Merge branch 'dev'

mittinatten · Sep 27, 2015 · 92d66ab · 92d66ab
2 parents 554983c + c548cbb
commit 92d66ab
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Showing 40 changed files with 2,478 additions and 18,157 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,26 +1,24 @@
 *.o
 *.so
 *.a
-freesasa
-example
-test
-.DS_Store
-*~
-a.out
 *.dvi
 *.aux
 *.log
 *.pdf
 *.ps
-doc/fig/lnr_*.eps
-doc/doxygen
-doc/Doxyfile
-doc/doxyfile.stamp
+*.svg
 *.gcda
 *.gcno
 *.out
 *.gcov
 *.trs
+*.tar.gz
+freesasa
+example
+test
+.DS_Store
+*~
+a.out
 *Makefile.in
 *Makefile
 *.deps
@@ -30,7 +28,6 @@ config.status
 configure.scan
 configure
 stamp-h1
-*.tar.gz
 missing
 install-sh
 depcomp
@@ -39,6 +36,12 @@ test-driver
 autom4te.cache
 aclocal.m4
 tmp*
-doc/doxygen
 bindings/python/*.c
+doc/doxygen
 doc/html/
+doc/fig/lnr_*.eps
+doc/doxygen
+doc/Doxyfile
+doc/doxyfile.stamp
+doc/manual.xml
+doc/LaTeXML.cache
diff --git a/bindings/python/cfreesasa.pxd b/bindings/python/cfreesasa.pxd
@@ -31,7 +31,7 @@ cdef extern from "freesasa.h":
         freesasa_algorithm alg
         double probe_radius
         int shrake_rupley_n_points
-        double lee_richards_delta
+        int lee_richards_n_slices
         int n_threads
 
     ctypedef struct freesasa_result:

diff --git a/bindings/python/freesasa.pyx b/bindings/python/freesasa.pyx
@@ -13,7 +13,7 @@ A minimal program would be something like
 See documentation of the classes and functions for how to customize behavior
 
 
-The private methods _assign_ptr allow access to the C structs that
+The private methods _get_address allow access to the C structs that
 these classes are wrapping, which are necessary in the functions
 calc() and classifyResults(). They are not intended to be used outside
 of this module.
@@ -44,8 +44,8 @@ defaultParameters = {'algorithm' : ShrakeRupley, #freesasa_default_parameters.al
                      'probe-radius' : freesasa_default_parameters.probe_radius,
                      'n-points' :
                        freesasa_default_parameters.shrake_rupley_n_points,
-                     'delta' :
-                       freesasa_default_parameters.lee_richards_delta,
+                     'n-slices' :
+                       freesasa_default_parameters.lee_richards_n_slices,
                      'n-threads' : freesasa_default_parameters.n_threads }
 """The default values for calculation parameters"""
 
@@ -72,7 +72,7 @@ cdef class Parameters:
                   if 'algorithm' in param:    self.setAlgorithm(param['algorithm'])
                   if 'probe-radius' in param: self.setProbeRadius(param['probe-radius'])
                   if 'n-points' in param:     self.setNPoints(param['n-points'])
-                  if 'delta' in param:        self.setDelta(param['delta'])
+                  if 'n-slices' in param:     self.setNSlices(param['n-slices'])
                   if 'n-threads' in param:    self.setNThreads(param['n-threads'])
 
       def setAlgorithm(self,alg):
@@ -130,12 +130,11 @@ cdef class Parameters:
             Set number of test points in Shrake & Rupley algorithm.
 
             Args:
-                n (int): Number of points. Must be one of 20, 50, 100, 200, 
-                  500, 1000, 2000 or 5000.
+                n (int): Number of points (> 0). 
             Raises:
-                AssertionError: n invalid.
+                AssertionError: n <= 0.
             """
-            assert(n in [20,50,100,200,500,1000,2000,5000])
+            assert(n > 0)
             self._c_param.shrake_rupley_n_points = n
 
       def nPoints(self):
@@ -147,26 +146,26 @@ cdef class Parameters:
             """
             return self._c_param.shrake_rupley_n_points
 
-      def setDelta(self,delta):
+      def setNSlices(self,n):
             """
-            Set the value of delta in Lee & Richards algorithm.
+            Set the number of slices per atom in Lee & Richards algorithm.
 
             Args:
-                delta: Value of delta
+                n: Number of slices (> 0)
             Raises:
-                AssertionError: delta must be > 0
+                AssertionError: n <= 0
             """
-            assert(delta > 0)
-            self._c_param.lee_richards_delta = delta
+            assert(n> 0)
+            self._c_param.lee_richards_n_slices = n
 
-      def delta(self):
+      def nSlices(self):
             """
-            Get the value of delta in Lee & Richards algorithm.
+            Get the number of slices per atom in Lee & Richards algorithm.
 
             Returns:
-                Value of delta.
+                Number of slices.
             """
-            return self._c_param.lee_richards_delta
+            return self._c_param.lee_richards_n_slices
 
       def setNThreads(self,n):
             """

diff --git a/bindings/python/test.py b/bindings/python/test.py
@@ -23,7 +23,7 @@ def testParameters(self):
         self.assertTrue(p.algorithm() == d['algorithm'])
         self.assertTrue(p.probeRadius() == d['probe-radius'])
         self.assertTrue(p.nPoints() == d['n-points'])
-        self.assertTrue(p.delta() == d['delta'])
+        self.assertTrue(p.nSlices() == d['n-slices'])
         self.assertTrue(p.nThreads() == d['n-threads'])
 
         p.setAlgorithm(ShrakeRupley)
@@ -38,11 +38,11 @@ def testParameters(self):
 
         p.setNPoints(20)
         self.assertTrue(p.nPoints() == 20)
-        self.assertRaises(AssertionError,lambda: p.setNPoints(21))
+        self.assertRaises(AssertionError,lambda: p.setNPoints(0))
 
-        p.setDelta(0.5)
-        self.assertTrue(p.delta() == 0.5)
-        self.assertRaises(AssertionError,lambda: p.setDelta(-0.5))
+        p.setNSlices(10)
+        self.assertTrue(p.nSlices() == 10)
+        self.assertRaises(AssertionError,lambda: p.setNSlices(0))
 
         p.setNThreads(2)
         self.assertTrue(p.nThreads() == 2)
@@ -184,7 +184,7 @@ def testStructureArray(self):
         self.assertTrue(len(ss) == 1)
         self.assertTrue(ss[0].nAtoms() == 602)
         result = calc(ss[0])
-        self.assertTrue(math.fabs(result.totalArea() - 4759.86096) < 1e-5)
+        self.assertTrue(math.fabs(result.totalArea() - 4779.5109924) < 1e-5)
 
         # Test exceptions
         setVerbosity(silent)
@@ -197,31 +197,31 @@ def testCalc(self):
         # test default settings
         structure = Structure("data/1ubq.pdb")
         result = calc(structure)
-        self.assertTrue(math.fabs(result.totalArea() - 4759.86096) < 1e-5)
+        self.assertTrue(math.fabs(result.totalArea() - 4779.5109924) < 1e-5)
         sasa_classes = classifyResults(result,structure)
-        self.assertTrue(math.fabs(sasa_classes['Polar'] - 2232.23039) < 1e-5)
-        self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2527.63057) < 1e-5)
+        self.assertTrue(math.fabs(sasa_classes['Polar'] - 2236.9298941) < 1e-5)
+        self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2542.5810983) < 1e-5)
 
         # test L&R
         result = calc(structure,Parameters({'algorithm' : LeeRichards, 'delta' : 0.25}))
         sasa_classes = classifyResults(result,structure)
-        self.assertTrue(math.fabs(result.totalArea() - 4728.26159) < 1e-5)
-        self.assertTrue(math.fabs(sasa_classes['Polar'] - 2211.41649) < 1e-5)
-        self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2516.84510) < 1e-5)
+        self.assertTrue(math.fabs(result.totalArea() - 4759.46651) < 1e-5)
+        self.assertTrue(math.fabs(sasa_classes['Polar'] - 2226.83182) < 1e-5)
+        self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2532.63469) < 1e-5)
 
         # test extending Classifier with derived class
         sasa_classes = classifyResults(result,structure,DerivedClassifier())
-        self.assertTrue(math.fabs(sasa_classes['bla'] - 4728.26159) < 1e-5)
+        self.assertTrue(math.fabs(sasa_classes['bla'] - 4759.46651) < 1e-5)
 
         ## test calculating with user-defined classifier ##
         classifier = Classifier("data/naccess.config")
         # classifier passed to assign user-defined radii, could also have used setRadiiWithClassifier()
         structure = Structure("data/1ubq.pdb",classifier) 
         result = calc(structure)
-        self.assertTrue(math.fabs(result.totalArea() - 4777.39) < 0.1)
+        self.assertTrue(math.fabs(result.totalArea() - 4823.29) < 0.1)
         sasa_classes = classifyResults(result,structure,classifier) # classifier passed to get user-classes
-        self.assertTrue(math.fabs(sasa_classes['polar'] - 2361.92) < 0.1)
-        self.assertTrue(math.fabs(sasa_classes['apolar'] - 2415.47) < 0.1)
+        self.assertTrue(math.fabs(sasa_classes['polar'] - 2360.52) < 0.1)
+        self.assertTrue(math.fabs(sasa_classes['apolar'] - 2462.77) < 0.1)
 
 
 if __name__ == '__main__':

diff --git a/configure.ac b/configure.ac
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.68])
-AC_INIT([FreeSASA], [0.4.1])
+AC_INIT([FreeSASA], [0.5.0])
 AM_INIT_AUTOMAKE([foreign])
 AC_CONFIG_SRCDIR([src/freesasa.c])
 AC_CONFIG_HEADERS([config.h])
@@ -60,29 +60,35 @@ fi
 # Enable LaTeX
 AC_ARG_ENABLE([latex],
  [AS_HELP_STRING([--enable-latex],
-   [build documentation from latex sources])],
- [enable_latex=yes], [enable_latex=no])
+   [build documentation from latex sources])])
 
 if test x$enable_latex = xyes ; then
   AC_CHECK_PROG(LATEX, latex, latex)
   AC_CHECK_PROG(DVIPS, dvips, dvips)
   AC_CHECK_PROG(PDFLATEX, pdflatex, pdflatex)
   AC_CHECK_PROG(EPSTOPDF, epstopdf, epstopdf)
+  AC_CHECK_PROG(PDFTOCAIRO, pdftocairo, pdftocairo)
+  AC_CHECK_PROG(LATEXML,latexml,latexml)
+  AC_CHECK_PROG(LATEXMLPOST,latexmlpost,latexmlpost)
   AM_CONDITIONAL([HAVE_LATEX], [test -n "$LATEX" && test -n "$DVIPS" \
                                 && test -n "$EPSTOPDF" && test -n "$PDFLATEX"])
+  AM_CONDITIONAL([HAVE_CAIRO], [test -n "$LATEX" && test -n "$DVIPS"])
+  AM_CONDITIONAL([BUILD_HTML_MANUAL], [test -n "$LATEXML" && test -n "$LATEXMLPOST" && test -n "$PDFTOCAIRO"])
   AM_COND_IF([HAVE_LATEX],[],
     [echo "LaTeX not available, option '--enable-latex' ignored"])
   AM_COND_IF([HAVE_LATEX],[build_doc=yes])
+  AM_COND_IF([BUILD_HTML_MANUAL],[],[echo "pdftocairo and/or latexml not available, HTML version of manual will not be built"])
 else
   AM_CONDITIONAL([HAVE_LATEX],FALSE)
+  AM_CONDITIONAL([HAVE_CAIRO],FALSE)
+  AM_CONDITIONAL([BUILD_HTML_MANUAL],FALSE)
 fi
 
 # Enable Doxygen
 AC_ARG_ENABLE([doxygen],
   [AS_HELP_STRING([--enable-doxygen],
-    [build doxygen html-documentation])],
-  [enable_doxygen=yes],
-  [enable_doxygen=no])
+    [build doxygen html-documentation])])
+
 if test x$enable_doxygen = xyes ; then
   AC_CHECK_PROG(DOXYGEN, doxygen, doxygen)
   AM_CONDITIONAL([HAVE_DOXYGEN],[test -n "$DOXYGEN"])
@@ -103,9 +109,7 @@ AM_CONDITIONAL([BUILD_DOC],[test -n "$build_doc"])
 # Enable testing
 AC_ARG_ENABLE([check],
   [AS_HELP_STRING([--enable-check],
-    [enable the Check unit testing framework])],
-    [enable_check=yes],
-    [enable_check=no])
+    [enable the Check unit testing framework])])
 
 if test x$enable_check = xyes ; then
   AC_CHECK_LIB([check],[suite_create],
@@ -119,8 +123,7 @@ fi
 # Enable gcov
 AC_ARG_ENABLE([gcov],
   [AS_HELP_STRING([--enable-gcov],
-    [compile with Gcov to measure coverage])],
-  [enable_gcov=yes],[enable_gcov=no])
+    [compile with Gcov to measure coverage])])
 AM_CONDITIONAL([COND_GCOV],[test "x$enable_gcov" = xyes])
 
 # Disable test for CLI

diff --git a/doc/HOWTO_BUILD_WEBPAGES b/doc/HOWTO_BUILD_WEBPAGES
@@ -0,0 +1 @@
+The makefile in this directory writes to the directory html, if that directory in turn has a clone of the branch 'gh-pages', the automatically generated HTML from doxygen and the manual will be put in the right place and can be committed in the gh-pages branch.
diff --git a/doc/Makefile.am b/doc/Makefile.am
@@ -1,12 +1,14 @@
 SUBDIRS = fig
 manual = manual.tex
-fig_eps = fig/lnr_circles.eps fig/lnr_slice.eps fig/scaling.eps fig/precision.eps fig/threads.eps
+fig_eps = fig/lnr_circles.eps fig/lnr_slice.eps fig/precision.eps fig/threads.eps
 fig_pdf = $(subst .eps,.pdf,$(fig_eps))
 
 CLEANFILES =
 ALLFILES =
 
-EXTRA_DIST = $(manual) doxy_main.md GPL.md README.md doxygen-footer.html doxygen-header.html
+EXTRA_DIST = $(manual) doxy_main.md GPL.md README.md \
+	doxygen-footer.html doxygen-header.html \
+	prepareHTML.pl HOWTO_BUILD_WEBPAGES
 
 if HAVE_LATEX
 
@@ -40,18 +42,41 @@ ps-local: manual.ps
 pdf-local: manual.pdf
 ALLFILES += manual.dvi manual.ps manual.pdf
 
-else
+if BUILD_HTML_MANUAL
+
+manual.xml: $(srcdir)/$(manual) $(fig_eps)
+	latexml --quiet $< > manual.xml
+
+html/manual.html: manual.xml
+	cd html; latexmlpost ../manual.xml  --format=html5 --destination=tmp.html --nodefaultresources --navigationtoc=context 
+	perl prepareHTML.pl html/tmp.html > $@
+	rm html/tmp.html html/LaTeXML.*
+
+html-local: html/manual.html
+
+ALLFILES += html/manual.html
+CLEANFILES += manual.xml
+
+else # BUILD_HTML_MANUAL
+
+html-local:
+	@echo latexml not available, html manual will not be built.
+
+endif # BUILD_HTML_MANUAL
+
+else # HAVE_LATEX
 nolatex:
-	@echo LaTex disabled, run configure script with option --enable-latex to enable
+	@echo LaTeX disabled, run configure script with option --enable-latex to enable
 dvi-local: nolatex
 ps-local: nolatex
 pdf-local: nolatex
 
-endif
+
+endif # HAVE_LATEX
 
 if HAVE_DOXYGEN
 
-doxyfile.stamp: $(top_srcdir)/src/*.h doxy_main.md $(top_srcdir)/README.md Doxyfile \
+doxyfile.stamp: $(top_srcdir)/src/freesasa.h doxy_main.md $(top_srcdir)/README.md Doxyfile \
 	doxygen-footer.html doxygen-header.html
 	@if [ ! -d "html/" ]; then mkdir html; fi
 	$(DOXYGEN) Doxyfile
@@ -75,4 +100,5 @@ endif
 clean-local:
 	rm -f *.ps *.dvi *.aux *.log *.pdf *.toc *~ 
 	rm -rf html/doxygen
+	rm -rf html/fig
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		The makefile in this directory writes to the directory html, if that directory in turn has a clone of the branch 'gh-pages', the automatically generated HTML from doxygen and the manual will be put in the right place and can be committed in the gh-pages branch.