Update pdbPCA, -oU -oM -oPDB

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/pdbPCA b/hostdepend/X86LINUX64/bin/X86LINUX64/pdbPCA
index b6644ab..374d966 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/pdbPCA and b/hostdepend/X86LINUX64/bin/X86LINUX64/pdbPCA differ

diff --git a/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbPCA/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbPCA/src/X86LINUX64/.Depend
index 1ec9323..1141b26 100644 (file)
--- a/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbPCA/src/X86LINUX64/.Depend
+++ b/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbPCA/src/X86LINUX64/.Depend
@@ -1,14 +1,15 @@
 argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -18,26 +19,27 @@ argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h ../inc/config.h ../inc/../inc/pdbPCA.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
 init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -47,26 +49,27 @@ init.o: init.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h ../inc/config.h ../inc/../inc/pdbPCA.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/float.h \
  /home/people/tacyas/Eos/include/String.h \
  /home/people/tacyas/Eos/include/File.h \
  /home/people/tacyas/Eos/include/Memory.h
 pdbPCA.o: pdbPCA.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -76,30 +79,32 @@ pdbPCA.o: pdbPCA.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h ../inc/config.h ../inc/../inc/pdbPCA.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/float.h \
  /home/people/tacyas/Eos/include/Array.h \
- /home/people/tacyas/Eos/include/pdbFile.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/pdbFile.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/mrcImage.h \
  /home/people/tacyas/Eos/include/genUtil.h \
  /home/people/tacyas/Eos/include/ctfInfo.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
@@ -107,14 +112,15 @@ usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
 util.o: util.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \

diff --git a/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbPCA/src/X86LINUX64/pdbPCA b/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbPCA/src/X86LINUX64/pdbPCA
index b6644ab..374d966 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbPCA/src/X86LINUX64/pdbPCA and b/hostdepend/X86LINUX64/src/Tools/pdbUtil/pdbPCA/src/X86LINUX64/pdbPCA differ

diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index 047848b..168e065 100755 (executable)
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -14,3 +14,5 @@ WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools

diff --git a/src/Tools/pdbUtil/Makefile b/src/Tools/pdbUtil/Makefile
deleted file mode 100755 (executable)
index dfd525eab555f9091108b34834053d364b8bf0ad..0000000000000000000000000000000000000000
--- a/src/Tools/pdbUtil/Makefile
+++ /dev/null
@@ -1,107 +0,0 @@
-include ../../Config/Define.inc
-include ../Config/Define.inc
-include Config/Define.inc
-include .Source
-
-all:
-       for dir in ${SOURCE} ; \
-       do \
-               if [ -d $${dir} ] ; then \
-                       $(CD) $${dir}; make all; $(CD) ..; \
-               fi \
-       done
-
-install:
-       for dir in ${SOURCE} ; \
-       do \
-               if [ -d $${dir} ] ; then \
-                       $(CD) $${dir}; make install; $(CD) ..; \
-               fi \
-       done
-
-put:
-       for dir in ${SOURCE} ; \
-       do \
-               if [ -d $${dir} ] ; then \
-                       $(CD) $${dir}; make put; $(CD) ..; \
-               fi \
-       done
-
-putSF:
-       if [ -f private ] ; then \
-               echo "$(WORLDNAME)/$(CLASSNAME) is private " ; \
-       else \
-               for dir in ${SOURCE} ; \
-               do \
-                       if [ -d $${dir} ] ; then \
-                               $(CD) $${dir}; make putSF; $(CD) ..; \
-                       fi \
-               done \
-       fi
-
-clean:
-       for dir in ${SOURCE} ; \
-       do \
-               $(CD) $${dir}; make clean; $(CD) ..; \
-       done
-
-check:
-       @for dir in ${SOURCE} ; do \
-               if [ -d $${dir} ] ; then \
-                       $(CD) $${dir}; \
-                       echo  $${dir}; \
-                       $(RM) Makefile; \
-                       $(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/Makefile Makefile ; \
-                       make check; \
-                       $(CD) ..; \
-               fi \
-       done
-
-depend: check
-       @for dir in ${SOURCE} ; \
-       do \
-               $(CD) $${dir}; make depend; $(CD) ..; \
-       done
-
-backup: 
-       cd ../../..; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
-       tar uvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
-       @for dir in ${SOURCE} ; \
-       do \
-               $(CD) $${dir}; make backup; $(CD) ..; \
-       done
-
-backup-all: 
-       cd ../../..; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
-       tar rvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
-       @for dir in ${SOURCE} ; \
-       do \
-               $(CD) $${dir}; make backup; $(CD) ..; \
-       done
-
-distribute: 
-       cd ../../..; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
-       @for dir in ${SOURCE} ; \
-       do \
-               $(CD) $${dir}; make distribute; $(CD) ..; \
-       done
-
-distribute-all: 
-       cd ../../..; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
-       @for dir in ${SOURCE} ; \
-       do \
-               $(CD) $${dir}; make distribute-all; $(CD) ..; \
-       done
-

diff --git a/src/Tools/pdbUtil/Makefile b/src/Tools/pdbUtil/Makefile
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..a4165b375ef689adb5a99ae2300a9bc3ad9431d5
--- /dev/null
+++ b/src/Tools/pdbUtil/Makefile
@@ -0,0 +1 @@
+/home/people/tacyas/Eos/src/Config/Template/ToolsClassTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/pdbUtil/pdbPCA/Config/OptionControlFile b/src/Tools/pdbUtil/pdbPCA/Config/OptionControlFile
index 9cda3e5..47c172f 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/Config/OptionControlFile
+++ b/src/Tools/pdbUtil/pdbPCA/Config/OptionControlFile
@@ -1,6 +1,9 @@
 # OptionControlFile
 # FileFormat
 "-i","-i[nput]","InputDataFile","Optional","1","1","In","inFile","stdin"
-"-o","-o[utput]","OutputDataFile","Optional","1","1","Out","outFile","stdout"
+"-o","-o[utput]","Output: Result","Optional","1","1","Out","outFile","stdout"
+"-oU","-o[utput]U[nit]","Output: Unit Vector Array","Optional","1","1","OutUnit","outFile","NULL"
+"-oM","-o[utput]M[atrix3D]","Output: Matrix3D from Unit Vector Array","Optional","1","1","OutMat3D","outFile","NULL"
+"-oPDB","-o[utput]PDB","Output: PDB rotated from Unit Vector Array","Optional","1","1","OutPDB","outFile","NULL"
 "-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
 "-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"

diff --git a/src/Tools/pdbUtil/pdbPCA/Makefile b/src/Tools/pdbUtil/pdbPCA/Makefile
deleted file mode 100755 (executable)
index cf583bda5caf22ea6b484fd2f57d17c251220e08..0000000000000000000000000000000000000000
--- a/src/Tools/pdbUtil/pdbPCA/Makefile
+++ /dev/null
@@ -1,103 +0,0 @@
-include ../../../Config/Define.inc
-include ../../Config/Define.inc
-include ../Config/Define.inc
-include Config/Define.inc
-
-all:
-       cd src; make all; cd ..
-
-install:
-       cd src; make install; cd ..
-
-
-putSF:
-       if [ -f private ] ; \
-       then \
-               echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
-       else \
-               cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
-       fi
-
-put:
-       cd src; make put; cd ..
-
-clean:
-       cd src; make clean; cd ..
-
-depend:
-       cd src; make depend; cd ..
-
-check:
-       @if [ ! -d src/$(OSTYPE) ]; then \
-               echo making directory; \
-               mkdir src/$(OSTYPE); \
-       fi
-       @$(RM) src/Makefile
-       @echo "New src/Makefile" 
-       @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
-       @cd src; touch $(OSTYPE)/.Depend; make depend
-
-cvsupdate::
-       cvs -d $(EOS_CVSROOT) update -d 
-
-cvscommit::
-       cvs -d $(EOS_CVSROOT) commit
-
-backup:
-       @cd ../../../..;     \
-       echo $(OBJECTNAME) ; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
-       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
-
-backup-all:
-       @cd ../../../..;     \
-       echo $(OBJECTNAME) ; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
-       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
-       
-distribute:
-       cd ../../../..;     \
-       echo $(OBJECTNAME) ; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
-       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
-       
-distribute-all:
-       @cd ../../../..;     \
-       echo $(OBJECTNAME) ; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
-       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
-
-eosintroduce:
-       ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ 
-
-include Config/Target.inc

diff --git a/src/Tools/pdbUtil/pdbPCA/Makefile b/src/Tools/pdbUtil/pdbPCA/Makefile
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..537735e6f10200cd5c886af6775498a31bbc041e
--- /dev/null
+++ b/src/Tools/pdbUtil/pdbPCA/Makefile
@@ -0,0 +1 @@
+/home/people/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/pdbUtil/pdbPCA/doc/Makefile b/src/Tools/pdbUtil/pdbPCA/doc/Makefile
new file mode 120000 (symlink)
index 0000000..e35804f
--- /dev/null
+++ b/src/Tools/pdbUtil/pdbPCA/doc/Makefile
@@ -0,0 +1 @@
+/home/people/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/doc/Makefile
\ No newline at end of file

diff --git a/src/Tools/pdbUtil/pdbPCA/inc/pdbPCA.h b/src/Tools/pdbUtil/pdbPCA/inc/pdbPCA.h
index db46f15..ffd9498 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/inc/pdbPCA.h
+++ b/src/Tools/pdbUtil/pdbPCA/inc/pdbPCA.h
@@ -21,6 +21,18 @@ typedef struct pdbPCAInfo {
     char* Out;
     FILE* fptOut;
     
+    long flagOutUnit;
+    char* OutUnit;
+    FILE* fptOutUnit;
+    
+    long flagOutMat3D;
+    char* OutMat3D;
+    FILE* fptOutMat3D;
+    
+    long flagOutPDB;
+    char* OutPDB;
+    FILE* fptOutPDB;
+    
     long flagconfigFile;
     char* configFile;
     FILE* fptconfigFile;

diff --git a/src/Tools/pdbUtil/pdbPCA/src/Makefile b/src/Tools/pdbUtil/pdbPCA/src/Makefile
index 82ced53..a547c12 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/src/Makefile
+++ b/src/Tools/pdbUtil/pdbPCA/src/Makefile
@@ -70,19 +70,19 @@ cudagdb: $(OSTYPE)/$(OBJECTNAME).cudagdb
 
 
 $(OSTYPE)/$(OBJECTNAME)::
-       $(RM) -f $(OSTYPE)/Makefile ; \
+       @$(RM) -f $(OSTYPE)/Makefile ; \
        $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
        cd $(OSTYPE); \
        $(MAKE) $(OBJECTNAME)  WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
 
 $(OSTYPE)/$(OBJECTNAME).debug::
-       $(RM) -f Makefile ; \
+       @$(RM) -f Makefile ; \
        $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
        cd $(OSTYPE); \
        $(MAKE) $(OBJECTNAME).debug  WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
 
 $(OSTYPE)/$(OBJECTNAME).cudagdb::
-       $(RM) -f Makefile ; \
+       @$(RM) -f Makefile ; \
        $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
        cd $(OSTYPE); \
        $(MAKE) $(OBJECTNAME).cudagdb WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)

diff --git a/src/Tools/pdbUtil/pdbPCA/src/argCheck.c b/src/Tools/pdbUtil/pdbPCA/src/argCheck.c
index 202cee7..9298753 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/src/argCheck.c
+++ b/src/Tools/pdbUtil/pdbPCA/src/argCheck.c
@@ -14,6 +14,17 @@ argCheck(pdbPCAInfo* info, int argc, char* argv[])
 {
     long i, j, nv;
     char s[1024];
+    FILE* fpt;
+    
+    if(NULL==(fpt=fopen(".EosLog", "a+"))) { 
+        
+    } else {
+        for(i=0; i<argc; i++) {
+            fprintf(fpt, "%s ", argv[i]);
+        }
+        fprintf(fpt, "\n");
+        fclose(fpt);
+    }
     for(i=1; i<argc; i++) {
         if(OPTION_FLAG==argv[i][OPTION_FLAG_POS]) {
             SSWITCH(argv[i]+OPTION_POS)
@@ -39,6 +50,39 @@ argCheck(pdbPCAInfo* info, int argc, char* argv[])
                     }
                     SBREAK;
                 }
+                SCASE("oU") {
+                    if(i+1<argc) {
+                        info->OutUnit = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagOutUnit++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("oM") {
+                    if(i+1<argc) {
+                        info->OutMat3D = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagOutMat3D++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("oPDB") {
+                    if(i+1<argc) {
+                        info->OutPDB = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagOutPDB++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
                 SCASE("c") {
                     if(i+1<argc) {
                         info->configFile = stringGetNthWord(argv[i+1], 1, " ,");

diff --git a/src/Tools/pdbUtil/pdbPCA/src/init.c b/src/Tools/pdbUtil/pdbPCA/src/init.c
index 42bf232..4614646 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/src/init.c
+++ b/src/Tools/pdbUtil/pdbPCA/src/init.c
@@ -14,6 +14,9 @@ init0(pdbPCAInfo* info)
 {
     info->fptIn = stdin;    info->flagIn = 0;
     info->fptOut = stdout;    info->flagOut = 0;
+    info->fptOutUnit = NULL;    info->flagOutUnit = 0;
+    info->fptOutMat3D = NULL;    info->flagOutMat3D = 0;
+    info->fptOutPDB = NULL;    info->flagOutPDB = 0;
     info->fptconfigFile = NULL;    info->flagconfigFile = 0;
     info->mode = 0;    info->flagmode = 0;
 }
@@ -31,6 +34,18 @@ init1(pdbPCAInfo* info)
         info->fptOut = fileOpen(info->Out, "w");
     }
     
+    if(info->flagOutUnit) {
+        info->fptOutUnit = fileOpen(info->OutUnit, "w");
+    }
+    
+    if(info->flagOutMat3D) {
+        info->fptOutMat3D = fileOpen(info->OutMat3D, "w");
+    }
+    
+    if(info->flagOutPDB) {
+        info->fptOutPDB = fileOpen(info->OutPDB, "w");
+    }
+    
     if(info->flagconfigFile) {
         info->fptconfigFile = fileOpen(info->configFile, "r");
     }

diff --git a/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.c b/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.c
index 890dd07..b62c5b7 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.c
+++ b/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.c
@@ -20,6 +20,7 @@ static char __sccs_id[] = "%Z%pdbPCA ver%I%; Date:%D% %Z%";
 #define DEBUG
 #include "genUtil.h"
 #include "Array.h"
+#include "Matrix3D.h"
 #include "pdbFile.h"
 
 int
@@ -33,6 +34,8 @@ main(int argc, char* argv[])
        Array X;
        int n;
        pdbFileParaTypeReal x, y, z;
+       Matrix3D mat;
+       int i, j;
 
        init0(&info);
     argCheck(&info, argc, argv);
@@ -76,6 +79,29 @@ main(int argc, char* argv[])
        arrayWriteToFile(info.fptOut, &u, "in main");
        fprintf(info.fptOut, "lambda^2: lambda^2\n");
        arrayWriteToFile(info.fptOut, &lambda, "in main");
+
+       if(info.flagOutUnit) {
+               arrayWriteToFile(info.fptOutUnit, &u, "in main");
+       }
+
+       if(info.flagOutMat3D || info.flagOutPDB) {
+               matrix3DInit(mat);
+               for(i=0; i<u.n[0]; i++) {
+               for(j=0; j<u.n[1]; j++) {
+                       mat[i][j] = arrayDataGet2(u, i, j);
+               }
+               }
+       }
+
+       if(info.flagOutMat3D) {
+               matrix3DFileWrite(info.fptOutMat3D, mat);
+       }
+
+       if(info.flagOutPDB) {
+               pdbTrans(&pdb, mat);
+               pdbFileWrite(info.fptOutPDB, &pdb);
+       }
+
        exit(EXIT_SUCCESS);
 }
 

diff --git a/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.html b/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.html
index 5bfd567..f2cedb4 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.html
+++ b/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.html
@@ -9,7 +9,10 @@
 Usage: pdbPCA
 Options:
     [-i[nput]            In                  (stdin     )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Result
+    [-o[utput]U[nit]     OutUnit             (NULL      )] :Optional  :Output: Unit Vector Array
+    [-o[utput]M[atrix3D] OutMat3D            (NULL      )] :Optional  :Output: Matrix3D from Unit Vector Array
+    [-o[utput]PDB        OutPDB              (NULL      )] :Optional  :Output: PDB rotated from Unit Vector Array
     [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
     [-m[ode]             mode                (0         )] :Optional  :Mode
 ----- Additional Usage -----

diff --git a/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.pane b/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.pane
index e8b08a6..4ce541c 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.pane
+++ b/src/Tools/pdbUtil/pdbPCA/src/pdbPCA.pane
@@ -8,9 +8,12 @@
         -H 1  5x1+41+0 'Help' 'help page' $EOS/src/Tools/pdbUtil/pdbPCA/doc/pdbPCA.doc help
         -Q 1 0 5.25x1+47+0 'Close'
         -I 1 0 1 0 0 1 -1x1+1+1.500000 ' ' 'In' 'InputDataFile' i
-        -O 1 0 1 0 0 1 -1x1+1+3.000000 ' ' 'Out' 'OutputDataFile' o
-        -I 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'configFile' 'ConfigurationFile' c
-        -i 1 0 1 0 0 -1x1+1+6.000000 0 0 0 0 0 'mode' 'Mode' m
+        -O 1 0 1 0 0 1 -1x1+1+3.000000 ' ' 'Out' 'Output: Result' o
+        -O 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'OutUnit' 'Output: Unit Vector Array' oU
+        -O 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'OutMat3D' 'Output: Matrix3D from Unit Vector Array' oM
+        -O 1 0 1 0 0 1 -1x1+1+7.500000 ' ' 'OutPDB' 'Output: PDB rotated from Unit Vector Array' oPDB
+        -I 1 0 1 0 0 1 -1x1+1+9.000000 ' ' 'configFile' 'ConfigurationFile' c
+        -i 1 0 1 0 0 -1x1+1+10.500000 0 0 0 0 0 'mode' 'Mode' m
     -E
   -E
 -E

diff --git a/src/Tools/pdbUtil/pdbPCA/src/test/Makefile b/src/Tools/pdbUtil/pdbPCA/src/test/Makefile
old mode 100644 (file)
new mode 100755 (executable)

diff --git a/src/Tools/pdbUtil/pdbPCA/src/usage.c b/src/Tools/pdbUtil/pdbPCA/src/usage.c
index 49059f5..242a176 100755 (executable)
--- a/src/Tools/pdbUtil/pdbPCA/src/usage.c
+++ b/src/Tools/pdbUtil/pdbPCA/src/usage.c
@@ -8,7 +8,10 @@ usage(char* thisProgram)
     fprintf(stderr, "Usage: %s\n", thisProgram);
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "    [-i[nput]            In                  (stdin     )] :Optional  :InputDataFile\n");
-    fprintf(stderr, "    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile\n");
+    fprintf(stderr, "    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Result\n");
+    fprintf(stderr, "    [-o[utput]U[nit]     OutUnit             (NULL      )] :Optional  :Output: Unit Vector Array\n");
+    fprintf(stderr, "    [-o[utput]M[atrix3D] OutMat3D            (NULL      )] :Optional  :Output: Matrix3D from Unit Vector Array\n");
+    fprintf(stderr, "    [-o[utput]PDB        OutPDB              (NULL      )] :Optional  :Output: PDB rotated from Unit Vector Array\n");
     fprintf(stderr, "    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile\n");
     fprintf(stderr, "    [-m[ode]             mode                (0         )] :Optional  :Mode\n");
     additionalUsage();