5 30.05.02 Changed PDB field from 'junk' to 'record_type'
V1.6 07.07.14 Use bl prefix for functions By: CTP
V1.7 15.08.14 Updated blReadCSSRasPDB() to use CLEAR_PDB() By: CTP

Definition in file ReadCSSR.c.

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.

Functions

Detailed Description

Description:

Usage:

Revision History:

Function Documentation