diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..a6cb8b615eb7a44af58c9563596ab6264ef6dbe6 --- /dev/null +++ b/.gitignore @@ -0,0 +1,54 @@ +# use glob syntax. +syntax: glob +*.ser +*.class +*~ +*.bak +#*.off +*.old +*.pyc +*.bk +*.swp +.DS_Store + +# logging files +detailed.log + +# eclipse conf file +.settings +.classpath +.project +.manager +.scala_dependencies + +# idea +.idea +*.iml + +# building +target +build +null +tmp* +temp* +dist +test-output +build.log + +# other scm +.svn +.CVS +.hg* + +# switch to regexp syntax. +# syntax: regexp +# ^\.pc/ + +#SHITTY output not in target directory +build.log + +#emacs TAGS +TAGS + +lib/ +env/ diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..2d443deb6d54c033cec97f550f65eb582cdc06b2 --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,19 @@ +stages: + - test + +testing: + stage: test + script: + - cd .. && rm -rf nomad-lab-base + - git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git + - cd nomad-lab-base + - git submodule foreach git checkout master + - git submodule foreach git pull + - sbt amber/full:test + - export PYTHONEXE=/labEnv/bin/python + - sbt amber/full:test + only: + - master + tags: + - test + - spec2 diff --git a/README.md b/README.md index 260a285243ed5d55b372af2ea56cc37ccd88615f..4263fa809f8abc35b358dc7b89753a5cd5713ab3 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # AMBER Parser -## Version 0.0.1a +## Version 0.0.2 +Fixed bugs on test issues + This is the parser for SANDER and PMEMD Molecular Dynamics codes in [AMBER](http://ambermd.org). The official version lives at: diff --git a/parser/parser-amber/trajectory_reader.py b/parser/parser-amber/trajectory_reader.py index a96031226b3bdedef819ae594a816e25ed1baba9..cc99029b566e2ac89b8a7d1c04504595e280a72a 100644 --- a/parser/parser-amber/trajectory_reader.py +++ b/parser/parser-amber/trajectory_reader.py @@ -197,15 +197,18 @@ class TrajectoryReader(object): """Returns an iterator that goes through the given trajectory file one configuration at a time. """ - iterator_object = iter(self.trajhandler) - try: - while True: - self.trajiter = next(iterator_object) - return self.trajiter - except StopIteration: - pass - finally: - del iterator_object + if self.trajhandler is not None: + iterator_object = iter(self.trajhandler) + try: + while True: + self.trajiter = next(iterator_object) + return self.trajiter + except StopIteration: + pass + finally: + del iterator_object + else: + return None def get_topology(self): """Returns an iterator that goes through the given trajectory file one