#!/bin/sh #!/usr/bin/ksh # file: dirdif < ddexec.unix [GBK Feb.97] Updt 14 July 1999 # ------ < ----------- # /bin/sh :Bourne shell for HP, IBM Risc, Silicon Gr., and Sun machines # /usr/bin/ksh : Korn shell for DEC machines # # |--------------------------------------------------------------------| # |--------------------------------------------------------------------| # | DIRDIF-99 | # | | # | Crystal Structure Determination by Patterson Methods and | # | Direct Methods applied to Difference Structure Factors | # | | # | Paul T. Beurskens, Gezina Beurskens, Rene de Gelder, | # | S. Garcia-Granda, R.O. Gould, Randy Israel, and Jan M.M. Smits | # | | # | Crystallography Laboratory, University of Nijmegen, | # | Toernooiveld 1, 6525 ED Nijmegen, The Netherlands | # | | # |--------------------------------------------------------------------| # |--------------------------------------------------------------------| # | | # | Script for EXECUTING the program system DIRDIF-99 | # | | # | Specifications of this script: Bourne shell or Korn shell | # | Tested and used on computers: | # | DEC Alpha (with Bourne and Korn shell) | # | DEC 5000 under ultrix (Korn shell, problems with Bourne shell) | # | IBM Risc 6000/320 (aix, Bourne shell) | # | Silicon Graphics Indigo and Irix (Bourne shell) | # | SUN under unix (Bourne shell) | # | We thank H.J. Bruins Slot, A.L. Spek, J.P. Declerq, | # | G. Baudoux and R. Driessen for their kind help in | # | setting up DIRDIF under Unix, Ultrix, AIX, in 1992. | # | HP computers (unix, Bourne shell) | # | Thanks are due to A. Meetsma and R.A. de Graaff | # | | # |--------------------------------------------------------------------| # | | # | In case of problems please contact one of the following persons: | # | Paul T. Beurskens, E-mail: ptb@sci.kun.nl | # | Jan M.M. Smits, E-mail: smits@sci.kun.nl | # | Rene de Gelder, E-mail: rdg@sci.kun.nl | # |--------------------------------------------------------------------| # # NOTE: The execution of dirdif has to be from the directory with the # structural data ! And no parallel runs from the same directory ! # # EDITING INSTRUCTIONS for this script file : # # First: check the definition of the shell to be used for this script: # ====> for some DEC machines it may be necessary to remove the first # line of this script, to change from Bourne to Korn shell. # # Next: define DDROOTPATH and ORUSERPATH as described here. # The dirdif-system files are stored in the directory xxxx/ddroot # and the path to this directory must be defined like: # DDROOTPATH=/root/users/local/ddroot # # or for instance in the situation in Leiden: # DDROOTPATH=/users/rag/dirdifhp/ddroot # # or as in the actual situation in Nijmegen: DDROOTPATH=/nsr/ptb/ddroot # # ===> IMPLEMENTATION: adapt DDROOTPATH=.... for your situation ! # # In addition we must define the path to the file oruser! # Oruser also is a dirdif-system file and has been stored # in the directory ..../ddroot # So, in general, ORUSERPATH=$DDROOTPATH would be correct. # # However, the file oruser should be used as a 'private' supplement # (with 'private' models appended by the individual user) to the file # orbase (wich contains molecular models for program ORIENT); # to enable the individual user access to his 'private' file oruser # during execution of dirdif, the path to oruser is defined as # the path to the user's home directory, for instance as follows: # # NAME=`whoami` # ORUSERPATH=/root/users/$NAME # # or more direct, as in Leiden: # ORUSERPATH=/users/rag # # and the actual situation in Nijmegen is: NAME=`whoami` ORUSERPATH=/nsr/$NAME # # The individual user is urged to add new structural models to oruser! # # In any dirdif run the presence of a 'private' oruser # (in the directory given by ORUSERPATH) is checked; # if not present, $DDROOTPATH/oruser is copied to $ORUSERPATH/oruser. # Then -when asked for by ORIENT- dirdif will search for a model # in oruser and in orbase in this order. # # ===> IMPLEMENTATION: adapt ORUSERPATH=.... for your situation !! # ===> then: exit , and proceed with the implementation instructions. # # Store and check user environment if [ `pwd` = $DDROOTPATH -o `pwd` = $ORUSERPATH ]; then echo "ATTENTION !!! Your working directory is `pwd`, however," echo "dirdif has to be called from a structure data directory." echo "Please, change your working directory to the appropriate" echo "structure data directory and call dirdif again." exit 1 fi echo "Execute DIRDIF-99.2 from pwd: `pwd` " # Initialize keys ? abort not yet, loop later? INDEX=$# # number of parameters given in the call # test first parameter (CCODE) and write file DDJOB if [ $INDEX -lt 1 ]; then CCODE=END else CCODE=$1 fi # to enforce the use of lower case in CCODE, capitals are converted: echo $CCODE > ddtemp1 tr [A-Z] [a-z] < ddtemp1 > ddtemp2 read CCODE < ddtemp2 rm ddtemp1 ddtemp2 # write DDJOB file if [ -f ddjob ]; then rm ddjob; fi echo $CCODE $2 $3 $4 > ddjob # Link files and check oruser ln -s $DDROOTPATH/ddhelp ddhelp ln -s $DDROOTPATH/orbase orbase # temp: if [ -f $DDROOTPATH/ddconfig ]; then ln -s $DDROOTPATH/ddconfig ddconfig; fi if [ -f $DDROOTPATH/ddcon ]; then ln -s $DDROOTPATH/ddcon ddcon; fi if [ -f $DDROOTPATH/ddlic ]; then ln -s $DDROOTPATH/ddlic ddlic; fi # # file oruser should also be available for personal use: if [ -f $ORUSERPATH/oruser ]; then ORU=0 # private oruser was present echo 'private oruser is present' else echo 'private oruser is initially not present' cp $DDROOTPATH/oruser $ORUSERPATH/oruser ORU=1 # private oruser made: print later fi ln -s $ORUSERPATH/oruser oruser # clean up and backup old output listing files if [ -f ddsyst ]; then rm ddsyst; fi if [ -f $CCODE.lis1 ]; then mv $CCODE.lis1 $CCODE.lis1.old echo "$CCODE.lis1 moved to $CCODE.lis1.old" fi if [ -f $CCODE.lis2 ]; then mv $CCODE.lis2 $CCODE.lis2.old echo "$CCODE.lis2 moved to $CCODE.lis2.old" fi # Start DIRDIF if everything is OK mind the capital names ! EXPROG=DDSTART loop=0 # Working loop while [ $loop -eq 0 ] do ln -s $DDROOTPATH/$EXPROG $EXPROG.EXE $EXPROG.EXE 2>dirdif.log retcod=$? if [ $retcod -ne 0 ]; then echo " Return code = $retcod : stop execution." echo " ERROR returning from $EXPROG" echo " Contents of dirdif.log:" more dirdif.log echo " " loop=1 fi if [ -f dirdif.log ]; then rm dirdif.log; fi # next program ? rm $EXPROG.EXE read EXPROG < ddsyst if [ $EXPROG = STOP ]; then loop=1; fi done # Remove linked and remove unnecessary files if [ -f ddhelp ]; then rm ddhelp; fi if [ -f orbase ]; then rm orbase; fi if [ -f oruser -a `pwd` != $ORUSERPATH ]; then rm oruser; fi if [ -f ddconfig ]; then rm ddconfig; fi if [ -f ddcon ]; then rm ddcon; fi if [ -f ddlic ]; then rm ddlic; fi if [ -f ddsyst ]; then rm ddsyst; fi if [ -f ddjob ]; then rm ddjob; fi # Finished echo "dirdif finished at " `date`. if [ $ORU -eq 1 ]; then echo " oruser has been copied to directory $ORUSERPATH , " echo " keep this file as your 'private' oruser and extend it with" echo " your own models (mol. fragments, e.g. ccode.atmod files)." echo " Next run dirdif will -when asked for by ORIENT- search" echo " oruser and orbase in this order for the requested model. " echo " " fi echo "Bye bye from dirdif --- DIRDIF-99.2 ---" echo "Current directory: `pwd` " # End of dirdif script -------------------------------------------