def global_logging_raw_input(prompt):
def get_stream(name):
if hasattr(sys, name):
stream = getattr(sys, name)
if isinstance(stream, file):
return stream
elif isinstance(stream, StreamTeeLogger):
return stream.stream
if hasattr(sys, '__%s__' % name):
stream = getattr(sys, '__%s__' % name)
if isinstance(stream, file):
return stream
return None
def check_interactive(stream, name):
try:
fd = stream.fileno()
except:
# Could be an AttributeError, an OSError, and IOError, or who
# knows what else...
return False
realfd = {'stdin': 0, 'stdout': 1, 'stderr': 2}[name]
return fd == realfd and os.isatty(fd)
stdout = get_stream('stdout')
stdin = get_stream('stdin')
stderr = get_stream('stderr')
if stdout is None:
raise RuntimeError('raw_input(): lost sys.stdout')
if stdin is None:
raise RuntimeError('raw_input(): lost sys.stdin')
if stderr is None:
raise RuntimeError('raw_input(): lost sys.stderr')
if (not check_interactive(stdin, 'stdin')
or not check_interactive(stdout, 'stdout')):
# Use the built-in raw_input(); this will repeat some of the checks
# we just did, but will save us from having to reimplement
# raw_input() in its entirety
retval = builtins._original_raw_input(prompt)
else:
stdout.flush()
infd = pythonapi.PyFile_AsFile(stdin)
outfd = pythonapi.PyFile_AsFile(stdout)
retval = pythonapi.PyOS_Readline(infd, outfd, str(prompt))
retval = retval.rstrip('\n')
if isinstance(sys.stdout, StreamTeeLogger):
sys.stdout.log_orig(str(prompt) + retval, echo=False)
return retval
libmdname = environ["GROMPY_LIBMD"]
if environ.has_key("GROMPY_LIBMDRUN"):
libmdrunname = environ["GROMPY_LIBMDRUN"]
libc = cdll.LoadLibrary(libcname)
libmd = cdll.LoadLibrary(libmdname)
libgmx = cdll.LoadLibrary(libgmxname)
libmdrun = cdll.LoadLibrary(libmdrunname)
# gromacs shuold be compiled with -lfftw3f!!!
# libmdrun = cdll.LoadLibrary(environ["HOME"]+"/src/gromacs-4.0.5_TEST/src/kernel/libmdrun0/mdrun.so") # for debugging purposes
#FILE * to stderr, stdout
pythonapi.PyFile_AsFile.restype = c_void_p
stderr = pythonapi.PyFile_AsFile(py_object(sys.stderr))
stdout = pythonapi.PyFile_AsFile(py_object(sys.stdout))
rvec = c_real * 3
dvec = c_double * 3
ivec = c_int * 3
splinevec = c_real * 3
matrix = c_real * 3 * 3
tensor = c_real * 3 * 3
class GMXctypesError(Exception):
def __init__(self, value):
self.value = value
def __str__(self):
def copy_file_pointer(self, f):
if not isinstance(f, file):
raise TypeError("f has to be a file")
self.fp = pythonapi.PyFile_AsFile(py_object(f))
def PrintCxxCompilerInfo(f=pythonapi.PyFile_AsFile(sys.stdout)):
lib.ElPrintCxxCompilerInfo(f)
def PrintConfig(f=pythonapi.PyFile_AsFile(sys.stdout)):
lib.ElPrintConfig(f)
def PrintVersion(f=pythonapi.PyFile_AsFile(sys.stdout)):
lib.ElPrintVersion(f)
