In practice, there are some minor changes to how rwbrook.f behaves:
Authors: John W. Campbell and Adam C. Ralph
| XYZINIT | initialises COMMON blocks must be called first. |
| XYZOPEN | opens co-ordinate file (by calling XYZOPEN2) |
| XYZOPEN2 | opens co-ordinate file with option to disable checks for CRYST and SCALE cards |
| XYZCLOSE | closes co-ordinate file |
| XYZADVANCE | reads/writes data from/to file to/from internal buffer. |
| XYZATOM | extracts various data items from internal buffer e.g. atom name, residue name. |
| XYZCOORD | extracts x, y, z, occupancy and B from internal buffer |
| XYZREWD | rewinds file to beginning |
| XYZBKSP | backspaces a line in the file |
| PDBREAD | reads data items from PDB file. |
| RBFROR | generates the various orthogonalising matrices |
| RBRINV | invert 4*4 matrices for conversion between fractional and orthogonal axes |
| RBFRAC2 | calc transformation matrices between orthogonal and fractional coordinates |
| RBRORF | fill or return RF and Ro matrice |
| RBFRO1 | duplicate of rbfror with a different call |
| CVFRAC2 | Convert between orthogonal and fractional coordinates and vice-versa |
| CVANISOB | convert between anisotropic orthogonal Us to crystallographic bs and vice-versa |
| RBRCEL | Returns Reciprocal cell dimensions, and reciprocal unit cell volume |
| RBCELL | Returns cell dimensions, and unit cell volume |
| WBCELL | Writes CRYST1 and SCALEn cards to output file. |
| RWNOHEAD | Suppress writing of CRYST1 and SCALEn cards to output file by XYZADVANCE or WBCELL |
| RES3TO1 | Find 3 character residue name from 1 character code and vice versa |
| RBRECIP | calculates 4SIN**2THETA/L**2 |
| WREMARK | write line to output file |
| SFREAD2 | matches atomic structure factor with inputted element id. |
| RWBFIN | copies remaining unread part of file to output. |
| RBSPGRP | stores a spacegroup name in common. |
| WBSPGRP | retrieves the spacegroup name from common. |
| RBINIT | Now obsolete, initialises various COMMON blocks and rewinds file. |
| RBROOK | Now obsolete, reads ATOM/HETATM card. |
| WBROOK | Now obsolete, writes ATOM/HETATM card. |
| RBFRAC | Now obsolete, similar function to RBFRAC2 but with different number of arguments |
| CVFRAC | Now obsolete, similar function to CVFRAC2 but with different number of arguments |
| SFREAD | Now obsolete, similar function to SFREAD2 but with different number of arguments |
It may seem a bit strange that simple functions such as CLOSE and REWIND are operated through a specific subroutine. In the future the working format may change, however it is hoped that procedures set out in this part will be independent of the format.
The old subroutines have been kept to ensure backwards compatibility. The compatibility is not absolute however, for instance XYZOPEN or XYZOPEN2 should still be used to open the co-ordinate file. Also, RWBROOK and WBROOK should only be used with orthogonal co-ordinates and not fractional ones.
All co-ordinate files should be opened with XYZOPEN or in special cases XYZOPEN2. The FORTRAN channel number can be assigned automatically. If this is done then it is best that all other files have their channel numbers assigned automatically as well. CCPDPN has been altered to make this easy.
It is also good practice to close all opened files before the program terminates normally. XYZCLOSE is the subroutine that will close the co-ordinate file.
The header information from the file is read when the file is opened. This includes the cell, orthogonalisation matrices (and in the future the symmetry). These are then stored in COMMON blocks which then should be extracted by subroutine calls rather than inclusion of the COMMON blocks in the main program.
If the cell is present in the file then the matrices for converting between fractional coordinates and orthogonal coordinates in the standard setting will be calculated. If the orthogonalisation matrix is present in the file then the co-ordinates need not be in a standard setting.
XYZADVANCE has a dual purpose in that it reads/writes data from/to the file into/out of an internal buffer. If the record name is recognised then the data is stored in the buffer. Otherwise the line is ignored but could be echoed to an output file (see the second example). XYZATOM and XYZCOORD then extract the data from the buffer and pass it to the calling program.
C PROGRAM TO READ BROOKHAVEN FILE
C ===============================
C
REAL X,Y,Z,OCC,BISO,U(6),CELL(6)
INTEGER IFAIL,ISER,IRS,IXYZIN,IZ,N
CHARACTER*4 ATNAM,RESNAM,RESNO,SEGID,ID
CHARACTER*1 CHNNAM,ALTCOD,INSCOD
EXTERNAL RBCELL,XYZADVANCE,XYZATOM,XYZCLOSE,XYZCOORD,
+ XYZINIT,XYZOPEN
C
C INITIALISATION CALL
C
CALL XYZINIT
C
C OPEN FILE
C
IFAIL = 0
IXYZIN = 0
CALL XYZOPEN('XYZIN','INPUT',' ',IXYZIN,IFAIL)
C
C READ COORDINATE RECORDS
C
N = 0
10 CALL XYZADVANCE(IXYZIN,0,0,*10,*100)
CALL XYZATOM(IXYZIN,ISER,ATNAM,RESNAM,CHNNAM,IRS,
+ RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
CALL XYZCOORD(IXYZIN,'O','U',X,Y,Z,OCC,BISO,U)
C
N = N + 1
.
.
process data
.
.
GO TO 10
C
C END OF FILE REACHED
C
100 CALL XYZCLOSE(IXYZIN)
WRITE(6,FMT='(A,I5,A)') ' There are ',N,
+ ' atoms in the file'
CALL RBCELL(CELL,VOL)
WRITE(6,FMT='(A,3F9.2,3F12.3)') ' The cell is ',CELL
END
Here is a further example which reads and writes a file. A set of coordinates are read in and processed. The input file is then re-read and an output file is created with the updated coordinate data. Notice that all the header records plus any REMARK cards will be echoed to the output file because of the second call to XYZADVANCE.
C PROGRAM TO READ AND UPDATE A BROOKHAVEN COORDINATE FILE
C =======================================================
C
C SPECIFICATION STATEMENTS
C
REAL XX,YY,ZZ,OCC,BISO
INTEGER IFAIL,ISER,IRESN,IXYZIN,IXYZOUT,IZ,N,NMAX
CHARACTER*4 ATNM,RESNM
CHARACTER*4 ATNAM(1000),RESNAM(1000),RESNO,SEGID,ID
CHARACTER*1 CHNNAM,ALTCOD,INSCOD
REAL X(1000),Y(1000),Z(1000),U(6)
EXTERNAL XYZADVANCE,XYZATOM,XYZCLOSE,XYZCOORD,XYZINIT,
+ XYZOPEN,XYZREWD
C
C INITIALISE FOR READING AND OPEN FILES
C
CALL XYZINIT
IFAIL = 0
IXYZIN = 0
IXYZOUT = 0
CALL XYZOPEN('XYZIN','INPUT',' ',IXYZIN,IFAIL)
CALL XYZOPEN('XYZOUT','OUTPUT',' ',IXYZOUT,IFAIL)
C
C READ COORDINATES AND STORE THEM
C
N=0
10 N=N+1
CALL XYZADVANCE(IXYZIN,0,0,*10,*100)
CALL XYZCOORD(IXYZIN,'O','U',X(N),Y(N),Z(N),OCC,BISO,U)
CALL XYZATOM(IXYZIN,ISER,ATNM,RESNM,CHNNAM,
+ IRESN,RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
ATNAM(N) = ATNM
RESNAM(N) = RESNM
GO TO 10
C
C REFINE COORDINATES
C
100 NMAX=N-1
CALL XYZREWD(IXYZIN)
.
.
refine coordinate values
.
.
C
C WRITE UPDATED COORDINATE FILE
C
150 CALL XYZADVANCE(IXYZIN,IXYZOUT,0,*200,*200)
CALL XYZATOM(IXYZIN,ISER,ATNM,RESNM,CHNNAM,IRESN,
+ RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
CALL XYZCOORD(IXYZIN,'O','U',XX,YY,ZZ,OCC,B,U)
C
C RESET DATA ITEMS AND WRITE TO OUTPUT FILE
C
CALL XYZATOM(IXYZOUT,ISER,ATNAM(N),RESNAM(N),CHNNAM,
+ IRES,RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
CALL XYZCOORD(IXYZOUT,'O','U',X(N),Y(N),Z(N),OCC,B,U)
CALL XYZADVANCE(IXYZOUT,0,0,*200,*200)
GOTO 150
200 CALL XYZCLOSE(IXYZIN)
CALL XYZCLOSE(IXYZOUT)
END
INTEGER MAXFILESOPEN,FILESOPEN,TYPE,UNIT
CHARACTER*80 LOGUNIT
COMMON /RBRKAA/ FILESOPEN,LOGUNIT(MAXFILESOPEN),
UNIT(MAXFILESOPEN),TYPE(MAXFILESOPEN)
MAXFILESOPEN maximum number of files that can be open at any
one time, = 10.
FILESOPEN no. of current coordinate files open.
LOGUNIT logical name of file
UNIT if the file is PDB then the unit is the physical
channel opened. If CIF then is related to blocks.
TYPE indicates whether PDB (1,-1) or CIF (2,-2). If
negative then file is output file.
LOGICAL IFCRYS,IFSCAL,IFEND,MATRIX
COMMON /RBRKXX/ IFCRYS,IFSCAL,IFEND,ITYP,MATRIX
IFCRYS Flag set to .TRUE. if CRYST1 card read,
otherwise .FALSE.
IFSCAL Flag set to .TRUE. if SCALE cards read,
otherwise .FALSE.
ITYP Type of last card read.
=0, No card read.
=1, 'CRYST1'
=2, 'SCALE'
=3, 'TER'
=4, 'ATOM'
=5, 'HETATM'
=6, 'ANISOU'
MATRIX Flag set to .TRUE. if orthogonalising
and fractionalising matrices set, otherwise
.FALSE.
IFHDOUT Flag set to .TRUE. if header records written out.
otherwise .FALSE.
CHARACTER*1 BROOK,WBROOK,WBROOK1
COMMON /RBRKYY/ BROOK(80),WBROOK(80),WBROOK1(80)
BROOK Internal buffer for holding data from input
file.
WBROOK Internal buffer for holding data for output
file.
WBROOK1 Additional buffer for holding data for the
output file (specifically for ANISOU card).
REAL CELL,RR,VOL,CELLAS
COMMON /RBRKZZ/ CELL(6),RR(3,3,5),VOL,CELLAS(6)
CELL Array holding cell dimensions read from
CRYST1 card if read (check IFCRYS)
RR Array holding some common orthogonalisation
matrices calculated if CRYST1 cards was read.
(See description of NCODE in common ORTHOG)
VOL Unit cell volume
CELLAS Reciprocal cell
INTEGER NCODE,IBRKFL
REAL RF,RO
COMMON /ORTHOG/ RO(4,4),RF(4,4),NCODE,IBRKFL
RO Orthogonalising matrix (only set if CRYST1 or
SCALE cards read (check the flag MATRIX)
RF Fractionalising matrix (only set if CRYST1 or
SCALE cards read (check the flag MATRIX)
NCODE Flag indicating setting found, =0 if not
recognised.
=1, a // XO, c* // ZO (Standard Brookhaven)
=2, b // XO, a* // ZO
=3, c // XO, b* // ZO
=4, Hexagonal a + b // XO, c* // ZO
=5, a* // XO, c // ZO (Rollett)
REAL AC
COMMON /RBREC/ AC(6)
AC Useful values for calculating d*.
CHARACTER*11 BRKSPGRP
COMMON /RBRKSPGRP/BRKSPGRP
BRKSPGRP Holds spacegroup name supplied from the s/r
RBSPGRP.
SUBROUTINE XYZINIT()
C =========================
C
C_BEGIN_XYZINIT
C
C This subroutine initialises the common block RBRKAA ready for reading
C and writing coordinate files. Also, the common blocks associated with
C storing the header information are initialised. It should be called only
C once from the top of the program.
C
C Parameters:
C
C NONE
C
C COMMONS:
C
C /RBRKAA/ FILESOPEN,LOGUNIT(MAXFILESOPEN),UNIT(MAXFILESOPEN),
C TYPE(MAXFILESOPEN)
C
C FILESOPEN no. of current coordinate files open.
C LOGUNIT logical name of file
C UNIT if the file is PDB then the unit is the physical
C channel opened. If CIF then is related to blocks.
C TYPE indicates whether PDB (1,-1) or CIF (2,-2). If
C negative then file is output file.
C
C_END_XYZINIT
C
SUBROUTINE XYZOPEN(LOGNAM,RWSTAT,FILTYP,IUNIT,IFAIL)
C ==========================================================
C
C_BEGIN_XYZOPEN
C
C
C Calls XYZOPEN2 which has an extra parameter for ignoring
C Symmetry and Cryst cards
C
C Parameters:
C
C LOGNAM (I) CHARACTER*(*) but maximum of eight? The logical unit
C to which the file is assigned
C RWSTAT (I) CHARACTER*(*) if 'INPUT' then file is read only
C if 'OUTPUT' then file is an output file.
C FILTYP (I) CHARACTER*(*) if 'CIF' then the file type is treated as
C CIF. If 'PDB' then the file type is
C treated as PDB. If blank then file type is
C automatically determined for input files
C and for output file the file type will be
C the same as the first file opened or
C defaulted to PDB.
C IUNIT (I/O) INTEGER If zero then unit is decided else
C file opened on that unit
C checked against previous data if
C applicable. NOT used with output files.
C IFAIL (I/O) INTEGER On input = 0 stop on failure
C = 1 continue on failure
C
C On output unchanged if OK
C = -1 if error
C
C
C_END_XYZOPEN
C
SUBROUTINE XYZOPEN2(LOGNAM,RWSTAT,FILTYP,IUNIT,IFAIL,ICRYST)
C =====================================================
C
C_BEGIN_XYZOPEN2
C
C Opens a coordinate file for input or output. The channel number can
C be determined automatically or set on input. The header info.
C is also read: cell, orthog. matrix and symmetry.
C This is a version of XYZOPEN with an extra argument to flag whether or
C not the CRYST and SCALE cards are required.
C
C Parameters:
C
C LOGNAM (I) CHARACTER*(*) but maximum of eight? The logical unit
C to which the file is assigned
C RWSTAT (I) CHARACTER*(*) if 'INPUT' then file is read only
C if 'OUTPUT' then file is an output file.
C FILTYP (I) CHARACTER*(*) if 'CIF' then the file type is treated as
C CIF. If 'PDB' then the file type is
C treated as PDB. If blank then file type is
C automatically determined for input files
C and for output file the file type will be
C the same as the first file opened or
C defaulted to PDB.
C IUNIT (I/O) INTEGER If zero then unit is decided else
C file opened on that unit
C checked against previous data if
C applicable. NOT used with output files.
C IFAIL (I/O) INTEGER On input = 0 stop on failure
C = 1 continue on failure
C
C On output unchanged if OK
C = -1 if error
C
C ICRYST (I/O) INTEGER If zero, then check for and use CRYST
C and SCALE cards in input PDB.
C If one, ignore these cards even if
C present.
C
C
C_END_XYZOPEN2
SUBROUTINE XYZCLOSE(IUNIT)
C ================================
C
C_BEGIN_XYZCLOSE
C
C This subroutine closes a coordinate file.
C
C Parameters:
C
C IUNIT (I) INTEGER Unit number for file
C
C_END_XYZCLOSE
C
SUBROUTINE XYZADVANCE(IUNIT,IOUT,ITER,*,*)
C ==================================================
C
C_BEGIN_XYZADVANCE
C
C This subroutine reads recognised data lines into a buffer. Optionally,
C if the card is unrecognised (eg REMARK) then the line can be echoed to an
C output file.
C
C Parameters:
C
C IUNIT (I) Channel number of the input coordinate file
C
C These arguments are not relevant for output files.
C IOUT (I) Logical unit number to which non-atom/hetatm/anisou records
C are to be written (may be blank if reading only)
C ITER (I) FLAG =1, return if 'ter' card found (via return 1)
C =0, do not return when 'ter' card found
C RETURN 1 Return on TER card if ITER=1
C RETURN 2 Return on end of file.
C
C_END_XYZADVANCE
C
SUBROUTINE XYZATOM(IUNIT,ISER,ATNAM,RESNAM,CHNNAM,IRESN,
*RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
C ==============================================================
C
C_BEGIN_XYZATOM
C
C This subroutine reads or writes the atom name, residue name,
C chain name etc. into the buffer. XYZADVANCE actually advances a line
C or atom. The character strings have undefined length in order to make
C change easier. However, these data items will be strictly defined in
C the working format.
C
C Parameters:
C
C IUNIT (I) Logical unit of the input coordinate file
C ISER (I/O) Atom serial number
C ATNAM (I/O) Atom name (left justified)
C RESNAM (I/O) Residue name
C CHNNAM (I/O) Chain name
C IRESN (I/O) Residue number as an integer
C RESNO (O) Residue number as character, NOT used for output file
C INSCOD (I/O) The insertion code
C ALTCOD (I/O) The alternate conformation code.
C SEGID (I/O) Segid is here to complete PDB standard.
C IZ (O) Atomic number (returned as 7 from ambiguous atoms),
C NOT used for output file
C ID (I/O) Atomic ID related to atomic number (element symbol
C right justified), plus the ionic state +2, +3 etc..
C
C_END_XYZATOM
C
SUBROUTINE XYZCOORD(IUNIT,XFLAG,BFLAG,X,Y,Z,OCC,BISO,B)
C =============================================================
C
C_BEGIN_XYZCOORD
C
C This subroutine reads or writes x, y, z, occupancy and b from/to
C the internal buffer. The buffer is updated from the file by
C XYZADVANCE. The coordinates can be input/output (to the subroutine)
C as orthogonal or fractional. The anisotropic temperature factors can be
C input/output as orthogonal Us or as crystallographic bs. These are
C defined below;
C T(aniso) = U(11)*H**2 + U(22)*K**2 + 2*U(12)*H*K + ...
C where H,K,L are orthogonal reciprocal lattice indices.
C T(aniso) = b(11)*h**2 + b(22)*k**2 + b(33)*k**2 + b(12)*h*k ... and
C Biso = 8*PI**2 (U(11) + U(22) + U(33)) / 3.0
C
C Parameters:
C
C IUNIT (I) Channel number of the input coordinate file
C XFLAG (I) For input file
C ='F' will get fractional coords.
C ='O' will get orthogonal coords.
C For output file
C ='F' passed coordinates are fractional
C ='O' passed coordinates are orthogonal
C BFLAG (I) For input file
C ='B' will get crystallographic bs
C ='U' will get orthogonal Us.
C For output file
C ='B' have crystallographic bs
C ='U' have othogonal Us
C X (I/O) Coordinates (orthogonal angstrom coordinates as
C Y (I/O) " stored)
C Z (I/O) "
C OCC (I/O) Occupancy
C BISO (O) Isotropic temperature factor, NOT used for output file.
C B(6) (I/O) Anisotropic temperature factor, unless only B(1) defined.
C
C_END_XYZCOORD
C
SUBROUTINE XYZREWD(IUNIT)
C ===============================
C
C_BEGIN_XYZREWD
C
C This routine resets pointer to the beginning of the file ie.
C rewind the file.
C
C Parameters:
C
C IUNIT (I) INTEGER Channel number for file.
C
C_END_XYZREWD
C
SUBROUTINE XYZBKSP(IUNIT)
C ===============================
C
C_BEGIN_XYZBKSP
C
C This routine is the opposite to XYZADVANCE in that it retreats
C one atom ie. backspacing.
C
C Parameters:
C
C IUNIT (I) INTEGER Channel number for file.
C
C_END_XYZBKSP
C
SUBROUTINE PDBREAD(ISER,ATNAM,RESNAM,CHNNAM,IRESN,RESNO,
*X,Y,Z,OCC,B,IZ,SEGID,ID)
C ========================================================
C
C_BEGIN_PDBREAD
C
C The subroutine PDBREAD is used to read coordinates from a Brookhaven
C format coordinate file. This routine should not be used stand alone
C but through XYZADVANCE.
C
C Parameters
C
C ISER (O) Atom serial number
C ATNAM (O) Atom name (character*4 left justified)
C RESNAM (O) Residue name (character*4)
C CHNNAM (O) Chain name (character*1)
C IRESN (O) Residue number as an integer
C RESNO (O) Residue number (character*4 or character*5)
C If character*5 then the 5th character will be the
C insertion code.
C X (O) Coordinates (orthogonal angstrom coordinates as
C Y (O) " stored)
C Z (O) "
C OCC (O) Occupancy
C B(6) (O) Temperature factor
C IZ (O) Atomic number (returned as 7 from ambiguous atoms)
C ID (O) Atomic ID related to atomic number + ionic state.
C (character*4)
C
C COMMON BLOCKS
C
C COMMON /RBRKXX/IFCRYS,IFSCAL,ITYP,MATRIX
C
C IFCRYS .TRUE. IF 'CRYST1' CARD READ, OTHERWISE .FALSE.
C IFSCAL .TRUE. IF 'SCALE' CARDS READ, OTHERWISE .FALSE.
C ITYP TYPE OF LAST CARD READ =1, 'CRYST1'
C =2, 'SCALE'
C =3, 'TER'
C =4, 'ATOM'
C =5, 'HETATM'
C MATRIX .TRUE. IF FRACT/ORTHOG MATRICES CALCULATED
C .FALSE. IF NOT
C
C COMMON /RBRKYY/BROOK(80)
C
C BROOK CHARACTER*1 ARRAY WHICH IS THE BUFFER FOR PDB FILES
C
C COMMON/RBRKZZ/CELL(6),RR(3,3,6),VOL,CELLAS(6)
C
C CELL CELL DIMENSIONS FROM 'CRYST1' CARD IF READ
C (CHECK IFCRYS)
C RR STANDARD ORTHOGONALISING MATRICES CALCULATED IF THE
C 'CRYST1' CARD WAS READ (CHECK IFCRYS)
C
C COMMON /ORTHOG/RO(4,4),RF(4,4),NCODE
C
C RO ORTHOGONALISING MATRIX (ONLY SET IF 'CRYST1' OR 'SCALE'
C CARDS PRESENT - CHECK 'MATRIX' FLAG)
C RF FRACTIONALISING MATRIX (ONLY SET IF 'CRYST1' OR 'SCALE'
C CARDS PRESENT - CHECK 'MATRIX' FLAG)
C NCODE FLAG INDICATING SETTING FOUND, 0 IF NOT ONE THAT WAS
C RECOGNISED
C
C_END_PDBREAD
C
SUBROUTINE RBFRAC2(A,B,C,AL,BE,GA,ARGNCODE)
C ================================================
C
C_BEGIN_RBFRAC2
C
C
C This subroutine is used to calculate the default transformation
C matrices between orthogonal angstrom and fractional coordinates
C
C
C PARAMETERS
C
C A,B,C,AL,BE,GA (I) (REAL) CELL PARAMETERS IN ANGSTROMS AND DEGREES
C ARGNCODE (I) (INTEGER) ORTHOGONALISATION CODE 1-6
C
C_END_RBFRAC2
C
SUBROUTINE RBRORF(ROO,RFF)
C =======================
C
C_BEGIN_RBRORF
C
C SUBROUTINE RBRORF(ROO,RFF)
C
C Subroutine to fill or return RF (fractionalising) and Ro
C (orthogonalising) matrices.
C
C PARAMETERS
C
C ROO (I) (REAL(4,4)) 4*4 MATRIX TO BE INVERTED
C RFF (O) (REAL(4,4)) INVERSE MATRIX
C
C common blocks
C
C COMMON /RBRKXX/IFCRYS,IFSCAL,ITYP,MATRIX
C COMMON /ORTHOG/RO(4,4),RF(4,4),NCODE
C
C_END_RBRORF
SUBROUTINE RBRINV(A,AI)
C =======================
C
C_BEGIN_RBRINV
C
C SUBROUTINE RBRINV(A,AI)
C
C
C Subroutine to invert 4*4 matrices for conversion between
C fractional and orthogonal axes.
C
C
C PARAMETERS
C
C A (I) (REAL(4,4)) 4*4 MATRIX TO BE INVERTED
C AI (O) (REAL(4,4)) INVERSE MATRIX
C
C_END_RBRINV
C
SUBROUTINE RBFROR
C =================
C
C_BEGIN_RBFROR
C
C SUBROUTINE RBFROR
C
C THIS SUBROUTINE CALCULATES MATRICES FOR STANDARD ORTHOGONALISATIONS
c and cell volume
C
C this generates the various orthogonalising matrices
C ' NCODE =1 - ORTHOG AXES ARE DEFINED TO HAVE'
C A PARALLEL TO XO CSTAR PARALLEL TO ZO'
C ' NCODE =2 - ORTHOG AXES ARE DEFINED TO HAVE'
C ' B PARALLEL TO XO ASTAR PARALLEL TO ZO'
C ' NCODE =3 - ORTHOG AXES ARE DEFINED TO HAVE'
C ' C PARALLEL TO XO BSTAR PARALLEL TO ZO'
C ' NCODE =4 - ORTHOG AXES ARE DEFINED TO HAVE'
C ' HEX A+B PARALLEL TO XO CSTAR PARALLEL TO ZO'
C ' NCODE =5 - ORTHOG AXES ARE DEFINED TO HAVE'
C ' ASTAR PARALLEL TO XO C PARALLEL TO ZO'
C ' NCODE =6 - ORTHOG AXES ARE DEFINED TO HAVE'
C A PARALLEL TO XO BSTAR PARALLEL TO YO'
C
C SET UP MATRICES TO ORTHOGONALISE H K L AND X Y Z FOR THIS CELL.
C
C Common Blocks
C
C COMMON/RBRKZZ/CELL(6),RR(3,3,6),VOL,CELLAS(6)
C COMMON /RBREC/AC(6)
C
C_END_RBFROR
C
SUBROUTINE RBFRO1(CEL,VOLL,RRR)
C ===============================
C
C_BEGIN_RBFRO1
C
C SUBROUTINE RBFRO1(CEL,VOLL,RRR)
C
C---- This subroutine is a duplicate of rbfror with a different call.
C
C PARAMETERS
C
C CEL (I) (REAL(6)) Cell dimensions
C VOLL (O) (REAL) Cell volume
C RRR (O) (REAL(3,3,6)) Standard orthogonisational matrices
C
C_END_RBFRO1
C
SUBROUTINE CVFRAC2(X,Y,Z,XX,YY,ZZ,IFLAG)
C =============================================
C
C_BEGIN_CVFRAC2
C
C This subroutine is used to convert between the stored orthogonal and
C fractional coordinates using the matrices set up in the common block
C /ORTHOG/ by the subroutine XYZOPEN. If no matrices have been set up then the
C program will stop with an error message.
C
C Call: CALL CVFRAC2(X,Y,Z,XX,YY,ZZ,IFLAG)
C
C Arguments:
C
C X (I) (REAL) Input coordinates.
C Y (I) (REAL) "
C Z (I) (REAL) "
C XX (O) (REAL) Output coordinates.
C YY (O) (REAL) "
C ZZ (O) (REAL) "
C IFLAG (I) (INTEGER) Flag =0, Convert coordinates from fractional to orthogonal
C =1, Convert coordinates from orthogonal to fractional
C
C_END_CVFRAC2
C
SUBROUTINE CVANISOB(B,IFLAG)
C =================================
C
C_BEGIN_CVANISOB
C
C This subroutine is used to convert between crystallographic bs and
C orthogonal Us. The orthogonal matrices are required, if no matrices have
C been set up then the program will stop with an error message. The
C temperature factors are defined below;
C T(anisoU) = U(1,1)*H**2 + U(2,2)*K**2 + U(1,2)*H*K + ...
C where H,K,L represent the orthogonal representation of the Miller indices
C T(anisob) = b(1,1)*h**2 + b(2,2)*k**2 + b(1,2)*h*k + ...
C thus U = A * B * AT / (2 * pi**2) where A is the orthogonalisation matrix
C
C Arguments:
C
C B(6) (I/O (REAL) Input coordinates.
C IFLAG (I) (INTEGER) Flag =0, Convert coordinates from fract. to orthog.
C =1, Convert coordinates from orthog. to fract.
C
C_END_CVFRAC
C
SUBROUTINE RBCELL(CELLD,CVOL)
C ============================
C
C_BEGIN_RBCELL
C
C SUBROUTINE RBCELL(CELLD,CVOL)
C
C Returns cell dimensions and unit cell volume.
C
C PARAMETERS
C CELLD (O) (REAL(6)) cell dimensions
C CVOL (O) (REAL) cell volume
C
C Common blocks
C
C COMMON/RBRKZZ/CELL(6),RR(3,3,6),VOL,CELLAS(6)
C
C_END_RBCELL
C
SUBROUTINE RBRCEL(RCEL,RVOL)
C ============================
C
C_BEGIN_RBRCEL
C
C SUBROUTINE RBRCEL(RCEL,RVOL)
C
C THIS SUBROUTINE RETURNS Reciprocal cell dimensions, and reciprocal
C unit cell volume.
C
C PARAMETERS
C RCEL (O) (REAL(6)) reciprocal cell dimensions
C RVOL (O) (REAL) reciprocal cell volume
C
C Common blocks
C
C COMMON/RBRKZZ/CELL(6),RR(3,3,6),VOL,CELLAS(6)
C
C_END_RBRCEL
C
SUBROUTINE RES3TO1(RESNM3,RESNM1)
C ================================
C
C_BEGIN_RES3TO1
C
C SUBROUTINE RES3TO1(RESNM3,RESNM1)
C
C FIND 3 CHARACTER RESIDUE NAME FROM 1 CHARACTER CODE OR
C FIND 1 CHARACTER RESIDUE NAME FROM 3 CHARACTER CODE.
C SUBROUTINE IS CALLED WITH EITHER RESNM3 OR RESNM1 PREVIOUSLY
C ASSIGNED, AND THE OTHER IS ASSIGNED HERE.
C
C Parameters
C
C RESNM3 (I/O) CHAR*4 3 character residue name
C RESNM1 (I/O) CHAR*1 1 character residue name
C
C_END_RES3TO1
C
SUBROUTINE RBRECIP(IH,IK,IL,S)
C ==============================
C
C_BEGIN_BRECIP
C
C SUBROUTINE RBRECIP(IH,IK,IL,S)
C
C---- This subroutine calculates 4SIN**2/L**2
C
C PARAMETERS
C IH,IK,IL (I) (INTEGER) reflection indices
C S (O) (REAL) 4SIN**2/L**2
C
C_END_BRECIP
C
SUBROUTINE SFREAD2(ID,NG,A,B,C,IWT,IELEC,CU,MO,Ifail)
C ==========================================================
C
C Inputs: ID atom identifier
C This should match an atom type in the atomsf.lib
C If an atom is identified as NE2+ say, characters are
C subtracted from the ID till a match is found, or there are
C no characters left.
C EG: Routine tests first NE2+, then NE2, then NE, then N.
C All matching checks UPPER CASE strings.
C
C NG num. of gaussian approximations (2 or 5 (default))
C IFILFF .TRUE. if want to open the library file assigned
C to ATOMSF (default `atomsf.lib')
C
C Output: A(4) coefficient for structure factor calculation
C B(4) coefficient for structure factor calculation
C C coefficient for structure factor calculation
C IWT atomic weight
C IELEC number of electrons
C CU(2) delta F' and delta F'' for Cu
C MO(2) delta F' and delta F'' for Mo
C Ifail = -1 if atom not found at all
C = 0 OK
C = 1 for two gaussian case that does not exist
C
SUBROUTINE WBCELL(IUNIT,ARGCELL,ARGNCODE)
C ===============================================
C
C_BEGIN_WBCELL
C
C This subroutine writes out the cell and orthogonalisation matrices, to
C the output file. If the input parameters are null then the cell etc. are
C taken from the COMMON blocks.
C
C PARAMETERS
C IUNIT (I) (INTEGER) Channel number for output file.
CC ARGCELL(6) (I) (REAL) crystallographic cell taken from COMMON
C if cell = 0
C ARGNCODE (I) (INTEGER) NCODE number taken from COMMON if NCODE=0
C
C_END_WBCELL
C
SUBROUTINE WREMARK(IUNIT,LINE)
C ====================================
C
C_BEGIN_WREMARK
C
C This subroutine writes a line to the output file. Its main use is for
C REMARK statements in PDB.
C
C Parameters:
C
C IUNIT (I) (CHARACTER*(*)) Channel number
C LINE (I) (CHARACTER*(*)) line to be written, best
C if declared as *80
C
C_END_WREMARK
C
SUBROUTINE RWBFIN(IUN,IOUT)
C ===========================
C
C_BEGIN_RWBFIN
C
C This subroutine copies remaining lines straight from input to
C output.
C
C_END_RWBFIN
C
SUBROUTINE RBSPGRP(SPGRP)
C ============================
C
C_BEGIN_RBSPGRP
C
C SUBROUTINE SUBROUTINE RBSPGRP(SPGRP)
C
C Returns spacegroup from pdb
C
C PARAMETERS
C SPGRP (O) (CHARACTER*11)
C
C Common blocks
C
C COMMON /RBRKSPGRP/BRKSPGRP
C
C_END_RBSPGRP
C
SUBROUTINE WBSPGRP(SPGRP)
C =============================
C
C_BEGIN_WBSPGRP
C
C SUBROUTINE WBSPGRP(SPGRP)
C
C Sets the internal spacegroup of a pdb file
C
C PARAMETERS
C SPGRP (I) (CHARACTER*11)
C
C Common Blocks
C
C COMMON /RBRKSPGRP/BRKSPGRP
C
C_END_WBSPGRP
C
These routines are now obsolete but are here to maintain backwards
compatibility with the version of RWBROOK that was in version 3.2 of CCP4.
SUBROUTINE RBINIT(IUNIT)
C ========================
C
C_BEGIN_RBINIT
C
C This routine is obsolete and should be removed. Initialises various
C COMMON block variables and rewinds the file.
C
C_END_RBINIT
C
SUBROUTINE RBROOK(IUNIT,ISER,ATNAM,RESNAM,CHNNAM,IRESN,RESNO,IS,
*X,Y,Z,OCC,B,IZ,IOUT,MSG1,MSG2,ITER,*,*)
C ================================================================
C
C_BEGIN_RBROOK
C
C This subroutine is obsolete and should be removed. May be
C PROBLEM in that routine returns orthogonal coordinates and not fractional
C ones. It presents a combination of XYZADVANCE, XYZATOM and XYZCOORD. The
C arguments IS, MSG1 and MSG2 are redundant
C
C_END_RBROOK
C
SUBROUTINE WBROOK(IUNIT,ISER,ATNAM,RESNAM,CHNNAM,IRESN,IS,
*X,Y,Z,OCC,B,IZ)
C ================================================================
C
C_BEGIN_RBROOK
C
C This subroutine is obsolete and should be removed. May be
C PROBLEM in that routine does not cater for IS.
C
C_END_RBROOK
C
SUBROUTINE RBFRAC(A,B,C,AL,BE,GA,MSG)
C =====================================
C
C_BEGIN_RBFRAC
C
C This routine is obsolete and should be removed. The argument
C MSG is redundant.
C
C_END_RBFRAC
C
SUBROUTINE CVFRAC(X,Y,Z,XX,YY,ZZ,IFLAG,MSG)
C ===========================================
C
C_BEGIN_CVFRAC
C
C Another silly obsolete routine that really should be deleted.
C MSG value is in fact useless. Library output controlled by CCPERR.
C
C_END_CVFRAC
C
SUBROUTINE SFREAD(ID,NG,A,B,C,IWT,IELEC,CU,MO,IFAIL,IFILFF)
C ===========================================================
C
C_BEGIN_SFREAD
C
C Obsolete routine should be deleted. IFILFF not used.
C
C_END_SFREAD
C
SUBROUTINE RWNOHEAD()
C =====================
C
C_BEGIN_RWNOHEAD
C
C This subroutine resets the logical variable IFHDOUT in the RWBROOK
C common block RBRKXX, and should be called once before either
C XYZADVANCE or WBCELL in order to prevent those routines from writing
C headers to an output pdb file.
C Effectively we are fooling the library that the header has already
C been written.
C
C_END_RWNOHEAD
C