Imported Upstream version 0.7

parent 37ae14ba
2012-09-28 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.7
2010-01-26 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.6.1
......
This diff is collapsed.
......@@ -28,11 +28,12 @@ ACLOCAL_AMFLAGS=-I macros
# coot-utils depends on mini-mol.
# geometry depends on utils
#
SUBDIRS = auxil scheme python macros compat utils protein_db geometry mini-mol \
SUBDIRS = auxil scheme python pdb-templates macros compat utils protein_db mini-mol geometry \
coot-utils surface coot-surface lidia-core \
coords angles skeleton ccp4mg-utils density-contour \
db-main ideal ligand high-res build greg-tests python-tests \
analysis tw lbg cootaneer src data rama-data doc
analysis tw libgtkgraph lbg cootaneer cootilus goograph src data \
rama-data doc rcrane
# po, no po today.
......@@ -65,7 +66,6 @@ EXTRA_DIST = \
fix-cif-loops.awk \
ifdef-for-create-aboutdialog.awk \
mtrix-to-ncs-matrix.awk \
theor-helix-70.pdb \
RELEASE-NOTES \
copyright-disclaimer.txt \
intltool-extract.in \
......@@ -100,6 +100,6 @@ dist-hook:
subpkgdatadir = $(pkgdatadir)
subpkgdata_DATA = cootrc standard-residues.pdb colours.def \
mtrix-to-ncs-matrix.awk theor-helix-70.pdb
mtrix-to-ncs-matrix.awk
......@@ -65,10 +65,8 @@ am__aclocal_m4_deps = $(top_srcdir)/macros/aclocal-include.m4 \
$(top_srcdir)/macros/clipper.m4 \
$(top_srcdir)/macros/coot-database.m4 \
$(top_srcdir)/macros/coot-windows.m4 \
$(top_srcdir)/macros/glib.m4 $(top_srcdir)/macros/glut.m4 \
$(top_srcdir)/macros/glut.m4 \
$(top_srcdir)/macros/goo-canvas.m4 \
$(top_srcdir)/macros/gtk-canvas.m4 $(top_srcdir)/macros/gtk.m4 \
$(top_srcdir)/macros/gtkgl.m4 \
$(top_srcdir)/macros/guile-gtk.m4 \
$(top_srcdir)/macros/guile-lib-guile-gui.m4 \
$(top_srcdir)/macros/guile.m4 \
......@@ -182,6 +180,7 @@ CFLAGS = @CFLAGS@
CLIPPER_CXXFLAGS = @CLIPPER_CXXFLAGS@
CLIPPER_LIBS = @CLIPPER_LIBS@
COOT_GSL_FLAGS = @COOT_GSL_FLAGS@
COOT_OPENGL_LIBS = @COOT_OPENGL_LIBS@
COOT_STDTYPES = @COOT_STDTYPES@
COOT_SYS_BUILD_TYPE = @COOT_SYS_BUILD_TYPE@
COOT_USE_GUILE = @COOT_USE_GUILE@
......@@ -207,7 +206,6 @@ ENTERPRISE_TOOLS_CFLAGS = @ENTERPRISE_TOOLS_CFLAGS@
EXEEXT = @EXEEXT@
FGREP = @FGREP@
GLIB_CFLAGS = @GLIB_CFLAGS@
GLIB_CONFIG = @GLIB_CONFIG@
GLIB_LIBS = @GLIB_LIBS@
GLUT_CFLAGS = @GLUT_CFLAGS@
GLUT_LIBS = @GLUT_LIBS@
......@@ -219,14 +217,9 @@ GREP = @GREP@
GSL_CFLAGS = @GSL_CFLAGS@
GSL_CONFIG = @GSL_CONFIG@
GSL_LIBS = @GSL_LIBS@
GTKCANVAS_CFLAGS = @GTKCANVAS_CFLAGS@
GTKCANVAS_LIBS = @GTKCANVAS_LIBS@
GTKGLEXT_CFLAGS = @GTKGLEXT_CFLAGS@
GTKGLEXT_LIBS = @GTKGLEXT_LIBS@
GTKGL_CFLAGS = @GTKGL_CFLAGS@
GTKGL_LIBS = @GTKGL_LIBS@
GTK_CFLAGS = @GTK_CFLAGS@
GTK_CONFIG = @GTK_CONFIG@
GTK_LIBS = @GTK_LIBS@
GUILE = @GUILE@
GUILE_CFLAGS = @GUILE_CFLAGS@
......@@ -274,7 +267,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
PACKAGE_NAME = @PACKAGE_NAME@
PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PKG_CONFIG = @PKG_CONFIG@
......@@ -355,11 +347,12 @@ ACLOCAL_AMFLAGS = -I macros
# coot-utils depends on mini-mol.
# geometry depends on utils
#
SUBDIRS = auxil scheme python macros compat utils protein_db geometry mini-mol \
SUBDIRS = auxil scheme python pdb-templates macros compat utils protein_db mini-mol geometry \
coot-utils surface coot-surface lidia-core \
coords angles skeleton ccp4mg-utils density-contour \
db-main ideal ligand high-res build greg-tests python-tests \
analysis tw lbg cootaneer src data rama-data doc
analysis tw libgtkgraph lbg cootaneer cootilus goograph src data \
rama-data doc rcrane
EXTRA_DIST = \
autogen.sh \
......@@ -386,7 +379,6 @@ EXTRA_DIST = \
fix-cif-loops.awk \
ifdef-for-create-aboutdialog.awk \
mtrix-to-ncs-matrix.awk \
theor-helix-70.pdb \
RELEASE-NOTES \
copyright-disclaimer.txt \
intltool-extract.in \
......@@ -395,7 +387,7 @@ EXTRA_DIST = \
subpkgdatadir = $(pkgdatadir)
subpkgdata_DATA = cootrc standard-residues.pdb colours.def \
mtrix-to-ncs-matrix.awk theor-helix-70.pdb
mtrix-to-ncs-matrix.awk
all: all-recursive
......
......@@ -308,6 +308,14 @@ Cygwin
To extend the available memory:
http://cygwin.com/cygwin-ug-net/setup-maxmem.html
Ligand Dialog, aka LIDIA
------------------------
To get ligand builder dialog you will need to comile with a
sufficiently recent version of gtk (2.16 or later) and goocavanvas.
extension language wrapper
--------------------------
......@@ -508,8 +516,8 @@ Code Thanks...
[1] Ethan Merritt, Gerard Kleywegt, George Sheldrick
[2] Eleanor Dodson, Miguel Ortiz Lombarda, Charlie Bond, Jan
Dohnalek, Garib Murshudov, Jean Wittingham, Florence Vincent,
[2] Eleanor Dodson, Miguel Ortiz Lombarda, Charlie Bond,
Jan Dohnalek, Garib Murshudov, Jean Wittingham, Florence Vincent,
Tracy Gloucester, Constantina Fotinou, Roberto Steiner, Adrian
Lapthorn, Claudia Schnick, Rosa Grenha, Ezra Peisach, Ben Luisi,
Frank von Delft, Karen McLuskey, Marcin Cymborowski, Stephen Graham.
......
Pre-release 0.6.2
------
Release 0.7
o FEATURE: Het-groups are now represented with bond orders.
o FEATURE: Ligand Builder - working in conjunction with cprodrg.
o FEATURE: RCrane [RNA builder]
o FEATURE: Cootaneer [RNA builder]
o FEATURE: PDBe Recent structure browser.
o FEATURE: JLigand interface.
o CHANGE: symmetry operator number are no longer zero indexed. Add
trans component to symmetry file names. [Steven Sheriff].
o CHANGE: Dotted surfaces now are coloured by atom type and are at
atomic radii rather than 1A.
o CHANGE: map transformation no longer has symmetry overwrite
problems [JED].
o BUG-FIX: Fix missing C7 on DA -> DT mutation [Sabine Schneider].
o BUG-FIX: TER records on base mutation [James Parker].
o BUG-FIX: DNA in sequence view [Miguel Ortiz Lombardia].
o BUG-FIX: Update Go To Atom dialog after water merging [Bob Nolte].
o BUG-FIX: fix memory leak in fit-protein function [Ed Pozharski].
o BUG-FIX: Improved "Place Helix Here".
------
Release 0.6.2
o FEATURE: PISA Interfaces can now be represented in Coot (requires
pisa version 1.06 or later).
......
This diff is collapsed.
This diff is collapsed.
lib_LTLIBRARIES=libcoot-analysis.la
include_HEADERS=bfkurt.hh
include_HEADERS=bfkurt.hh mogul-interface.hh
INCLUDES = \
-I$(top_srcdir)/geometry \
-I$(top_srcdir)/coot-utils \
-I$(top_srcdir)/mini-mol \
-I$(top_srcdir)/utils \
$(CLIPPER_CXXFLAGS) \
$(MMDB_CXXFLAGS)
libcoot_analysis_la_SOURCES = bfkurt.cc
libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc
libcoot_analysis_la_LIBADD = \
../coot-utils/libcoot-coord-utils.la \
$(top_builddir)/coot-utils/libcoot-coord-utils.la \
$(top_builddir)/geometry/libcoot-geometry.la \
$(top_builddir)/mini-mol/libcoot-mini-mol.la \
$(top_builddir)/utils/libcoot-utils.la \
$(MMDB_LIBS)
bin_PROGRAMS = bfactan
check_PROGRAMS = test-mogul
bfactan_SOURCES = bfactan.cc
test_mogul_SOURCES = test-mogul.cc
test_mogul_LDADD = libcoot-analysis.la
bfactan_LDADD = \
libcoot-analysis.la \
$(top_builddir)/coot-utils/libcoot-coord-utils.la \
$(top_builddir)/geometry/libcoot-geometry.la \
$(top_builddir)/mini-mol/libcoot-mini-mol.la \
$(top_builddir)/utils/libcoot-utils.la \
$(CLIPPER_LIBS) \
$(MMDB_LIBS)
......
......@@ -37,6 +37,7 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
bin_PROGRAMS = bfactan$(EXEEXT)
check_PROGRAMS = test-mogul$(EXEEXT)
subdir = analysis
DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \
$(srcdir)/Makefile.in
......@@ -45,10 +46,8 @@ am__aclocal_m4_deps = $(top_srcdir)/macros/aclocal-include.m4 \
$(top_srcdir)/macros/clipper.m4 \
$(top_srcdir)/macros/coot-database.m4 \
$(top_srcdir)/macros/coot-windows.m4 \
$(top_srcdir)/macros/glib.m4 $(top_srcdir)/macros/glut.m4 \
$(top_srcdir)/macros/glut.m4 \
$(top_srcdir)/macros/goo-canvas.m4 \
$(top_srcdir)/macros/gtk-canvas.m4 $(top_srcdir)/macros/gtk.m4 \
$(top_srcdir)/macros/gtkgl.m4 \
$(top_srcdir)/macros/guile-gtk.m4 \
$(top_srcdir)/macros/guile-lib-guile-gui.m4 \
$(top_srcdir)/macros/guile.m4 \
......@@ -95,8 +94,11 @@ am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)" \
LTLIBRARIES = $(lib_LTLIBRARIES)
am__DEPENDENCIES_1 =
libcoot_analysis_la_DEPENDENCIES = \
../coot-utils/libcoot-coord-utils.la $(am__DEPENDENCIES_1)
am_libcoot_analysis_la_OBJECTS = bfkurt.lo
$(top_builddir)/coot-utils/libcoot-coord-utils.la \
$(top_builddir)/geometry/libcoot-geometry.la \
$(top_builddir)/mini-mol/libcoot-mini-mol.la \
$(top_builddir)/utils/libcoot-utils.la $(am__DEPENDENCIES_1)
am_libcoot_analysis_la_OBJECTS = bfkurt.lo mogul.lo
libcoot_analysis_la_OBJECTS = $(am_libcoot_analysis_la_OBJECTS)
PROGRAMS = $(bin_PROGRAMS)
am_bfactan_OBJECTS = bfactan.$(OBJEXT)
......@@ -104,8 +106,12 @@ bfactan_OBJECTS = $(am_bfactan_OBJECTS)
bfactan_DEPENDENCIES = libcoot-analysis.la \
$(top_builddir)/coot-utils/libcoot-coord-utils.la \
$(top_builddir)/geometry/libcoot-geometry.la \
$(top_builddir)/mini-mol/libcoot-mini-mol.la \
$(top_builddir)/utils/libcoot-utils.la $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
am_test_mogul_OBJECTS = test-mogul.$(OBJEXT)
test_mogul_OBJECTS = $(am_test_mogul_OBJECTS)
test_mogul_DEPENDENCIES = libcoot-analysis.la
DEFAULT_INCLUDES = -I.@am__isrc@
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
......@@ -119,8 +125,10 @@ CXXLD = $(CXX)
CXXLINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
$(LDFLAGS) -o $@
SOURCES = $(libcoot_analysis_la_SOURCES) $(bfactan_SOURCES)
DIST_SOURCES = $(libcoot_analysis_la_SOURCES) $(bfactan_SOURCES)
SOURCES = $(libcoot_analysis_la_SOURCES) $(bfactan_SOURCES) \
$(test_mogul_SOURCES)
DIST_SOURCES = $(libcoot_analysis_la_SOURCES) $(bfactan_SOURCES) \
$(test_mogul_SOURCES)
HEADERS = $(include_HEADERS)
ETAGS = etags
CTAGS = ctags
......@@ -140,6 +148,7 @@ CFLAGS = @CFLAGS@
CLIPPER_CXXFLAGS = @CLIPPER_CXXFLAGS@
CLIPPER_LIBS = @CLIPPER_LIBS@
COOT_GSL_FLAGS = @COOT_GSL_FLAGS@
COOT_OPENGL_LIBS = @COOT_OPENGL_LIBS@
COOT_STDTYPES = @COOT_STDTYPES@
COOT_SYS_BUILD_TYPE = @COOT_SYS_BUILD_TYPE@
COOT_USE_GUILE = @COOT_USE_GUILE@
......@@ -165,7 +174,6 @@ ENTERPRISE_TOOLS_CFLAGS = @ENTERPRISE_TOOLS_CFLAGS@
EXEEXT = @EXEEXT@
FGREP = @FGREP@
GLIB_CFLAGS = @GLIB_CFLAGS@
GLIB_CONFIG = @GLIB_CONFIG@
GLIB_LIBS = @GLIB_LIBS@
GLUT_CFLAGS = @GLUT_CFLAGS@
GLUT_LIBS = @GLUT_LIBS@
......@@ -177,14 +185,9 @@ GREP = @GREP@
GSL_CFLAGS = @GSL_CFLAGS@
GSL_CONFIG = @GSL_CONFIG@
GSL_LIBS = @GSL_LIBS@
GTKCANVAS_CFLAGS = @GTKCANVAS_CFLAGS@
GTKCANVAS_LIBS = @GTKCANVAS_LIBS@
GTKGLEXT_CFLAGS = @GTKGLEXT_CFLAGS@
GTKGLEXT_LIBS = @GTKGLEXT_LIBS@
GTKGL_CFLAGS = @GTKGL_CFLAGS@
GTKGL_LIBS = @GTKGL_LIBS@
GTK_CFLAGS = @GTK_CFLAGS@
GTK_CONFIG = @GTK_CONFIG@
GTK_LIBS = @GTK_LIBS@
GUILE = @GUILE@
GUILE_CFLAGS = @GUILE_CFLAGS@
......@@ -232,7 +235,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
PACKAGE_NAME = @PACKAGE_NAME@
PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PKG_CONFIG = @PKG_CONFIG@
......@@ -305,22 +307,31 @@ top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
lib_LTLIBRARIES = libcoot-analysis.la
include_HEADERS = bfkurt.hh
include_HEADERS = bfkurt.hh mogul-interface.hh
INCLUDES = \
-I$(top_srcdir)/geometry \
-I$(top_srcdir)/coot-utils \
-I$(top_srcdir)/mini-mol \
-I$(top_srcdir)/utils \
$(CLIPPER_CXXFLAGS) \
$(MMDB_CXXFLAGS)
libcoot_analysis_la_SOURCES = bfkurt.cc
libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc
libcoot_analysis_la_LIBADD = \
../coot-utils/libcoot-coord-utils.la \
$(top_builddir)/coot-utils/libcoot-coord-utils.la \
$(top_builddir)/geometry/libcoot-geometry.la \
$(top_builddir)/mini-mol/libcoot-mini-mol.la \
$(top_builddir)/utils/libcoot-utils.la \
$(MMDB_LIBS)
bfactan_SOURCES = bfactan.cc
test_mogul_SOURCES = test-mogul.cc
test_mogul_LDADD = libcoot-analysis.la
bfactan_LDADD = \
libcoot-analysis.la \
$(top_builddir)/coot-utils/libcoot-coord-utils.la \
$(top_builddir)/geometry/libcoot-geometry.la \
$(top_builddir)/mini-mol/libcoot-mini-mol.la \
$(top_builddir)/utils/libcoot-utils.la \
$(CLIPPER_LIBS) \
$(MMDB_LIBS)
......@@ -436,9 +447,21 @@ clean-binPROGRAMS:
list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
echo " rm -f" $$list; \
rm -f $$list
clean-checkPROGRAMS:
@list='$(check_PROGRAMS)'; test -n "$$list" || exit 0; \
echo " rm -f" $$list; \
rm -f $$list || exit $$?; \
test -n "$(EXEEXT)" || exit 0; \
list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
echo " rm -f" $$list; \
rm -f $$list
bfactan$(EXEEXT): $(bfactan_OBJECTS) $(bfactan_DEPENDENCIES)
@rm -f bfactan$(EXEEXT)
$(CXXLINK) $(bfactan_OBJECTS) $(bfactan_LDADD) $(LIBS)
test-mogul$(EXEEXT): $(test_mogul_OBJECTS) $(test_mogul_DEPENDENCIES)
@rm -f test-mogul$(EXEEXT)
$(CXXLINK) $(test_mogul_OBJECTS) $(test_mogul_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
......@@ -448,6 +471,8 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bfactan.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bfkurt.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mogul.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/test-mogul.Po@am__quote@
.cc.o:
@am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
......@@ -579,6 +604,7 @@ distdir: $(DISTFILES)
fi; \
done
check-am: all-am
$(MAKE) $(AM_MAKEFLAGS) $(check_PROGRAMS)
check: check-am
all-am: Makefile $(LTLIBRARIES) $(PROGRAMS) $(HEADERS)
install-binPROGRAMS: install-libLTLIBRARIES
......@@ -614,8 +640,8 @@ maintainer-clean-generic:
@echo "it deletes files that may require special tools to rebuild."
clean: clean-am
clean-am: clean-binPROGRAMS clean-generic clean-libLTLIBRARIES \
clean-libtool mostlyclean-am
clean-am: clean-binPROGRAMS clean-checkPROGRAMS clean-generic \
clean-libLTLIBRARIES clean-libtool mostlyclean-am
distclean: distclean-am
-rm -rf ./$(DEPDIR)
......@@ -684,19 +710,19 @@ ps-am:
uninstall-am: uninstall-binPROGRAMS uninstall-includeHEADERS \
uninstall-libLTLIBRARIES
.MAKE: install-am install-strip
.MAKE: check-am install-am install-strip
.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
clean-generic clean-libLTLIBRARIES clean-libtool ctags \
distclean distclean-compile distclean-generic \
distclean-libtool distclean-tags distdir dvi dvi-am html \
html-am info info-am install install-am install-binPROGRAMS \
install-data install-data-am install-dvi install-dvi-am \
install-exec install-exec-am install-html install-html-am \
install-includeHEADERS install-info install-info-am \
install-libLTLIBRARIES install-man install-pdf install-pdf-am \
install-ps install-ps-am install-strip installcheck \
installcheck-am installdirs maintainer-clean \
clean-checkPROGRAMS clean-generic clean-libLTLIBRARIES \
clean-libtool ctags distclean distclean-compile \
distclean-generic distclean-libtool distclean-tags distdir dvi \
dvi-am html html-am info info-am install install-am \
install-binPROGRAMS install-data install-data-am install-dvi \
install-dvi-am install-exec install-exec-am install-html \
install-html-am install-includeHEADERS install-info \
install-info-am install-libLTLIBRARIES install-man install-pdf \
install-pdf-am install-ps install-ps-am 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-binPROGRAMS \
......
......@@ -12,7 +12,7 @@
#include <vector>
#endif // HAVE_VECTOR
#include "mmdb_manager.h"
#include <mmdb/mmdb_manager.h>
namespace coot_extras {
......
#ifndef MOGUL_INTERFACE_HH
#define MOGUL_INTERFACE_HH
#include <string>
#include <vector>
#include "protein-geometry.hh"
namespace coot {
// this can throw a std::runtime_error
class mogul_distribution {
public:
mogul_distribution(const std::vector<std::string> &bits);
mogul_distribution() {}
float bin_start;
float bin_end;
float bin_width;
int n_bins;
std::vector<int> counts;
};
class mogul_item {
public:
enum type_t { BOND, ANGLE, TORSION, PLANE };
// 1-based counting
int idx_1;
int idx_2;
int idx_3;
int idx_4;
std::vector<int> plane_indices;
int counts;
float value, mean, median, std_dev, z;
type_t type;
float max_badness;
mogul_distribution distribution;
public:
mogul_item() { max_badness = 5.0; }
mogul_item(int atom_idx_1_in, int atom_idx_2_in,
float value_in,
int counts_in, float mean_in, float median_in, float std_dev_in, float z_in) {
type = BOND;
value = value_in;
idx_1 = atom_idx_1_in;
idx_2 = atom_idx_2_in;
counts = counts_in;
mean = mean_in;
median = median_in;