Support CIF

.gitignore

@@ -47,3 +47,5 @@ doc/html/
 doc/Doxyfile
 doc/doxyfile.stamp
 doc/man/freesasa.1
+.ionide
+.fake

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "third-party/gemmi"]
+	path = third-party/gemmi
+	url = https://github.com/project-gemmi/gemmi.git

.travis.yml

@@ -1,20 +1,12 @@
-
-language: c
+language: c++
 git:
   depth: 3
-dist:
-  trusty
-cache:
-  pip
-
-branches:
-  only:
-    - master
-    - dev
+dist: xenial
+cache: pip
 
 before_install:
-    - sudo apt-get update -qq
-    - sudo apt-get install -qq check libjson-c-dev libxml2-dev libxml2-utils
+  - sudo apt-get update -qq
+  - sudo apt-get install -qq check libjson-c-dev libxml2-dev libxml2-utils libc++-dev libc++abi-dev
 
 matrix:
   include:
@@ -24,7 +16,7 @@ matrix:
       before_install:
         - pip install --user cpp-coveralls
         - sudo apt-get update -qq
-        - sudo apt-get install -qq check libjson-c-dev libxml2-dev libxml2-utils
+        - sudo apt-get install -qq check libjson-c-dev libxml2-dev libxml2-utils libc++-dev libc++abi-dev
       after_success:
         - coveralls --exclude tests --exclude src/lexer.l --exclude src/lexer.c --exclude src/parser.c --exclude src/parser.y --exclude src/example.c --exclude src/util.c  --gcov-options '\-lp'
 
@@ -45,5 +37,5 @@ before_script:
 script: make && make check
 
 after_failure:
-    - cat tests/test-api.log
-    - cat tests/test-cli.log
+  - cat tests/test-api.log
+  - cat tests/test-cli.log

CHANGELOG.md

@@ -7,6 +7,14 @@ FreeSASA uses semantic versioning. Changelog added for versions 2.x
 - Fix bug in JSON output where relative SASA for amino acids without sidechan
   were written as `NaN`, which is not valid JSON. These values are now
   simply skipped.
+- Support for mmCIF input with the CLI option `--cif`.
+  - The CLI was ported to C++ to allow using Gemmi for CIF import.
+  - Gemmi is imported as a git submodule, see README for details.
+  - A test runner was added to verify that CIF and PDB input files
+    give the same result.
+  - The C API does not support CIF for now (this would require conversion to C++).
+- Fix bug where elements with H or D as second element, such as CD, were classified
+  as hydrogens.
 
 ## 2.0.3
 

Makefile.am

@@ -1,6 +1,6 @@
 SUBDIRS = src doc tests share
 
-EXTRA_DIST = README.md scripts/chemcomp2config.pl scripts/config2c.pl scripts/rsa
+EXTRA_DIST = README.md scripts/chemcomp2config.pl scripts/config2c.pl scripts/rsa third-party/gemmi/include/gemmi/*.hpp
 
 # we want to test all features for dist-check
 DISTCHECK_CONFIGURE_FLAGS = --enable-check

README.md

@@ -36,6 +36,11 @@ information.
 
 ## Building and installing
 
+After cloning the repository, add git submodules
+
+    git submodules init
+    git supmodules update
+
 FreeSASA can be compiled and installed using the following
 
     ./configure

configure.ac

@@ -7,12 +7,14 @@ AM_INIT_AUTOMAKE([foreign])
 AC_CONFIG_SRCDIR([config.h.in])
 AC_CONFIG_HEADERS([config.h])
 m4_include([m4/ax_compare_version.m4])
+m4_include([m4/ax_cxx_compile_stdcxx.m4])
 AC_DEFINE([REPORTBUG], ["Report bugs to <https://github.com/mittinatten/freesasa/issues>"], [Bug report string])
 AC_DEFINE([HOMEPAGE], ["<http://freesasa.github.io>"], [Project homepage])
 AC_DEFINE([FREESASA_XMLNS], ["http://freesasa.github.io/"], [XML namespace])
 
 # Checks for programs.
 AC_PROG_CC
+AC_PROG_CXX
 AC_PROG_RANLIB
 AC_PROG_INSTALL
 
@@ -45,6 +47,9 @@ AC_FUNC_MALLOC
 AC_FUNC_REALLOC
 AC_CHECK_FUNCS([memset mkdir sqrt strchr strdup strerror strncasecmp getopt_long getline])
 
+# C++ 14
+AX_CXX_COMPILE_STDCXX([14])
+
 AC_CONFIG_FILES([Makefile src/Makefile doc/Makefile doc/Doxyfile doc/man/freesasa.1 tests/Makefile share/Makefile])
 AC_CONFIG_FILES([tests/test-cli], [chmod +x tests/test-cli])
 
@@ -152,9 +157,11 @@ AC_ARG_ENABLE([check],
 
 AM_CONDITIONAL([USE_CHECK],false)
 AC_DEFINE([USE_CHECK],[0],[Build with Check unit testing framework])
+AM_CONDITIONAL([USE_SUBUNIT], false)
 
 if test "x$enable_check" = "xyes" ; then
   AC_CHECK_LIB(rt, setitimer) # necessary on some platforms
+  AC_CHECK_LIB([subunit], [subunit_test_start]) # necessary on some platforms
   AC_CHECK_LIB([check],[suite_create],
     [],
     [AC_MSG_ERROR[Library Check not available, install libary or configure without flag --enable-check]])