Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4957
Modified Files:
coot.info coot.patch clipper.info mmdb.info ssm.info
Log Message:
updates for coot dependencies
Index: coot.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- coot.patch 4 Aug 2011 14:10:11 -0000 1.1
+++ coot.patch 9 Aug 2013 04:09:02 -0000 1.2
@@ -33,3 +33,327 @@
;; run raster3d
(define render-image
+
+
+diff -crB ./src/graphics-info.h ../coot-patched/src/graphics-info.h
+*** ./src/graphics-info.h 2013-04-27 16:04:58.000000000 +0200
+--- ../coot-patched/src/graphics-info.h 2013-07-25 04:09:17.861265837
+0200
+***************
+*** 3307,3313 ****
+ short int move_copy_of_imol2_flag);
+
+ #ifdef HAVE_SSMLIB
+! void print_ssm_sequence_alignment(CSSMAlign *SSMAlign,
+ atom_selection_container_t asc_ref,
+ atom_selection_container_t asc_mov,
+ PCAtom *atom_selection1,
+--- 3307,3313 ----
+ short int move_copy_of_imol2_flag);
+
+ #ifdef HAVE_SSMLIB
+! void print_ssm_sequence_alignment(ssm::Align *SSMAlign,
+ atom_selection_container_t asc_ref,
+ atom_selection_container_t asc_mov,
+ PCAtom *atom_selection1,
+***************
+*** 3315,3321 ****
+ int n_selected_atoms_1, int
n_selected_atoms_2,
+ short int move_copy_of_imol2_flag);
+
+! void make_and_print_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign,
+
atom_selection_container_t asc_ref,
+
atom_selection_container_t asc_mov,
+ PCAtom
*atom_selection1,
+--- 3315,3321 ----
+ int n_selected_atoms_1, int
n_selected_atoms_2,
+ short int move_copy_of_imol2_flag);
+
+! void make_and_print_horizontal_ssm_sequence_alignment(ssm::Align
*SSMAlign,
+
atom_selection_container_t asc_ref,
+
atom_selection_container_t asc_mov,
+ PCAtom
*atom_selection1,
+***************
+*** 3325,3331 ****
+ void print_horizontal_ssm_sequence_alignment(std::pair<std::string,
std::string> aligned_sequences) const;
+
+ std::pair<std::string, std::string>
+! get_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign,
+ atom_selection_container_t asc_ref,
+ atom_selection_container_t asc_mov,
+ PCAtom *atom_selection1, PCAtom
*atom_selection2,
+--- 3325,3331 ----
+ void print_horizontal_ssm_sequence_alignment(std::pair<std::string,
std::string> aligned_sequences) const;
+
+ std::pair<std::string, std::string>
+! get_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign,
+ atom_selection_container_t asc_ref,
+ atom_selection_container_t asc_mov,
+ PCAtom *atom_selection1, PCAtom
*atom_selection2,
+diff -crB ./src/graphics-info-superpose.cc
../coot-patched/src/graphics-info-superpose.cc
+*** ./src/graphics-info-superpose.cc 2013-01-16 17:40:31.000000000 +0100
+--- ../coot-patched/src/graphics-info-superpose.cc 2013-07-25
04:42:47.876256551 +0200
+***************
+*** 22,27 ****
+--- 22,31 ----
+ #include "Python.h" // before system includes to stop "POSIX_C_SOURCE"
redefined problems
+ #endif
+
++ #ifdef HAVE_SSMLIB
++ #include "ssm_defs.h"
++ #endif
++
+ #if defined _MSC_VER
+ #include <windows.h>
+ #endif
+***************
+*** 168,179 ****
+
+ #ifdef HAVE_SSMLIB
+
+! int precision = SSMP_Normal;
+! int connectivity = CSSC_Flexible;
+
+ // probably not necessary, not sure:
+! SetSSConnectivityCheck ( CSSC_Flexible );
+! SetSSMatchPrecision ( SSMP_Normal );
+
+ if (asc_ref.n_selected_atoms > 0) {
+ if (asc_mov.n_selected_atoms > 0) {
+--- 172,183 ----
+
+ #ifdef HAVE_SSMLIB
+
+! ssm::PRECISION precision = ssm::PREC_Normal;
+! ssm::CONNECTIVITY connectivity = ssm::CONNECT_Flexible;
+
+ // probably not necessary, not sure:
+! ssm::SetConnectivityCheck ( ssm::CONNECT_Flexible );
+! ssm::SetMatchPrecision ( ssm::PREC_Normal );
+
+ if (asc_ref.n_selected_atoms > 0) {
+ if (asc_mov.n_selected_atoms > 0) {
+***************
+*** 199,234 ****
+
+ // Remove the pointer one day.
+ //
+! CSSMAlign *SSMAlign = new CSSMAlign();
+! int rc = SSMAlign->Align(mol2, mol1, precision, connectivity,
+ asc_mov.SelectionHandle,
+ asc_ref.SelectionHandle);
+
+ if (rc) {
+ std::string ws;
+ switch (rc) {
+! case SSM_noHits :
+ std::cout << " *** secondary structure does not match.\n";
+ ws = "secondary structure does not match";
+ break;
+! case SSM_noSPSN :
+ std::cout << " *** structures are too remote.\n";
+ ws = "structures are too remote";
+ break;
+! case SSM_noGraph :
+ std::cout << " *** can't make graph for " << name1 << "\n";
+ ws = "can't make graph for " + name1;
+ ws += " structure";
+ break;
+! case SSM_noVertices :
+ std::cout << " *** empty graph for " << name1 << "\n";
+ ws = "empty graph for " + name1;
+ break;
+! case SSM_noGraph2 :
+ std::cout << " *** can't make graph for " << name2 << "\n";
+ ws = "can't make graph for " + name2;
+ break;
+! case SSM_noVertices2 :
+ std::cout << " *** empty graph for " << name2 << "\n";
+ ws = "empty graph for " + name2;
+ break;
+--- 203,238 ----
+
+ // Remove the pointer one day.
+ //
+! ssm::Align *SSMAlign = new ssm::Align();
+! int rc = SSMAlign->align(mol2, mol1, precision, connectivity,
+ asc_mov.SelectionHandle,
+ asc_ref.SelectionHandle);
+
+ if (rc) {
+ std::string ws;
+ switch (rc) {
+! case ssm::RC_NoHits :
+ std::cout << " *** secondary structure does not match.\n";
+ ws = "secondary structure does not match";
+ break;
+! case ssm::RC_NoSuperposition :
+ std::cout << " *** structures are too remote.\n";
+ ws = "structures are too remote";
+ break;
+! case ssm::RC_NoGraph :
+ std::cout << " *** can't make graph for " << name1 << "\n";
+ ws = "can't make graph for " + name1;
+ ws += " structure";
+ break;
+! case ssm::RC_NoVertices :
+ std::cout << " *** empty graph for " << name1 << "\n";
+ ws = "empty graph for " + name1;
+ break;
+! case ssm::RC_NoGraph2 :
+ std::cout << " *** can't make graph for " << name2 << "\n";
+ ws = "can't make graph for " + name2;
+ break;
+! case ssm::RC_NoVertices2 :
+ std::cout << " *** empty graph for " << name2 << "\n";
+ ws = "empty graph for " + name2;
+ break;
+***************
+*** 298,304 ****
+ // mat44 tmat;
+ // realtype rmsdAchieved, seqIdentity, nCombs;
+ // int nAligned, nGaps, nMisD;
+! // CSuperpose Superpose; type in class CSSMAlign
+ //
+ // Superpose->GetSuperposition(Ca1, dist1, nCa1, Ca2,
+ // nCa2, tmat, rmsdAchieved, nAligned, nGaps, seqIdentity,
+--- 302,308 ----
+ // mat44 tmat;
+ // realtype rmsdAchieved, seqIdentity, nCombs;
+ // int nAligned, nGaps, nMisD;
+! // CSuperpose Superpose; type in class ssm::Align
+ //
+ // Superpose->GetSuperposition(Ca1, dist1, nCa1, Ca2,
+ // nCa2, tmat, rmsdAchieved, nAligned, nGaps, seqIdentity,
+***************
+*** 331,337 ****
+
+ #ifdef HAVE_SSMLIB
+ void
+! graphics_info_t::make_and_print_horizontal_ssm_sequence_alignment(CSSMAlign
*SSMAlign,
+
atom_selection_container_t asc_ref,
+
atom_selection_container_t asc_mov,
+ PCAtom
*atom_selection1, PCAtom *atom_selection2,
+--- 335,341 ----
+
+ #ifdef HAVE_SSMLIB
+ void
+! graphics_info_t::make_and_print_horizontal_ssm_sequence_alignment(ssm::Align
*SSMAlign,
+
atom_selection_container_t asc_ref,
+
atom_selection_container_t asc_mov,
+ PCAtom
*atom_selection1, PCAtom *atom_selection2,
+***************
+*** 394,400 ****
+
+ #ifdef HAVE_SSMLIB
+ std::pair<std::string, std::string>
+! graphics_info_t::get_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign,
+
atom_selection_container_t asc_ref,
+
atom_selection_container_t asc_mov,
+ PCAtom *atom_selection1,
PCAtom *atom_selection2,
+--- 398,404 ----
+
+ #ifdef HAVE_SSMLIB
+ std::pair<std::string, std::string>
+! graphics_info_t::get_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign,
+
atom_selection_container_t asc_ref,
+
atom_selection_container_t asc_mov,
+ PCAtom *atom_selection1,
PCAtom *atom_selection2,
+***************
+*** 483,489 ****
+
+ #ifdef HAVE_SSMLIB
+ void
+! graphics_info_t::print_ssm_sequence_alignment(CSSMAlign *SSMAlign,
+ atom_selection_container_t
asc_ref,
+ atom_selection_container_t
asc_mov,
+ PCAtom *atom_selection1, PCAtom
*atom_selection2,
+--- 487,493 ----
+
+ #ifdef HAVE_SSMLIB
+ void
+! graphics_info_t::print_ssm_sequence_alignment(ssm::Align *SSMAlign,
+ atom_selection_container_t
asc_ref,
+ atom_selection_container_t
asc_mov,
+ PCAtom *atom_selection1, PCAtom
*atom_selection2,
+diff -crB ./src/molecule-class-info-ncs.cc
../coot-patched/src/molecule-class-info-ncs.cc
+*** ./src/molecule-class-info-ncs.cc 2013-01-16 17:40:31.000000000 +0100
+--- ../coot-patched/src/molecule-class-info-ncs.cc 2013-07-25
04:44:45.450071527 +0200
+***************
+*** 51,56 ****
+--- 51,57 ----
+
+ #ifdef HAVE_SSMLIB
+ #include "ssm_align.h"
++ #include "ssm_defs.h"
+ #endif
+
+ // This is called by make_bonds_type_checked(), which is called by
+***************
+*** 514,546 ****
+ if (graphics_info_t::ncs_matrix_flag == coot::NCS_SSM) {
+ #ifdef HAVE_SSMLIB
+
+! int precision = SSMP_Normal;
+! int connectivity = CSSC_Flexible;
+! CSSMAlign *SSMAlign = new CSSMAlign();
+! int rc = SSMAlign->Align(atom_sel.mol, atom_sel.mol,
+ precision, connectivity, SelHandle2, SelHandle1);
+
+ if (rc) {
+ std::string ws;
+ switch (rc) {
+! case SSM_noHits :
+ std::cout << " *** secondary structure does not match.\n";
+ ws = "secondary structure does not match";
+ break;
+! case SSM_noSPSN :
+ std::cout << " *** structures are too remote.\n";
+ ws = "structures are too remote";
+ break;
+! case SSM_noGraph :
+ std::cout << " *** can't make graph for 1\n";
+ break;
+! case SSM_noVertices :
+ std::cout << " *** empty graph for 1\n";
+ break;
+! case SSM_noGraph2 :
+ std::cout << " *** can't make graph for 2\n";
+ break;
+! case SSM_noVertices2 :
+ std::cout << " *** empty graph for 2\n";
+ break;
+ default :
+--- 515,547 ----
+ if (graphics_info_t::ncs_matrix_flag == coot::NCS_SSM) {
+ #ifdef HAVE_SSMLIB
+
+! ssm::PRECISION precision = ssm::PREC_Normal;
+! ssm::CONNECTIVITY connectivity = ssm::CONNECT_Flexible;
+! ssm::Align *SSMAlign = new ssm::Align();
+! int rc = SSMAlign->align(atom_sel.mol, atom_sel.mol,
+ precision, connectivity, SelHandle2, SelHandle1);
+
+ if (rc) {
+ std::string ws;
+ switch (rc) {
+! case ssm::RC_NoHits :
+ std::cout << " *** secondary structure does not match.\n";
+ ws = "secondary structure does not match";
+ break;
+! case ssm::RC_NoSuperposition :
+ std::cout << " *** structures are too remote.\n";
+ ws = "structures are too remote";
+ break;
+! case ssm::RC_NoGraph :
+ std::cout << " *** can't make graph for 1\n";
+ break;
+! case ssm::RC_NoVertices :
+ std::cout << " *** empty graph for 1\n";
+ break;
+! case ssm::RC_NoGraph2 :
+ std::cout << " *** can't make graph for 2\n";
+ break;
+! case ssm::RC_NoVertices2 :
+ std::cout << " *** empty graph for 2\n";
+ break;
+ default :
Index: mmdb.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/mmdb.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- mmdb.info 4 Jul 2013 19:48:21 -0000 1.6
+++ mmdb.info 9 Aug 2013 04:09:02 -0000 1.7
@@ -1,6 +1,6 @@
Package: mmdb
-Version: 1.25.0
-Revision: 32
+Version: 1.25.3
+Revision: 1
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
DescPackaging: <<
Based on package created by Morten Kjeldgaard <m...@bioxray.dk> with minor
@@ -10,11 +10,10 @@
License: LGPL
GCC:4.0
HomePage: http://www.ebi.ac.uk/pdbe/docs/cldoc/
-Source:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/dependencies/%n-%v.tar.gz
-Source-MD5: 8d20c3b752b7b604d3ef2b3f01a04f70
-# build-time stuff in %N-dev, runtime stuff in %N-shlibs, nothing in %N
-RuntimeDepends: fink-obsolete-packages, %n-shlibs (= %v-%r)
-BuildDepends: libtool2, automake1.11, autoconf2.6, fink (>= 0.32)
+Source: ftp://ftp.ccp4.ac.uk/opensource//%n-%v.tar.gz
+Source-MD5: 1216462ac8c542bd45ffe5792fd6b723
+RuntimeDepends: %n-shlibs (= %v-%r)
+BuildDepends: fink (>= 0.32)
DescDetail: <<
MMDB is CCP4\'s macromolecular coordinate library, written by Eugene
Krissinel of the EBI. The Coordinate Library is designed to assist
@@ -36,39 +35,15 @@
<<
CompileScript: <<
#!/bin/bash -evf
-%p/bin/libtoolize
-%p/bin/aclocal
-%p/bin/automake --gnu
-%p/bin/autoconf
LDFLAGS="-L%p/lib -L/usr/lib" \
- ./configure --prefix=%p
+ ./configure --prefix=%p --enable-shared
make
-# create missing mmdb.pc
-mkdir -p lib/pkgconfig
-cd lib/pkgconfig
-cat > mmdb.pc << eof
-prefix=%p
-exec_prefix=\$prefix
-libdir=\$prefix/lib
-includedir=\$prefix/include
-
-Name: %n
-Description: Macromolecular coordinate library
-Version: %v
-Requires:
-Conflicts:
-Libs: -L\${libdir} -lmmdb
-Cflags: -I\${includedir}
-
-eof
<<
InstallScript: <<
make install DESTDIR=%d
-mkdir -p %i/lib/pkgconfig
-cp lib/pkgconfig/%n.pc %i/lib/pkgconfig/.
# dpkg requires every package to contain at least one actual file
-mkdir -p %i/share/doc/installed-packages
-touch %i/share/doc/installed-packages/%n
+ mkdir -p %i/share/doc/installed-packages
+ touch %i/share/doc/installed-packages/%n
<<
SplitOff: <<
Package: %N-shlibs
Index: clipper.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/clipper.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- clipper.info 3 Jul 2013 00:31:19 -0000 1.5
+++ clipper.info 9 Aug 2013 04:09:02 -0000 1.6
@@ -1,24 +1,25 @@
Package: clipper
Epoch: 1
-Version: 2.1
-Revision: 32
+Version: 2.1.20130601
+Revision: 1
GCC:4.0
BuildDepends: <<
fftw (>= 2.1.5-1010) | fftw-mpi (>= 2.1.5-1010),
-mmdb-dev (>= 1.23.2-31),
-ssm-dev (>= 0.1-31),
-gpp4-dev (>= 1.2.0-31),
-gcc48
+mmdb-dev (>= 1.25.3-1),
+ssm-dev (>= 1.3-1),
+libccp4-dev (>= 6.3.1-1),
+gcc48,
+gcc48-compiler
<<
Depends: <<
%n-shlibs (>= %e:%v-%r)
<<
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
Homepage: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html
-Source: http://www.ysbl.york.ac.uk/~cowtan/%n/%n-%v-091215-ac.tar.gz
-Source-MD5: 003d8c8dd5e3b7bf6b09ef10e9fa31cb
+Source: ftp://ftp.ccp4.ac.uk/opensource/%n-%v.tar.gz
+Source-MD5: 2e0d3faec7cc5a1eb377392122e6e254
SourceDirectory: %n-%v
-DocFiles: README AUTHORS NEWS COPYING
+DocFiles: README AUTHORS COPYING ChangeLog
Description: Object-oriented crystallographic libraries
DescDetail: <<
The aim of the project is to produce a set of object-oriented libraries
@@ -27,12 +28,12 @@
for new crystallographic software, which will allow the full power of
modern programming techniques to be exploited by the developer.
<<
-SetCXX programming techniques to be exploited by the developer. of
-%v.tar.gz c s sequences)
const; réHëG+ \ñÿ \ñÿ ujHëG+ IëG+
iëG+ xeìG+ \ñÿ ìG+ p\ñÿ @\ñÿ kHëG+ 6
è è ! è ! \ñÿ \ñÿ x4eìG+ p\ñÿ bHëG+ HëG+ \ñÿ `bHëG+ O\ñÿ À/ÉìG+ ujHëG+
ÉìG+ Ø$ÉìG+ ¨)ÉìG+ IëG+ x4eìG+ p\ñÿ @\ñÿ kHëG+ à! à! \ñÿ \ñÿ HþDìG+ P\ñÿ bHëG+ HëG+ \ñÿ `bHëG+ O\ñÿ @\ñÿ 8\ñÿ 8iëG+ p \ñÿ ujHëG+ IëG+ P\ñÿ
\ñÿ kHëG+ G H I J K M N O P \ñÿ \ñÿ HµìG+ ð
\ñÿ bHëG+ HëG+ \ñÿ 0/ÉìG+ ujHëG+ @eìG+
éøëG+ ÉìG+ Ø$ÉìG+ ¨)ÉìG+ IëG+ HµìG+ ð
\ñÿ
0\ñÿ kHëG+ 8µìG+ ð
\ñÿ `\ñÿ kHëG+ (µìG+ ð
\ñÿ \ñÿ kHëG+ µìG+ ð
\ñÿ À\ñÿ kHëG+
¨.ÉìG+ ujHëG+ ¨)ÉìG+ @\ñÿ 8ùëG+ eiHëG+ Ø$ÉìG+ `
\ñÿ y8ùëG+ eiHëG+ ÉìG+
\ñÿ Z8ùëG+ eiHëG+ ØäøëG+ @eìG+ éøëG+
ÉìG+ ØDeìG+ Ø$ÉìG+ ¨)ÉìG+ IëG+ 8iëG+ ÄëG+ \ñÿ p{øëG+ @\ñÿ \ñÿ kHëG+ 5 6 7 8 : < = > ? @ B D \ñÿ \ñÿ
±ÁëG+ \ñÿ ujHëG+
iëG+ À
\ñÿ ÄëG+ eiHëG+
iëG+ Õ_@f ÆS
Qöl±í ìÃëG+ \ñÿ ±ÁëG+ P\ñÿ
\ñÿ kHëG+ u]ÞÓ 4Q
÷U^Qʧ ¶uª¹ñìò*Äv\ñÿ \ñÿ HþëG+ `\ñÿ bHëG+ HëG+ \ñÿ `bHëG+ O\ñÿ @\ñÿ 8\ñÿ OeìG+ ujHëG+ ØDeìG+
IeìG+ IëG+ `\ñÿ \ñ
ÿ kHëG+ 8þëG+ `\ñÿ @\ñÿ kFLAGS:
-fno-strict-aliasing -I%p/include -I%p/include/mmdb -I%p/include/ssm
-I%p/include/gpp4 -I%p/include/gpp4/ccp4
+SetCXXFLAGS: -fno-strict-aliasing -I%p/include -I%p/include/mmdb
-I%p/include/ssm -I%p/include/ccp4
License: LGPL
CompileScript: <<
#!/bin/bash -evf
-LDFLAGS="-L%p/lib -L/usr/lib" \
- ./configure --prefix=%p --enable-shared --with-gpp4=%p --with-mmdb=%p
--with-fftw=%p --enable-mmdb --enable-minimol --enable-cif --enable-cns
--enable-gpp4
+LDFLAGS="-L%p/lib -L/usr/lib" F77="%p/bin/gfortran-fsf-4.8"
FFLAGS="-L%p/lib/gcc4.8/lib -lgfortran " \
+ ./configure --prefix=%p --enable-shared --enable-ccp4 --enable-fortran
--with-ccp4=%p --with-mmdb=%p --with-fftw=%p --enable-mmdb --enable-minimol
--enable-cif --enable-cns
perl -pi -e 's|examples||g' Makefile
# Fix for 10.4 libtool issue
if [[ $(sw_vers -productVersion) < 10.5 ]]; then
@@ -49,9 +50,9 @@
Package: %N-shlibs
Depends: <<
fftw-shlibs (>= 2.1.5-1010) | fftw-mpi-shlibs (>= 2.1.5-1010),
- mmdb-shlibs (>= 1.23.2-1),
- ssm-shlibs (>= 0.1-26),
- gpp4-shlibs (>= 1.2.0-26),
+ mmdb-shlibs (>= 1.25.3-1),
+ ssm-shlibs (>= 1.3-1),
+ libccp4-shlibs (>= 6.3.1-1),
gcc48-shlibs
<<
Files: <<
@@ -62,7 +63,8 @@
lib/libclipper-core.2.*dylib
lib/libclipper-minimol.2.*dylib
lib/libclipper-mmdb.2.*dylib
- lib/libclipper-phs.2.*dylib
+ lib/libclipper-phs.2.*dylib
+ lib/libclipper-fortran.2.*dylib
<<
Shlibs: <<
%p/lib/libclipper-ccp4.2.dylib 3.0.0 %n (>= 1:2.1-1)
@@ -73,6 +75,7 @@
%p/lib/libclipper-minimol.2.dylib 3.0.0 %n (>= 1:2.1-1)
%p/lib/libclipper-mmdb.2.dylib 3.0.0 %n (>= 1:2.1-1)
%p/lib/libclipper-phs.2.dylib 3.0.0 %n (>= 1:2.1-1)
+ %p/lib/libclipper-fortran.2.dylib 3.0.0 %n (>= 1:2.1-1)
<<
<<
SplitOff2: <<
@@ -92,7 +95,7 @@
lib/libclipper-minimol.dylib
lib/libclipper-mmdb.dylib
lib/libclipper-phs.dylib
+ lib/libclipper-fortran.dylib
include/*
- bin/clipper-config
<<
<<
Index: coot.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -d -r1.24 -r1.25
--- coot.info 30 Jul 2013 16:33:10 -0000 1.24
+++ coot.info 9 Aug 2013 04:09:02 -0000 1.25
@@ -1,6 +1,6 @@
Package: coot
Version: 0.7.1.0
-Revision: 3
+Revision: 4
SourceDirectory: %n-0.7.1
Distribution: 10.6, 10.7, 10.8
GCC: 4.0
@@ -39,10 +39,10 @@
BuildDepends: <<
fink (>= 0.24.12) ,
boost1.53.python27 (>= 1.53.0-1),
- clipper-dev (>= 1:2.1-32) ,
- gpp4-dev (>= 1.2.0-32) ,
- mmdb-dev (>= 1.25.0-32) ,
- ssm-dev (>= 0.1-31) ,
+ clipper-dev (>= 1:2.1.20130601-1),
+ libccp4-dev (>= 6.3.1-1) ,
+ mmdb-dev (>= 1.25.3-1) ,
+ ssm-dev (>= 1.3-1) ,
atk1 (>= 1.28.0-1) ,
cairo (>= 1.8.8-3) ,
expat1 ,
@@ -88,10 +88,11 @@
Depends: <<
coot-shlibs (= 0.7.1.0-%r) ,
boost1.53.python27-shlibs (>= 1.53.0-1),
- clipper-shlibs (>= 1:2.1-32) ,
- gpp4-shlibs (>= 1.2.0-32) ,
- mmdb-shlibs (>= 1.25.0-32) ,
- ssm-shlibs (>= 0.1-32) ,
+ clipper-shlibs (>= 1:2.1.20130601-1),
+ libccp4-shlibs (>= 6.3.1-1) ,
+ libccp4-lib (>= 6.3.1-1) | ccp4 (>= 6.3.0-1),
+ mmdb-shlibs (>= 1.25.3-1) ,
+ ssm-shlibs (>= 1.3-1) ,
atk1-shlibs (>= 1.28.0-1) ,
fftw-shlibs | fftw-mpi-shlibs ,
freeglut-shlibs ,
@@ -135,16 +136,15 @@
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
PatchFile: %n.patch
-PatchFile-MD5: 847c69ea1ded1d4238b66ab4840a8141
+PatchFile-MD5: ac51a219f71aae370e33b68dbd80030d
PatchScript: <<
sed 's|@PREFIX@|%p|g' <%{PatchFile} | patch -p1
-perl -pi -e 's|ccp4c=ccp4c|ccp4c=gpp4|g' configure
+#perl -pi -e 's|ccp4c=ccp4c|ccp4c=gpp4|g' configure
perl -pi -e 's|CXX\=\"libtool --mode\=link \$CXX\"|#CXX|g' configure
-#cp ../cod-types.hh lidia-core/cod-types.hh
<<
###############################################################################
ConfigureParams: <<
---disable-openmp --with-gpp4=%p --with-mmdb=%p --with-ssmlib-prefix=%p
--with-clipper-prefix=%p \
+--disable-openmp --with-ccp4=%p --with-mmdb=%p --with-ssmlib-prefix=%p
--with-clipper-prefix=%p \
--with-fftw=%p --with-gnomecanvas-prefix=%p --with-gtk2 --with-glut-prefix=%p
\
--with-guile-gtk --with-guile-gtk-prefix=%p --with-gl-prefix=/usr/X11R6
\
--with-gtkgl-prefix=%p --with-glib-prefix=%p --with-goocanvas-prefix=%p
\
@@ -169,7 +169,7 @@
rdkit_libs='-lMolChemicalFeatures -lDescriptors -lSubgraphs -lPartialCharges
-lForceFieldHelpers -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers
-lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lFileParsers
-lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral
-lboost_python ' \
rdkit_prefix=%p \
FLIBS="-L%p/lib -L%p/lib/rdkit" \
- CPPFLAGS="-I%p/include/rdkit -I%b/lidia-core -I%p/include/libglade-2.0/glade
-I%p/include/libglade-2.0 -I%p/include/python2.7 -I%p/include/mmdb
-I%p/include/ssm -I%p/include/gpp4/ccp4 -I%p/include/clipper -I%p/include
-I/usr/X11R6/include" \
+ CPPFLAGS="-I%p/include/rdkit -I%b/lidia-core -I%p/include/libglade-2.0/glade
-I%p/include/libglade-2.0 -I%p/include/python2.7 -I%p/include/mmdb
-I%p/include/ssm -I%p/include/ccp4 -I%p/include/clipper -I%p/include
-I/usr/X11R6/include" \
LDFLAGS="-Wl,-dylib_file,%p/lib/libboost_python.dylib:%p/lib/python2.7/site-packages/libboost_python-1_53.dylib:%p/lib/python2.7/config/libpython2.7.dylib:%p/lib/libsfftw.2.0.7.dylib:%p/lib/libsrfftw.2.0.7.dylib:%p/lib/pango-ft219/lib/libpango-1.0.dylib:%p/lib/pango-ft219/lib/libpangocairo-1.0.dylib:%p/lib/pango-ft219/lib/libpangoft2-1.0.dylib:%p/lib/pango-ft219/lib/libpangox-1.0.dylib:%p/lib/pango-ft219/lib/libpangoxft-1.0.dylib
-L%p/lib -L/usr/lib -flat_namespace
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \
DYLD_LIBRARY_PATH="" \
RDKIT_CXXFLAGS=-I$rdkit_prefix/include/rdkit \
@@ -189,8 +189,8 @@
fi
perl -pi -e 's|lidia_LDFLAGS = -Wl,--export-dynamic||g' lbg/Makefile
#
-# NUMPROC="$(sysctl -n hw.ncpu)"
- NUMPROC="1"
+ NUMPROC="$(sysctl -n hw.ncpu)"
+# NUMPROC="1"
PYTHON=%p/bin/python2.7 make -j $NUMPROC
<<
###############################################################################
@@ -236,14 +236,20 @@
# Replace with a new wrapper to set the required PYTHONPATH variable
# and a few others as follows:
/bin/rm -f %i/bin/coot
-echo '#!/bin/sh -f ' > %i/bin/coot
-echo "export LC_NUMERIC=C" >> %i/bin/coot
-echo "export COOT_REFMAC_LIB_DIR=%p/share/coot/lib" >> %i/bin/coot
-echo "export COOT_PYTHON_DIR=%p/share/coot/python" >> %i/bin/coot
-echo 'export COOT_SBASE_DIR="$CCP4/share/sbase"' >> %i/bin/coot
-echo 'export CLIBD="$CCP4/lib/data"' >> %i/bin/coot
+echo '#!/bin/sh -f ' > %i/bin/coot
+echo 'export GUILE_WARN_DEPRECATED="no"' >> %i/bin/coot
+echo "export LC_NUMERIC=C" >> %i/bin/coot
+echo "export COOT_REFMAC_LIB_DIR=%p/share/coot/lib" >> %i/bin/coot
+echo "export COOT_PYTHON_DIR=%p/share/coot/python" >> %i/bin/coot
+echo 'export COOT_SBASE_DIR="$CCP4/share/sbase"' >> %i/bin/coot
+echo 'export CLIBD="$CCP4/lib/data"' >> %i/bin/coot
+echo 'if [[ -f $CCP4/lib/data/symop.lib ]];then' >> %i/bin/coot
+echo ' export SYMINFO="$CCP4/lib/data/syminfo.lib"' >> %i/bin/coot
+echo 'else' >> %i/bin/coot
+echo " export SYMINFO=\"%p/share/ccp4/syminfo.lib\"" >> %i/bin/coot
+echo 'fi' >> %i/bin/coot
echo "export
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python"
>> %i/bin/coot
-echo "%p/bin/coot-real \"\$@\" " >> %i/bin/coot
+echo "%p/bin/coot-real \"\$@\" " >> %i/bin/coot
chmod a+x %i/bin/coot
# Clean up the rest of the mess.
/bin/rm -rf %i/include %i/**/.libs %i/lib/*.la %i/share/coot/etc/**/*.la
Index: ssm.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/ssm.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- ssm.info 3 Jul 2013 00:31:19 -0000 1.5
+++ ssm.info 9 Aug 2013 04:09:02 -0000 1.6
@@ -1,6 +1,6 @@
Package: ssm
-Version: 0.1
-Revision: 32
+Version: 1.3
+Revision: 1
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
DescPackaging: <<
Based on package created by Morten Kjeldgaard <m...@bioxray.dk> with minor
@@ -12,13 +12,13 @@
License: LGPL
GCC:4.0
HomePage: http://www.bioxray.dk/~mok/%N
-Source: ftp://ftp.bioxray.au.dk/pub/mok/src/%N-%v.tar.gz
-Source-MD5: 317d9cc78a88fa5652a4a4b06f329823
+Source: ftp://ftp.ccp4.ac.uk/opensource/%n-%v.tar.bz2
+Source-MD5: a7f4eee0ccb4831d2d5d0e06f9327041
NoSourceDirectory: false
Depends: %n-shlibs (= %v-%r)
-BuildDepends: mmdb-dev (>= 1.25.0-32)
+BuildDepends: mmdb-dev (>= 1.25.3-1)
BuildDependsOnly: true
-DocFiles: README AUTHORS NEWS COPYING
+DocFiles: AUTHORS COPYING COPYING.LESSER
DescDetail: <<
SSM is a macromolecular coordinate superposition library, written by
Eugene Krissinel of the EBI.
@@ -35,7 +35,6 @@
Acta Crystallogr D Biol Crystallogr. 60, 2256-68.
<<
PatchScript: <<
-#
# To avoid a conflict with python
#
perl -pi -e 's|FF1|FF1RENAMED|g' src/ssm_superpose.*
@@ -45,7 +44,7 @@
CompileScript: <<
#!/bin/bash -evf
LDFLAGS="-L%p/lib -L/usr/lib" \
- ./configure --prefix=%p
+ ./configure --prefix=%p --enable-shared
make
<<
InstallScript: <<
@@ -54,11 +53,10 @@
SplitOff: <<
Package: %N-shlibs
Files: <<
- lib/libssm.0.dylib
- lib/libssm.0.0.0.dylib
+ lib/libssm.1.dylib
<<
Shlibs: <<
- %p/lib/libssm.0.dylib 1.0.0 %n (>= 0.1-3)
+ %p/lib/libssm.1.dylib 2.0.0 %n (>= 1.3-1)
<<
<<
SplitOff2: <<
@@ -71,6 +69,5 @@
lib/*.la
lib/libssm.dylib
include/ssm/*.h
- lib/pkgconfig/ssm.pc
<<
<<
------------------------------------------------------------------------------
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