#endif
/* prototype begin */
-double eosBeseel_I(double x, int n);
+extern double eosBeseel_I(double x, int n);
/* prototype end */
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/contourCreate.c:
-
-../src/lcontour2ps.c:
-
-../src/lmrc2contour.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/tkImgFmtMRC.c:
-
-../src/tkImgFmtlargeIP.c:
-
-../src/tkctfInfo.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/avsFileInit.c:
-
-../src/avsFileSet.c:
-
-../src/avsFileWrite.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/density_sphere.c:
-
-../src/drawWireFrame.c:
-
-../src/lmolvieCamera.c:
-
-../src/lmolvieDisplayLib.c:
-
-../src/lmolvieDisplayListMake.c:
-
-../src/lmolvieDisplayNormal.c:
-
-../src/lmolvieDisplayParallel.c:
-
-../src/lmolvieDockDisplay.c:
-
-../src/lmolvieDockKeyboard.c:
-
-../src/lmolvieFlightDisplay.c:
-
-../src/lmolvieFlightIdle.c:
-
-../src/lmolvieFlightKeyboard.c:
-
-../src/lmolvieIdleNormal.c:
-
-../src/lmolvieInitNormal.c:
-
-../src/lmolvieInitParallel.c:
-
-../src/lmolvieKeyboard.c:
-
-../src/lmolvieKeyboardDrive.c:
-
-../src/lmolvieKeyboardMulti.c:
-
-../src/lmolvieKeyboardNormal.c:
-
-../src/lmolvieKeyboardParallel.c:
-
-../src/lmolvieKeyboardSurface.c:
-
-../src/lmolvieLight.c:
-
-../src/lmolvieMRCread.c:
-
-../src/lmolvieMouse.c:
-
-../src/lmolvieMouseDrive.c:
-
-../src/lmolvieMouseMulti.c:
-
-../src/lmolvieMouseNormal.c:
-
-../src/lmolvieMouseParallel.c:
-
-../src/lmolvieMrcViewerDisplay.c:
-
-../src/lmolvieMrcViewerKeyboard.c:
-
-../src/lmolvieMrcViewerMouse.c:
-
-../src/lmolvieOperation.c:
-
-../src/lmolviePDBread.c:
-
-../src/lmolvieProjectionKeyboard.c:
-
-../src/lmolvieProjectionMouse.c:
-
-../src/lmolvieProteinStatus.c:
-
-../src/lmolvieReshapeNormal.c:
-
-../src/lmolvieReshapeParallel.c:
-
-../src/lmolvieTest.c:
-
-../src/lmolvieTexture.c:
-
-../src/lmolvieViewerDisplay.c:
-
-../src/lmolvieViewerIdle.c:
-
-../src/lmolvieViewerKeyboard.c:
-
-../src/lmolvieViewerMouse.c:
-
-../src/lmolvieViewerSpecial.c:
-
-../src/lmolvieVoice.c:
-
-../src/loadPDB.c:
-
-../src/loadPPM.c:
-
-../src/marching_cubes.c:
-
-../src/multiPDB.c:
-
-../src/openGLKey.c:
-
-../src/savePPM.c:
</PRE>
<HR>
<A NAME="include">
-have_library: checking for main() in -lGL... -------------------- yes
+have_library: checking for -lGL... -------------------- no
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lruby -lpthread -lrt -ldl -lcrypt -lm -lc"
+"xcrun clang -o conftest -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/universal-darwin22 -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/ruby/backward -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0 -I. -I/Users/tacyas/Eos/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT -g -Os -pipe -DHAVE_GCC_ATOMIC_BUILTINS -DUSE_FFI_CLOSURE_ALLOC conftest.c -L. -L/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib -L/usr/lib -L/Users/tacyas/Eos/lib/ARM64MAC64 -L/Users/tacyas/Eos/util/ARM64MAC64/lib -L. -L/AppleInternal/Library/BuildRoots/aaefcfd1-5c95-11ed-8734-2e32217d8374/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.Internal.sdk/usr/local/lib -lruby.2.6 "
+ld: warning: directory not found for option '-L/AppleInternal/Library/BuildRoots/aaefcfd1-5c95-11ed-8734-2e32217d8374/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.Internal.sdk/usr/local/lib'
checked program was:
/* begin */
1: #include "ruby.h"
6: }
/* end */
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lruby -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
+"xcrun clang -o conftest -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/universal-darwin22 -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/ruby/backward -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0 -I. -I/Users/tacyas/Eos/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT -g -Os -pipe -DHAVE_GCC_ATOMIC_BUILTINS -DUSE_FFI_CLOSURE_ALLOC conftest.c -L. -L/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib -L/usr/lib -L/Users/tacyas/Eos/lib/ARM64MAC64 -L/Users/tacyas/Eos/util/ARM64MAC64/lib -L. -L/AppleInternal/Library/BuildRoots/aaefcfd1-5c95-11ed-8734-2e32217d8374/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.Internal.sdk/usr/local/lib -lruby.2.6 -lGL "
+ld: warning: directory not found for option '-L/AppleInternal/Library/BuildRoots/aaefcfd1-5c95-11ed-8734-2e32217d8374/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.1.Internal.sdk/usr/local/lib'
+ld: library not found for -lGL
+clang: error: linker command failed with exit code 1 (use -v to see invocation)
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: /*top*/
4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lruby -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
---------------------
-
-have_library: checking for main() in -lGLU... -------------------- yes
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lGL -lruby -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lGL -lruby -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
---------------------
-
-have_library: checking for main() in -lglut... -------------------- yes
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lGLU -lGL -lruby -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lGLU -lGL -lruby -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
---------------------
-
-have_library: checking for main() in -ltcl... -------------------- yes
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lglut -lGLU -lGL -lruby -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lglut -lGLU -lGL -lruby -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
---------------------
-
-have_library: checking for main() in -ltk... -------------------- yes
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -ltcl -lglut -lGLU -lGL -lruby -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -ltcl -lglut -lGLU -lGL -lruby -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
---------------------
-
-have_library: checking for main() in -lBLT... -------------------- yes
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -ltk -ltcl -lglut -lGLU -lGL -lruby -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -ltk -ltcl -lglut -lGLU -lGL -lruby -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
---------------------
-
-have_library: checking for main() in -lasound... -------------------- yes
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lBLT -ltk -ltcl -lglut -lGLU -lGL -lruby -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lBLT -ltk -ltcl -lglut -lGLU -lGL -lruby -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
---------------------
-
-have_library: checking for main() in -lgif... -------------------- yes
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lruby -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lruby -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
---------------------
-
-have_library: checking for main() in -lfftw3f... -------------------- yes
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lruby -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lruby -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
---------------------
-
-have_library: checking for main() in -lnr... -------------------- no
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lruby -lnr -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:57: エラー: ‘main’ が宣言されていません (この関数内での最初の使用)
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-conftest.c:5:57: 備考: 未宣言の識別子は出現した各関数内で一回のみ報告されます
-conftest.c:5:32: 警告: 変数 ‘p’ が設定されましたが使用されていません [-Wunused-but-set-variable]
- int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
-/* end */
-
-"gcc -o conftest -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -I/home/tacyas/Eos/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC conftest.c -L. -L/usr/lib64 -L/usr/lib -L/home/tacyas/Eos/lib/X86LINUX64 -L/home/tacyas/Eos/util/X86LINUX64/lib -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lruby -lnr -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-conftest.c: 関数 ‘t’ 内:
-conftest.c:5:1: 警告: 関数 ‘main’ の暗黙的な宣言です [-Wimplicit-function-declaration]
- int t(void) { main(); return 0; }
- ^
-/usr/bin/ld: -lnr が見つかりません
-collect2: エラー: ld はステータス 1 で終了しました
-checked program was:
-/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
+ 5: int main(int argc, char **argv)
+ 6: {
+ 7: if (argc > 1000000) {
+ 8: int (* volatile tp)(void)=(int (*)(void))&t;
+ 9: printf("%d", (*tp)());
10: }
11:
12: return 0;
13: }
+14:
+15: int t(void) { ; return 0; }
/* end */
--------------------
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/decoder.c:
-
-../src/gifFileInit.c:
-
-../src/gifFileWrite.c:
-
-../src/gifUtil.c:
-
-../src/gifcompr.c:
-
-../src/gifencod.c:
-
-../src/lmrc2gif.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lmrc2png.c:
-
-../src/pngFileInit.c:
-
-../src/pngFileWrite.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/psFileCircle.c:
-
-../src/psFileContour.c:
-
-../src/psFileContour3D.c:
-
-../src/psFileEnd.c:
-
-../src/psFileImage.c:
-
-../src/psFileInit.c:
-
-../src/psFileLine.c:
-
-../src/psFilePage.c:
-
-../src/psFileRead.c:
-
-../src/psFileString.c:
-
-../src/psFileUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lmrc2bild.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/bmpFileInfo.c:
-
-../src/bmpFileRead.c:
-
-../src/lbmp2mrc.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/ctfDeterminationFromPhaseComparison.c:
-
-../src/ctfFunction.c:
-
-../src/ctfInfoPVM.c:
-
-../src/ctfInfoRead.c:
-
-../src/ctfInfoWrite.c:
-
-../src/ctfInfoWrite2.c:
-
-../src/ctfWeight.c:
-
-../src/ctfZeroPoint.c:
-
-../src/ctfforbayes.c:
-
-../src/ctfforbayescheck.c:
-
-../src/defocuslikelihood.c:
-
-../src/lastigmatismDetection.c:
-
-../src/lctfDetermination.c:
-
-../src/lctfDetermine.c:
-
-../src/lmolecularEnvelope.c:
-
-../src/lmrcFSInfoScatteringAngularDistributionAverageSection.c:
-
-../src/powerspectraTangentLine.c:
-
-../src/thonRing.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/dmFileInfo.c:
-
-../src/dmFileInit.c:
-
-../src/dmFileRead.c:
-
-../src/dmFileUtil.c:
-
-../src/ldm2mrc.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/dsn6Init.c:
-
-../src/dsn6Write.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/emDataRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosStarFileDataGet.c:
-
-../src/eosStarFileLoopDataGet.c:
-
-../src/eosStarFileRead.c:
-
-../src/eosStarFileWrite.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lmrc2viff.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/largeIPRead.c:
-
-../src/tkImgFmtlargeIP.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/llDataCheck.c:
-
-../src/llDataETC.c:
-
-../src/llDataError.c:
-
-../src/llDataGet.c:
-
-../src/llDataInfo.c:
-
-../src/llDataInit.c:
-
-../src/llDataIntensityInformationGet.c:
-
-../src/llDataPVM.c:
-
-../src/llDataRead.c:
-
-../src/llDataSet.c:
-
-../src/llDataUtil.c:
-
-../src/llDataWrite.c:
-
-../src/lll2ltlg.c:
-
-../src/lllDataAdd.c:
-
-../src/lllDataAverage.c:
-
-../src/lllDataAvgTo.c:
-
-../src/lllDataAxisSearch.c:
-
-../src/lllDataAxisSearch2.c:
-
-../src/lllDataAxisSearchAndAverage.c:
-
-../src/lllDataCTFCompensate.c:
-
-../src/lllDataCTFObservation.c:
-
-../src/lllDataCompare.c:
-
-../src/lllDataContributionCalcDifferentN.c:
-
-../src/lllDataDifferenceCalc.c:
-
-../src/lllDataEquatorAdd.c:
-
-../src/lllDataExtract.c:
-
-../src/lllDataFit.c:
-
-../src/lllDataFit2.c:
-
-../src/lllDataFitAndAverage.c:
-
-../src/lllDataFitMergedLL.c:
-
-../src/lllDataFitOut.c:
-
-../src/lllDataFitParamInverse.c:
-
-../src/lllDataFitUtil.c:
-
-../src/lllDataFitUtilPVM.c:
-
-../src/lllDataInterpolate.c:
-
-../src/lllDataLowPassFiltering.c:
-
-../src/lllDataMergeDifferentN.c:
-
-../src/lllDataMultiCTFCompensation.c:
-
-../src/lllDataPhaseShift.c:
-
-../src/lllDataPrint.c:
-
-../src/lllDataRescaling.c:
-
-../src/lllDataSingleCTFCompensation.c:
-
-../src/lllDataWeightSet.c:
-
-../src/lllDatarMaxLimit.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lltlg2mrc.c:
-
-../src/ltlgDataAllocate.c:
-
-../src/ltlgDataGet.c:
-
-../src/ltlgDataPrint.c:
-
-../src/ltlgDataReadFile.c:
-
-../src/ltlgDataWeightModify.c:
-
-../src/ltlgDataWriteFile.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/mapFileRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/fftn.c:
-
-../src/lmrcFETnormalizeBySD.c:
-
-../src/lmrcFFTCentralSection.c:
-
-../src/lmrcFFTCentralSectionCompare.c:
-
-../src/lmrcFFTCentralSectionCompareInfoWrite.c:
-
-../src/lmrcFFTCentralSectionsGet.c:
-
-../src/lmrcFFTExpression.c:
-
-../src/lmrcFFTFGconj.c:
-
-../src/lmrcFFTFxG.c:
-
-../src/lmrcFFTInfo.c:
-
-../src/lmrcImage3DPad.c:
-
-../src/lmrcImage3DWindowing.c:
-
-../src/lmrcImageAddValue.c:
-
-../src/lmrcImageAsProbability.c:
-
-../src/lmrcImageAverage.c:
-
-../src/lmrcImageBandPassFilter.c:
-
-../src/lmrcImageBilateralFilter.c:
-
-../src/lmrcImageBinarization.c:
-
-../src/lmrcImageBottomHatTransform.c:
-
-../src/lmrcImageBoundaryInfo.c:
-
-../src/lmrcImageCTFCompensation.c:
-
-../src/lmrcImageCTFDetermination.c:
-
-../src/lmrcImageCTFObservation.c:
-
-../src/lmrcImageCTFSN.c:
-
-../src/lmrcImageCVE.c:
-
-../src/lmrcImageCalcArea.c:
-
-../src/lmrcImageCenterGet.c:
-
-../src/lmrcImageCentre.c:
-
-../src/lmrcImageClosing.c:
-
-../src/lmrcImageClusterAnalysis.c:
-
-../src/lmrcImageCommonLine.c:
-
-../src/lmrcImageConnection.c:
-
-../src/lmrcImageConnectivityNumberCalc.c:
-
-../src/lmrcImageContourSurface.c:
-
-../src/lmrcImageContraction.c:
-
-../src/lmrcImageCorrelation.c:
- $lmrcImageEuclidDistanceCalc: Calculate Euclid distance between two images $
- $arg: in1: input mrcImage1 $
- $arg: in2: input mrcImage2 $
- $arg: mode: input int $
- $mode: 0 Sum of SQR $
- $mode: 1 Distance $
- $return: EuclidDistance $
-
-../src/lmrcImageCorrelationPVM.c:
-
-../src/lmrcImageCorrelationWithCTFCompensation.c:
-
-../src/lmrcImageCorrelationinSpace.c:
-
-../src/lmrcImageCrystalCreate.c:
-
-../src/lmrcImageDataMaxAndMinGetByImage.c:
-
-../src/lmrcImageDataStraightCopy.c:
-
-../src/lmrcImageDeconvolution.c:
-
-../src/lmrcImageDensity.c:
-
-../src/lmrcImageDensityInverse.c:
-
-../src/lmrcImageDensityNormalizationByImage.c:
-
-../src/lmrcImageDifferential.c:
-
-../src/lmrcImageDilation.c:
-
-../src/lmrcImageDistanceConversion.c:
-
-../src/lmrcImageEdge.c:
-
-../src/lmrcImageEdgeAverage.c:
-
-../src/lmrcImageEdgeEnhancement.c:
-
-../src/lmrcImageErosion.c:
-
-../src/lmrcImageFFT.c:
-
-../src/lmrcImageFOMCalc.c:
-
-../src/lmrcImageFeatureCalc.c:
-
-../src/lmrcImageFeatureExtraction.c:
-
-../src/lmrcImageFeatureExtractionCoOccurrence.c:
-
-../src/lmrcImageFeatureExtractionRunLength.c:
-
-../src/lmrcImageFilterCreate.c:
-
-../src/lmrcImageFirstNoiseReductionByRelaxation.c:
-
-../src/lmrcImageFloating.c:
-
-../src/lmrcImageFourierNeighborCorrelation.c:
-
-../src/lmrcImageFourierPowerSpectrum.c:
-
-../src/lmrcImageFourierShellCorrelation.c:
-
-../src/lmrcImageHighPassFilter.c:
-
-../src/lmrcImageHighlighting.c:
-
-../src/lmrcImageHoleFilling.c:
-
-../src/lmrcImageHoughTransform.c:
-
-../src/lmrcImageLabeling.c:
-
-../src/lmrcImageLocalMaximumValuesFind.c:
-
-../src/lmrcImageLogicalOperation.c:
-
-../src/lmrcImageLowPassFilter.c:
-
-../src/lmrcImageMasking.c:
-
-../src/lmrcImageMaxDataGet.c:
-
-../src/lmrcImageMirroring.c:
- $lmrcImageMirroring: (mrcImage* out, mrcImage* in, lmrcImageMirroring mode) $
-
-../src/lmrcImageModeChange.c:
-
-../src/lmrcImageModelCreate.c:
-
-../src/lmrcImageMontageCreate.c:
-
-../src/lmrcImageMorphology.c:
-
-../src/lmrcImageMove.c:
-
-../src/lmrcImageMultiCTFCompensation.c:
-
-../src/lmrcImageMultiplying.c:
-
-../src/lmrcImageNegativeLaplacian.c:
-
-../src/lmrcImageNoiseCreate.c:
-
-../src/lmrcImageNormalizing.c:
-
-../src/lmrcImageOneLineSimilarityCalc.c:
-
-../src/lmrcImageOpening.c:
-
-../src/lmrcImagePad.c:
-
-../src/lmrcImagePartImageSegmentation.c:
-
-../src/lmrcImagePattersonFunctionCalc.c:
-
-../src/lmrcImagePixelSummationOfProbabilityGetByImage.c:
-
-../src/lmrcImagePixelValueSort.c:
-
-../src/lmrcImagePosterization.c:
-
-../src/lmrcImagePrewitt.c:
-
-../src/lmrcImageProjection.c:
-
-../src/lmrcImageProportionalDensityLevelSetByImage.c:
-
-../src/lmrcImagePyramidal.c:
-
-../src/lmrcImageROI2D.c:
-
-../src/lmrcImageROI3D.c:
-
-../src/lmrcImageROInotChangeHeaderLength.c:
-
-../src/lmrcImageRadialDistribution.c:
-
-../src/lmrcImageRhoFiltering.c:
-
-../src/lmrcImageRoberts.c:
-
-../src/lmrcImageRotation.c:
-
-../src/lmrcImageSSDA.c:
-
-../src/lmrcImageSamplingUnitChange.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxation.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationDijDimensionSet.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationDijValueSet.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationQValueSet.c:
-
-../src/lmrcImageSecondNoiseReductionByRelaxationRValueSet.c:
-
-../src/lmrcImageShapePCA.c:
-
-../src/lmrcImageShift.c:
-
-../src/lmrcImageShrink.c:
-
-../src/lmrcImageSigmaCalculate.c:
-
-../src/lmrcImageSinogram.c:
-
-../src/lmrcImageSinogramCorrelation.c:
-
-../src/lmrcImageSinogramFFT.c:
-
-../src/lmrcImageSmoothing.c:
-
-../src/lmrcImageSobel.c:
-
-../src/lmrcImageSoftEdge.c:
-
-../src/lmrcImageSolventFlattening.c:
-
-../src/lmrcImageSpatialFrequencyFilter.c:
-
-../src/lmrcImageSphere.c:
-
-../src/lmrcImageSplit.c:
-
-../src/lmrcImageStack.c:
-
-../src/lmrcImageStudentCalculate.c:
-
-../src/lmrcImageSubtractionCalc.c:
-
-../src/lmrcImageSummationCalculate.c:
-
-../src/lmrcImageSurfaceAreaCalc.c:
-
-../src/lmrcImageSymmetryFind.c:
-
-../src/lmrcImageTfunction.c:
-
-../src/lmrcImageToneReversal.c:
-
-../src/lmrcImageTopHatTransform.c:
-
-../src/lmrcImageTrans.c:
-
-../src/lmrcImageTransformDescartesIntoPolar.c:
-
-../src/lmrcImageTranspose.c:
-
-../src/lmrcImageTriming.c:
-
-../src/lmrcImageUnsharpening.c:
-
-../src/lmrcImageVolumeCalc.c:
-
-../src/lmrcImageWindowing.c:
-
-../src/lmrcImagesFTest.c:
-
-../src/lmrcImagesStatDataGet.c:
-
-../src/lmrcImagesTTest.c:
-
-../src/lmrcImagesVarianceAnalysis.c:
-
-../src/lmrcImagesVarianceMap.c:
-
-../src/lmrcMultiFFTCentralSectionsCompare.c:
-
-../src/lmrcMultiFFTCentralSectionsSigma.c:
-
-../src/lmrcSinogramFET.c:
-
-../src/lmrcSinogramFETPCA.c:
-
-../src/lmrcSinogramFETcalcWeight.c:
-
-../src/lmrcSinogramFETcorrelationMap.c:
-
-../src/lmrcSinogramFETnormalizedMap.c:
-
-../src/lmrcSinogramFETreferredCorrelation.c:
-
-../src/lmrcSinogramFETsmoothParameterMatching.c:
-
-../src/mrcImageCheckFFT.c:
-
-../src/mrcImageCheckSameSize.c:
-
-../src/mrcImageCopy.c:
-
-../src/mrcImageDataSet.c:
-
-../src/mrcImageError.c:
-
-../src/mrcImageGet.c:
-
-../src/mrcImageGetPixels.c:
-
-../src/mrcImageInfo.c:
-
-../src/mrcImageInit.c:
-
-../src/mrcImageOperation.c:
-
-../src/mrcImagePVM.c:
-
-../src/mrcImagePrint.c:
-
-../src/mrcImageRead.c:
-
-../src/mrcImageSectionGet.c:
-
-../src/mrcImageSectionSet.c:
-
-../src/mrcImageSet.c:
-
-../src/mrcImageTailer.c:
-
-../src/mrcImageToIntImage.c:
-
-../src/mrcImageUtil.c:
-
-../src/mrcImageUtilityforVariance.c:
-
-../src/mrcImageWrite.c:
-
-../src/mrcImageWrite2.c:
-
-../src/mrcImagefuncmin.c:
-
-../src/mrcRefUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lmrcImageMeanFreePath.c:
-
-../src/lmrcImageShapeModePrint.c:
-
-../src/lmrcImageShapeSearch.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lpdb2mrc2d.c:
-
-../src/lpdb2mrc3d.c:
-
-../src/lpdbCoord.c:
-
-../src/lpdbCoordInfo.c:
-
-../src/lpdbSelectedAtom.c:
-
-../src/lpdbSurface.c:
-
-../src/pdbFileRead.c:
-
-../src/pdbFileWrite.c:
-
-../src/pdbGet.c:
-
-../src/pdbInfoGet.c:
-
-../src/pdbRotation.c:
-
-../src/pdbSecondaryStructure.c:
-
-../src/pdbSet.c:
-
-../src/pdbTrans.c:
-
-../src/pdbUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/rigakuImageRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/tgaFileInit.c:
-
-../src/tgaFilePrint.c:
-
-../src/tgaFileRead.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/lAllCommonLineCalculation.c:
-
-../src/lAngularWeightCalculation.c:
-
-../src/lCommonLineCalculation.c:
-
-../src/lCommonLineDataSetInPlaneRotation.c:
-
-../src/lCommonLinesDataSet.c:
-
-../src/lDescartesIntoPolar.c:
-
-../src/lEvaluateCorrelationMapwithCommonLine.c:
-
-../src/lFETOrientationSearchByAnnealing.c:
-
-../src/lFETOrientationSearchByFeatureAlignment.c:
-
-../src/lFETOrientationSearchByFeatureAlignmentInitSet.c:
-
-../src/lFETOrientationSearchByFeatureAlignmentSphere.c:
-
-../src/lFETmapOrientationSearchBySimultaneousFitting.c:
-
-../src/lFETsmallMapSetCreate_forSimultaneousMinimization.c:
-
-../src/lInitialDataFileRead.c:
-
-../src/lJcalulation.c:
-
-../src/lLcalculation.c:
-
-../src/lPlaneRotationAngleSet.c:
-
-../src/lllDataSeparationInfoPrint.c:
-
-../src/lllDataSeparationInfoRead.c:
-
-../src/lllDataSeparationInfoSet.c:
-
-../src/lllDatarMaxLimitForSeparation.c:
-
-../src/lllExtract.c:
-
-../src/lllExtractCtfinfFileCreate.c:
-
-../src/lllExtractWithSeparation.c:
-
-../src/lllExtractdYEstimate.c:
-
-../src/lmrc2Dto3D.c:
-
-../src/lmrc2Dto3DSIRT.c:
-
-../src/lmrc3Dto2D.c:
-
-../src/lmrc3Dto2DFFT.c:
-
-../src/lmrcImageFileListAndEulerAngleDataRead.c:
-
-../src/lmrcImageOneLineGet.c:
-
-../src/lmrcImageSinogramCorrelationAdditionalWeight.c:
-
-../src/lmrcImageToFFT.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/clusterLogAnalysis.c:
-
-../src/clusterLogInit.c:
-
-../src/clusterLogRead.c:
-
-../src/clusterLogUtil.c:
-
-../src/clusterLogWrite.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/crystalHelix.c:
- $Revision: 1.1 $
- $Date: 2002/02/14 10:18:46 $
- $Author: tacyas $
- $State: Exp $
- $Log: crystalHelix.c,v $
-
-../src/crystalInfoFile.c:
-
-../src/crystalInit.c:
-
-../src/crystalUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/map2DCoordGet.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/matrix3DEulerAngleGet.c:
-
-../src/matrix3DEulerAngleSet.c:
-
-../src/matrix3DEulerAngles.c:
-
-../src/matrix3DFile.c:
-
-../src/matrix3DInit.c:
-
-../src/matrix3DMultiply.c:
-
-../src/matrix3DMultiplyMatrix.c:
-
-../src/matrix3DMultiplyVector.c:
-
-../src/matrix3DRotation.c:
-
-../src/matrix3DTranslation.c:
-
-../src/matrix3DUtil.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/memoryAllocate.c:
-
-../src/memoryByteSwap.c:
-
-../src/memoryClear.c:
-
-../src/memoryCopy.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/pvmStart.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/randomNormal.c:
-
-../src/randomUniform.c:
-
-../src/srandom.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/socketClient.c:
-
-../src/socketServer.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/pow2nn.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/Vector.c:
-
-../src/VectorRead.c:
-
-../src/VectorScalarProduct.c:
-
-../src/lVectorSpline2D.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosBayesCondition.c:
-
-../src/eosBayesDistributionInit.c:
-
-../src/eosBayesDistributionInitialProbabilitySet.c:
-
-../src/eosBayesEstimation.c:
-
-../src/eosBayesFree.c:
-
-../src/eosBayesParameterOfMaxPosterior.c:
-
-../src/eosBayesRead.c:
-
-../src/eosBayesWrite.c:
-
-../src/eosBayesflag.c:
-
-../src/leosBayesInit.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosFunc.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosMathStatistics.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosPThread.c:
-
-../src/eosPThreadCreate.c:
-
-../src/eosPThreadInit.c:
-
-../src/eosPThreadJoin.c:
-
-../src/eosPThreadMutex.c:
</PRE>
<HR>
<A NAME="include">
<H2>Information from source codes</H2>
</A>
<PRE>
-../src/eosPointCopy.c:
-
-../src/eosPointProject.c:
-
-../src/eosPointRead.c:
-
-../src/eosPointRotate.c:
-
-../src/eosPointUtil.c:
-
-../src/eosPointWrite.c:
-
-../src/leosPointPositionCorrection.c:
</PRE>
<HR>
<A NAME="include">
-/bin/bash: dcdCompareCA: そのようなファイルやディレクトリはありません
+/bin/bash: dcdCompareCA: No such file or directory
-/bin/bash: dcdDistanceAtomBetweenAtom: そのようなファイルやディレクトリはありません
+/bin/bash: dcdDistanceAtomBetweenAtom: No such file or directory
-/bin/bash: Display3: そのようなファイルやディレクトリはありません
+/bin/bash: Display3: No such file or directory
-/bin/bash: Eos: そのようなファイルやディレクトリはありません
+/bin/bash: Eos: No such file or directory
-/bin/bash: StereoDisplay: そのようなファイルやディレクトリはありません
+/bin/bash: StereoDisplay: No such file or directory
-/bin/bash: Visualmake: そのようなファイルやディレクトリはありません
+/bin/bash: Visualmake: No such file or directory
-/bin/bash: imagesClustering: そのようなファイルやディレクトリはありません
+/bin/bash: imagesClustering: No such file or directory
-/bin/bash: obj3Don2DImageView: そのようなファイルやディレクトリはありません
+/bin/bash: obj3Don2DImageView: No such file or directory
-/bin/bash: smolet: そのようなファイルやディレクトリはありません
+/bin/bash: smolet: No such file or directory
-/bin/bash: crystalGetLatticeVolume: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>crystalGetLatticeVolume</TITLE>
+</HEAD>
+<BODY>
+<H1>crystalGetLatticeVolume</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: crystalGetLatticeVolume
+Options:
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :Input:
+ [-a[Axis] ax (2 ).as(Real )
+ ay (3 ).as(Real )
+ az (0 ).as(Real ) ] :Optional :Input:
+ [-b[Axis] bx (2 ).as(Real )
+ by (3 ).as(Real )
+ bz (0 ).as(Real ) ] :Optional :Input:
+ [-c[Axis] cx (2 ).as(Real )
+ cy (3 ).as(Real )
+ cz (1 ).as(Real ) ] :Optional :Input:
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+> crystaInfo
+aAxis %15.6g %15.6g %15.6g
+bAxis %15.6g %15.6g %15.6g
+cAxis %15.6g %15.6g %15.6g
+CellLength %15.6g %15.6g %15.6g
+Origin %15.6g %15.6g %15.6g
+N %15d %15d %15d
+StartN %15d %15d %15d
+SpaceGroup %15d
+HelixInfo %10d %10d %10d
+### Attention ###
+Parameter Order is important: Dependent between CellLength and a|b|cAxis.
+ Because each of aAxis, bAxis, cAxis must be a unit vector.
+HelixInfo t u n
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: crystalGetReciprocalLattice: そのようなファイルやディレクトリはありません
+/bin/bash: crystalGetReciprocalLattice: No such file or directory
-/bin/bash: ctfDeterminationFromPhaseComparison: そのようなファイルやディレクトリはありません
+/bin/bash: ctfDeterminationFromPhaseComparison: No such file or directory
-/bin/bash: ctfDeterminationFromThonRing: そのようなファイルやディレクトリはありません
+/bin/bash: ctfDeterminationFromThonRing: No such file or directory
-/bin/bash: ctfFunctionServer: そのようなファイルやディレクトリはありません
+/bin/bash: ctfFunctionServer: No such file or directory
-/bin/bash: ctfZeroPoint: そのようなファイルやディレクトリはありません
+/bin/bash: ctfZeroPoint: No such file or directory
-/bin/bash: defocusDeterminationFromThonRing: そのようなファイルやディレクトリはありません
+/bin/bash: defocusDeterminationFromThonRing: No such file or directory
-/bin/bash: homology2PG: そのようなファイルやディレクトリはありません
+/bin/bash: homology2PG: No such file or directory
-/bin/bash: pgDataBaseSelectServer: そのようなファイルやディレクトリはありません
+/bin/bash: pgDataBaseSelectServer: No such file or directory
-/bin/bash: pgJournalSelect: そのようなファイルやディレクトリはありません
+/bin/bash: pgJournalSelect: No such file or directory
-/bin/bash: pgJournalSelectCORBAClient: そのようなファイルやディレクトリはありません
+/bin/bash: pgJournalSelectCORBAClient: No such file or directory
-/bin/bash: pgJournalSelectCORBAServer: そのようなファイルやディレクトリはありません
+/bin/bash: pgJournalSelectCORBAServer: No such file or directory
-/bin/bash: pgMemoSelectCORBAServer: そのようなファイルやディレクトリはありません
+/bin/bash: pgMemoSelectCORBAServer: No such file or directory
-/bin/bash: pgSelect: そのようなファイルやディレクトリはありません
+/bin/bash: pgSelect: No such file or directory
-/bin/bash: eosBayesInit: そのようなファイルやディレクトリはありません
+/bin/bash: eosBayesInit: No such file or directory
-/bin/bash: eosPointAffineTransform: そのようなファイルやディレクトリはありません
+/bin/bash: eosPointAffineTransform: No such file or directory
-/bin/bash: eosPointCurvatureInfo: そのようなファイルやディレクトリはありません
+/bin/bash: eosPointCurvatureInfo: No such file or directory
-/bin/bash: eosPointPositionCorrection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>eosPointPositionCorrection</TITLE>
+</HEAD>
+<BODY>
+<H1>eosPointPositionCorrection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: eosPointPositionCorrection
+Options:
+ [-i[nput] In (NULL ).as(inFile::eosPoint ) ] :Essential :Input:eosPoint
+ [-i[nput]t[ype] InType (0 ).as(Integer ) ] :Optional :Input:eosPointMode
+ [-n[umber] N (-1 ).as(Integer ) ] :Optional :Input:number of Point, n, dependent upon m=n/(n-1)/2, a point number in In
+ [-o[utput] Out (stdout ).as(outFile::eosPoint ) ] :Optional :Output:eosPoint
+ [-o[utput]t[ype] OutType (0 ).as(Integer ) ] :Optional :Output:eosPoint
+ [-delta OutDelta (stdout ).as(outFile::eosPoint ) ] :Optional :Output:eosPoint
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+type-0: x y z
+type-1: x y z sig
+type-2: x y z sigx sigy sigz
+type-3: x y z sig sigx sigy sigz
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: eosPointProjector: そのようなファイルやディレクトリはありません
+/bin/bash: eosPointProjector: No such file or directory
-/bin/bash: mrc2gif: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2gif: No such file or directory
-/bin/bash: mrc2lattice: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2lattice: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>mrc2png</TITLE>
-</HEAD>
-<BODY>
-<H1>mrc2png</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrc2png
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-z[section] z (0 ).as(Integer ) ] :Optional :z-section
- [-Format Format (%s.%03d.png).as(String ) ] :Optional :OutputFileNameFormat
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrc2png: No such file or directory
-/bin/bash: mrc2pov: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2pov: No such file or directory
-/bin/bash: mrc2viff: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2viff: No such file or directory
-/bin/bash: hf2000Init: そのようなファイルやディレクトリはありません
+/bin/bash: hf2000Init: No such file or directory
-/bin/bash: hf2000LenzCurrent: そのようなファイルやディレクトリはありません
+/bin/bash: hf2000LenzCurrent: No such file or directory
-/bin/bash: hf2000SpecimenPosition: そのようなファイルやディレクトリはありません
+/bin/bash: hf2000SpecimenPosition: No such file or directory
-/bin/bash: khorosFilterGenerate: そのようなファイルやディレクトリはありません
+/bin/bash: khorosFilterGenerate: No such file or directory
-/bin/bash: llDataFitServer: そのようなファイルやディレクトリはありません
+/bin/bash: llDataFitServer: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>llDataPrint</TITLE>
-</HEAD>
-<BODY>
-<H1>llDataPrint</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: llDataPrint
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
- [-i[nput]s Ins (NULL ).as(inFileList ) ] :Optional :InputDataFileList
- [-i2[nput] Nea (NULL ).as(inFile )
- Far (NULL ).as(inFile ) ] :Optional :InputDataFile(nea and far)
- [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
- [-Rmax Rmax (0.1 ).as(Real ) ] :Optional :Input: Rmax [/A]
- [-I[nteractive] ] :Optional :Interactive
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: llDataPrint: No such file or directory
-/bin/bash: llDataRotation: そのようなファイルやディレクトリはありません
+/bin/bash: llDataRotation: No such file or directory
-/bin/bash: llDataSeparate: そのようなファイルやディレクトリはありません
+/bin/bash: llDataSeparate: No such file or directory
-/bin/bash: fft2d: そのようなファイルやディレクトリはありません
+/bin/bash: fft2d: No such file or directory
-/bin/bash: mrc2dsn6: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2dsn6: No such file or directory
-/bin/bash: mrc2hdf: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2hdf: No such file or directory
-/bin/bash: mrcImage1dCutAverage: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImage1dCutAverage: No such file or directory
-/bin/bash: mrcImage3DCTFObservation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImage3DCTFObservation: No such file or directory
-/bin/bash: mrcImage3DPeakGet: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImage3DPeakGet: No such file or directory
-/bin/bash: mrcImageAddValue: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAddValue</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAddValue</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAddValue
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrc
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: mrc
+ [-v[alue] Value (0.0 ).as(Real ) ] :Optional :Value: o=i+v
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :UseCuda
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImageAutoFilamentExtract: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageAutoFilamentExtract: No such file or directory
-/bin/bash: mrcImageAutoRotationCorrelationResultPrint: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageAutoRotationCorrelationResultPrint: No such file or directory
-/bin/bash: mrcImageAutoTriming: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageAutoTriming: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>mrcImageBilateralFilter</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageBilateralFilter</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageBilateralFilter
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-s[igma]D[ensity] SigmaDensity (2.0 ).as(Real ) ] :Optional :SigmaDensity
- [-k[ernal]T[type]D[ensity]KernelTypeDensity (0 ).as(Integer ) ] :Optional :KernelTypeForDensity
- [-s[igma]S[pace] SigmaSpace (1.0 ).as(Real ) ] :Optional :SigmaSpace
- [-s[igma]S[pace]3 SigmaSpaceX (1.0 ).as(Real )
- SigmaSpaceY (1.0 ).as(Real )
- SigmaSpaceZ (1.0 ).as(Real ) ] :Optional :SigmaSpace(3D)
- [-k[ernel]T[ype]S[pace]KernelTypeSpace (0 ).as(Integer ) ] :Optional :KernelTypeForSpace
- [-k[ernel]S[ize] KernelSize (5 ).as(Integer ) ] :Optional :KernelSize
- [-k[ernel]S[ize]3 KernelSizeX (5 ).as(Integer )
- KernelSizeY (5 ).as(Integer )
- KernelSizeZ (5 ).as(Real ) ] :Optional :KernelSize(3D)
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-Bilateral Filter
- by Tomashi and Manduchi
- C. Tomasi and R. Manduchi, Bilateral Filtering for Gray and Color Images, Proceedings of the 1998 IEEE International Conference on Computer Vision, Bombay, India
- fi = Sigma_j(W(i,j)*Ij)/ Sigma_j(Wj)
- ,where W(i,j)=W_x(xi,xj)*W_I(Ii,Ij)
-------- linfo.mode : 0
- W_x(xi,xj) = exp(-|xi-xj|^2/2 sigmaSpace^2 )
- W_I(Ii,Ij) = exp(-|Ii-Ij|^2/2 sigmaDensity^2)
-------- linfo.mode : 1
- W_x(xi,xj) = 1/(1+|xi-xj|^2/sigmaSpace^2 )
- W_I(Ii,Ij) = 1/(1+|Ii-Ij|^2/sigmaDensity^2)
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageBilateralFilter: No such file or directory
-/bin/bash: mrcImageBlurByTemperatureFactor: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageBlurByTemperatureFactor: No such file or directory
-/bin/bash: mrcImageColoring: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageColoring: No such file or directory
-/bin/bash: mrcImageConvolution: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageConvolution: No such file or directory
-/bin/bash: mrcImageCorrelationServer: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCorrelationServer: No such file or directory
-/bin/bash: mrcImageCorrelationWithCTFCompensation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCorrelationWithCTFCompensation: No such file or directory
-/bin/bash: mrcImageCrystalDeform: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCrystalDeform: No such file or directory
-/bin/bash: mrcImageCutAndSetInArray: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCutAndSetInArray: No such file or directory
-/bin/bash: mrcImageDeconvolution: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDeconvolution</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDeconvolution</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDeconvolution
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: Src
+ [-k[ernel] Kernel (NULL ).as(inFile::mrcImage ) ] :Essential :Input: Kernel
+ [-k[ernel]centre KernelCentre (1 ).as(Integer ) ] :Optional :Input: Kernel Centre
+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: Dst
+ [-o[utput]conv OutConv (NULL ).as(outFile::mrcImage ) ] :Optional :Output: Conv*Dst to compare with in
+ [-O[utput] OutASCII (stdout ).as(outFile::ASCII ) ] :Optional :Output: Param
+ [-O[utput]RMSD OutRMSD (NULL ).as(outFile::mrcImage ) ] :Optional :Output: Param
+ [-thresCTF thresCTF (1e-4 ).as(Real ) ] :Optional :threshold CTF for InverseFilter
+ [-NSRatio NSRatio (0.0 ).as(Real ) ] :Optional :N/S Ratio for R-dependent Wiener Filter
+ [-NSCoeff NSCoeff (0.0 ).as(Real ) ] :Optional :N/S Coeff for R-dependent Wiener Filter
+ [-Pad3DMode Pad3DMode (1 ).as(Integer ) ] :Optional :lmrcImage3DPad Mode
+ [-r[max] r (0 ).as(Real ) ] :Optional :Pad3D: [pix] Threshold radius of signal.Default is min(Nx,Ny).
+ [-w[idth] w (1 ).as(Real ) ] :Optional :Pad3D: [pix] Width of slope. For mode 1.
+ [-v[alue] v (0 ).as(Real ) ] :Optional :Pad3D: Value of out of threshold.
+ [-Floating ] :Optional :Pad3D: Floating
+ [-maxIter maxIter (0 ).as(Integer ) ] :Optional :maxIteration for Iterative
+ [-minRMSD minRMSD (0.0 ).as(Real ) ] :Optional :min of MRSD for Iterative
+ [-lambda lambda (0.5 ).as(Real ) ] :Optional :lambda for Iterative
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+Deconvolution Mode
+0: No deconvolution
+1: CTF/|CTF| (phase flipping)
+2: CTF (CTF-Multi)
+3: 1/CTF (Inverse Filter)
+4: CTF/(SQR(CTF)+SQR(NS)) (Wiener Filter)
+5: SQR(CTF) x CTF/|CTF| (phase flipping + ctfWeighted)
+6: 1/|CTF| (No phase-flipping: Inverse Filter)
+7: |CTF|/(SQR(CTF)+SQR(NS)) (No phase-flipping: Wiener Filter)
+8: CTF /(SQR(CTF)+SQR(NS*exp(a*R))) (phase-flipping: Wiener Filter + Noise)
+9: |CTF|/(SQR(CTF)+SQR(NS*exp(a*R))) (No phase-flipping: Wiener Filter + Noise)
+</PRE>
+</BODY>
+</HTML>
Options:
[-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
[-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
- [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 5.533535e-322ach
+ [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 3.025695e-314ach
[-log Log (NULL ).as(appendFile ) ] :Optional :OutputDataFile
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
-/bin/bash: mrcImageEnhancementWithFuzzySets: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageEnhancementWithFuzzySets: No such file or directory
-/bin/bash: mrcImageFilamentSearch: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageFilamentSearch: No such file or directory
--- /dev/null
+../../../../../hostdepend/ARM64MAC64/src/Tools/mrcImage/mrcImageFilamentSearchResultShow/src/ARM64MAC64
\ No newline at end of file
-/bin/bash: mrcImageFractalFrourierShellCorrelation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageFractalFrourierShellCorrelation: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>mrcImageMeanFreePathCalc</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageMeanFreePathCalc</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageMeanFreePathCalc
-Options:
- [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:mrcImage
- [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:distribution
- [-O[utput]w[hite]all OutWhiteAll (NULL ).as(outFile::mrcImage ) ] :Optional :Output: white+whiteEdge
- [-O[utput]w[hite] OutWhite (NULL ).as(outFile::mrcImage ) ] :Optional :Output: white
- [-O[utput]b[lack]all OutBlackAll (NULL ).as(outFile::mrcImage ) ] :Optional :Output: black+blackEdge
- [-O[utput]b[lack] OutBlack (NULL ).as(outFile::mrcImage ) ] :Optional :Output: black
- [-O[utput]w[hite]e[dge]OutWhiteEdge (NULL ).as(outFile::mrcImage ) ] :Optional :Output: whiteEdge
- [-O[utput]b[lack]e[dge]OutBlackEdge (NULL ).as(outFile::mrcImage ) ] :Optional :Output: blackEdge
- [-O[utput]dir[ection]Direction (direction ).as(String ) ] :Optional :Output: basename.[0|1|2] vector for any
- [-l[ine]t[hickness] LineThicknessX (1 ).as(Real )
- LineThicknessY (1 ).as(Real ) ] :Optional :[pixel]
- [-l[ine]m[ode] LineMode (0 ).as(Integer ) ] :Optional :LineMode
- [-l[ine]s[hape] LineShape (0 ).as(Integer ) ] :Optional :LineShape
- [-deltaPhi deltaPhi (30 ).as(Real ) ] :Optional :deltaPhi
- [-deltaTheta deltaTheta (30 ).as(Real ) ] :Optional :deltaTheta
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
->>>> mode
-0: Along Z-axis
-1: Along X-axis
-2: Along Y-axis
-3: For any direction
-+16: Length is shown in real using HeaderLength
->>>> line shape
-0: LineShape-Rectangle
-1: LineShape-Disk
->>>> line mode
-0: LineMode-And
-1: LineMode-Or
-2: LineMode-GE(Greater than or equal to)
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageMeanFreePathCalc: No such file or directory
-/bin/bash: mrcImageMergeFFT: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageMergeFFT: No such file or directory
-/bin/bash: mrcImageNLMeansFilter: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageNLMeansFilter: No such file or directory
-/bin/bash: mrcImagePad: そのようなファイルやディレクトリはありません
+dyld[97779]: symbol not found in flat namespace '_cblas_caxpy'
-/bin/bash: mrcImagePeakSearch: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImagePeakSearch: No such file or directory
-/bin/bash: mrcImagePixelDataGet: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImagePixelDataGet</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImagePixelDataGet</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImagePixelDataGet
+Options:
+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrcImage
+ [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :OutputDataFile
+ [-x x (0.0 ).as(Real ) ] :Optional :Input: x
+ [-y y (0.0 ).as(Real ) ] :Optional :Input: y
+ [-z z (0.0 ).as(Real ) ] :Optional :Input: z
+ [-In[put] InCoord (stdin ).as(inFile::ASCII ) ] :Optional :Input:eosPoint
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :cudaDeviceID
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-o[utput]m[ode] outMode (0 ).as(Integer ) ] :Optional :Mode:Output
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode:Interpolation
+----- Additional Usage -----
+-m InterpolationMode ; refer to mrcImageROI
+-om outputMode
+ +1 : with coordinates
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: mrcImagePrint: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImagePrint: No such file or directory
-/bin/bash: mrcImagePrint3D: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImagePrint3D: No such file or directory
-/bin/bash: mrcImagePut3D: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImagePut3D: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>mrcImageRadialDistribution</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageRadialDistribution</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageRadialDistribution
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: ASCII
- [-O[utputMRC] Out2 (NULL ).as(outFile ) ] :Optional :Output: MRC
- [-centre Cx (0.0 ).as(Real )
- Cy (0.0 ).as(Real ) ] :Optional :[pixel]
- [-Cs[phere] Csx (0.0 ).as(Real )
- Csy (0.0 ).as(Real )
- Csz (0.0 ).as(Real ) ] :Optional :[pixel]
- [-Avg ] :Optional :flagAvg: Averaged Intensity
- [-Inv ] :Optional :flagInv: Inversed Intensity
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
->> Mode
- 0: 2D or 3D(Cylindrical Coordinates)
- 1: 2D or 3D(Spherical Coordinates)
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageRadialDistribution: No such file or directory
-/bin/bash: mrcImageSNEstimate: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageSNEstimate: No such file or directory
-/bin/bash: mrcImageShapePCA: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageShapePCA: No such file or directory
-/bin/bash: mrcImageShapePCAFit: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageShapePCAFit: No such file or directory
-/bin/bash: mrcImageShapeRelaxation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageShapeRelaxation: No such file or directory
-/bin/bash: mrcImageShapeSearch: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageShapeSearch: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>mrcImageSphereCheck</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageSphereCheck</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageSphereCheck
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:
- [-n[ormalized] OutNOr (NULL ).as(outFile ) ] :Optional :Output: NormalizedImage
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageSphereCheck: No such file or directory
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Essential :RealSpaceCalculating
[-LabelingMode labelingmode (0 ).as(Integer ) ] :Optional :LabelingMode
- [-max[value] max (800 ).as(Integer ) ] :Optional :Density Max value:Support Constraint(%)
- [-min[value] min (200 ).as(Integer ) ] :Optional :Density Min value:Support Constraint(%)
+ [-max[value] max (800 ).as(Integer ) ] :Optional :Density Max value:Support Constraint()
+ [-min[value] min (200 ).as(Integer ) ] :Optional :Density Min value:Support Constraint()
[-sh[ape] shape (0 ).as(Integer ) ] :Optional :Shape:0(Rectangule),1(Globe)
[-h[alf]v[alue]p[oint]hvp (0.0 ).as(Real ) ] :Optional :Half value point(/[A])
[-Inverse ] :Optional :Inverse
-<HTML>
-<HEAD>
-<TITLE>mrcImageUnsharpening</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageUnsharpening</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageUnsharpening
-Options:
- [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input: mrcImage
- [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: mrcImage
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
---UnsharpeningMode--
-0: 0 -1 0
- -1 5 -1
- 0 -1 0
-1:-1 -1 -1
- -1 9 -1
- -1 -1 -1
-2: 1 -2 1
- -2 5 -2
- 1 -2 1
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageUnsharpening: No such file or directory
[-D[elta] Delta (5.0 ).as(Real ) ] :Optional :Delta[A]
[-R[ange] MinVol (0.0 ).as(Real )
MaxVol (200.0 ).as(Real )
- DeltaVol (10.0 ).as(Real ) ] :Optional :vol%
+ DeltaVol (10.0 ).as(Real ) ] :Optional :vol
[-I[nverse] ] :Optional :Inverse
[-format Format (ContourLevel(%3g): %g %lu).as(StringAll ) ] :Optional :Format
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
-<HTML>
-<HEAD>
-<TITLE>mrcMultiFFTCentralSectionsSigmaCalc</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcMultiFFTCentralSectionsSigmaCalc</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcMultiFFTCentralSectionsSigmaCalc
-Options:
- [-i[nput] In (NULL ).as(inFileNoOpen::mrcImage)
- PathIn (./ ).as(String ) ] :Essential :Input:2DFT
- [-i[nput]L[ikelihood]InLikelihood (NULL ).as(inFileListNoOpen )
- PathL (./ ).as(String ) ] :Essential :Input: LikelihoodList
- [-i[nput]3d[SectionList]In3D (NULL ).as(inFileListNoOpen )
- Path3D (./ ).as(String ) ] :Essential :Input: CentralSectionList
- [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output: 2DSigma
- [-EulerMode EulerMode (YOYS ).as(String ) ] :Optional :Input: EulerMode
- [-Rot1 Rot1Start (0.0 ).as(Real )
- Rot1End (360.0 ).as(Real )
- Rot1Delta (10 ).as(Real ) ] :Optional :OutputDataFile
- [-Rot2 Rot2Start (0.0 ).as(Real )
- Rot2End (360.0 ).as(Real )
- Rot2Delta (10 ).as(Real ) ] :Optional :OutputDataFile
- [-Rot3 Rot3Start (0.0 ).as(Real )
- Rot3End (360.0 ).as(Real )
- Rot3Delta (10 ).as(Real ) ] :Optional :OutputDataFile
- [-trans[late] TransX (0.0 ).as(Real )
- TransY (0.0 ).as(Real ) ] :Optional :Input: Translation
- [-InterpMode InterpMode (0 ).as(Integer ) ] :Optional :Interpolation Mode
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcMultiFFTCentralSectionsSigmaCalc: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>mrcRefNormalizing</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcRefNormalizing</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcRefNormalizing
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcRefNormalizing: No such file or directory
-/bin/bash: mrcView: そのようなファイルやディレクトリはありません
+/bin/bash: mrcView: No such file or directory
-/bin/bash: molvie: そのようなファイルやディレクトリはありません
+/bin/bash: molvie: No such file or directory
-/bin/bash: molvieDock: そのようなファイルやディレクトリはありません
+/bin/bash: molvieDock: No such file or directory
-/bin/bash: molvieFlight: そのようなファイルやディレクトリはありません
+/bin/bash: molvieFlight: No such file or directory
-/bin/bash: molvieMrcViewer: そのようなファイルやディレクトリはありません
+/bin/bash: molvieMrcViewer: No such file or directory
-/bin/bash: molvieProjection: そのようなファイルやディレクトリはありません
+/bin/bash: molvieProjection: No such file or directory
-/bin/bash: molvieViewer: そのようなファイルやディレクトリはありません
+/bin/bash: molvieViewer: No such file or directory
-/bin/bash: pdb2mrc2d: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdb2mrc2d</TITLE>
+</HEAD>
+<BODY>
+<H1>pdb2mrc2d</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdb2mrc2d
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile(2D)
+ [-O[utput] Out3D (NULL ).as(outFile ) ] :Optional :OutputDataFile(3D)
+ [-d[elta] dx (5.0 ).as(Real )
+ dy (5.0 ).as(Real ) ] :Essential :delta: dx[A] dy[A]
+ [-s[tart] sx (0.0 ).as(Real )
+ sy (0.0 ).as(Real ) ] :Optional :start: startx[A] starty[A]: When -s was not set, image centre is the origin(0,0,0)
+ [-n[umber] nx (0 ).as(Integer )
+ ny (0 ).as(Integer ) ] :Essential :N: nx ny (image size)
+ [-Rot[ation] rotnx (1 ).as(Integer )
+ rotny (1 ).as(Integer ) ] :Optional :rotnx rotny
+ [-S[tart] srotx (0.0 ).as(Real )
+ sroty (0.0 ).as(Real )
+ srotz (0.0 ).as(Real ) ] :Optional :start(rotx roty rotz):ZXY
+ [-startE[uler]A[ngle]sRotMode (YOYS ).as(String )
+ sRot1 (0.0 ).as(Real )
+ sRot2 (0.0 ).as(Real )
+ sRot3 (0.0 ).as(Real ) ] :Optional :EulerAngle: Start Angle
+ [-E[uler]A[ngle]Mode RotMode (YOYS ).as(String ) ] :Optional :RotationMode
+ [-E[uler]A[ngle]Rot1 dRot1 (5.0 ).as(Real )
+ minRot1 (0.0 ).as(Real )
+ maxRot1 (180.0 ).as(Real ) ] :Optional :FirstRotation
+ [-E[uler]A[ngle]Rot2 dRot2 (5.0 ).as(Real )
+ minRot2 (0.0 ).as(Real )
+ maxRot2 (180.0 ).as(Real ) ] :Optional :SecondRotation
+ [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :weight
+ [-sig[ma] Sigma (0.0 ).as(Real ) ] :Optional :Sigma[A]:Atom radius
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :UseCuda
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode: 0 Merc; 1: Earth
+----- Attention1 -----
+If both of -s and -startEA, first -s and second -startEA will be performed
+----- Attention2 -----
+Bug fixed: rotation around x-axis. + is changed to -
+----- Mode -----
+1: 0: equal angle 1: equal area
+2: 0: Mercatol 1: Morwide
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdb2mrc2dWithCTF: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdb2mrc2dWithCTF</TITLE>
+</HEAD>
+<BODY>
+<H1>pdb2mrc2dWithCTF</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdb2mrc2dWithCTF
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: PDB
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: MRC
+ [-N Nx (2048 ).as(Integer )
+ Ny (2048 ).as(Integer ) ] :Optional :Input: Nx Ny [pixel]
+ [-d dx (1.72 ).as(Real )
+ dy (1.72 ).as(Real ) ] :Optional :Input: dx dy [A]
+ [-Centre cx (0 ).as(Real )
+ cy (0 ).as(Real )
+ cz (0 ).as(Real ) ] :Optional :Input: CentreX CentreY [A]
+ [-n nx (64 ).as(Integer )
+ ny (64 ).as(Integer ) ] :Optional :Input: nx ny for subimage [pixel]
+ [-kV kV (200. ).as(Real ) ] :Optional :kV
+ [-Cs Cs (1.7 ).as(Real ) ] :Optional :Cs
+ [-d[e]f[ocus] Defocus (10000 ).as(Real ) ] :Optional :Defocus [A] at z = 0
+ [-A[overP] AoverP (0.07 ).as(Real ) ] :Optional :AoverP
+ [-Ain Ain (0.2 ).as(Real ) ] :Optional :Beta: IlluminationAngle [mrad]
+ [-ctfMode ctfMode (33 ).as(Integer ) ] :Optional :ctfMode
+ [-E[uler]A[ngle] EulerAngle (XEYS ).as(String )
+ Rot1 (0 ).as(Real )
+ Rot2 (0 ).as(Real )
+ Rot3 (0 ).as(Real ) ] :Optional :EulerAngle: [degree]
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbChargeFit: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbChargeFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbChargeFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbChargeFit
+Options:
+ [-i[nput]f[ixed pdb] InFix (NULL ).as(inFile ) ] :Essential :InputFixedPdbFile
+ [-i[nput]m[oved pdb] InMove (NULL ).as(inFile ) ] :Essential :InputMovedPdbFile
+ [-o[utput] OutTxt (NULL ).as(outFile ) ] :Essential :OutputTextFile
+ [-s[ymmetry of helix(degree/A)]symmetry (0.47096 ).as(Real ) ] :Optional :default: 13/28
+ [-zmin zmin (-28 ).as(Real ) ] :Optional :minimum z
+ [-zmax zmax (28 ).as(Real ) ] :Optional :maximum z
+ [-zDel[ta] zDel (1 ).as(Real ) ] :Optional :delta z
+ [-mind[istance] mind (1 ).as(Real ) ] :Optional :set atoms distance to mind
+ [-maxd[istance] maxd (5 ).as(Real ) ] :Optional :ignore atoms distance
+ [-a[xis coordinate] axisX (70 ).as(Real )
+ axisY (70 ).as(Real ) ] :Optional :(x, y)
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Algorythm -----
+score = Sum(1/SQR(length))
+, where length is the set of length between charged atoms
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbCrystalCreate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbCrystalCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbCrystalCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbCrystalCreate
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input:PDB
+ [-I[nfo] Info (NULL ).as(inFile ) ] :Essential :Input:Crystal Information
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output:PDB
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+----- CrystalInfo -----
+aAxis %15.6g %15.6g %15.6g
+bAxis %15.6g %15.6g %15.6g
+cAxis %15.6g %15.6g %15.6g
+CellLength %15.6g %15.6g %15.6g
+Origin %15.6g %15.6g %15.6g
+N %15d %15d %15d
+StartN %15d %15d %15d
+SpaceGroup %15d
+HelixInfo %10d %10d %10d
+### Attention ###
+Parameter Order is important: Dependent between CellLength and a|b|cAxis.
+ Because each of aAxis, bAxis, cAxis must be a unit vector.
+HelixInfo t u n
+----- CrystalSpaceGroup -----
+ 0 P1
+ 1 HelicalSymmmetry
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbHelix: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbHelix</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbHelix</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbHelix
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-3[D] Out3D (NULL ).as(outFile ) ] :Optional :OutputDataFile(3D-mrc)
+ [-2[D] Out2D (NULL ).as(outFile ) ] :Optional :OutputDataFile(2D-mrc projection(y-z))
+ [-d[elta] delta (5 ).as(Real ) ] :Optional :delta[A](mrc-file)
+ [-p[delphi] delphi (165 ).as(Real ) ] :Essential :deltaPhi
+ [-dp[delphi] deldelphi (5 ).as(Real ) ] :Optional :deltaDeltaPhi
+ [-z[deltaz] delz (5 ).as(Real ) ] :Essential :deltaz
+ [-n[Molecule] nMolecule (1 ).as(Integer ) ] :Essential :NumberOfMolecules
+ [-nx nx (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-ny ny (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-nz nz (1 ).as(Integer ) ] :Optional :Pixel[Def:]
+ [-Sx[tart] Startx (0.0 ).as(Real ) ] :Optional :Startx[A]
+ [-Sy[tart] Starty (0.0 ).as(Real ) ] :Optional :Starty[A]
+ [-Sz[tart] Startz (0.0 ).as(Real ) ] :Optional :Startz[A]
+ [-w[eight] Weight (1.0 ).as(Real ) ] :Optional :Weight
+ [-dx dx (2.5 ).as(Real ) ] :Optional :dx
+ [-dy dy (2.5 ).as(Real ) ] :Optional :dy
+ [-dz dz (2.5 ).as(Real ) ] :Optional :dz
+ [-startn startn (0 ).as(Integer ) ] :Optional :start molecule's index
+ [-startC startID (A ).as(Character ) ] :Optional :start chain ID
+ [-deltaSeq deltaSeq (1000 ).as(Integer ) ] :Optional :start chain ID
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbHomologySearch: そのようなファイルやディレクトリはありません
+/bin/bash: pdbHomologySearch: No such file or directory
-/bin/bash: pdbMatrixCreate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbMatrixCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbMatrixCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbMatrixCreate
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataToBeFitted
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :InputReference
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-M[atrixFile] Matrix (NULL ).as(outFile ) ] :Essential :OutputMatrixFile
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbMove: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbMove</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbMove</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbMove
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-x X (0.0 ).as(Real ) ] :Optional :Move X[A]
+ [-y Y (0.0 ).as(Real ) ] :Optional :Move Y[A]
+ [-z Z (0.0 ).as(Real ) ] :Optional :Move Z[A]
+ [-originTo toX (0.0 ).as(Real )
+ toY (0.0 ).as(Real )
+ toZ (0.0 ).as(Real ) ] :Optional :move (0,0,0) to (X,Y,Z)
+ [-toOrigin fromX (0.0 ).as(Real )
+ fromY (0.0 ).as(Real )
+ fromZ (0.0 ).as(Real ) ] :Optional :move (X,Y,Z) to (0,0,0)
+ [-GCtoOrigin ] :Optional :GC(Gravity Centre) to origin
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbPCA: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbPCA</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbPCA</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbPCA
+Options:
+ [-i[nput] In (stdin ).as(inFile ) ] :Optional :InputDataFile
+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output: Result
+ [-o[utput]U[nit] OutUnit (NULL ).as(outFile ) ] :Optional :Output: Unit Vector Array
+ [-o[utput]M[atrix3D] OutMat3D (NULL ).as(outFile ) ] :Optional :Output: Matrix3D from Unit Vector Array
+ [-o[utput]PDB OutPDB (NULL ).as(outFile ) ] :Optional :Output: PDB rotated from Unit Vector Array
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbRhoFit: そのようなファイルやディレクトリはありません
+/bin/bash: pdbRhoFit: No such file or directory
-/bin/bash: pdbRhoFitTm: そのようなファイルやディレクトリはありません
+/bin/bash: pdbRhoFitTm: No such file or directory
-/bin/bash: pdbRotation: そのようなファイルやディレクトリはありません
+/bin/bash: pdbRotation: No such file or directory
-/bin/bash: pdbShapeFit: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbShapeFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbShapeFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbShapeFit
+Options:
+ [-i[nput]pdb[File] InPDB (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]mrc[File] InMRC (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-C[ontour] Contour (0.0 ).as(Real ) ] :Essential :Contour
+ [-C[ontour]M[ode] ContourMode (0 ).as(Integer ) ] :Optional :ContourMode: refer to mrcImageContourSurfaceCreate
+ [-o[utput of ]mrc OutMRC (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]txt OutTxt (stdout ).as(outFile ) ] :Optional :OutputDataFile
+ [-o[utput of ]pdb OutPDB (NULL ).as(outFile ) ] :Optional :OutputDataFile
+ [-xmin xmin (0 ).as(Real ) ] :Optional :xmin for fitting
+ [-xmax xmax (0 ).as(Real ) ] :Optional :xmax for fitting
+ [-xd[elta] xDelta (1 ).as(Real ) ] :Optional :delta x for fitting
+ [-ymin ymin (0 ).as(Real ) ] :Optional :ymin for fitting
+ [-ymax ymax (0 ).as(Real ) ] :Optional :ymax for fitting
+ [-yd[elta] yDelta (1 ).as(Real ) ] :Optional :delta y for fitting
+ [-zmin zmin (0 ).as(Real ) ] :Optional :zmin for fitting
+ [-zmax zmax (82 ).as(Real ) ] :Optional :zmax for fitting
+ [-zd[elta] zDelta (1 ).as(Real ) ] :Optional :delta z for fitting
+ [-E[uler]A[ngle] EulerAngle (ZOYS ).as(String ) ] :Optional :Euler Angle for three-angle
+ [-phimin phimin (0 ).as(Real ) ] :Optional :phimin for fitting(degree)
+ [-phimax phimax (194 ).as(Real ) ] :Optional :phimax for fitting(degree)
+ [-phid[elta] phiDelta (2 ).as(Real ) ] :Optional :delta phi for fitting(degree)
+ [-psimin psimin (0 ).as(Real ) ] :Optional :psimin for fitting(degree)
+ [-psimax psimax (0 ).as(Real ) ] :Optional :psimax for fitting(degree)
+ [-psid[elta] psiDelta (2 ).as(Real ) ] :Optional :delta psi for fitting(degree)
+ [-thetamin thetamin (0 ).as(Real ) ] :Optional :thetamin for fitting(degree)
+ [-thetamax thetamax (0 ).as(Real ) ] :Optional :thetamax for fitting(degree)
+ [-thetad[elta] thetaDelta (2 ).as(Real ) ] :Optional :delta theta for fitting(degree)
+ [-P[DB]C[ontour]M[ode]surfaceMode (0 ).as(Integer ) ] :Optional :PDB SurfaceMode: refer to pdbSurface
+ [-order order (1.7 ).as(Real ) ] :Optional :order: refer to pdbSurface
+ [-refine refine (2 ).as(Integer ) ] :Optional :refine: refer to pdbSurface
+ [-size size (3 ).as(Integer ) ] :Optional :size: refer to pdbSurface
+ [-weight weight (100 ).as(Real ) ] :Optional :weight: refer to pdbSurface
+ [-mergin mergin (3.0 ).as(Real ) ] :Optional :mergin: refer to pdbSurface
+ [-thres thresHold (0.0 ).as(Real ) ] :Optional :threshold: refer to pdbSurface
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-Centre ] :Optional :Filament-axis is x=0, y=0
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+----- Additional Usage -----
+ -ipdb : Filename : An atomic model to be fitted (PDB)
+ -imrc : Filename : 3-D density map (mrc-formated)
+ -omrc : Filename : fitting score map (MRC)
+ z=0: a max-score map of an phi-z plane which includes a max score point.
+ The max score mean a maximum score in all x-y-psi-theta plane with specific values of phi and z.
+ z=1: a max-score map of an psi-theta plane which includes a max score point.
+ The max score mean a maximum score in all x-y plane with specific values of psi, theta, phi and z.
+ z=2: a score map of an x-y plane which includes a max score point.
+ -otxt : Filename : fitting results (Text)
+ -opdb : Filename : An atomic model with a maximum score after fitting
+ -x|y|zmin : Initial value of z (should <= zmax)
+ -x|y|zmax : Final value of z
+ -x|y|zd : Delta z for fitting (should !=0)
+ -phi|psi|thetamin : Initial value of phi (should <= phimax; initial value of phi is 0)
+ -phi|psi|thetamax : Final value of phi (should !=0)
+ -phi|psi|thetad : Delta phi for fitting (should >0)
+ -C : Contour level of map file
+ -Inverse: Protein has high density on the image
+ -Centre : Filament-axis in an inPDBFile is along the line of x=0, y=0
+ -EA : Euler Angle Set : ZOYS: z -> y -> x
+ -c : Not used now
+ -m 0 : Count the atom number inside the contour.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbTrans: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbTrans</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbTrans</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbTrans
+Options:
+ [-i[nput] inFile (NULL ).as(inFile ) ] :Essential :Input: DataFile
+ [-o[utput] outFile (NULL ).as(outFile ) ] :Essential :Output: DataFile
+ [-M[atrix] matFile (NULL ).as(inFile ) ] :Optional :Input: MatrixFile[4][4]
+ [-E[uler]A[ngle] RotMode (YOYS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :Input:
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :cuda
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+>>> Matrix3D File Format y = Ax + b<<<
+a11 a21 a31 : Rotation Array : y=Ax
+a12 a22 a32
+a13 a23 a33
+b1 b2 b3 : Translation Array : y = x + b
+--- Attention ---
+If both options of -M and -EA are set,
+ first, translation and rotation by -M will be performed
+ then, rotation by -EA will be done.
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbTwoProteinFit: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>pdbTwoProteinFit</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbTwoProteinFit</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbTwoProteinFit
+Options:
+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
+ [-i[nput]res[idue] InResidue (NULL ).as(inFile ) ] :Optional :ResidueInformationOfInputData
+ [-i[nput]sel[ectResidue]SelectIn (NULL ).as(outFile ) ] :Optional :Output: Selected residue of in after fitting
+ [-r[ef] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
+ [-r[ef]res[idue] RefResidue (NULL ).as(inFile ) ] :Optional :ResidueInfomationOfReferenceData
+ [-r[ef]sel[ectResidue]SelectRef (NULL ).as(outFile ) ] :Optional :Output: Selected residue of after fitting
+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
+ [-o[utput]Matrix Matrix (stdout ).as(outFile ) ] :Optional :OutputMatrix
+ [-o[utput]Param Param (stdout ).as(outFile ) ] :Optional :OutputParam
+ [-o[utput]Dis[tance] outDis (stdout ).as(outFile ) ] :Optional :Output: PDB Distance as Temp
+ [-o[utput]Dis[tance]2outDis2 (stdout ).as(outFile ) ] :Optional :Output: Distance List for Ca
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+>>>> Input and Reference File Format<<<<
+ResidueNumberToBeFitted
+...
+If |, all residules are sellected till the residue in the next line
+</PRE>
+</BODY>
+</HTML>
-/bin/bash: pdbView: そのようなファイルやディレクトリはありません
+/bin/bash: pdbView: No such file or directory
-/bin/bash: mrcImageNeuralNetParticleExtraction: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageNeuralNetParticleExtraction: No such file or directory
-/bin/bash: CheckOrientationByDegree: そのようなファイルやディレクトリはありません
+/bin/bash: CheckOrientationByDegree: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>calcCommonLine</TITLE>
-</HEAD>
-<BODY>
-<H1>calcCommonLine</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: calcCommonLine
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputEulerAnglesList
- [-R[ot]1 EMode1 (YOYS ).as(String )
- Rot1_1 (0.0 ).as(Real )
- Rot1_2 (0.0 ).as(Real )
- Rot1_3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle1[degree]
- [-R[ot]2 EMode2 (YOYS ).as(String )
- Rot2_1 (0.0 ).as(Real )
- Rot2_2 (0.0 ).as(Real )
- Rot2_3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle2[degree]
- [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:Degrees
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: calcCommonLine: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>commonLinesSearchByVoting</TITLE>
-</HEAD>
-<BODY>
-<H1>commonLinesSearchByVoting</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: commonLinesSearchByVoting
-Options:
- [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputCorrelationMapList
- [-i[nput]c[ommonLines]InC (NULL ).as(inFile ) ] :Optional :InputCommonLinesList
- [-i[nput]c[orrect]c[ommonLines]InCC (NULL ).as(inFile ) ] :Optional :InputCorrectCommonLinesList
- [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputFilteredCommonLinesList
- [-o[utput]a[ll] OutA (NULL ).as(outFile ) ] :Optional :OutputAllCommonLinesList
- [-o[utput]d[etecting]r[ate]OutDR (NULL ).as(outFile ) ] :Optional :OutputDetectingRate
- [-o[utput]d[etecting]r[ate]a[ll]OutDRA (NULL ).as(outFile ) ] :Optional :OutputDetectingRateALL
- [-o[utput]p[eaks]h[istgram]OutPH (NULL ).as(outFile ) ] :Optional :OutputPeaksHistgram
- [-e[stimation]n[umber]en (1 ).as(Integer ) ] :Optional :EstimationNumber
- [-th[resholdLevel] th (1 ).as(Integer ) ] :Optional :ThresholdLevel
- [-histgramCreate[Flag] ] :Optional :HistgramCreateFlag
- [-extend[VotingFlag] ] :Optional :ExtendVotingFlag
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-Common lines are filtered only top G*100/sqrt(N) %, where N is the number of projections.
--extend Option
- Execute extended voting.
--m Option
- 0: normal
- 1: self voting (each angle histgram peak is multiplyed by its correlation value)
--th Option
- :
- -1: G = 2^(-1)
- 0: G = 2^0
- 1: G = 2^1
- 2: G = 2^2
- :
--en Option
- Estimation number of common line in a map.
- Running time is proportional to this number.
- Default; 1: the largest value in a correlation map is detected as common line.
-MapList Format
- numOfProjection1 numOfProjection2 mapFileName
- : : :
-CLinesList Format
- numOfProjection1 numOfProjection2 [ degOfProjection1 degOfProjection2 degDiff cor ] mapFileName
- : : : : : : :
-Voting Algorithm by Amit Singer et al (2010),
-"Detecting consistent common lines in cryo-EM by voting " (doi:10.1016/j.jsb.2009.11.003)
-----------------------------
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: commonLinesSearchByVoting: No such file or directory
-/bin/bash: llExtractWithLayerSeparationServer: そのようなファイルやディレクトリはありません
+/bin/bash: llExtractWithLayerSeparationServer: No such file or directory
-/bin/bash: llExtractWithLayerSeparationSingle: そのようなファイルやディレクトリはありません
+/bin/bash: llExtractWithLayerSeparationSingle: No such file or directory
-/bin/bash: ltlg2ps: そのようなファイルやディレクトリはありません
+/bin/bash: ltlg2ps: No such file or directory
-/bin/bash: mrc2Dto3DforVariation: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2Dto3DforVariation: No such file or directory
-/bin/bash: mrcImageOrientationSearch: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageOrientationSearch: No such file or directory
-/bin/bash: muscleSimulation: そのようなファイルやディレクトリはありません
+/bin/bash: muscleSimulation: No such file or directory
-<HTML>
-<HEAD>
-<TITLE>anglediffchk</TITLE>
-</HEAD>
-<BODY>
-<H1>anglediffchk</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: anglediffchk
-Options:
- [-t[estAngle] Test (0.0 ).as(Real ) ] :Essential :test
- [-r[eferenceAngle] Reference (0.0 ).as(Real ) ] :Essential :reference
- [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :configFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: anglediffchk: No such file or directory
+#
+#
+#
+
+check:
+ for i in $(UTILS) ; do echo $$i; \
+ make $${i}Check; \
+ done
+
+config:
+ for i in $(UTILS) ; do echo $$i; \
+ make $${i}Config; \
+ done
+
+all:
+ for i in $(UTILS) ; do echo $$i; \
+ make $${i}All; \
+ done
+
+clean:
+ for i in $(UTILS) ; do echo $$i; \
+ make $${i}Clean; \
+ done
+
+cleanAll:
+ for i in $(UTILS) ; do echo $$i; \
+ make $${i}CleanAll; \
+ done
+
make clean
make config
make all
+ make cleanAll
check:
cd src$(OSTYPE) ; \
-include ${EOS_HOME}/src/Config/${EOS_HOST}.inc
+include ../../Config/Define.inc
+include ../../Config/Target.inc
+
+UTILS= hdf5
PREFIX=$$EOS_HOME/util/$$EOS_HOSTDIR
make cif_api
make libcif
-
-init:: init-hdf5 init-cif_api init-icu
-config:: config-hdf5 config-icu config-cif_api
-all:: all-hdf5
-clean::
-cleanAll::
-
init-pkg-config::
curl https://pkgconfig.freedesktop.org/releases/pkg-config-$(PKG-CONFIG-VERSION).tar.gz -O
cd cif_api; ./configure --enable-static --enable-shared --prefix=$(PREFIX) ICU_LIBS=$(PREFIX)/lib
-
hdf5::
- make init-hdf5
- make config-hdf5
- make all-hdf5
- make clean-hdf5
- make cleanAll-hdf5
+ make hdf5Check
+ make hdf5Config
+ make hdf5All
+ make hdf5Clean
+ make hdf5CleanAll
-init-hdf5::
+hdf5Check::
if [ ! -f hdf5-$(HDF5-VERSION3).tar.gz ] ; then \
curl -o hdf5-$(HDF5-VERSION3).tar.gz -L https://www.hdfgroup.org/package/hdf5-$(HDF5-VERSION2)-tar-gz/?wpdmdl=14582&refresh=5f54487ee2f341599359102 ; \
fi
tar xvzf hdf5-$(HDF5-VERSION3).tar.gz
-config-hdf5::
+hdf5Config::
cd hdf5-$(HDF5-VERSION3); ./configure --prefix=${EOS_HOME}/util/$(OSTYPE)/
-all-hdf5::
+hdf5All::
cd hdf5-$(HDF5-VERSION3); make; make test; make install
-clean-hdf5::
+hdf5Clean::
cd hdf5-$(HDF5-VERSION3); make clean
-cleanAll-hdf5::
+hdf5CleanAll::
rm -f hdf5-$(HDF5-VERSION3).tar.gz; rm -rf hdf5-$(HDF5-VERSION3)
libcif:
--- /dev/null
+Subproject commit 410ca90707c641dfb5dad09974211d27e4c2e664
include ${EOS_HOME}/src/Config/${EOS_HOST}.inc
include ../../Config/Define.inc
+include ../../Config/Target.inc
+
+UTILS=tiff jpeg gif
help:
@echo "make tiff"
-init:
-
TIFFWHERE=http://download.osgeo.org/libtiff/
TIFFNAME=tiff
TIFFVERSION=4.3.0
JPEGWHERE=https://www.ijg.org/files/
JPEGNAME=jpeg
JPEGVERSION=9e
+GIFWHERE=https://sourceforge.net/projects/giflib/files/
+GIFNAME=giflib
+GIFVERSION=5.2.1
+#
+# TIFF
+#
tiff:
- make tiffInit
+ make tiffCheck
make tiffConfig
make tiffAll
make tiffClean
make tiffCleanAll
-tiffInit:
+tiffCheck:
curl -o $(TIFFNAME)-$(TIFFVERSION).tar.gz -L $(TIFFWHERE)/$(TIFFNAME)-$(TIFFVERSION).tar.gz
tar xvzf $(TIFFNAME)-$(TIFFVERSION).tar.gz
tiffCleanAll:
rm -rf $(TIFFNAME)-$(TIFFVERSION); rm $(TIFFNAME)-$(TIFFVERSION).tar.gz
-cleanAll:
-
-
+#
+# JPEG
+#
jpeg:
- make jpegInit
+ make jpegCheck
make jpegConfig
make jpegAll
make jpegClean
make jpegCleanAll
-jpegInit:
+jpegCheck:
curl -o $(JPEGNAME)src.v$(JPEGVERSION).tar.gz -L $(JPEGWHERE)/$(JPEGNAME)src.v$(JPEGVERSION).tar.gz
tar xvzf $(JPEGNAME)src.v$(JPEGVERSION).tar.gz
cd $(JPEGNAME)-$(JPEGVERSION); make -i install
jpegClean:
- cd $(jpegNAME)-$(JEPGVERSION); make clean
+ cd $(JPEGNAME)-$(JPEGVERSION); make clean
jpegCleanAll:
- rm -rf $(jpegNAME)-$(JEPGERSION); rm $(JEPGNAME)-$(JEPGVERSION).tar.gz
+ rm -rf $(JPEGNAME)-$(JPEGVERSION); rm $(JPEGNAME)src.v$(JPEGVERSION).tar.gz
+
+#
+# GIF
+#
+
+giflib:
+ make gifCheck
+ make gifConfig
+ make gifgAll
+ make gifClean
+ make gifCleanAll
+
+gifCheck:
+ curl -o $(GIFNAME)-$(GIFVERSION).tar.gz -L $(GIFWHERE)/$(GIFNAME)-$(GIFVERSION).tar.gz
+ tar xvzf $(GIFNAME)-$(GIFVERSION).tar.gz
+
+gifConfig:
+ cd $(GIFNAME)-$(GIFVERSION); ./configure --prefix=${EOS_HOME}/util/${EOS_HOSTDIR}/
+
+gifAll:
+ cd $(GIFNAME)-$(GIFVERSION); make -i PREFIX=${EOS_HOME}/util/${EOS_HOSTDIR}/ install
+
+gifClean:
+ cd $(GIFNAME)-$(GIFVERSION); make clean
+
+gifCleanAll:
+ rm -rf $(GIFNAME)-$(GIFVERSION); rm $(GIFNAME)-$(GIFVERSION).tar.gz
-cleanAll:
include ${EOS_HOME}/src/Config/${EOS_HOST}${FLAG_ICC}.inc
+include ../../Config/Define.inc
+include ../../Config/Target.inc
-include Config/Define.inc
+UTILS=fftw gsl
FFTWWHERE=http://www.fftw.org/
FFTWVERSION=3.3.10
@echo "make fftw"
@echo "make gsl"
-check: fftwCheck gslCheck
-config: fftwConfig glsConfig
-all: fftwAll gslAll
-clean: fftwClean gslClean
-cleanAll: fftwCleanAll gslCleanAll
-
fftw::
make fftwCheck
make fftwConfig
include ${EOS_HOME}/src/Config/${EOS_HOST}.inc
+include ../../Config/Define.inc
+include ../../Config/Target.inc
+
+UTILS=AlsaLIb AlsaOS
ALSALIBVERSION=1.0.29
ALSALIBNAME=alsa-lib
ALSAOSSNAME=alsa-oss
ALSAOSSWHERE=ftp://ftp.alsa-project.org/pub/oss-lib/$(ALSAOSSNAME)-$(ALSAOSSVERSION).tar.bz2
-check: AlsaLibCheck AlsaOSSCheck
-
-config: AlsaLibConfig AlsaOSSCheck
-
-all: AlsaLibAll AlsaOSSAll
-
-clean: AlsaLibClean AlsaOSSClean
-
-cleanAll: AlsaLibCleanAll AlsaOSSCleanAll
-
#
# ALSA-LIB
#
-.SUFFIXES:
+include ../../Config/Define.inc
+include ../../Config/Target.inc
-.IGNORE:
+UTILS=Tcl Tk BLT VTK
SHELL=/bin/ksh
VTKWHERE=http://www.vtk.org/files/release/6.3/
#VTKWHERE=http://www.vtk.org/files/release/6.2/
-check: TclCheck TkCheck TcllibCheck TkImgCheck BLTCheck VTKCheck
-
-config: TclConfig TkConfig TkImgCheck BLTConfig VTKConfig
-
-all: Tcl Tk TkImg BLT VTK
-
-clean: TclClean TkClean TkImgClean BLTClean VTKClean
-
-cleanAll: TclCleanAll TkCleanAll TkImgCleanAll BLTCleanAll VTKCleanAll
-
tcl::
make TclCheck
make TclConfig
TclCleanAll::
@rm -rf tcl$(TCLVERSION) ;
- @rm tcl$(TCLVERSION)-src.tar.gz ;
+ @rm -f tcl$(TCLVERSION)-src.tar.gz ;
#@rm -f tcl$(TCLVERSION)-src.zip ;
TkClean::
cd vtk$(VTKVERSION) ; \
$(MAKE) distclean
+VTKCleanAll::
+ @rm -rf vtk$(VTKVERSION)
+ @rm -f $(VTKNAME).zip
+
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