the Fink project is an effort to port
popular Unix programs to Mac OS X
Package: ccp4-onlylibs-dev
# Use version numbering to sync with the current CCP4 release:
Version: 6.0.99
Revision: 1
GCC: 4.0
Source: http://sage.ucsc.edu/xtal/%n/%n-%v.tgz
#Source: ftp://ftp.ccp4.ac.uk/prerelease/ccp4-onlylibs-dev.tar.gz
# Source-MD5: 67de45f1d718627ab96939f5443937ae
#Source-MD5: e778478de628c75792d2401248c63350
Source-MD5: 04d79e0c72544ec1ba447bb1e91b4b54
#
SourceDirectory: %n
#Source2: http://chemistry.ucsc.edu/~wgscott/xtal/%n/%n-extras-0.1.tgz
#Source2-MD5: ea307964e3786bef0868ea56aaaa0471
#
Depends: gcc43-shlibs
BuildDepends: gcc43
# BuildDepends: fort77
BuildDependsOnly: false
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
###############################################################################
#Patch: %n.patch
PatchScript: <<
#!/bin/zsh -efv
umask 0022
# Use my patched configure and ccp4.setup-zsh files
#cp ../ccp4.setup-zsh include/.
# cp ../configure .
# setup scripts for tcsh, zsh and bash users
export TEMPXTAL=$PWD:h
#
perl -pi.bak -e 's|/xtal|\$TEMPXTAL|g' include/ccp4.setup*
# build prefix (changed in install)
perl -pi.bak -e 's|/prefix|%p|g' include/ccp4.setup*
# location of tcktk, blt (not needed here, but doesn't hurt).
perl -pi.bak -e 's|/usr/local/bin|%p/bin|g' include/ccp4.setup*
# same
# make copy for tcsh users (CCP4 convention is no suffix)
cp include/ccp4.setup-dist include/ccp4.setup
#
# Enable everything.
# We need the mmdbold clipper libraries built for COOT:
perl -pi.bak -e 's|enable_mmdbold=no|enable_mmdbold=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_phs=no|enable_phs=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_mmdb=no|enable_mmdb=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_minimol=no|enable_minimol=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_cif=no|enable_cif=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_ccp4=no|enable_ccp4=yes|g' lib/clipper/configure*
# perl -pi.bak -e 's|enable_cctbx=no|enable_cctbx=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_cns=no|enable_cns=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_fortran=no|enable_fortran=yes|g' lib/clipper/configure*
# clean up:
rm -f include/*.bak lib/clipper/*.bak
<<
###############################################################################
CompileScript: <<
#!/bin/zsh -efv
umask 0022
#cp -R ../src/* lib/clipper/src/.
export TEMPXTAL=$PWD:h
source include/ccp4.setup-zsh
export DYLD_LIBRARY_PATH=$CLIB
#
./configure --disable-cctbx --disable-phaser --disable-pdb_extract --disable-diffractionImg --onlylibs Darwin
#FC="fort77" ./configure --onlylibs Darwin
#ln -s $CCP4/lib/src $CCP4/lib/clipper/ccp4
#
# fix some post-configure bugs
#
make 2>../make.log |tee ../make.log
make install 2>../makeinst.log |tee ../makeinst.log
#
echo "Ignoring error messages. They are harmless"
#
command ls -1 lib/*.a
sleep 10
#
# rm $CCP4/lib/clipper/ccp4
# make realclean
<<
###############################################################################
InstallScript: <<
#!/bin/zsh -efv
umask 0022
export TEMPXTAL=$PWD:h
source include/ccp4.setup-zsh
export DYLD_LIBRARY_PATH=$CLIB
ORIGDIR=$(dirname $PWD)
#
# Change environment scripts to match final installation install prefix:
perl -pi.bak -e 's|\$TEMPXTAL|%p/share/xtal|g' include/ccp4.setup*
perl -pi.bak -e 's|CCP4_MASTER/%n|CCP4_MASTER/%n-%v|g' include/ccp4.setup-zsh
perl -pi.bak -e 's|ccp4-6.0.99|%n-%v|g' include/ccp4.setup*
rm -f include/*.bak
perl -pi.bak -e 's|%b|%p/share/xtal/%n-%v|g' bin/clipper-config
rm -f bin/clipper-config.bak
perl -pi.bak -e 's|%b|%p/share/xtal/%n-%v|g' lib/*.la
rm -f lib/*.la.bak
#
cp include/ssm/ssm_superpose.h include/ssm/ssm_superpose.h-orig
perl -pi -e 's|ivector FF1,FF2;||g' include/ssm/ssm_superpose.h
#
# Now install:
mkdir -p %i/bin
mkdir -p %i/share/xtal/%n-%v
cp bin/* %i/bin/.
cp -R * %i/share/xtal/%n-%v/.
ranlib %i/share/xtal/%n-%v/lib/**/*.a
<<
###############################################################################
SplitOff:<<
Package: clipper
Depends: clipper-bin, ccp4-onlylibs-dev
BuildDependsOnly: true
InstallScript: <<
mkdir -p %i/share/doc/installed-packages
touch %i/share/doc/installed-packages/%n
<<
Description: Working Clipper static libs and binaries
DescDetail:<<
Placeholder to install working static clipper libraries and binary
executables for packages that require both to be present for linking.
The aim of the project is to produce a set of object-oriented libraries
for the organisation of crystallographic data and the performance of
crystallographic computation. The libraries are designed as a framework
for new crystallographic software, which will allow the full power of
modern programming techniques to be exploited by the developer. This
will lead to greater functionality from simpler code which will be easier
to develop and debug. NOTE: This is a static version of clipper required
to build COOT and various clipper binary executables like CPIRATE with the
g++-4.0 compiler.
<<
<<
###############################################################################
SplitOff2: <<
Package: clipper-bin
BuildDependsOnly: false
Files: <<
bin/*
<<
Description: Working Clipper executables including cpirate
DescDetail:<<
The package clipper-bin installs statically-linked versions of the following
binary executable files that are broken in the ccp4-clipper-bin package in
the 10.4 branch of fink: cecalc cfft chltofom cinvfft clipper-config
cmakereference cpatterson cphasecombine cphasematch cpirate csfcalc csigmaa
superpose. These executables will be installed in %p/bin.
<<
<<
###############################################################################
###############################################################################
Description: CCP4 and CLIPPER static libraries
DescDetail: <<
This package installs CCP4 libraries, only. If you need all
of CCP4, install the self-contained CCP4 package instead of, or
in addition to, this. The splitoff package clipper-bin builds
and installs statically-linked clipper executable programs such
as cpirate. CCP4 itself will also install these, but cpirate in
CCP4 suffers from a run-time error. Installation of clipper-bin
will put working copies in %p/bin, and thus at the head of the path.
The licensing for the CCP4 library loosely conforms to the LGPL,
unlike the more restrictive CCP4 license. The clipper libraries
and programs explicitly adhere to the LGPL.
This version compiles with the Apple Lapack/Blas framework
but uses its own static lib build of fftw to avoid a run-time
error that appears in cpirate and coot fft calculations.
CCP4lib files will be installed under
%p/share/xtal/ccp4-onlylibs-dev-6.0.2. This is slightly newer
in content relative to the corresponding files in CCP4 6.0.2.
Programs requiring these libraries to build or run need to
source the appropriate
%p/share/xtal/ccp4-onlylibs-dev-6.0.2/include/ccp4.setup
file for the shell, as is done in the coot.info file. Unless
you are building something external to fink, there is no need
to source that file.
The primary use for this package, currently, is for compiling COOT.
The primary use for the clipper-bin split-off package is to provide
stand-alone, functioning versions of cpirate and colleagues.
<<
DocFiles: conditions.txt
Homepage: http://www.ccp4.ac.uk
License: LGPL
Maintainer: W. G. Scott
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.am ccp4-onlylibs-dev/lib/src/mmdb/Makefile.am
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.am 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-onlylibs-dev/lib/src/mmdb/Makefile.am 2007-10-21 22:33:35.000000000 -0700
@@ -0,0 +1,29 @@
+
+AUTOMAKE_OPTIONS = foreign
+
+lib_LTLIBRARIES = libmmdb.la
+
+library_includedir = $(pkgincludedir)
+
+# includedir = $(pkgincludedir)/mmdb
+
+library_include_HEADERS = \
+bfgs_min.h mmdb_atom.h mmdb_ficif.h mmdb_rwbrook.h mmdb_uddata.h \
+file_.h mmdb_bondmngr.h mmdb_file.h mmdb_sbase0.h mmdb_utils.h \
+linalg_.h mmdb_chain.h mmdb_graph.h mmdb_sbase.h mmdb_xml.h \
+machine_.h mmdb_cifdefs.h mmdb_manager.h mmdb_selmngr.h random_n.h \
+math_.h mmdb_coormngr.h mmdb_mask.h mmdb_symop.h stream_.h \
+mattype_.h mmdb_cryst.h mmdb_mmcif.h mmdb_tables.h \
+mmdb_align.h mmdb_defs.h mmdb_model.h mmdb_title.h
+
+libmmdb_la_SOURCES = \
+bfgs_min.cpp mmdb_bondmngr.cpp mmdb_manager.cpp mmdb_symop.cpp \
+file_.cpp mmdb_chain.cpp mmdb_mask.cpp mmdb_tables.cpp \
+linalg_.cpp mmdb_cifdefs.cpp mmdb_mmcif.cpp mmdb_title.cpp \
+machine_.cpp mmdb_coormngr.cpp mmdb_model.cpp mmdb_uddata.cpp \
+math_.cpp mmdb_cryst.cpp mmdb_rwbrook.cpp mmdb_utils.cpp \
+mattype_.cpp mmdb_ficif.cpp mmdb_sbase0.cpp mmdb_xml.cpp \
+mmdb_align.cpp mmdb_file.cpp mmdb_sbase.cpp random_n.cpp \
+mmdb_atom.cpp mmdb_graph.cpp mmdb_selmngr.cpp stream_.cpp
+
+
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.in ccp4-onlylibs-dev/lib/src/mmdb/Makefile.in
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.in 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-onlylibs-dev/lib/src/mmdb/Makefile.in 2007-10-21 22:33:35.000000000 -0700
@@ -0,0 +1,533 @@
+# Makefile.in generated by automake 1.9.6 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+
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+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
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+ mmdb_symop.lo file_.lo mmdb_chain.lo mmdb_mask.lo \
+ mmdb_tables.lo linalg_.lo mmdb_cifdefs.lo mmdb_mmcif.lo \
+ mmdb_title.lo machine_.lo mmdb_coormngr.lo mmdb_model.lo \
+ mmdb_uddata.lo math_.lo mmdb_cryst.lo mmdb_rwbrook.lo \
+ mmdb_utils.lo mattype_.lo mmdb_ficif.lo mmdb_sbase0.lo \
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+lib_LTLIBRARIES = libmmdb.la
+library_includedir = $(pkgincludedir)
+
+# includedir = $(pkgincludedir)/mmdb
+library_include_HEADERS = \
+bfgs_min.h mmdb_atom.h mmdb_ficif.h mmdb_rwbrook.h mmdb_uddata.h \
+file_.h mmdb_bondmngr.h mmdb_file.h mmdb_sbase0.h mmdb_utils.h \
+linalg_.h mmdb_chain.h mmdb_graph.h mmdb_sbase.h mmdb_xml.h \
+machine_.h mmdb_cifdefs.h mmdb_manager.h mmdb_selmngr.h random_n.h \
+math_.h mmdb_coormngr.h mmdb_mask.h mmdb_symop.h stream_.h \
+mattype_.h mmdb_cryst.h mmdb_mmcif.h mmdb_tables.h \
+mmdb_align.h mmdb_defs.h mmdb_model.h mmdb_title.h
+
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+bfgs_min.cpp mmdb_bondmngr.cpp mmdb_manager.cpp mmdb_symop.cpp \
+file_.cpp mmdb_chain.cpp mmdb_mask.cpp mmdb_tables.cpp \
+linalg_.cpp mmdb_cifdefs.cpp mmdb_mmcif.cpp mmdb_title.cpp \
+machine_.cpp mmdb_coormngr.cpp mmdb_model.cpp mmdb_uddata.cpp \
+math_.cpp mmdb_cryst.cpp mmdb_rwbrook.cpp mmdb_utils.cpp \
+mattype_.cpp mmdb_ficif.cpp mmdb_sbase0.cpp mmdb_xml.cpp \
+mmdb_align.cpp mmdb_file.cpp mmdb_sbase.cpp random_n.cpp \
+mmdb_atom.cpp mmdb_graph.cpp mmdb_selmngr.cpp stream_.cpp
+
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+
+clean-libLTLIBRARIES:
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+
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+
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+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_align.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_atom.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_bondmngr.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_chain.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_cifdefs.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_coormngr.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_cryst.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_ficif.Plo@am__quote@
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+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_mmcif.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_model.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_rwbrook.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_sbase.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_sbase0.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_selmngr.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_symop.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_tables.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_title.Plo@am__quote@
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+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_utils.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mmdb_xml.Plo@am__quote@
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+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stream_.Plo@am__quote@
+
+.cpp.o:
+@am__fastdepCXX_TRUE@ if $(CXXCOMPILE) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" -c -o $@ $<; \
+@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.Po"; else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+
+.cpp.obj:
+@am__fastdepCXX_TRUE@ if $(CXXCOMPILE) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" -c -o $@ `$(CYGPATH_W) '$<'`; \
+@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.Po"; else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+.cpp.lo:
+@am__fastdepCXX_TRUE@ if $(LTCXXCOMPILE) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" -c -o $@ $<; \
+@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.Plo"; else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@ $(LTCXXCOMPILE) -c -o $@ $<
+
+mostlyclean-libtool:
+ -rm -f *.lo
+
+clean-libtool:
+ -rm -rf .libs _libs
+
+distclean-libtool:
+ -rm -f libtool
+uninstall-info-am:
+install-library_includeHEADERS: $(library_include_HEADERS)
+ @$(NORMAL_INSTALL)
+ test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)"
+ @list='$(library_include_HEADERS)'; for p in $$list; do \
+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
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+ done
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+ @$(NORMAL_UNINSTALL)
+ @list='$(library_include_HEADERS)'; for p in $$list; do \
+ f=$(am__strip_dir) \
+ echo " rm -f '$(DESTDIR)$(library_includedir)/$$f'"; \
+ rm -f "$(DESTDIR)$(library_includedir)/$$f"; \
+ done
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+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
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+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ mkid -fID $$unique
+tags: TAGS
+
+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ tags=; \
+ here=`pwd`; \
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+ test -n "$$unique" || unique=$$empty_fix; \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ $$tags $$unique; \
+ fi
+ctags: CTAGS
+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ tags=; \
+ here=`pwd`; \
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ test -z "$(CTAGS_ARGS)$$tags$$unique" \
+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+ $$tags $$unique
+
+GTAGS:
+ here=`$(am__cd) $(top_builddir) && pwd` \
+ && cd $(top_srcdir) \
+ && gtags -i $(GTAGS_ARGS) $$here
+
+distclean-tags:
+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
+ list='$(DISTFILES)'; for file in $$list; do \
+ case $$file in \
+ $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
+ $(top_srcdir)/*) file=`echo "$$file" | sed "s|^$$topsrcdirstrip/|$(top_builddir)/|"`;; \
+ esac; \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test "$$dir" != "$$file" && test "$$dir" != "."; then \
+ dir="/$$dir"; \
+ $(mkdir_p) "$(distdir)$$dir"; \
+ else \
+ dir=''; \
+ fi; \
+ if test -d $$d/$$file; then \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ fi; \
+ cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ else \
+ test -f $(distdir)/$$file \
+ || cp -p $$d/$$file $(distdir)/$$file \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile $(LTLIBRARIES) $(HEADERS)
+installdirs:
+ for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(library_includedir)"; do \
+ test -z "$$dir" || $(mkdir_p) "$$dir"; \
+ done
+install: install-am
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+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
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+installcheck: installcheck-am
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+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic clean-libLTLIBRARIES clean-libtool \
+ mostlyclean-am
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+distclean: distclean-am
+ -rm -rf ./$(DEPDIR)
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+ distclean-libtool distclean-tags
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+ distclean-compile distclean-generic distclean-libtool \
+ distclean-tags distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-exec \
+ install-exec-am install-info install-info-am \
+ install-libLTLIBRARIES install-library_includeHEADERS \
+ install-man install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic \
+ mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \
+ uninstall-am uninstall-info-am uninstall-libLTLIBRARIES \
+ uninstall-library_includeHEADERS
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/README ccp4-onlylibs-dev/lib/src/mmdb/README
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/README 2006-08-16 03:55:13.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/README 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-$Id: README,v 1.4 2006/08/16 10:55:13 fr45 Exp $
+$Id: README,v 1.2 2004/04/22 16:36:01 keb Exp $
CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/bfgs_min.cpp ccp4-onlylibs-dev/lib/src/mmdb/bfgs_min.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/bfgs_min.cpp 2006-08-16 03:55:13.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/bfgs_min.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: bfgs_min.cpp,v 1.12 2006/08/16 10:55:13 fr45 Exp $
+// $Id: bfgs_min.cpp,v 1.4 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/bfgs_min.h ccp4-onlylibs-dev/lib/src/mmdb/bfgs_min.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/bfgs_min.h 2006-08-16 03:55:13.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/bfgs_min.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: bfgs_min.h,v 1.13 2006/08/16 10:55:13 fr45 Exp $
+// $Id: bfgs_min.h,v 1.6 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/file_.cpp ccp4-onlylibs-dev/lib/src/mmdb/file_.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/file_.cpp 2006-08-16 06:03:35.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/file_.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: file_.cpp,v 1.18 2006/08/16 13:03:35 fr45 Exp $
+// $Id: file_.cpp,v 1.17 2007/01/30 12:33:45 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -40,7 +40,7 @@
#include
#endif
-#ifndef _MSC_VER
+#ifndef _MVS
#ifndef __UNISTD_H
#include
#endif
@@ -177,7 +177,7 @@
void CFile::assign ( const pstr FileName, Boolean Text, Boolean UniB,
byte gzMode ) {
-#ifndef _MSC_VER
+#ifndef _MVS
pstr p;
#endif
@@ -195,7 +195,7 @@
UniBin = UniB;
-#ifndef _MSC_VER
+#ifndef _MVS
gzipMode = gzMode;
gzipIO = ARCH_NONE;
@@ -273,7 +273,7 @@
}
Boolean CFile::reset ( Boolean ReadOnly, int retry ) {
-#ifndef _MSC_VER
+#ifndef _MVS
pstr p;
int i;
#endif
@@ -305,7 +305,7 @@
StdIO = False;
if (gzipIO==ARCH_GZIP) {
-#ifndef _MSC_VER
+#ifndef _MVS
p = NULL;
CreateConcat ( p,ungzip_path,FName );
for (i=0;(i<=retry) && (!hFile);i++) {
@@ -316,7 +316,7 @@
#endif
} else if (gzipIO==ARCH_COMPRESS) {
-#ifndef _MSC_VER
+#ifndef _MVS
p = NULL;
CreateConcat ( p,uncompress_path,FName );
for (i=0;(i<=retry) && (!hFile);i++) {
@@ -328,7 +328,7 @@
} else {
-#ifndef _MSC_VER
+#ifndef _MVS
for (i=0;(i<=retry) && (!hFile);i++) {
if (i>0) sleep ( 1 );
#endif
@@ -339,7 +339,7 @@
if (ReadOnly) hFile = fopen ( FName,"r" );
else hFile = fopen ( FName,"r+b" );
}
-#ifndef _MSC_VER
+#ifndef _MVS
}
#endif
@@ -370,7 +370,7 @@
}
Boolean CFile::rewrite() {
-#ifndef _MSC_VER
+#ifndef _MVS
pstr p;
#endif
@@ -391,7 +391,7 @@
BufCnt = 0;
if (gzipIO==ARCH_GZIP) {
-#ifndef _MSC_VER
+#ifndef _MVS
p = NULL;
CreateConcat ( p,gzip_path,pstr(" > "),FName );
hFile = popen ( p,"w" );
@@ -401,7 +401,7 @@
#endif
StdIO = False;
} else if (gzipIO==ARCH_COMPRESS) {
-#ifndef _MSC_VER
+#ifndef _MVS
p = NULL;
CreateConcat ( p,compress_path,pstr(" > "),FName );
hFile = popen ( p,"w" );
@@ -434,7 +434,7 @@
}
Boolean CFile::append() {
-#ifndef _MSC_VER
+#ifndef _MVS
pstr p;
#endif
@@ -455,7 +455,7 @@
BufLen = 0;
BufCnt = 0;
if (gzipIO==ARCH_GZIP) {
-#ifndef _MSC_VER
+#ifndef _MVS
p = NULL;
CreateConcat ( p,gzip_path,pstr(" >> "),FName );
hFile = popen ( p,"w" );
@@ -465,7 +465,7 @@
#endif
StdIO = False;
} else if (gzipIO==ARCH_COMPRESS) {
-#ifndef _MSC_VER
+#ifndef _MVS
p = NULL;
CreateConcat ( p,compress_path,pstr(" >> "),FName );
hFile = popen ( p,"w" );
@@ -596,7 +596,7 @@
if (hFile!=NULL) {
if (!StdIO) {
-#ifndef _MSC_VER
+#ifndef _MVS
if (gzipIO!=ARCH_NONE) pclose ( hFile );
else fclose ( hFile );
#else
@@ -1426,7 +1426,8 @@
return IOSuccess;
}
-Boolean CFile::CreateReadVector ( rvector & V, int & len, int Shift ) {
+Boolean CFile::CreateReadVector ( rvector & V, int & len,
+ int Shift ) {
intUniBin iUB;
realUniBin rUB;
int i;
@@ -1462,7 +1463,8 @@
return CreateReadVector ( V,len,Shift );
}
-Boolean CFile::CreateReadVector ( ivector & iV, int & len, int Shift ) {
+Boolean CFile::CreateReadVector ( ivector & iV, int & len,
+ int Shift ) {
intUniBin iUB;
int i,iB;
FreeVectorMemory ( iV,Shift );
@@ -1496,7 +1498,8 @@
return CreateReadVector ( iV,len,Shift );
}
-Boolean CFile::CreateReadVector ( lvector & lV, int & len, int Shift ) {
+Boolean CFile::CreateReadVector ( lvector & lV, int & len,
+ int Shift ) {
intUniBin iUB;
longUniBin lUB;
int i;
@@ -1533,7 +1536,8 @@
}
-Boolean CFile::CreateReadVector ( bvector & B, int & len, int Shift ) {
+Boolean CFile::CreateReadVector ( bvector & B, int & len,
+ int Shift ) {
intUniBin iUB;
int i;
byte t;
@@ -1591,7 +1595,8 @@
return IOSuccess;
}
-Boolean CFile::CreateReadMatrix ( rmatrix & A, int ShiftN, int ShiftM ) {
+Boolean CFile::CreateReadMatrix ( rmatrix & A, int ShiftN,
+ int ShiftM ) {
int N,M;
return CreateReadMatrix ( A,N,M,ShiftN,ShiftM );
}
@@ -1686,7 +1691,8 @@
int CFile::CreateReadColumns ( rvector & X, rvector & Y, rvector & Z,
- int xCol, int yCol, int zCol, int Shift ) {
+ int xCol, int yCol, int zCol,
+ int Shift ) {
// ReadColumns reads data stored by WriteColumns. X, Y, and Z
// must be set to NULL prior to call. They will be allocated
// within the procedure.
@@ -1721,7 +1727,8 @@
Ok = Ok && GetVectorMemory(Z,DataLen,Shift);
if (Ok) {
reset();
- _ReadColumns ( DataLen,S,sizeof(S),X,Y,Z,xCol,yCol,zCol,Shift );
+ _ReadColumns ( DataLen,S,sizeof(S),X,Y,Z,xCol,yCol,
+ zCol,Shift );
} else ErrCode = FileError_NoMemory;
} else ErrCode = FileError_NoDataFound;
} else ErrCode = FileError_NoDataFound;
@@ -1735,7 +1742,8 @@
void CFile::_ReadColumns ( int & DLen, pstr S, int SLen,
rvector X, rvector Y, rvector Z,
- int xCol, int yCol, int zCol, int Shift ) {
+ int xCol, int yCol, int zCol,
+ int Shift ) {
int i,is,j,k,m,n,cmax;
char SV[256];
realtype Res;
@@ -1810,13 +1818,13 @@
pstr FileError ( int ErrCode ) {
switch (ErrCode) {
- case 0 : return pstr("Ok");
- case FileError_NoMemory : return pstr("Insufficient memory");
- case FileError_NoDataFound : return pstr("No data found");
- case FileError_NoColumn : return pstr("No column structure");
- case FileError_BadData : return pstr("Incorrect data format");
+ case 0 : return pstr("Ok");
+ case FileError_NoMemory : return pstr("Insufficient memory");
+ case FileError_NoDataFound : return pstr("No data found");
+ case FileError_NoColumn : return pstr("No column structure");
+ case FileError_BadData : return pstr("Incorrect data format");
case FileError_WrongMemoryAllocation
- : return pstr("Wrong Memory Allocation");
+ : return pstr("Wrong Memory Allocation");
default : return pstr("Unknown I/O error");
}
}
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/file_.h ccp4-onlylibs-dev/lib/src/mmdb/file_.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/file_.h 2006-08-16 03:55:13.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/file_.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: file_.h,v 1.15 2006/08/16 10:55:13 fr45 Exp $
+// $Id: file_.h,v 1.14 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/linalg_.cpp ccp4-onlylibs-dev/lib/src/mmdb/linalg_.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/linalg_.cpp 2006-08-16 03:55:13.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/linalg_.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: linalg_.cpp,v 1.13 2006/08/16 10:55:13 fr45 Exp $
+// $Id: linalg_.cpp,v 1.6 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/linalg_.h ccp4-onlylibs-dev/lib/src/mmdb/linalg_.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/linalg_.h 2006-08-16 03:55:14.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/linalg_.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: linalg_.h,v 1.13 2006/08/16 10:55:14 fr45 Exp $
+// $Id: linalg_.h,v 1.8 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/machine_.cpp ccp4-onlylibs-dev/lib/src/mmdb/machine_.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/machine_.cpp 2006-08-16 03:55:14.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/machine_.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: machine_.cpp,v 1.12 2006/08/16 10:55:14 fr45 Exp $
+// $Id: machine_.cpp,v 1.4 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/machine_.h ccp4-onlylibs-dev/lib/src/mmdb/machine_.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/machine_.h 2006-08-16 06:18:17.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/machine_.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: machine_.h,v 1.19 2006/08/16 13:18:17 fr45 Exp $
+// $Id: machine_.h,v 1.5 2007/04/04 13:59:58 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -46,7 +46,7 @@
*/
-// =================== List of known machines ========================
+// ================== List of known machines ========================
#define MACHINE_SGI 1
#define MACHINE_RS6000 2
@@ -118,12 +118,8 @@
# define CALL_LIKE_VMS 1
// MVS stands for Microsoft Visual Studio
-#elif defined(_MSC_VER)
-# if (_MSC_VER) >= 800
-# define CALL_LIKE_MVS 2
-# else
+#elif defined(_MVS)
# define CALL_LIKE_MVS 1
-# endif
#elif defined(F2C) || defined(G77)
# define CALL_LIKE_SUN 8
@@ -139,7 +135,7 @@
-// ================= Machine-dependent definitions ===================
+// ================= Machine-dependent definitions ==================
#ifdef CALL_LIKE_STARDENT
// SStrParam is used in Ardent-like machines' fortran calls
@@ -395,36 +391,6 @@
#elif defined(CALL_LIKE_MVS)
-# if ( CALL_LIKE_MVS == 2 )
-
- typedef pstr fpstr;
-
-# define FTN_STR(s) s
-# define FTN_LEN(s) s##_len
-
-# define char_struct(s) \
- pstr s; \
- int s##_len;
-# define fill_char_struct(s,str) \
- s = str; \
- s##_len = strlen(str);
-
-# ifdef __cplusplus
-# define FORTRAN_SUBR(NAME,name,p_sun,p_stardent,p_mvs) \
- extern "C" void NAME p_sun
-# else
-# define FORTRAN_SUBR(NAME,name,p_sun,p_stardent,p_mvs) \
- void NAME p_sun
-# endif
-
-# define FORTRAN_EXTERN(NAME,name,p_sun,p_stardent,p_mvs) \
- extern "C" void NAME p_sun
-
-# define FORTRAN_CALL(NAME,name,p_sun,p_stardent,p_mvs) \
- NAME p_sun
-
-# else
-
typedef pstr fpstr;
# define FTN_STR(s) s
@@ -450,7 +416,7 @@
# define FORTRAN_CALL(NAME,name,p_sun,p_stardent,p_mvs) \
NAME p_mvs
-# endif
+
#else
# error Unknown machine!!!
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/math_.cpp ccp4-onlylibs-dev/lib/src/mmdb/math_.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/math_.cpp 2006-08-16 03:55:14.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/math_.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: math_.cpp,v 1.12 2006/08/16 10:55:14 fr45 Exp $
+// $Id: math_.cpp,v 1.5 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/math_.h ccp4-onlylibs-dev/lib/src/mmdb/math_.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/math_.h 2006-08-16 03:55:14.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/math_.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: math_.h,v 1.12 2006/08/16 10:55:14 fr45 Exp $
+// $Id: math_.h,v 1.5 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mattype_.cpp ccp4-onlylibs-dev/lib/src/mmdb/mattype_.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mattype_.cpp 2006-08-16 03:55:14.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mattype_.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mattype_.cpp,v 1.17 2006/08/16 10:55:14 fr45 Exp $
+// $Id: mattype_.cpp,v 1.11 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mattype_.h ccp4-onlylibs-dev/lib/src/mmdb/mattype_.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mattype_.h 2006-08-16 06:03:36.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mattype_.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mattype_.h,v 1.17 2006/08/16 13:03:36 fr45 Exp $
+// $Id: mattype_.h,v 1.9 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -87,7 +87,7 @@
#define strchr FirstOccurence
#define fstrchr FirstOccurence
-#ifdef _MSC_VER
+#ifdef _MVS
#define strncasecmp _strnicmp
#define strcasecmp _stricmp
#define strlen (int)strlen
@@ -292,20 +292,27 @@
// the same as those at allocation !
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-extern void FreeMatrix3Memory ( rmatrix3 & A, word N, word M,
- word ShiftN=1, word ShiftM=1, word ShiftK=1 );
-extern void FreeMatrix3Memory ( imatrix3 & A, word N, word M,
- word ShiftN=1, word ShiftM=1, word ShiftK=1 );
-extern void FreeMatrix3Memory ( wmatrix3 & A, word N, word M,
- word ShiftN=1, word ShiftM=1, word ShiftK=1 );
-extern void FreeMatrix3Memory ( bmatrix3 & A, word N, word M,
- word ShiftN=1, word ShiftM=1, word ShiftK=1 );
-extern void FreeMatrix3Memory ( lmatrix3 & A, word N, word M,
- word ShiftN=1, word ShiftM=1, word ShiftK=1 );
-extern void FreeMatrix3Memory ( lwmatrix3 & A, word N, word M,
- word ShiftN=1, word ShiftM=1, word ShiftK=1 );
-extern void FreeMatrix3Memory ( psmatrix3 & A, word N, word M,
- word ShiftN=1, word ShiftM=1, word ShiftK=1 );
+extern void FreeMatrix3Memory
+ ( rmatrix3 & A, word N, word M,
+ word ShiftN=1, word ShiftM=1, word ShiftK=1 );
+extern void FreeMatrix3Memory
+ ( imatrix3 & A, word N, word M,
+ word ShiftN=1, word ShiftM=1, word ShiftK=1 );
+extern void FreeMatrix3Memory
+ ( wmatrix3 & A, word N, word M,
+ word ShiftN=1, word ShiftM=1, word ShiftK=1 );
+extern void FreeMatrix3Memory
+ ( bmatrix3 & A, word N, word M,
+ word ShiftN=1, word ShiftM=1, word ShiftK=1 );
+extern void FreeMatrix3Memory
+ ( lmatrix3 & A, word N, word M,
+ word ShiftN=1, word ShiftM=1, word ShiftK=1 );
+extern void FreeMatrix3Memory
+ ( lwmatrix3 & A, word N, word M,
+ word ShiftN=1, word ShiftM=1, word ShiftK=1 );
+extern void FreeMatrix3Memory
+ ( psmatrix3 & A, word N, word M,
+ word ShiftN=1, word ShiftM=1, word ShiftK=1 );
// -------------------------------------------------------------
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_align.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_align.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_align.cpp 2006-08-16 03:55:15.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_align.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_align.cpp,v 1.13 2006/08/16 10:55:15 fr45 Exp $
+// $Id: mmdb_align.cpp,v 1.8 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_align.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_align.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_align.h 2006-08-16 03:55:15.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_align.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_align.h,v 1.13 2006/08/16 10:55:15 fr45 Exp $
+// $Id: mmdb_align.h,v 1.6 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_atom.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_atom.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_atom.cpp 2006-08-16 03:55:15.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_atom.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_atom.cpp,v 1.17 2006/08/16 10:55:15 fr45 Exp $
+// $Id: mmdb_atom.cpp,v 1.22 2007/08/15 10:59:31 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -633,7 +633,8 @@
WhatIsSet |= ASET_Anis_tFac;
- if (WhatIsSet & (ASET_Coordinates | ASET_CoordSigma | ASET_Anis_tFSigma))
+ if (WhatIsSet & (ASET_Coordinates | ASET_CoordSigma |
+ ASET_Anis_tFSigma))
// something was already submitted. check complience
return CheckData ( S );
else
@@ -1727,7 +1728,7 @@
-// ============================ CResidue ============================
+// =========================== CResidue ===========================
void SAtomStat::Init() {
@@ -2279,8 +2280,10 @@
}
-void CResidue::_copy ( PCResidue res, PPCAtom atm, int & atom_index ) {
-// modify both CResidue::_copy and CResidue::Copy methods simultaneously!
+void CResidue::_copy ( PCResidue res, PPCAtom atm,
+ int & atom_index ) {
+// modify both CResidue::_copy and CResidue::Copy methods
+// simultaneously!
//
// This function physically copies the atoms, creating new atom
// instances and putting them into array 'atm' sequentially from
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_atom.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_atom.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_atom.h 2006-08-16 03:55:15.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_atom.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_atom.h,v 1.16 2006/08/16 10:55:15 fr45 Exp $
+// $Id: mmdb_atom.h,v 1.15 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_bondmngr.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_bondmngr.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_bondmngr.cpp 2006-08-16 03:55:15.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_bondmngr.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_bondmngr.cpp,v 1.12 2006/08/16 10:55:15 fr45 Exp $
+// $Id: mmdb_bondmngr.cpp,v 1.6 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_bondmngr.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_bondmngr.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_bondmngr.h 2006-08-16 03:55:15.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_bondmngr.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_bondmngr.h,v 1.12 2006/08/16 10:55:15 fr45 Exp $
+// $Id: mmdb_bondmngr.h,v 1.4 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_chain.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_chain.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_chain.cpp 2007-07-09 08:39:28.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_chain.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_chain.cpp,v 1.16 2007/07/09 15:39:28 ccb Exp $
+// $Id: mmdb_chain.cpp,v 1.14 2007/05/18 13:50:51 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_chain.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_chain.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_chain.h 2006-08-16 03:55:16.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_chain.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_chain.h,v 1.14 2006/08/16 10:55:16 fr45 Exp $
+// $Id: mmdb_chain.h,v 1.10 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -21,15 +21,15 @@
// ~~~~~~~~~
// **** Project : MacroMolecular Data Base (MMDB)
// ~~~~~~~~~
-// **** Classes : CProModel ( a virtue of CModel )
-// ~~~~~~~~~ CChainContainer ( container of in-chain classes )
-// CContainerChain ( chain containered class template )
-// CDBReference ( DBREF records )
-// CSeqAdv ( SEQADV records )
-// CSeqRes ( SEQRES records )
-// CModRes ( MODRES records )
-// CHetRec ( HET records )
-// CChain ( chain class )
+// **** Classes : CProModel ( a virtue of CModel )
+// ~~~~~~~~~ CChainContainer ( container of in-chain classes )
+// CContainerChain ( chain containered class template)
+// CDBReference ( DBREF records )
+// CSeqAdv ( SEQADV records )
+// CSeqRes ( SEQRES records )
+// CModRes ( MODRES records )
+// CHetRec ( HET records )
+// CChain ( chain class )
//
// Copyright (C) E. Krissinel 2001-2004
//
@@ -86,8 +86,11 @@
// GetNumberOfModels() returns TOTAL number of models
virtual int GetNumberOfModels() { return 0; }
- // GetNumberOfAllAtoms() returns TOTAL number of atoms in all models
+
+ // GetNumberOfAllAtoms() returns TOTAL number of atoms in
+ // all models
virtual int GetNumberOfAllAtoms() { return 0; }
+
// returns pointer to the general Atom array
virtual PPCAtom GetAllAtoms() { return NULL; }
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_cifdefs.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_cifdefs.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_cifdefs.cpp 2006-08-16 03:55:16.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_cifdefs.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_cifdefs.cpp,v 1.12 2006/08/16 10:55:16 fr45 Exp $
+// $Id: mmdb_cifdefs.cpp,v 1.4 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_cifdefs.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_cifdefs.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_cifdefs.h 2007-07-09 08:40:17.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_cifdefs.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_cifdefs.h,v 1.13 2007/07/09 15:40:17 ccb Exp $
+// $Id: mmdb_cifdefs.h,v 1.5 2007/05/18 13:50:51 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_coormngr.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_coormngr.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_coormngr.cpp 2006-08-16 03:55:16.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_coormngr.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_coormngr.cpp,v 1.18 2006/08/16 10:55:16 fr45 Exp $
+// $Id: mmdb_coormngr.cpp,v 1.22 2007/08/15 10:59:31 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -13,7 +13,7 @@
//
// =================================================================
//
-// 08.03.06 <-- Date of Last Modification.
+// 29.05.07 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -25,7 +25,7 @@
// ~~~~~~~~~ CMBrick ( "multiple" space brick )
// CMMDBCoorManager ( MMDB atom coordinate manager )
//
-// Copyright (C) E. Krissinel 2001-2006
+// Copyright (C) E. Krissinel 2001-2007
//
// =================================================================
//
@@ -580,6 +580,25 @@
return DefPath.SetPath ( CID );
}
+PCModel CMMDBCoorManager::GetFirstDefinedModel() {
+PCModel mdl;
+int i;
+ mdl = NULL;
+ for (i=0;(i
+ return mdl;
+}
+
+int CMMDBCoorManager::GetFirstModelNum() {
+PCModel mdl;
+int i;
+ mdl = NULL;
+ for (i=0;(i
+ if (mdl) return mdl->GetSerNum();
+ return 1;
+}
+
PCModel CMMDBCoorManager::GetModel ( int modelNo ) {
if ((modelNo>=1) && (modelNo<=nModels))
@@ -4119,7 +4138,6 @@
V[j][k] = -V[j][k];
}
-
// 4.3 Calculate rotational part of T
for (j=1;j<=3;j++)
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_coormngr.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_coormngr.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_coormngr.h 2006-08-16 03:55:16.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_coormngr.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_coormngr.h,v 1.18 2006/08/16 10:55:16 fr45 Exp $
+// $Id: mmdb_coormngr.h,v 1.17 2007/08/15 10:59:31 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -13,7 +13,7 @@
//
// =================================================================
//
-// 26.11.03 <-- Date of Last Modification.
+// 29.05.07 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -24,7 +24,7 @@
// **** Classes : CBrick ( space brick )
// ~~~~~~~~~ CMMDBCoorManager ( MMDB atom coordinate manager )
//
-// E. Krissinel 2001-2003
+// (C) E. Krissinel 2001-2007
//
// =================================================================
//
@@ -243,6 +243,8 @@
// ---------------- Extracting models ---------------------
int GetNumberOfModels () { return nModels; }
+ int GetFirstModelNum ();
+ PCModel GetFirstDefinedModel();
PCModel GetModel ( int modelNo ); // 1<=modelNo<=nModels
PCModel GetModel ( const pstr CID );
void GetModelTable ( PPCModel & modTable,
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_cryst.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_cryst.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_cryst.cpp 2007-07-09 08:40:57.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_cryst.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_cryst.cpp,v 1.18 2007/07/09 15:40:57 ccb Exp $
+// $Id: mmdb_cryst.cpp,v 1.23 2007/01/08 16:42:41 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_cryst.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_cryst.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_cryst.h 2007-07-09 08:41:12.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_cryst.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_cryst.h,v 1.17 2007/07/09 15:41:12 ccb Exp $
+// $Id: mmdb_cryst.h,v 1.17 2007/01/08 16:42:41 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_defs.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_defs.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_defs.h 2007-07-09 08:41:42.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_defs.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_defs.h,v 1.16 2007/07/09 15:41:42 ccb Exp $
+// $Id: mmdb_defs.h,v 1.10 2007/05/18 13:50:51 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -13,7 +13,7 @@
//
// =================================================================
//
-// 11.05.07 <-- Date of Last Modification.
+// 10.09.07 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -221,7 +221,7 @@
#define ClassID_Helix 19
#define ClassID_Turn 20
#define ClassID_Link 21
-
+#define ClassID_CisPep 22
// ===================== classes ===============================
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_ficif.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_ficif.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_ficif.cpp 2006-08-16 03:55:17.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_ficif.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_ficif.cpp,v 1.12 2006/08/16 10:55:17 fr45 Exp $
+// $Id: mmdb_ficif.cpp,v 1.5 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_ficif.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_ficif.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_ficif.h 2006-08-16 03:55:17.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_ficif.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_ficif.h,v 1.12 2006/08/16 10:55:17 fr45 Exp $
+// $Id: mmdb_ficif.h,v 1.4 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_file.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_file.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_file.cpp 2007-07-09 08:42:22.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_file.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_file.cpp,v 1.22 2007/07/09 15:42:22 ccb Exp $
+// $Id: mmdb_file.cpp,v 1.27 2007/05/18 13:50:51 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -238,7 +238,7 @@
int CMMDBFile::ReadPDBASCII ( RCFile f ) {
PCContString ContString;
word cleanKey;
-int RC;
+int RC,modNum;
Boolean fixSpaceGroup,fend;
// remove previous data
@@ -325,7 +325,13 @@
strncmp(S,"ENDMDL",6)) {
if (!strncmp(S,"LINK ",6))
crModel->ConvertPDBString(S);
- else {
+ else if (!strncmp(S,"CISPEP",6)) {
+ GetInteger ( modNum,&(S[43]),3 );
+ if (modNum<=0) modNum = 1;
+ if (modNum!=1) SwitchModel ( modNum );
+ crModel->ConvertPDBString(S);
+ if (modNum!=1) SwitchModel ( 1 );
+ } else {
ContString = new CContString(S);
SA.AddData ( ContString );
}
@@ -1784,11 +1790,13 @@
int CMMDBFile::PutAtom ( int index, // same meaning as above
- PCAtom A, // pointer to completed atom class
- int serNum // 0 means that the serial number
- // will be set equal to index.
- // Otherwise the serial number
- // is set to the specified value
+ PCAtom A, // pointer to completed atom
+ // class
+ int serNum // 0 means that the serial
+ // number will be set equal
+ // to "index". Otherwise,
+ // the serial number is set
+ // to the specified value
) {
int i,kndex,RC,sn;
@@ -2264,6 +2272,11 @@
if (i
+ // output cispep records
+ for (i=0;i
+ Model[i]->PDBASCIIDumpCP ( f );
+
SA .PDBASCIIDump ( f );
Footnote.PDBASCIIDump ( f );
Cryst .PDBASCIIDump ( f );
@@ -2273,7 +2286,7 @@
if (Model[i])
Model[i]->PDBASCIIDump ( f );
- SC .PDBASCIIDump ( f );
+ SC.PDBASCIIDump ( f );
f.WriteLine ( pstr("END") );
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_file.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_file.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_file.h 2007-07-09 08:42:32.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_file.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_file.h,v 1.19 2007/07/09 15:42:32 ccb Exp $
+// $Id: mmdb_file.h,v 1.22 2007/03/30 17:08:04 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_graph.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_graph.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_graph.cpp 2007-07-09 08:42:51.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_graph.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_graph.cpp,v 1.16 2007/07/09 15:42:51 ccb Exp $
+// $Id: mmdb_graph.cpp,v 1.17 2007/08/15 10:59:32 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -700,7 +700,7 @@
e1--;
for (j=i+1;j
- e2 = Vertex[i]->type;
+ e2 = Vertex[j]->type;
if (e2>nElementNames) e2 = 6;
e2--;
dx = R->atom[a2]->x - R->atom[a1]->x;
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_graph.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_graph.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_graph.h 2007-07-09 08:43:11.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_graph.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_graph.h,v 1.15 2007/07/09 15:43:11 ccb Exp $
+// $Id: mmdb_graph.h,v 1.13 2007/04/04 13:59:58 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_manager.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_manager.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_manager.cpp 2007-07-09 08:43:24.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_manager.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_manager.cpp,v 1.15 2007/07/09 15:43:24 ccb Exp $
+// $Id: mmdb_manager.cpp,v 1.9 2007/05/18 13:50:51 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_manager.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_manager.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_manager.h 2007-07-09 08:43:48.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_manager.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_manager.h,v 1.14 2007/07/09 15:43:48 ccb Exp $
+// $Id: mmdb_manager.h,v 1.6 2007/05/18 13:50:51 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_mask.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_mask.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_mask.cpp 2006-08-16 03:55:18.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_mask.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_mask.cpp,v 1.12 2006/08/16 10:55:18 fr45 Exp $
+// $Id: mmdb_mask.cpp,v 1.5 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_mask.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_mask.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_mask.h 2006-08-16 03:55:19.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_mask.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_mask.h,v 1.12 2006/08/16 10:55:19 fr45 Exp $
+// $Id: mmdb_mask.h,v 1.4 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_mmcif.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_mmcif.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_mmcif.cpp 2006-08-16 03:55:19.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_mmcif.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_mmcif.cpp,v 1.14 2006/08/16 10:55:19 fr45 Exp $
+// $Id: mmdb_mmcif.cpp,v 1.10 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_mmcif.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_mmcif.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_mmcif.h 2006-08-16 03:55:19.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_mmcif.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_mmcif.h,v 1.13 2006/08/16 10:55:19 fr45 Exp $
+// $Id: mmdb_mmcif.h,v 1.8 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_model.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_model.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_model.cpp 2007-07-09 08:44:09.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_model.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_model.cpp,v 1.16 2007/07/09 15:44:09 ccb Exp $
+// $Id: mmdb_model.cpp,v 1.16 2007/05/18 13:50:51 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -13,7 +13,7 @@
//
// =================================================================
//
-// 14.05.07 <-- Date of Last Modification.
+// 10.09.07 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -29,8 +29,10 @@
// CSheet ( sheet info )
// CSheets ( container for sheets )
// CTurn ( turn info )
-// CLinkContainer ( container for link data )
-// CLink ( link data )
+// CLinkContainer ( container for link data )
+// CLink ( link data )
+// CCisPepContainer ( container for CisPep data )
+// CCisPep ( CisPep data )
// CModel ( PDB model )
//
// Copyright (C) E. Krissinel 2000-2007
@@ -2040,6 +2042,7 @@
MakeStreamFunctions(CLinkContainer)
+
// ======================== CLink ===========================
CLink::CLink() : CContainerClass() {
@@ -2380,6 +2383,158 @@
MakeStreamFunctions(CLink)
+// =================== CCisPepContainer ======================
+
+PCContainerClass CCisPepContainer::MakeContainerClass ( int ClassID ) {
+ switch (ClassID) {
+ default :
+ case ClassID_Template : return
+ CClassContainer::MakeContainerClass(ClassID);
+ case ClassID_CisPep : return new CCisPep();
+ }
+}
+
+MakeStreamFunctions(CCisPepContainer)
+
+
+// ======================== CCisPep ==========================
+
+CCisPep::CCisPep() : CContainerClass() {
+ InitCisPep();
+}
+
+CCisPep::CCisPep ( const pstr S ) : CContainerClass() {
+ InitCisPep();
+ ConvertPDBASCII ( S );
+}
+
+CCisPep::CCisPep ( RPCStream Object ) : CContainerClass(Object) {
+ InitCisPep();
+}
+
+CCisPep::~CCisPep() {}
+
+void CCisPep::InitCisPep() {
+ serNum = 1; // record serial number
+ strcpy ( pep1 ,"---" ); // residue name
+ strcpy ( chainID1," " ); // chain identifier 1
+ seqNum1 = 0; // residue sequence number 1
+ strcpy ( icode1 ," " ); // insertion code 1
+ strcpy ( pep2 ,"---" ); // residue name 2
+ strcpy ( chainID2," " ); // chain identifier 2
+ seqNum2 = 0; // residue sequence number 2
+ strcpy ( icode2 ," " ); // insertion code 2
+ modNum = 0; // model number
+ measure = 0.0; // measure of the angle in degrees.
+}
+
+void CCisPep::PDBASCIIDump ( pstr S, int N ) {
+
+ strcpy ( S,"CISPEP" );
+ PadSpaces ( S,80 );
+
+ PutInteger ( &(S[7]),serNum,3 );
+
+ strcpy_n1 ( &(S[11]),pep1 ,3 );
+ strcpy_n1 ( &(S[15]),chainID1,1 );
+ PutIntIns ( &(S[17]),seqNum1 ,4,icode1 );
+
+ strcpy_n1 ( &(S[25]),pep2 ,3 );
+ strcpy_n1 ( &(S[29]),chainID2,1 );
+ PutIntIns ( &(S[31]),seqNum2 ,4,icode1 );
+
+ PutInteger ( &(S[43]),modNum,3 );
+ PutRealF ( &(S[53]),measure,6,2 );
+
+}
+
+
+int CCisPep::ConvertPDBASCII ( const pstr S ) {
+
+ GetInteger ( serNum ,&(S[7]) ,3 );
+
+ strcpy_ncss ( pep1 ,&(S[11]),3 );
+ strcpy_ncss ( chainID1,&(S[15]),1 );
+ GetIntIns ( seqNum1,icode1,&(S[17]),4 );
+
+ strcpy_ncss ( pep2 ,&(S[25]),3 );
+ strcpy_ncss ( chainID2,&(S[29]),1 );
+ GetIntIns ( seqNum2,icode2,&(S[31]),4 );
+
+ GetInteger ( modNum ,&(S[43]),3 );
+ GetReal ( measure ,&(S[53]),6 );
+
+ return 0;
+
+}
+
+
+void CCisPep::Copy ( PCContainerClass CisPep ) {
+
+ serNum = PCCisPep(CisPep)->serNum;
+
+ strcpy ( pep1 ,PCCisPep(CisPep)->pep1 );
+ strcpy ( chainID1,PCCisPep(CisPep)->chainID1 );
+ seqNum1 = PCCisPep(CisPep)->seqNum1;
+ strcpy ( icode1 ,PCCisPep(CisPep)->icode1 );
+
+ strcpy ( pep2 ,PCCisPep(CisPep)->pep2 );
+ strcpy ( chainID2,PCCisPep(CisPep)->chainID2 );
+ seqNum2 = PCCisPep(CisPep)->seqNum2;
+ strcpy ( icode2 ,PCCisPep(CisPep)->icode2 );
+
+ modNum = PCCisPep(CisPep)->modNum;
+ measure = PCCisPep(CisPep)->measure;
+
+}
+
+void CCisPep::write ( RCFile f ) {
+byte Version=1;
+
+ f.WriteByte ( &Version );
+
+ f.WriteInt ( &serNum );
+
+ f.WriteTerLine ( pep1 ,False );
+ f.WriteTerLine ( chainID1,False );
+ f.WriteInt ( &seqNum1 );
+ f.WriteTerLine ( icode1 ,False );
+
+ f.WriteTerLine ( pep2 ,False );
+ f.WriteTerLine ( chainID2,False );
+ f.WriteInt ( &seqNum2 );
+ f.WriteTerLine ( icode2 ,False );
+
+ f.WriteInt ( &modNum );
+ f.WriteReal ( &measure );
+
+}
+
+void CCisPep::read ( RCFile f ) {
+byte Version;
+
+ f.ReadByte ( &Version );
+
+ f.ReadInt ( &serNum );
+
+ f.ReadTerLine ( pep1 ,False );
+ f.ReadTerLine ( chainID1,False );
+ f.ReadInt ( &seqNum1 );
+ f.ReadTerLine ( icode1 ,False );
+
+ f.ReadTerLine ( pep2 ,False );
+ f.ReadTerLine ( chainID2,False );
+ f.ReadInt ( &seqNum2 );
+ f.ReadTerLine ( icode2 ,False );
+
+ f.ReadInt ( &modNum );
+ f.ReadReal ( &measure );
+
+}
+
+MakeStreamFunctions(CCisPep)
+
+
// ===================== CModel =======================
@@ -2422,6 +2577,7 @@
RemoveSecStructure();
RemoveHetInfo ();
RemoveLinks ();
+ RemoveCisPeps ();
}
@@ -3482,6 +3638,7 @@
PCHelix helix;
PCTurn turn;
PCLink link;
+PCCisPep cispep;
int RC;
// pad input line with spaces, if necessary
@@ -3563,6 +3720,14 @@
else delete link;
return RC;
+ } else if (!strncmp(PDBString,"CISPEP",6)) {
+
+ cispep = new CCisPep();
+ RC = cispep->ConvertPDBASCII(PDBString);
+ if (RC==0) CisPeps.AddData ( cispep );
+ else delete cispep;
+ return RC;
+
} else
return Error_WrongSection;
@@ -3600,6 +3765,10 @@
}
+void CModel::PDBASCIIDumpCP ( RCFile f ) {
+ CisPeps.PDBASCIIDump ( f );
+}
+
void CModel::PDBASCIIDump ( RCFile f ) {
char S[100];
int i;
@@ -4205,6 +4374,24 @@
}
+
+int CModel::GetNumberOfCisPeps() {
+ return CisPeps.Length();
+}
+
+PCCisPep CModel::GetCisPep ( int CisPepNum ) {
+ return (PCCisPep)CisPeps.GetContainerClass ( CisPepNum-1 );
+}
+
+void CModel::RemoveCisPeps() {
+ CisPeps.FreeContainer();
+}
+
+void CModel::AddCisPep ( PCCisPep CisPep ) {
+ CisPeps.AddData ( CisPep );
+}
+
+
void CModel::ApplyTransform ( mat44 & TMatrix ) {
// transforms all coordinates by multiplying with matrix TMatrix
int i;
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_model.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_model.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_model.h 2007-07-09 08:44:54.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_model.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_model.h,v 1.15 2007/07/09 15:44:54 ccb Exp $
+// $Id: mmdb_model.h,v 1.10 2007/05/18 13:50:51 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -13,7 +13,7 @@
//
// =================================================================
//
-// 14.05.07 <-- Date of Last Modification.
+// 10.09.07 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -29,8 +29,10 @@
// CSheet ( sheet info )
// CSheets ( container for sheets )
// CTurn ( turn info )
-// CLinkContainer ( container for link data )
-// CLink ( link data )
+// CLinkContainer ( container for link data )
+// CLink ( link data )
+// CCisPepContainer ( container for CisPep data )
+// CCisPep ( CisPep data )
// CModel ( PDB model )
//
// Copyright (C) E. Krissinel 2000-2007
@@ -381,6 +383,7 @@
};
+
// =================== CLinkContainer =====================
DefineClass(CLinkContainer)
@@ -446,6 +449,72 @@
};
+
+// =================== CCisPepContainer =====================
+
+DefineClass(CCisPepContainer)
+DefineStreamFunctions(CCisPepContainer)
+
+class CCisPepContainer : public CClassContainer {
+
+ public :
+
+ CCisPepContainer () : CClassContainer() {}
+ CCisPepContainer ( RPCStream Object )
+ : CClassContainer ( Object ) {}
+ ~CCisPepContainer () {}
+
+ PCContainerClass MakeContainerClass ( int ClassID );
+
+};
+
+
+// ===================== CCisPep ===========================
+
+DefineClass(CCisPep)
+DefineStreamFunctions(CCisPep)
+
+class CCisPep : public CContainerClass {
+
+ public :
+ int serNum; // record serial number
+ ResName pep1; // residue name
+ ChainID chainID1; // chain identifier 1
+ int seqNum1; // residue sequence number 1
+ InsCode icode1; // insertion code 1
+ ResName pep2; // residue name 2
+ ChainID chainID2; // chain identifier 2
+ int seqNum2; // residue sequence number 2
+ InsCode icode2; // insertion code 2
+ int modNum; // model number
+ realtype measure; // measure of the angle in degrees.
+
+ CCisPep ();
+ CCisPep ( const pstr S );
+ CCisPep ( RPCStream Object );
+ ~CCisPep();
+
+ void PDBASCIIDump ( pstr S, int N );
+ int ConvertPDBASCII ( const pstr S );
+
+// void MakeCIF ( PCMMCIFData CIF, int N );
+// void GetCIF ( PCMMCIFData CIF, int & Signal );
+
+ int GetClassID () { return ClassID_CisPep; }
+
+ void Copy ( PCContainerClass CisPep );
+
+ void write ( RCFile f );
+ void read ( RCFile f );
+
+ protected :
+
+ void InitCisPep();
+
+};
+
+
+
// ==================== CModel ===============================
#define SSERC_Ok 0
@@ -714,9 +783,13 @@
int ConvertPDBString ( pstr PDBString );
// PDBASCIIDumpPS(..) makes output of PDB primary structure records
+ // excluding cispeps
void PDBASCIIDumpPS ( RCFile f );
- // PDBASCIIDumpPS(..) makes output of PDB coordinate (ATOM etc.)
+ // PDBASCIIDumpCP(..) makes output of cispep records
+ void PDBASCIIDumpCP ( RCFile f );
+
+ // PDBASCIIDump(..) makes output of PDB coordinate (ATOM etc.)
// records
void PDBASCIIDump ( RCFile f );
@@ -789,14 +862,24 @@
void RemoveHetInfo ();
- // ---- Getting Links
+ // ---- Working Links
int GetNumberOfLinks ();
PCLink GetLink ( int serialNum ); // 1<=serNum<=NofLinks
PCLinkContainer GetLinks() { return &Links; }
- void RemoveLinks ();
- void AddLink ( PCLink Link );
+ void RemoveLinks();
+ void AddLink ( PCLink Link );
+
+
+ // ---- Working CisPeps
+
+ int GetNumberOfCisPeps();
+ PCCisPep GetCisPep ( int CisPepNum );
+ PCCisPepContainer GetCisPeps() { return &CisPeps; }
+
+ void RemoveCisPeps();
+ void AddCisPep ( PCCisPep CisPep );
@@ -825,20 +908,21 @@
protected :
- int serNum; // the model serial number
- PCMMDBManager manager; // pointer to mmdbmanager class
+ int serNum; // the model serial number
+ PCMMDBManager manager; // pointer to mmdbmanager class
- CHetCompounds HetCompounds; // information on heterocompounds
- CSSContainer Helices; // information on helices
- CSheets Sheets; // information on sheets
- CSSContainer Turns; // information on turns
- CLinkContainer Links; // information on links
-
- int nChains; // number of chains
- int nChainsAlloc; // actual length of Chain[]
- PPCChain Chain; // array of chains
+ CHetCompounds HetCompounds; // information on heterocompounds
+ CSSContainer Helices; // information on helices
+ CSheets Sheets; // information on sheets
+ CSSContainer Turns; // information on turns
+ CLinkContainer Links; // information on links
+ CCisPepContainer CisPeps; // information on cispeps
+
+ int nChains; // number of chains
+ int nChainsAlloc; // actual length of Chain[]
+ PPCChain Chain; // array of chains
- Boolean Exclude; // used internally
+ Boolean Exclude; // used internally
void InitModel ();
void FreeMemory ();
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_rwbrook.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_rwbrook.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_rwbrook.cpp 2007-10-15 03:45:54.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_rwbrook.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_rwbrook.cpp,v 1.35 2007/10/15 10:45:54 nds65 Exp $
+// $Id: mmdb_rwbrook.cpp,v 1.15 2006/07/28 10:57:23 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -1469,6 +1469,7 @@
SegID sgID;
Element element;
PCAtom atom;
+pstr p;
char charge[10];
strcpy ( LastFunc,"MMDB_F_Atom" );
@@ -1544,7 +1545,7 @@
if (FTN_STR(ID)[0]==' ') {
atomName[0] = char(0);
- if ((FTN_STR(AtNam)[1]=='H') && (FTN_STR(AtNam)[0]!='H') ||
+ if ((FTN_STR(AtNam)[1]=='H') ||
((FTN_STR(AtNam)[1]=='D') && (FTN_STR(ID)[2]=='D'))) {
i = 0;
while ((i
if (i
}
-
- if ((FTN_STR(AtNam)[0]=='A') || ((FTN_STR(AtNam)[0]=='N') && (FTN_STR(ID)[1]!='N'))) {
- GetStrTer ( atomName,FTN_STR(AtNam),4,5,FTN_LEN(AtNam) );
- } else if ((FTN_STR(ID)[1]=='N') && ( (FTN_STR(AtNam)[0]=='N') && (FTN_STR(AtNam)[1]=='N') )) {
- GetStrTer ( atomName,FTN_STR(AtNam),4,5,FTN_LEN(AtNam) );
- } else if (!atomName[0]) {
+ if (!atomName[0]) {
atomName[0] = ' ';
GetStrTer ( &(atomName[1]),FTN_STR(AtNam),3,4,FTN_LEN(AtNam) );
}
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_rwbrook.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_rwbrook.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_rwbrook.h 2006-08-16 03:55:20.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_rwbrook.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_rwbrook.h,v 1.12 2006/08/16 10:55:20 fr45 Exp $
+// $Id: mmdb_rwbrook.h,v 1.4 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_sbase.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_sbase.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_sbase.cpp 2006-08-16 03:55:20.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_sbase.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_sbase.cpp,v 1.15 2006/08/16 10:55:20 fr45 Exp $
+// $Id: mmdb_sbase.cpp,v 1.11 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_sbase.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_sbase.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_sbase.h 2006-08-16 03:55:20.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_sbase.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_sbase.h,v 1.14 2006/08/16 10:55:20 fr45 Exp $
+// $Id: mmdb_sbase.h,v 1.9 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_sbase0.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_sbase0.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_sbase0.cpp 2007-07-09 08:45:24.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_sbase0.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,10 +1,10 @@
-// $Id: mmdb_sbase0.cpp,v 1.9 2007/07/09 15:45:24 ccb Exp $
+// $Id: mmdb_sbase0.cpp,v 1.7 2007/08/15 10:59:32 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
-// Copyright (C) Eugene Krissinel 2000-2006.
+// Copyright (C) Eugene Krissinel 2000-2007.
//
// This code is distributed under the terms and conditions of the
// CCP4 Program Suite Licence Agreement as a CCP4 Library.
@@ -13,7 +13,7 @@
//
// =================================================================
//
-// 24.02.06 <-- Date of Last Modification.
+// 14.08.07 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -25,7 +25,7 @@
// CSBStructure ( SB structure (monomer) class )
// CSBIndex ( SB index class )
//
-// E. Krissinel 2001-2006
+// (C) E. Krissinel 2001-2007
//
// =================================================================
//
@@ -66,33 +66,35 @@
CSBAtom::~CSBAtom() {}
void CSBAtom::SBAtomInit() {
- sca_name [0] = char(0);
- pdb_name [0] = char(0);
- element [0] = char(0);
- energyType[0] = char(0);
- x = -MaxReal;
- y = -MaxReal;
- z = -MaxReal;
- x_esd = 0.0;
- y_esd = 0.0;
- z_esd = 0.0;
- ccp4_charge = 0.0; // atom charge from ccp4 libs
- sca_charge = 0.0; // formal atom charge (MSD)
- partial_charge = 0.0; // partial atom charge (MSD)
- vdw_radius = 0.0;
- vdwh_radius = 0.0;
- ion_radius = 0.0;
- valency = 0;
- chirality = 'N';
- leaving = 'N';
- hb_type = 'N';
+ sca_name [0] = char(0);
+ pdb_name [0] = char(0);
+ old_pdb_name[0] = char(0);
+ element [0] = char(0);
+ energyType [0] = char(0);
+ x = -MaxReal;
+ y = -MaxReal;
+ z = -MaxReal;
+ x_esd = 0.0;
+ y_esd = 0.0;
+ z_esd = 0.0;
+ ccp4_charge = 0.0; // atom charge from ccp4 libs
+ sca_charge = 0.0; // formal atom charge (MSD)
+ partial_charge = 0.0; // partial atom charge (MSD)
+ vdw_radius = 0.0;
+ vdwh_radius = 0.0;
+ ion_radius = 0.0;
+ valency = 0;
+ chirality = 'N';
+ leaving = 'N';
+ hb_type = 'N';
}
void CSBAtom::Copy ( PCSBAtom A ) {
- strcpy ( sca_name ,A->sca_name );
- strcpy ( pdb_name ,A->pdb_name );
- strcpy ( element ,A->element );
- strcpy ( energyType,A->energyType );
+ strcpy ( sca_name ,A->sca_name );
+ strcpy ( pdb_name ,A->pdb_name );
+ strcpy ( old_pdb_name,A->old_pdb_name );
+ strcpy ( element ,A->element );
+ strcpy ( energyType ,A->energyType );
x = A->x;
y = A->y;
z = A->z;
@@ -133,12 +135,13 @@
void CSBAtom::write ( RCFile f ) {
-int Version=4;
+int Version=5;
f.WriteInt ( &Version );
- f.WriteFile ( sca_name ,sizeof(sca_name) );
- f.WriteFile ( pdb_name ,sizeof(pdb_name) );
- f.WriteFile ( element ,sizeof(element) );
- f.WriteFile ( energyType,sizeof(energyType) );
+ f.WriteFile ( sca_name ,sizeof(sca_name) );
+ f.WriteFile ( pdb_name ,sizeof(pdb_name) );
+ f.WriteFile ( old_pdb_name,sizeof(old_pdb_name) );
+ f.WriteFile ( element ,sizeof(element) );
+ f.WriteFile ( energyType ,sizeof(energyType) );
f.WriteReal ( &x );
f.WriteReal ( &y );
f.WriteReal ( &z );
@@ -162,6 +165,9 @@
f.ReadInt ( &Version );
f.ReadFile ( sca_name ,sizeof(sca_name) );
f.ReadFile ( pdb_name ,sizeof(pdb_name) );
+ if (Version>4)
+ f.ReadFile ( old_pdb_name,sizeof(old_pdb_name) );
+ else strcpy ( old_pdb_name,pdb_name );
f.ReadFile ( element ,sizeof(element) );
f.ReadFile ( energyType,sizeof(energyType) );
f.ReadReal ( &x );
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_sbase0.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_sbase0.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_sbase0.h 2006-08-16 03:55:20.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_sbase0.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,10 +1,10 @@
-// $Id: mmdb_sbase0.h,v 1.7 2006/08/16 10:55:20 fr45 Exp $
+// $Id: mmdb_sbase0.h,v 1.5 2007/08/15 10:59:32 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
-// Copyright (C) Eugene Krissinel 2000-2006.
+// Copyright (C) Eugene Krissinel 2000-2007.
//
// This code is distributed under the terms and conditions of the
// CCP4 Program Suite Licence Agreement as a CCP4 Library.
@@ -13,7 +13,7 @@
//
// =================================================================
//
-// 21.02.06 <-- Date of Last Modification.
+// 14.08.07 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -25,7 +25,7 @@
// CSBStructure ( SB structure (monomer) class )
// CSBIndex ( SB index class )
//
-// E. Krissinel 2001-2006
+// (C) E. Krissinel 2001-2007
//
// =================================================================
//
@@ -78,6 +78,7 @@
public :
char sca_name [sca_name_len+1]; // SCA atom name
char pdb_name [pdb_name_len+1]; // PDB atom name (aligned)
+ char old_pdb_name[pdb_name_len+1]; // old PDB atom name (aligned)
char element [element_len+1]; // chemical element (aligned)
char energyType[energy_type_len+1]; // energy type; set to empty
// string "" if not provided
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_selmngr.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_selmngr.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_selmngr.cpp 2006-08-16 03:55:21.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_selmngr.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_selmngr.cpp,v 1.15 2006/08/16 10:55:21 fr45 Exp $
+// $Id: mmdb_selmngr.cpp,v 1.24 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -777,7 +777,7 @@
}
-#define hetIndicator '¬'
+#define hetIndicator '@'
void CMMDBSelManager::Select (
int selHnd, // must be obtained from NewSelection()
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_selmngr.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_selmngr.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_selmngr.h 2006-08-16 03:55:21.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_selmngr.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_selmngr.h,v 1.14 2006/08/16 10:55:21 fr45 Exp $
+// $Id: mmdb_selmngr.h,v 1.13 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_symop.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_symop.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_symop.cpp 2006-08-16 03:55:21.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_symop.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_symop.cpp,v 1.16 2006/08/16 10:55:21 fr45 Exp $
+// $Id: mmdb_symop.cpp,v 1.13 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_symop.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_symop.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_symop.h 2007-07-09 08:45:44.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_symop.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_symop.h,v 1.14 2007/07/09 15:45:44 ccb Exp $
+// $Id: mmdb_symop.h,v 1.10 2007/01/08 16:42:41 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_tables.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_tables.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_tables.cpp 2006-08-16 03:55:21.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_tables.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_tables.cpp,v 1.16 2006/08/16 10:55:21 fr45 Exp $
+// $Id: mmdb_tables.cpp,v 1.13 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_tables.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_tables.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_tables.h 2006-08-16 03:55:22.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_tables.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_tables.h,v 1.16 2006/08/16 10:55:22 fr45 Exp $
+// $Id: mmdb_tables.h,v 1.12 2007/08/15 10:59:32 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
@@ -31,7 +31,7 @@
// RName1 ( 1-characters amino acid names )
//
//
-// E. Krissinel 2001-2002
+// (C) E. Krissinel 2001-2002
//
// =================================================================
//
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_title.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_title.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_title.cpp 2006-08-16 03:55:22.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_title.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_title.cpp,v 1.14 2006/08/16 10:55:22 fr45 Exp $
+// $Id: mmdb_title.cpp,v 1.9 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_title.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_title.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_title.h 2006-08-16 03:55:22.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_title.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_title.h,v 1.13 2006/08/16 10:55:22 fr45 Exp $
+// $Id: mmdb_title.h,v 1.7 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_uddata.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_uddata.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_uddata.cpp 2006-08-16 03:55:22.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_uddata.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_uddata.cpp,v 1.12 2006/08/16 10:55:22 fr45 Exp $
+// $Id: mmdb_uddata.cpp,v 1.8 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_uddata.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_uddata.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_uddata.h 2006-08-16 03:55:22.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_uddata.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_uddata.h,v 1.12 2006/08/16 10:55:22 fr45 Exp $
+// $Id: mmdb_uddata.h,v 1.5 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_utils.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_utils.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_utils.cpp 2006-08-16 03:55:22.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_utils.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_utils.cpp,v 1.22 2006/08/16 10:55:22 fr45 Exp $
+// $Id: mmdb_utils.cpp,v 1.23 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_utils.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_utils.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_utils.h 2006-08-16 03:55:22.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_utils.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_utils.h,v 1.17 2006/08/16 10:55:22 fr45 Exp $
+// $Id: mmdb_utils.h,v 1.15 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_xml.cpp ccp4-onlylibs-dev/lib/src/mmdb/mmdb_xml.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_xml.cpp 2006-08-16 03:55:23.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_xml.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_xml.cpp,v 1.17 2006/08/16 10:55:23 fr45 Exp $
+// $Id: mmdb_xml.cpp,v 1.10 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_xml.h ccp4-onlylibs-dev/lib/src/mmdb/mmdb_xml.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/mmdb_xml.h 2006-08-16 03:55:23.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/mmdb_xml.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: mmdb_xml.h,v 1.13 2006/08/16 10:55:23 fr45 Exp $
+// $Id: mmdb_xml.h,v 1.5 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/random_n.cpp ccp4-onlylibs-dev/lib/src/mmdb/random_n.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/random_n.cpp 2006-08-16 03:55:23.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/random_n.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: random_n.cpp,v 1.11 2006/08/16 10:55:23 fr45 Exp $
+// $Id: random_n.cpp,v 1.4 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/random_n.h ccp4-onlylibs-dev/lib/src/mmdb/random_n.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/random_n.h 2006-08-16 03:55:23.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/random_n.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: random_n.h,v 1.11 2006/08/16 10:55:23 fr45 Exp $
+// $Id: random_n.h,v 1.4 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.cpp ccp4-onlylibs-dev/lib/src/mmdb/stream_.cpp
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.cpp 2006-08-16 03:55:23.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/stream_.cpp 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: stream_.cpp,v 1.12 2006/08/16 10:55:23 fr45 Exp $
+// $Id: stream_.cpp,v 1.4 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.h ccp4-onlylibs-dev/lib/src/mmdb/stream_.h
--- ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.h 2006-08-16 03:55:23.000000000 -0700
+++ ccp4-onlylibs-dev/lib/src/mmdb/stream_.h 2007-10-21 22:33:35.000000000 -0700
@@ -1,4 +1,4 @@
-// $Id: stream_.h,v 1.12 2006/08/16 10:55:23 fr45 Exp $
+// $Id: stream_.h,v 1.4 2006/07/28 10:57:24 keb Exp $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
Package: ccp4-onlylibs-dev
# Use version numbering to sync with the current CCP4 release:
Version: 6.0.99
Revision: 2
GCC: 4.0
Source: http://sage.ucsc.edu/xtal/%n/%n-%v.tgz
Source-MD5: 04d79e0c72544ec1ba447bb1e91b4b54
SourceDirectory: %n
Source2: http://www.ysbl.york.ac.uk/~emsley/software/mmdb-1.12.tar.gz
Source2-MD5: b46e31159b85d6742f4014822f2240f4
Depends: gcc43-shlibs
BuildDepends: gcc43
BuildDependsOnly: false
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
###############################################################################
#Patch: %n.patch
PatchScript: <<
#!/bin/zsh -efv
umask 0022
# Use my patched configure and ccp4.setup-zsh files
#cp ../ccp4.setup-zsh include/.
# cp ../configure .
# setup scripts for tcsh, zsh and bash users
export TEMPXTAL=$PWD:h
#
perl -pi.bak -e 's|/xtal|\$TEMPXTAL|g' include/ccp4.setup*
# build prefix (changed in install)
perl -pi.bak -e 's|/prefix|%p|g' include/ccp4.setup*
# location of tcktk, blt (not needed here, but doesn't hurt).
perl -pi.bak -e 's|/usr/local/bin|%p/bin|g' include/ccp4.setup*
# same
# make copy for tcsh users (CCP4 convention is no suffix)
cp include/ccp4.setup-dist include/ccp4.setup
#
# Enable everything.
# We need the mmdbold clipper libraries built for COOT:
perl -pi.bak -e 's|enable_mmdbold=no|enable_mmdbold=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_phs=no|enable_phs=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_mmdb=no|enable_mmdb=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_minimol=no|enable_minimol=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_cif=no|enable_cif=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_ccp4=no|enable_ccp4=yes|g' lib/clipper/configure*
# perl -pi.bak -e 's|enable_cctbx=no|enable_cctbx=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_cns=no|enable_cns=yes|g' lib/clipper/configure*
perl -pi.bak -e 's|enable_fortran=no|enable_fortran=yes|g' lib/clipper/configure*
# clean up:
rm -f include/*.bak lib/clipper/*.bak
<<
###############################################################################
CompileScript: <<
#!/bin/zsh -efv
umask 0022
rm -rf lib/src/mmdb
cp -R ../mmdb-1.12/src lib/src/mmdb
export TEMPXTAL=$PWD:h
source include/ccp4.setup-zsh
export DYLD_LIBRARY_PATH=$CLIB
#
./configure --disable-cctbx --disable-phaser --disable-pdb_extract --disable-diffractionImg --onlylibs Darwin
#FC="fort77" ./configure --onlylibs Darwin
#ln -s $CCP4/lib/src $CCP4/lib/clipper/ccp4
#
# fix some post-configure bugs
#
make 2>../make.log |tee ../make.log
make install 2>../makeinst.log |tee ../makeinst.log
#
echo "Ignoring error messages. They are harmless"
#
command ls -1 lib/*.a
sleep 10
#
# rm $CCP4/lib/clipper/ccp4
# make realclean
<<
###############################################################################
InstallScript: <<
#!/bin/zsh -efv
umask 0022
export TEMPXTAL=$PWD:h
source include/ccp4.setup-zsh
export DYLD_LIBRARY_PATH=$CLIB
ORIGDIR=$(dirname $PWD)
#
# Change environment scripts to match final installation install prefix:
perl -pi.bak -e 's|\$TEMPXTAL|%p/share/xtal|g' include/ccp4.setup*
perl -pi.bak -e 's|CCP4_MASTER/%n|CCP4_MASTER/%n-%v|g' include/ccp4.setup-zsh
perl -pi.bak -e 's|ccp4-6.0.99|%n-%v|g' include/ccp4.setup*
rm -f include/*.bak
perl -pi.bak -e 's|%b|%p/share/xtal/%n-%v|g' bin/clipper-config
rm -f bin/clipper-config.bak
perl -pi.bak -e 's|%b|%p/share/xtal/%n-%v|g' lib/*.la
rm -f lib/*.la.bak
#
cp include/ssm/ssm_superpose.h include/ssm/ssm_superpose.h-orig
perl -pi -e 's|ivector FF1,FF2;||g' include/ssm/ssm_superpose.h
#
# Now install:
mkdir -p %i/bin
mkdir -p %i/share/xtal/%n-%v
cp bin/* %i/bin/.
cp -R * %i/share/xtal/%n-%v/.
ranlib %i/share/xtal/%n-%v/lib/**/*.a
<<
###############################################################################
SplitOff:<<
Package: clipper
Depends: clipper-bin, ccp4-onlylibs-dev
BuildDependsOnly: true
InstallScript: <<
mkdir -p %i/share/doc/installed-packages
touch %i/share/doc/installed-packages/%n
<<
Description: Working Clipper static libs and binaries
DescDetail:<<
Placeholder to install working static clipper libraries and binary
executables for packages that require both to be present for linking.
The aim of the project is to produce a set of object-oriented libraries
for the organisation of crystallographic data and the performance of
crystallographic computation. The libraries are designed as a framework
for new crystallographic software, which will allow the full power of
modern programming techniques to be exploited by the developer. This
will lead to greater functionality from simpler code which will be easier
to develop and debug. NOTE: This is a static version of clipper required
to build COOT and various clipper binary executables like CPIRATE with the
g++-4.0 compiler.
<<
<<
###############################################################################
SplitOff2: <<
Package: clipper-bin
BuildDependsOnly: false
Files: <<
bin/*
<<
Description: Working Clipper executables including cpirate
DescDetail:<<
The package clipper-bin installs statically-linked versions of the following
binary executable files that are broken in the ccp4-clipper-bin package in
the 10.4 branch of fink: cecalc cfft chltofom cinvfft clipper-config
cmakereference cpatterson cphasecombine cphasematch cpirate csfcalc csigmaa
superpose. These executables will be installed in %p/bin.
<<
<<
###############################################################################
###############################################################################
Description: CCP4 and CLIPPER static libraries
DescDetail: <<
This package installs CCP4 libraries, only. If you need all
of CCP4, install the self-contained CCP4 package instead of, or
in addition to, this. The splitoff package clipper-bin builds
and installs statically-linked clipper executable programs such
as cpirate. CCP4 itself will also install these, but cpirate in
CCP4 suffers from a run-time error. Installation of clipper-bin
will put working copies in %p/bin, and thus at the head of the path.
The licensing for the CCP4 library loosely conforms to the LGPL,
unlike the more restrictive CCP4 license. The clipper libraries
and programs explicitly adhere to the LGPL.
This version compiles with the Apple Lapack/Blas framework
but uses its own static lib build of fftw to avoid a run-time
error that appears in cpirate and coot fft calculations.
CCP4lib files will be installed under
%p/share/xtal/ccp4-onlylibs-dev-6.0.2. This is slightly newer
in content relative to the corresponding files in CCP4 6.0.2.
Programs requiring these libraries to build or run need to
source the appropriate
%p/share/xtal/ccp4-onlylibs-dev-6.0.2/include/ccp4.setup
file for the shell, as is done in the coot.info file. Unless
you are building something external to fink, there is no need
to source that file.
The primary use for this package, currently, is for compiling COOT.
The primary use for the clipper-bin split-off package is to provide
stand-alone, functioning versions of cpirate and colleagues