def __init__(self, soundfile, parent):
self.soundfile = soundfile
self.isplaying = False
self.time = 0 # current audio position in frames
self.audio = pyaudio.PyAudio()
if AudioSegment:
if which("ffmpeg") != None:
AudioSegment.converter = which("ffmpeg")
elif which("avconv") != None:
AudioSegment.converter = which("avconv")
else:
if platform.system() == "Windows":
AudioSegment.converter = os.path.dirname(os.path.realpath(__file__)) + "\\ffmpeg.exe"
else:
# TODO: Check if we have ffmpeg or avconv installed
AudioSegment.converter = "ffmpeg"
try:
if AudioSegment:
tempsound = AudioSegment.from_file(self.soundfile, format = os.path.splitext(self.soundfile)[1][1:])
tempsound.export(os.path.dirname(os.path.realpath(__file__)) +"\\temp.wav", format = "wav")
self.wave_reference = wave.open(os.path.dirname(os.path.realpath(__file__)) + "\\temp.wav")
else:
self.wave_reference = wave.open(self.soundfile)
self.isvalid = True
except:
traceback.print_exc()
self.wave_reference = None
self.isvalid = False
def main(vers=None):
try:
if vers:pause=False
else:pause=True
svn=which('svn')
makensis=which('makensis')
if not svn:
print 'Install an SVN command line client (e.g. http://www.sliksvn.com) or ensure that it is on your PATH'
if pause:raw_input('Press enter to exit.')
sys.exit(1)
if not makensis:
print 'Install NSIS (http://nsis.sourceforge.net) or ensure that it is on your PATH'
if pause:raw_input('Press enter to exit.')
sys.exit(1)
if not vers:
try:vers = raw_input('Enter the version to build, options are: \n1.N (eg. 1.1 release) \ncurr (latest release) \nbranches/<branch> \ntrunk (unstable development) \nVersion: ')
except:sys.exit(0)#vers = 'trunk'
repo=''
if vers in ['curr','']:
cmd='svn ls http://metageta.googlecode.com/svn/tags'
exit_code,stdout,stderr=runcmd(cmd)
if exit_code != 0:
if stderr: print stderr
elif stdout: print stdout
else : print 'SVN command failed'
if pause:raw_input('Press enter to exit.')
sys.exit(exit_code)
else:
def check_requirements():
if which("adb") is None:
print(t.red("This program requires adb executable to be in path."))
sys.exit(-3)
ffmpeg_path = which("ffmpeg")
if ffmpeg_path is None:
print(t.red("This program requires ffmpeg in path."))
sys.exit(-4)
# Check if ffmpeg supports all capabilities we need
try:
ffmpeg_p = subprocess.Popen([ffmpeg_path, "-codecs"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
output = ffmpeg_p.stdout.read().decode("utf-8")
ffmpeg_p.communicate()
if ffmpeg_p.returncode != 0:
print(
t.red(
"Incompatible ffmpeg version detected, please update to newest ffmpeg."
))
sys.exit(-4)
if "gif" not in output:
print(
t.red(
"Missing GIF encoder in your installed ffmpeg, cannot create gifs."
))
sys.exit(-4)
if "libx264" not in output:
print(
t.yellow(
"Missing libx264 encoder in your installed ffmpeg, will not be able to create videos."
))
ffmpeg_p = subprocess.Popen([ffmpeg_path, "-filters"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
output = ffmpeg_p.stdout.read().decode("utf-8")
ffmpeg_p.communicate()
if ffmpeg_p.returncode != 0:
print(
t.red(
"Incompatible ffmpeg version detected, please update to newest ffmpeg."
))
sys.exit(-4)
if not ("format" in output and "scale" in output and "palettegen"
in output and "paletteuse" in output and "fps" in output):
print(t.red("Missing required filters in installed ffmpeg, installed ffmpeg requires"), \
t.green("format, fps, scale, palettegen and paletteuse"), t.red("filters."))
sys.exit(-4)
except OSError:
print(t.red("This program requires a newish ffmpeg in path."))
sys.exit(-4)
def submit_ask(self, print_result=True, after_job=None):
""" Submits the job, but prints the jobfile and asks first """
import utilities
qsub = utilities.which('qsub')
qstat = utilities.which('qstat')
if not qsub: raise PBSMissingError('Cannot find qsub!')
sub_script = self._get_sub_script()
# Determine if we have to submit this with a dependency
if after_job:
# Make sure we have qstat, since that's how we check that the job
# we're depending on exists in the first place
if not qstat:
raise PBSMissingError('Cannot find qstat!')
process = Popen([qstat, after_job],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
(output, error) = process.communicate('')
# If we get a non-zero exit status, that job doesn't exist!
if process.wait():
raise PBSDependError('Job %s does not exist. Bad dependency!' %
after_job)
# If it does exist,
ending_prompt = 'OK? > '
if after_job:
ending_prompt = 'with "qsub -W depend=afterok:%s", OK? > ' % after_job
stdout.write('Going to submit the following script:' + linesep)
stdout.write('=============' + linesep + sub_script + linesep +
'=============' + linesep + ending_prompt)
response = stdin.readline()
if response.strip().lower() == 'yes' or response.strip().lower(
) == 'y':
if after_job:
process = Popen(
[qsub, '-W', 'depend=afterok:%s' % after_job],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
else:
process = Popen([qsub], stdin=PIPE, stdout=PIPE, stderr=PIPE)
(output, error) = process.communicate(sub_script)
if process.wait():
raise QsubError('problem submitting job: %s' % error)
if print_result: print output
return output
return None
def _check_member_accnt(self, user):
if which('getent'):
xcmd = ['getent', 'passwd', user]
elif which('pwget'):
xcmd = ['pwget', '-n', user]
else:
return 0
xp = Popen(xcmd, stdout=PIPE, stderr=PIPE, close_fds=True)
xout, xerr = xp.communicate()
return xp.returncode
def __init__(self, soundfile, parent):
self.soundfile = soundfile
self.isplaying = False
self.time = 0 # current audio position in frames
self.audio = QMediaPlayer()
self.is_loaded = False
self.volume = 100
self.isplaying = False
self.max_bits = 32768
# File Loading is Asynchronous, so we need to be creative here, doesn't need to be duration but it works
self.audio.durationChanged.connect(self.on_durationChanged)
# self.decoder.finished.connect(self.decode_finished_signal)
self.audio.setMedia(QUrl.fromLocalFile(soundfile))
# self.decoder.setSourceFilename(soundfile) # strangely inconsistent file-handling
# It will hang here forever if we don't process the events.
while not self.is_loaded:
QCoreApplication.processEvents()
time.sleep(0.1)
self.isvalid = True
self.pydubfile = None
if AudioSegment:
if which("ffmpeg") is not None:
AudioSegment.converter = which("ffmpeg")
elif which("avconv") is not None:
AudioSegment.converter = which("avconv")
else:
if platform.system() == "Windows":
AudioSegment.converter = os.path.join(
get_main_dir(), "ffmpeg.exe")
# AudioSegment.converter = os.path.dirname(os.path.realpath(__file__)) + "\\ffmpeg.exe"
else:
# TODO: Check if we have ffmpeg or avconv installed
AudioSegment.converter = "ffmpeg"
try:
if AudioSegment:
print(self.soundfile)
self.pydubfile = AudioSegment.from_file(
self.soundfile,
format=os.path.splitext(self.soundfile)[1][1:])
else:
self.wave_reference = wave.open(self.soundfile)
self.isvalid = True
except:
traceback.print_exc()
self.wave_reference = None
self.isvalid = False
def check_requirements():
if which("adb") is None:
print(t.red("This program requires adb executable to be in path."))
sys.exit(-3)
ffmpeg_path = which("ffmpeg")
if ffmpeg_path is None:
print(t.red("This program requires ffmpeg in path."))
sys.exit(-4)
# Check if ffmpeg supports all capabilities we need
try:
ffmpeg_p = subprocess.Popen([ffmpeg_path, "-codecs"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
output = ffmpeg_p.stdout.read().decode("utf-8")
ffmpeg_p.communicate()
if ffmpeg_p.returncode != 0:
print(t.red("Incompatible ffmpeg version detected, please update to newest ffmpeg."))
sys.exit(-4)
if "gif" not in output:
print(t.red("Missing GIF encoder in your installed ffmpeg, cannot create gifs."))
sys.exit(-4)
if "libx264" not in output:
print(t.yellow("Missing libx264 encoder in your installed ffmpeg, will not be able to create videos."))
ffmpeg_p = subprocess.Popen([ffmpeg_path, "-filters"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
output = ffmpeg_p.stdout.read().decode("utf-8")
ffmpeg_p.communicate()
if ffmpeg_p.returncode != 0:
print(t.red("Incompatible ffmpeg version detected, please update to newest ffmpeg."))
sys.exit(-4)
if not (
"format" in output
and "scale" in output
and "palettegen" in output
and "paletteuse" in output
and "fps" in output
):
print(
t.red("Missing required filters in installed ffmpeg, installed ffmpeg requires"),
t.green("format, fps, scale, palettegen and paletteuse"),
t.red("filters."),
)
sys.exit(-4)
except OSError:
print(t.red("This program requires a newish ffmpeg in path."))
sys.exit(-4)
def submit_ask(self, print_result=True, after_job=None):
""" Submits the job, but prints the jobfile and asks first """
import utilities
qsub = utilities.which("qsub")
qstat = utilities.which("qstat")
if not qsub:
raise PBSMissingError("Cannot find qsub!")
sub_script = self._get_sub_script()
# Determine if we have to submit this with a dependency
if after_job:
# Make sure we have qstat, since that's how we check that the job
# we're depending on exists in the first place
if not qstat:
raise PBSMissingError("Cannot find qstat!")
process = Popen([qstat, after_job], stdin=PIPE, stdout=PIPE, stderr=PIPE)
(output, error) = process.communicate("")
# If we get a non-zero exit status, that job doesn't exist!
if process.wait():
raise PBSDependError("Job %s does not exist. Bad dependency!" % after_job)
# If it does exist,
ending_prompt = "OK? > "
if after_job:
ending_prompt = 'with "qsub -W depend=afterok:%s", OK? > ' % after_job
stdout.write("Going to submit the following script:" + linesep)
stdout.write("=============" + linesep + sub_script + linesep + "=============" + linesep + ending_prompt)
response = stdin.readline()
if response.strip().lower() == "yes" or response.strip().lower() == "y":
if after_job:
process = Popen([qsub, "-W", "depend=afterok:%s" % after_job], stdin=PIPE, stdout=PIPE, stderr=PIPE)
else:
process = Popen([qsub], stdin=PIPE, stdout=PIPE, stderr=PIPE)
(output, error) = process.communicate(sub_script)
if process.wait():
raise QsubError("problem submitting job: %s" % error)
if print_result:
print output
return output
return None
def create_optimized_gif(in_file, out_file, size, fps):
print(t.green("Converting video to GIF..."))
tmp_pal_file = get_new_temp_file_path("png")
gifsicle_path = which("gifsicle")
if gifsicle_path is not None:
convert_output_path = get_new_temp_file_path("gif")
else:
convert_output_path = out_file
FFMPEG_FILTERS = "fps={fps},scale=w='if(gt(iw,ih),-1,{size})':h='if(gt(iw,ih),{size},-1)':flags=lanczos".format(fps=fps, size=size)
FFMPEG_PALLETE = ["ffmpeg", "-v", "warning", "-i", in_file, "-vf", FFMPEG_FILTERS + ",palettegen", "-y", tmp_pal_file]
FFMPEG_CONVERT = ["ffmpeg", "-v", "warning", "-i", in_file, "-i", tmp_pal_file, "-lavfi", FFMPEG_FILTERS + "[x];[x][1:v]paletteuse=dither=floyd_steinberg", "-y", "-f", "gif", convert_output_path]
GIFSICLE_OPTIMIZE = ["gifsicle", "-O3", convert_output_path, "-o", out_file]
try:
subprocess.check_call(FFMPEG_PALLETE)
subprocess.check_call(FFMPEG_CONVERT)
if gifsicle_path is not None:
subprocess.check_call(GIFSICLE_OPTIMIZE)
print(t.green("Done!"))
except:
print(t.red("Could not convert downloaded recording to GIF!"))
raise
finally:
try:
os.remove(tmp_pal_file)
if gifsicle_path is not None:
os.remove(convert_output_path)
except:
pass
print(t.yellow("Created " + out_file))
def pwconv(self):
if not cap_shadow or not os.path.exists('/etc/shadow'):
return
if not which('pwconv'):
return
p = Popen(['pwconv'])
p.communicate()
def main(vers=None):
try:
if vers: pause = False
else: pause = True
svn = which('svn')
if not svn:
print 'Install an SVN command line client (e.g. http://www.sliksvn.com) or ensure that it is on your PATH'
if pause: raw_input('Press enter to exit.')
sys.exit(1)
if not vers:
try:
vers = raw_input(
'Enter the version to build, options are: \n1.N (eg. 1.1 release) \ncurr (latest release) \nbranches/<branch> \ntrunk (unstable development) \nVersion: '
)
except:
sys.exit(0) #vers = 'trunk'
repo = ''
if vers in ['curr', '']:
cmd = 'svn ls http://metageta.googlecode.com/svn/tags'
exit_code, stdout, stderr = runcmd(cmd)
if exit_code != 0:
if stderr: print stderr
elif stdout: print stdout
else: print 'SVN command failed'
if pause: raw_input('Press enter to exit.')
sys.exit(exit_code)
else:
def set_radii(self, igb=0, radius_set='mbondi'):
""" Sets the radius set to a new one using parmed """
# If someone sets an igb, change to the appropriate radius set
if igb:
if igb == 1: radius_set = 'mbondi'
elif igb == 2: radius_set = 'mbondi2'
elif igb == 5: radius_set = 'mbondi2'
elif igb == 7: radius_set = 'bondi'
elif igb == 8: radius_set = 'mbondi3'
if not radius_set in [
'mbondi', 'mbondi2', 'mbondi3', 'bondi', 'amber6'
]:
raise InputError('Bad radius set! Choose from ' +
'mbondi, mbondi2, mbondi3, bondi, and amber6')
parmed = which('parmed.py')
change_str = ("setOverwrite True\n" + "changeRadii %s\n" % radius_set +
"parmout %s\n" % self.prmtop + "go\n")
process = Popen(
[parmed, '-q', '-n', str(self.prmtop)],
stdin=PIPE,
stderr=PIPE,
stdout=PIPE)
(output, error) = process.communicate(change_str)
if process.wait():
raise ProgramError('parmed.py failed to change radii!')
# Reload our topology file now that we've changed radius sets
self.prmtop = AmberParm(str(self.prmtop))
def create_optimized_gif(in_file, out_file, size, fps):
print(t.green("Converting video to GIF..."))
tmp_pal_file = get_new_temp_file_path("png")
gifsicle_path = which("gifsicle")
if gifsicle_path is not None:
convert_output_path = get_new_temp_file_path("gif")
else:
convert_output_path = out_file
FFMPEG_FILTERS = "fps={fps},scale=w='if(gt(iw,ih),-1,{size})':h='if(gt(iw,ih),{size},-1)':flags=lanczos".format(fps=fps, size=size)
FFMPEG_PALLETE = ["ffmpeg", "-v", "warning", "-i", in_file, "-vf", FFMPEG_FILTERS + ",palettegen", "-y", tmp_pal_file]
FFMPEG_CONVERT = ["ffmpeg", "-v", "warning", "-i", in_file, "-i", tmp_pal_file, "-lavfi", FFMPEG_FILTERS + "[x];[x][1:v]paletteuse=dither=floyd_steinberg", "-y", "-f", "gif", convert_output_path]
GIFSICLE_OPTIMIZE = ["gifsicle", "-O3", convert_output_path, "-o", out_file]
try:
subprocess.check_call(FFMPEG_PALLETE)
subprocess.check_call(FFMPEG_CONVERT)
if gifsicle_path is not None:
subprocess.check_call(GIFSICLE_OPTIMIZE)
print(t.green("Done!"))
except:
print(t.red("Could not convert downloaded recording to GIF!"))
raise
finally:
try:
os.remove(tmp_pal_file)
if gifsicle_path is not None:
os.remove(convert_output_path)
except:
pass
print(t.yellow("Created " + out_file))
def set_radii(self, igb=0, radius_set='mbondi'):
""" Sets the radius set to a new one using parmed """
# If someone sets an igb, change to the appropriate radius set
if igb:
if igb == 1: radius_set = 'mbondi'
elif igb == 2: radius_set = 'mbondi2'
elif igb == 5: radius_set = 'mbondi2'
elif igb == 7: radius_set = 'bondi'
elif igb == 8: radius_set = 'mbondi3'
if not radius_set in ['mbondi', 'mbondi2', 'mbondi3', 'bondi', 'amber6']:
raise InputError('Bad radius set! Choose from ' +
'mbondi, mbondi2, mbondi3, bondi, and amber6')
parmed = which('parmed.py')
change_str = ("setOverwrite True\n" +
"changeRadii %s\n" % radius_set +
"parmout %s\n" % self.prmtop +
"go\n")
process = Popen([parmed, '-q', '-n', str(self.prmtop)], stdin=PIPE,
stderr=PIPE, stdout=PIPE)
(output, error) = process.communicate(change_str)
if process.wait():
raise ProgramError('parmed.py failed to change radii!')
# Reload our topology file now that we've changed radius sets
self.prmtop = AmberParm(str(self.prmtop))
def __init__(self, soundfile, parent):
self.soundfile = soundfile
self.isplaying = False
self.time = 0 # current audio position in frames
self.audio = QMediaPlayer()
self.is_loaded = False
self.volume = 100
self.isplaying = False
self.max_bits = 32768
# File Loading is Asynchronous, so we need to be creative here, doesn't need to be duration but it works
self.audio.durationChanged.connect(self.on_durationChanged)
# self.decoder.finished.connect(self.decode_finished_signal)
self.audio.setMedia(QUrl.fromLocalFile(soundfile))
# self.decoder.setSourceFilename(soundfile) # strangely inconsistent file-handling
# It will hang here forever if we don't process the events.
self.audio_file = audioread.audio_open(self.soundfile)
self.audio_data = []
for buf in self.audio_file:
self.audio_data.extend(
struct.unpack("<{}H".format(int(len(list(buf)) / 2)), buf))
print(self.audio_data)
print(len(self.audio_data))
print(len(self.audio_data) / self.audio_file.samplerate)
print(self.audio_file.duration)
print(self.audio_file.channels)
print("DATAEND")
while not self.is_loaded:
QCoreApplication.processEvents()
time.sleep(0.1)
self.isvalid = True
self.pydubfile = None
if AudioSegment:
if which("ffmpeg") is not None:
AudioSegment.converter = which("ffmpeg")
elif which("avconv") is not None:
AudioSegment.converter = which("avconv")
else:
if platform.system() == "Windows":
AudioSegment.converter = os.path.join(
get_main_dir(), "ffmpeg.exe")
# AudioSegment.converter = os.path.dirname(os.path.realpath(__file__)) + "\\ffmpeg.exe"
else:
# TODO: Check if we have ffmpeg or avconv installed
AudioSegment.converter = "ffmpeg"
self.isvalid = True
def pushpkg(self):
bin = 'nodemgr'
if which(bin) is None:
return
cmd = [bin, 'pushpkg']
pinfo(' '.join(cmd))
p = Popen(cmd)
p.communicate()
def __init__(self,
parm,
traj_list,
start=1,
stride=1,
end=99999999,
logfile=None,
overwrite=False):
# Get cpptraj
self.cpptraj = which('cpptraj')
if not self.cpptraj:
raise TrajError('Could not find cpptraj!')
# Load instance data
self.parm = str(parm)
# Order matters
self.traj_name_list = []
# Start, end, stride
self.start, self.stride, self.end = [], [], []
# traj_list is a dictionary that matches the trajectory name to the
# number of frames in that trajectory
self.traj_list = {}
if type(traj_list).__name__ in ['list', 'tuple']:
for item in traj_list:
self.traj_list[item] = -1
self.traj_name_list.append(item)
self.start.append(start)
self.stride.append(stride)
self.end.append(end)
elif type(traj_list).__name__ == 'str':
self.traj_list[traj_list] = -1
self.traj_name_list.append(traj_list)
self.start.append(start)
self.stride.append(stride)
self.end.append(end)
else:
raise TypeError(
'AmberTraj: trajectory(s) must be a list/tuple or str')
# Now set up num_frames
self._query()
# Can we overwrite files?
self.overwrite = overwrite
# what is our logfile?
if type(logfile).__name__ == 'str':
if os.path.exists(logfile) and not self.overwrite:
raise TrajError('Cannot overwrite %s' % logfile)
self.logfile = open(logfile, 'w', 0)
else:
self.logfile = sys.stdout
# Start keeping track of the commands we want to run
self._cpptraj_commands = ''
def submit(self, print_result=True, after_job=None):
""" Submits the job """
import utilities
qsub = utilities.which('qsub')
qstat = utilities.which('qstat')
if not qsub: raise PBSMissingError('Cannot find qsub!')
sub_script = self._get_sub_script()
# Determine if we have to submit this with a dependency
if after_job:
# Make sure we have qstat, since that's how we check that the job
# we're depending on exists in the first place
if not qstat:
raise PBSMissingError('Cannot find qstat!')
process = Popen([qstat, after_job],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
(output, error) = process.communicate('')
# If we get a non-zero exit status, that job doesn't exist!
if process.wait():
raise PBSDependError('Job %s does not exist. Bad dependency!' %
after_job)
# If it does exist,
if after_job:
process = Popen(
[qsub, '-W', 'depend=afterok:%s' % after_job],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
else:
process = Popen([qsub], stdin=PIPE, stdout=PIPE, stderr=PIPE)
(output, error) = process.communicate(sub_script)
if process.wait():
raise QsubError('problem submitting job: %s' % error)
if print_result: print output
return output
def __init__(self, soundfile, parent):
self.soundfile = soundfile
self.isplaying = False
self.time = 0 # current audio position in frames
self.audio = sd
self.pydubfile = None
self.volume = 100
if AudioSegment:
if which("ffmpeg") is not None:
AudioSegment.converter = which("ffmpeg")
elif which("avconv") is not None:
AudioSegment.converter = which("avconv")
else:
if platform.system() == "Windows":
AudioSegment.converter = os.path.join(
get_main_dir(), "ffmpeg.exe")
#AudioSegment.converter = os.path.dirname(os.path.realpath(__file__)) + "\\ffmpeg.exe"
else:
# TODO: Check if we have ffmpeg or avconv installed
AudioSegment.converter = "ffmpeg"
try:
if AudioSegment:
print(self.soundfile)
self.pydubfile = AudioSegment.from_file(
self.soundfile,
format=os.path.splitext(self.soundfile)[1][1:])
else:
self.wave_reference = wave.open(self.soundfile)
self.isvalid = True
except:
traceback.print_exc()
self.wave_reference = None
self.isvalid = False
if AudioSegment:
self.pydubfile = self.pydubfile.set_sample_width(2)
self.audio.default.samplerate = self.pydubfile.frame_rate * self.pydubfile.channels
else:
self.audio.default.samplerate = self.wave_reference.getframerate()
def __init__(self, soundfile, parent):
self.soundfile = soundfile
self.isplaying = False
self.time = 0 # current audio position in frames
self.audio = pyaudio.PyAudio()
self.pydubfile = None
self.volume = 100
if which("ffmpeg") is not None:
self.converter = which("ffmpeg")
elif which("avconv") is not None:
self.converter = which("avconv")
else:
if platform.system() == "Windows":
self.converter = os.path.join(get_main_dir(), "ffmpeg.exe")
#AudioSegment.converter = os.path.dirname(os.path.realpath(__file__)) + "\\ffmpeg.exe"
else:
# TODO: Check if we have ffmpeg or avconv installed
self.converter = "ffmpeg"
if AudioSegment:
AudioSegment.converter = self.converter
try:
format = os.path.splitext(self.soundfile)[1][1:]
if AudioSegment:
self.pydubfile = AudioSegment.from_file(self.soundfile, format=format)
else:
wave_file = self.soundfile
if format != "wav":
wave_file = tempfile._get_default_tempdir() + "/" + next(tempfile._get_candidate_names()) + ".wav"
subprocess.call([self.converter, '-i', self.soundfile, wave_file])
self.wave_reference = wave.open(wave_file)
self.isvalid = True
except:
traceback.print_exc()
self.wave_reference = None
self.isvalid = False
def vglist_Linux(self):
if not which("vgs"):
perror('vgs command not found')
raise ComplianceError()
cmd = ['vgs', '-o', 'vg_name', '--noheadings']
p = Popen(cmd, stdout=PIPE, stderr=PIPE)
out, err = p.communicate()
if p.returncode != 0:
perror('failed to list volume groups')
raise ComplianceError()
out = bdecode(out)
self.vg = out.split()
def submit(self, print_result=True, after_job=None):
""" Submits the job """
import utilities
qsub = utilities.which("qsub")
qstat = utilities.which("qstat")
if not qsub:
raise PBSMissingError("Cannot find qsub!")
sub_script = self._get_sub_script()
# Determine if we have to submit this with a dependency
if after_job:
# Make sure we have qstat, since that's how we check that the job
# we're depending on exists in the first place
if not qstat:
raise PBSMissingError("Cannot find qstat!")
process = Popen([qstat, after_job], stdin=PIPE, stdout=PIPE, stderr=PIPE)
(output, error) = process.communicate("")
# If we get a non-zero exit status, that job doesn't exist!
if process.wait():
raise PBSDependError("Job %s does not exist. Bad dependency!" % after_job)
# If it does exist,
if after_job:
process = Popen([qsub, "-W", "depend=afterok:%s" % after_job], stdin=PIPE, stdout=PIPE, stderr=PIPE)
else:
process = Popen([qsub], stdin=PIPE, stdout=PIPE, stderr=PIPE)
(output, error) = process.communicate(sub_script)
if process.wait():
raise QsubError("problem submitting job: %s" % error)
if print_result:
print output
return output
def __init__(self, parm, traj_list, start=1, stride=1, end=99999999,
logfile=None, overwrite=False):
# Get cpptraj
self.cpptraj = which('cpptraj')
if not self.cpptraj:
raise TrajError('Could not find cpptraj!')
# Load instance data
self.parm = str(parm)
# Order matters
self.traj_name_list = []
# Start, end, stride
self.start, self.stride, self.end = [], [], []
# traj_list is a dictionary that matches the trajectory name to the
# number of frames in that trajectory
self.traj_list = {}
if type(traj_list).__name__ in ['list', 'tuple']:
for item in traj_list:
self.traj_list[item] = -1
self.traj_name_list.append(item)
self.start.append(start)
self.stride.append(stride)
self.end.append(end)
elif type(traj_list).__name__ == 'str':
self.traj_list[traj_list] = -1
self.traj_name_list.append(traj_list)
self.start.append(start)
self.stride.append(stride)
self.end.append(end)
else:
raise TypeError('AmberTraj: trajectory(s) must be a list/tuple or str')
# Now set up num_frames
self._query()
# Can we overwrite files?
self.overwrite = overwrite
# what is our logfile?
if type(logfile).__name__ == 'str':
if os.path.exists(logfile) and not self.overwrite:
raise TrajError('Cannot overwrite %s' % logfile)
self.logfile = open(logfile, 'w', 0)
else:
self.logfile = sys.stdout
# Start keeping track of the commands we want to run
self._cpptraj_commands = ''
def __init__(self, soundfile, parent):
self.soundfile = soundfile
self.isplaying = False
self.time = 0 # current audio position in frames
self.audio = sd
self.pydubfile = None
self.volume = 100
if AudioSegment:
if which("ffmpeg") is not None:
AudioSegment.converter = which("ffmpeg")
elif which("avconv") is not None:
AudioSegment.converter = which("avconv")
else:
if platform.system() == "Windows":
AudioSegment.converter = os.path.join(get_main_dir(), "ffmpeg.exe")
#AudioSegment.converter = os.path.dirname(os.path.realpath(__file__)) + "\\ffmpeg.exe"
else:
# TODO: Check if we have ffmpeg or avconv installed
AudioSegment.converter = "ffmpeg"
try:
if AudioSegment:
print(self.soundfile)
self.pydubfile = AudioSegment.from_file(self.soundfile, format=os.path.splitext(self.soundfile)[1][1:])
else:
self.wave_reference = wave.open(self.soundfile)
self.isvalid = True
except:
traceback.print_exc()
self.wave_reference = None
self.isvalid = False
if AudioSegment:
self.audio.default.samplerate = self.pydubfile.frame_rate
else:
self.audio.default.samplerate = self.wave_reference.getframerate()
def __init__(self, soundfile, parent):
self.soundfile = soundfile
self.isplaying = False
self.time = 0 # current audio position in frames
self.audio = pyaudio.PyAudio()
if AudioSegment:
if which("ffmpeg") != None:
AudioSegment.converter = which("ffmpeg")
elif which("avconv") != None:
AudioSegment.converter = which("avconv")
else:
if platform.system() == "Windows":
AudioSegment.converter = os.path.dirname(
os.path.realpath(__file__)) + "\\ffmpeg.exe"
else:
# TODO: Check if we have ffmpeg or avconv installed
AudioSegment.converter = "ffmpeg"
try:
if AudioSegment:
tempsound = AudioSegment.from_file(self.soundfile,
format=os.path.splitext(
self.soundfile)[1][1:])
tempsound.export(os.path.dirname(os.path.realpath(__file__)) +
"\\temp.wav",
format="wav")
self.wave_reference = wave.open(
os.path.dirname(os.path.realpath(__file__)) + "\\temp.wav")
else:
self.wave_reference = wave.open(self.soundfile)
self.isvalid = True
except:
traceback.print_exc()
self.wave_reference = None
self.isvalid = False
def submit_jobfiles(job_list, dependent=True, previous_job=None):
""" Submits multiple job files one after another """
import utilities
qsub = utilities.which('qsub')
if not qsub: raise PBSMissingError('Cannot find qsub!')
for job in job_list:
cl_array = [qsub]
if dependent and previous_job:
cl_array.extend(['-W', 'depend=afterok:%s' % previous_job])
cl_array.append(job)
process = Popen(cl_array, stdout=PIPE, stderr=PIPE)
(previous_job, error) = process.communicate('')
if process.wait():
raise QsubError('Problem submitting job file %s:\n%s' %
(job, error))
print previous_job
def submit_jobfiles(job_list, dependent=True, previous_job=None):
""" Submits multiple job files one after another """
import utilities
qsub = utilities.which("qsub")
if not qsub:
raise PBSMissingError("Cannot find qsub!")
for job in job_list:
cl_array = [qsub]
if dependent and previous_job:
cl_array.extend(["-W", "depend=afterok:%s" % previous_job])
cl_array.append(job)
process = Popen(cl_array, stdout=PIPE, stderr=PIPE)
(previous_job, error) = process.communicate("")
if process.wait():
raise QsubError("Problem submitting job file %s:\n%s" % (job, error))
print previous_job
def grpconv(self):
if not cap_shadow or not os.path.exists('/etc/gshadow'):
return
if not which('grpconv'):
return
with open('/etc/group', 'r') as f:
buff = f.read()
l = []
for line in buff.split('\n'):
u = line.split(':')[0]
if u in l:
perror(
"duplicate group %s in /etc/group. skip grpconv (grpconv bug workaround)"
% u)
return
l.append(u)
p = Popen(['grpconv'])
p.communicate()
def select_optional_executable(self, field):
""" We try to choose amount avaible tools specified
optianally in a class like image_viewer or file_manager.
"""
# self.config['image_viewer'] is a list of a number of viewers
# [('rv', ""), ...], second tuple element is optional path.
# If None, it is to be found in PATH,
for candidate in self[field]:
assert(len(candidate) == 2)
exec_, path = candidate
if not path:
exec_ = utilities.which(exec_)
if exec_:
return exec_
else:
path = self.convert_platform_path(path)
if os.path.isfile(path):
return path
return None
def select_optional_executable(self, field):
""" We try to choose amount avaible tools specified
optianally in a class like image_viewer or file_manager.
"""
# self.config['image_viewer'] is a list of a number of viewers
# [('rv', ""), ...], second tuple element is optional path.
# If None, it is to be found in PATH,
for candidate in self[field]:
assert (len(candidate) == 2)
exec_, path = candidate
if not path:
exec_ = utilities.which(exec_)
if exec_:
return exec_
else:
path = self.convert_platform_path(path)
if os.path.isfile(path):
return path
return None
def init(self):
self.rules = []
if not which('ansible-playbook'):
perror('ansible-playbook binary not found')
raise NotApplicable()
self.inventory = os.path.join(os.environ["OSVC_PATH_COMP"],
".ansible-inventory")
for rule in self.get_rules():
try:
self.rules += self.add_rule(rule)
except InitError:
continue
except ValueError:
perror('ansible_playbook: failed to parse variable',
os.environ[k])
if len(self.rules) == 0:
raise NotApplicable()
def __init__(self):
"""Load up the applications and connect to the X Server"""
# The list of .desktop files' relevant details. A list of dicts with keys "FullPath", "StartupWMClass", "Exec"
self.applications = []
## Load up all the .desktop files
for fullPath in self._get_xdg_application_files():
# Make sure this is a .desktop file
if not os.path.isfile(fullPath) or os.path.splitext(fullPath)[1].lower() != ".desktop":
continue
# Try to parse the desktop file; catching any exceptions
try:
entry = DesktopEntry.DesktopEntry(fullPath)
except xdg.Exceptions.Error:
continue
# Make sure this is an application and isn't hidden (which is equivalent to not existing at all),
if entry.getType() != "Application" or entry.getHidden():
continue
# Test the `TryExec` key, if it exists
if entry.getTryExec() != "" and which(entry.getTryExec()) == None:
continue
# Add the relevant details to the list of applications
self.applications.append({
"FullPath": fullPath,
"StartupWMClass": entry.getStartupWMClass(),
"Exec": entry.getExec()
})
# Connect to the X server, re-raising any Xerror.DisplayError
try:
self.display = Xdisplay.Display()
except Xerror.DisplayError as exception:
raise XServerError from exception
def fix_process(self, process):
if process['state'] == 'on':
if self.check_present(process, verbose=False) == RET_OK:
if ('uid' in process and self.check_uid(process, process['uid'], verbose=False) == RET_ERR) or \
('user' in process and self.check_user(process, process['user'], verbose=False) == RET_ERR):
perror(process, "runs with the wrong user. can't fix.")
return RET_ERR
return RET_OK
elif process['state'] == 'off':
if self.check_not_present(process, verbose=False) == RET_OK:
return RET_OK
if 'start' not in process or len(process['start'].strip()) == 0:
perror("undefined fix method for process", process['comm'])
return RET_ERR
v = process['start'].split(' ')
if not which(v[0]):
perror("fix command", v[0], "is not present or not executable")
return RET_ERR
pinfo('exec:', process['start'])
try:
p = Popen(v, stdout=PIPE, stderr=PIPE)
out, err = p.communicate()
except Exception as e:
perror(e)
return RET_ERR
out = bdecode(out)
err = bdecode(err)
if len(out) > 0:
pinfo(out)
if len(err) > 0:
perror(err)
if p.returncode != 0:
perror("fix up command returned with error code", p.returncode)
return RET_ERR
return RET_OK
def get_ogm(self):
if not which(self.ogm_script):
r = files.CompFiles(prefix="OSVC_COMP_OGM_SCRIPT").fix()
if r != 0:
raise Exception()
default=None,
help='Reference file for RMSDs')
parser.add_option('-m',
'--mask',
dest='mask',
default='@CA',
help='Mask to calculate RMSd for. Default [%default]')
opt, args = parser.parse_args()
if not args or not opt.rmsfile or not os.path.exists(opt.prmtop):
print >> sys.stderr, 'Error: Missing key CL arguments or missing topology!'
parser.print_help()
sys.exit(1)
if opt.rmsbin:
binner = which('1Dbinning.py')
if not binner:
print >> sys.stderr, 'Error: Binning requires 1Dbinning.py!'
sys.exit(1)
trajs = AmberTraj(opt.prmtop, args)
trajs.rmsd(mask=opt.mask, outfile=opt.rmsfile, ref=opt.reffile)
trajs.run()
if opt.rmsbin:
process = Popen(
[binner, '-f', opt.rmsfile, '-o', opt.rmsbin, '-n', '-c', 2])
if process.wait():
print >> sys.stderr, 'Error: Binning program (%s) failed!' % binner
sys.exit(1)
def init(self):
self.rules = self.get_rules()
if which("openssl") is None:
raise NotApplicable("openssl command not found")
x += 1
while x < len(sys.argv) and not sys.argv[x].startswith('-'):
mdcrds.append(sys.argv[x])
x += 1
except IndexError:
print 'Error: Improper command!'
printusage()
except ValueError:
print 'Error: "percent" must be a floating point decimal!'
printusage()
parm = amberParm(prmtop)
if len(mdcrds) == 0: # if no mdcrd supplied, give default
mdcrds.append('mdcrd')
ptraj = utilities.which('cpptraj') # look for ptraj
if ptraj is None:
print 'Error: cpptraj needed for FindSaltbridge.py!'
sys.exit() # quit if not found
if not parm.valid:
printusage()
for x in range(len(mdcrds)): # check for mdcrd existences
if utilities.fileexists(mdcrds[x]) == -1:
printusage()
residues = parm.parm_data['RESIDUE_LABEL']
for x in range(len(residues)): # build acceptor list and donor list
help='MPI Command to run MPI programs on your machine. ('
'Default "%default")', default='mpiexec -n 6')
group.add_option('-d', '--intdiel', dest='intdiel', type='float', default=1.0,
metavar='FLOAT', help='Internal dielectric to use. Default is '
'1.0')
parser.add_option_group(group)
(options, args) = parser.parse_args()
# Make sure we have enough arguments
if options.res is None or options.pKa is None:
parser.print_help()
sys.exit(1)
# Now determine where required programs are
sander = which('sander')
sanderMPI = which('sander.MPI')
tleap = which('tleap')
cpinutil = which('cpinutil.py')
converter = which('parmed.py')
if options.nreps % 2 != 0:
print >> sys.stderr, 'Error: Even number of replicas required!'
sys.exit(1)
if None in [sander, sanderMPI, tleap, cpinutil]:
print >> sys.stderr, 'sander, tleap, and cpinutil.py are all necessary!'
sys.exit(1)
if options.igb == 8 and converter is None:
print >> sys.stderr, 'parmed.py is needed for igb = 8!'
print "Error: Invalid topology file " + topname + "!"
sys.exit()
for x in range(len(residues)):
if residues[x] < 1:
print "Error: You chose a nonsensical residue (residue 0 or less)"
sys.exit()
elif residues[x] > residue_number:
print "Error: The residue you chose is out of range!"
sys.exit()
for x in range(len(mdcrds)):
if utilities.fileexists(mdcrds[x]) == -1:
sys.exit()
ptraj = utilities.which("ptraj")
if ptraj == "none":
print "Error: ptraj needed for phipsigen.py!"
sys.exit()
else:
print "ptraj Found! Using " + ptraj
os.system("rm -f _CHI1CHI2_*")
ptrajin = open("_CHI1CHI2_ptraj.in", "w")
for x in range(len(mdcrds)):
ptrajin.write("trajin " + mdcrds[x] + "\n")
ptrajin.write("\n")
for x in range(len(residues)):
intdiel={1},
/
""".format(igb, intdiel)
# Groupfiles -- 1 is for the first run, 2 is for each one after
TI_groupfile1 = """-O -i mdin -p {0}0.prmtop -c {0}0.inpcrd -o 0_0.mdout -r 0_0.restrt -x 0_0.mdcrd
-O -i mdin -p {0}1.prmtop -c {0}1.inpcrd -o 0_1.mdout -r 0_1.restrt -x 0_1.mdcrd
""".format(resname.lower())
TI_groupfile2 = """-O -i mdin -p {0}0.prmtop -c {1}_0.restrt -o {2}_0.mdout -r {2}_0.restrt -x {2}_0.mdcrd
-O -i mdin -p {0}1.prmtop -c {1}_1.restrt -o {2}_1.mdout -r {2}_1.restrt -x {2}_1.mdcrd
"""
# Find sander and tleap or quit
sander = which("sander.MPI")
sandermin = which("sander")
tleap = which("tleap")
if sander is None or tleap is None or sandermin is None:
sys.exit("Error: You need sander.MPI and tleap to run this program!")
# Make tleap script and build the residue
extras = ''
if opt.off:
extras += 'loadOFF %s\n' % opt.off
if opt.frcmod:
extras += 'loadAmberParams %s\n' % opt.frcmod
if isolated:
prev_str, next_str = '', ''
for x in range(len(residues)):
if residues[x] == 1 or residues[x] == residue_number:
print 'Error: You cannot get phi/psi dihedrals for either terminus!'
sys.exit()
elif residues[x] < 1:
print 'Error: You chose a nonsensical residue (residue 0 or less)'
sys.exit()
elif residues[x] > residue_number:
print 'Error: The residue you chose is out of range!'
sys.exit()
for x in range(len(mdcrds)):
if utilities.fileexists(mdcrds[x]) == -1:
sys.exit()
ptraj = utilities.which('cpptraj')
if ptraj == 'none':
print 'Error: ptraj needed for phipsigen.py!'
sys.exit()
else:
print 'ptraj Found! Using ' + ptraj
os.system('rm -f _PHIPSI_*')
ptrajin = open('_PHIPSI_ptraj.in','w')
for x in range(len(mdcrds)):
ptrajin.write('trajin ' + mdcrds[x] + '\n')
ptrajin.write('\n')
for x in range(len(residues)):
parser.add_option('-i', '--right-residue', dest='rightres', default=None,
help='Which residue to cap with on the right terminus')
parser.add_option('--frcmod', dest='frcmod', metavar='FILE', default=None,
help='File with additional parameters for the compound')
parser.add_option('--lib', dest='lib', metavar='FILE', default=None,
help='File with the residue definition (OFF file)')
(options, args) = parser.parse_args()
# Make sure we have enough arguments
if options.res == None or options.pH == None:
parser.print_help()
commworld.Abort()
# Now determine where required programs are
sander = which('sander')
pmemd = which('pmemd.cuda')
tleap = which('tleap')
cpinutil = which('cpinutil.py')
if None in [sander, pmemd, tleap, cpinutil]:
print('sander, pmemd.cuda, tleap, cpinutil.py, and parmed.py are all '
'necessary!')
commworld.Abort()
print(" Found necessary programs!")
# Keep a log of all stdout
log = open('%s.log' % os.path.split(sys.argv[0])[1].strip('.py'), 'w')
md_mdin = """Mdin file for titrating stuff
pmemd_input.write('pmemd_pH.mdin')
pmemd_energy.minimization(maxcyc=1)
pmemd_energy.change('cntrl', 'ntpr', 1)
pmemd_energy.write('pmemd_min.mdin')
# Now it's time to enter the actual MD loop
numsteps = int(total_time / dt)
try:
mpi_cmd = os.environ['DO_PARALLEL']
except KeyError:
mpi_cmd = 'none'
if mpi_cmd == 'none':
pmemd = which('pmemd')
exe = '%s' % pmemd
else:
pmemd = which('pmemd.MPI')
exe = '%s %s' % (mpi_cmd, pmemd)
if pmemd == 'none':
print >> sys.stderr, 'Error: PMEMD cannot be found! It must be in your PATH for cph_pmemd.py to work.'
sys.exit()
cpout_file = open(cpout, 'w')
cpout_file.write("""Solvent pH: %8.5f
Monte Carlo step size: %8i
Time step: %8i
Time: %10.3f
""" % (pH, dt, 0, 0))
help='File with additional parameters for the compound')
parser.add_option('--lib',
dest='lib',
metavar='FILE',
default=None,
help='File with the residue definition (OFF file)')
(options, args) = parser.parse_args()
# Make sure we have enough arguments
if options.res == None or options.pH == None:
parser.print_help()
commworld.Abort()
# Now determine where required programs are
sander = which('sander')
pmemd = which('pmemd.cuda')
tleap = which('tleap')
cpinutil = which('cpinutil.py')
if None in [sander, pmemd, tleap, cpinutil]:
print(
'sander, pmemd.cuda, tleap, cpinutil.py, and parmed.py are all '
'necessary!')
commworld.Abort()
print(" Found necessary programs!")
# Keep a log of all stdout
log = open('%s.log' % os.path.split(sys.argv[0])[1].strip('.py'), 'w')
(options, args) = parser.parse_args()
# Make sure we have enough arguments
if options.res is None or options.pKa is None:
parser.print_help()
sys.exit(1)
if options.dielc != 1 and options.dielc != 2:
sys.exit('--intdiel must be 1 or 2!')
if options.mccycles <= 0:
sys.exit('--mccycles must be a positive integer!')
# Now determine where required programs are
sander = which('sander.MPI')
pmemd = which('pmemd.MPI')
pmemd_cuda = which('pmemd.cuda')
tleap = which('tleap')
cpinutil = which('cpinutil.py')
converter = which('parmed.py')
if options.nreps % 2 != 0:
print >> sys.stderr, 'Error: Even number of replicas required!'
sys.exit(1)
if 'none' in [sander, tleap, cpinutil]:
print >> sys.stderr, 'sander, tleap, and cpinutil.py are all necessary!'
sys.exit(1)
if options.igb == 8 and converter == 'none':
opt, args = clparser.parse_args()
if not opt.mdout or not opt.prmtop or not opt.mdcrd:
clparser.print_help()
sys.exit()
try:
mdout = open(opt.mdout,'r')
if not os.path.exists(opt.mdcrd): raise IOError('mdcrd doesn\'t exist')
if not os.path.exists(opt.prmtop): raise IOError('mdcrd doesn\'t exist')
except IOError:
print >> sys.stderr, "Error: mdout, prmtop, and/or mdcrd files don't exist!"
clparser.print_help()
sys.exit(1)
ptraj = utilities.which('ptraj')
if ptraj == "none":
print "Error: ptraj is needed to analyze coordinate files!"
sys.exit(1)
mdoutlines = mdout.readlines()
mdout.close()
# parse this block:
# NSTEP = 100000 TIME(PS) = 200.000 TEMP(K) = 308.77 PRESS = 0.0
# Etot = -18650.7357 EKtot = 4532.3000 EPtot = -23183.0357
# BOND = 11.0060 ANGLE = 19.7379 DIHED = 12.5913
# 1-4 NB = 5.9918 1-4 EEL = -372.1093 VDWAALS = 3276.9971
# EELEC = -26139.9559 EHBOND = 0.0000 RESTRAINT = 2.7054
# EAMBER (non-restraint) = -23185.7411
def __init__(self, soundfile, parent):
self.soundfile = soundfile
self.isplaying = False
self.time = 0 # current audio position in frames
self.audio = QMediaPlayer()
self.decoder = QAudioDecoder()
self.is_loaded = False
self.volume = 100
self.isplaying = False
self.decoded_audio = {}
self.only_samples = []
self.decoding_is_finished = False
self.max_bits = 32768
# File Loading is Asynchronous, so we need to be creative here, doesn't need to be duration but it works
self.audio.durationChanged.connect(self.on_durationChanged)
#self.decoder.finished.connect(self.decode_finished_signal)
self.audio.setMedia(QUrl.fromLocalFile(soundfile))
#self.decoder.setSourceFilename(soundfile) # strangely inconsistent file-handling
# It will hang here forever if we don't process the events.
while not self.is_loaded:
QCoreApplication.processEvents()
time.sleep(0.1)
#self.decode_audio()
#self.np_data = np.array(self.only_samples)
#self.np_data = np.abs(self.np_data / self.max_bits)
# A simple normalisation, with this the samples should all be between 0 and 1
# for i in self.decoded_audio.items():
# self.only_samples.extend(i[1][0])
# t = []
# for i in self.only_samples:
# if i != []:
# t.append(i + -(min(self.only_samples)))
#
# t2 = []
# for i in t:
# t2.append(i / max(t))
# self.only_samples = t2
#print(len(self.only_samples))
#print(self.max_bits)
self.isvalid = True
self.pydubfile = None
if AudioSegment:
if which("ffmpeg") is not None:
AudioSegment.converter = which("ffmpeg")
elif which("avconv") is not None:
AudioSegment.converter = which("avconv")
else:
if platform.system() == "Windows":
AudioSegment.converter = os.path.join(get_main_dir(), "ffmpeg.exe")
#AudioSegment.converter = os.path.dirname(os.path.realpath(__file__)) + "\\ffmpeg.exe"
else:
# TODO: Check if we have ffmpeg or avconv installed
AudioSegment.converter = "ffmpeg"
try:
if AudioSegment:
print(self.soundfile)
self.pydubfile = AudioSegment.from_file(self.soundfile, format=os.path.splitext(self.soundfile)[1][1:])
else:
self.wave_reference = wave.open(self.soundfile)
self.isvalid = True
except:
traceback.print_exc()
self.wave_reference = None
self.isvalid = False
default=None, help='Data file to dump RMSDs to')
parser.add_option('-b', '--rmsd-bin-file', dest='rmsbin', metavar='FILE',
default=None, help='Data file to dump RMSD bins to')
parser.add_option('-f', '--reference', dest='reffile', metavar='FILE',
default=None, help='Reference file for RMSDs')
parser.add_option('-m', '--mask', dest='mask', default='@CA',
help='Mask to calculate RMSd for. Default [%default]')
opt, args = parser.parse_args()
if not args or not opt.rmsfile or not os.path.exists(opt.prmtop):
print >> sys.stderr, 'Error: Missing key CL arguments or missing topology!'
parser.print_help()
sys.exit(1)
if opt.rmsbin:
binner = which('1Dbinning.py')
if not binner:
print >> sys.stderr, 'Error: Binning requires 1Dbinning.py!'
sys.exit(1)
trajs = AmberTraj(opt.prmtop, args)
trajs.rmsd(mask=opt.mask, outfile=opt.rmsfile, ref=opt.reffile)
trajs.run()
if opt.rmsbin:
process = Popen([binner, '-f', opt.rmsfile, '-o', opt.rmsbin, '-n', '-c', 2])
if process.wait():
print >> sys.stderr, 'Error: Binning program (%s) failed!' % binner
sys.exit(1)
else:
(options, args) = parser.parse_args()
# Make sure we have enough arguments
if options.res is None or options.pKa is None:
parser.print_help()
sys.exit(1)
if options.dielc != 1 and options.dielc != 2:
sys.exit('--intdiel must be 1 or 2!')
if options.mccycles <= 0:
sys.exit('--mccycles must be a positive integer!')
# Now determine where required programs are
sander = which('sander.MPI')
pmemd = which('pmemd.MPI')
pmemd_cuda = which('pmemd.cuda')
tleap = which('tleap')
cpinutil = which('cpinutil.py')
converter = which('parmed.py')
if options.nreps % 2 != 0:
print >> sys.stderr, 'Error: Even number of replicas required!'
sys.exit(1)
if 'none' in [sander, tleap, cpinutil]:
print >> sys.stderr, 'sander, tleap, and cpinutil.py are all necessary!'
sys.exit(1)
if options.igb == 8 and converter == 'none':
print 'Error: Invalid topology file ' + topname + '!'
sys.exit()
for x in range(len(residues)):
if residues[x] < 1:
print 'Error: You chose a nonsensical residue (residue 0 or less)'
sys.exit()
elif residues[x] > residue_number:
print 'Error: The residue you chose is out of range!'
sys.exit()
for x in range(len(mdcrds)):
if utilities.fileexists(mdcrds[x]) == -1:
sys.exit()
ptraj = utilities.which('ptraj')
if ptraj == 'none':
print 'Error: ptraj needed for phipsigen.py!'
sys.exit()
else:
print 'ptraj Found! Using ' + ptraj
os.system('rm -f _CHI1CHI2_*')
ptrajin = open('_CHI1CHI2_ptraj.in','w')
for x in range(len(mdcrds)):
ptrajin.write('trajin ' + mdcrds[x] + '\n')
ptrajin.write('\n')
for x in range(len(residues)):
x += 1
while x < len(sys.argv) and not sys.argv[x].startswith('-'):
mdcrds.append(sys.argv[x])
x += 1
except IndexError:
print 'Error: Improper command!'
printusage()
except ValueError:
print 'Error: "percent" must be a floating point decimal!'
printusage()
parm = amberParm(prmtop)
if len(mdcrds) == 0: # if no mdcrd supplied, give default
mdcrds.append('mdcrd')
ptraj = utilities.which('cpptraj') # look for ptraj
if ptraj is None:
print 'Error: cpptraj needed for FindSaltbridge.py!'
sys.exit() # quit if not found
if not parm.valid:
printusage()
for x in range(len(mdcrds)): # check for mdcrd existences
if utilities.fileexists(mdcrds[x]) == -1:
printusage()
residues = parm.parm_data['RESIDUE_LABEL']
for x in range(len(residues)): # build acceptor list and donor list
def to_png(self, out_file, bit_depth = 16, clip_on_percentiles = False, crush = False):
"""
Converts the FITS file to a PNG.
:param out_file: User specified filename for the PNG
:param clip_on_percentiles: Clips flux values to a lower and upper percentile
:param crush: Call pngcrush on the output image
.. warning:: Setting bit_depth to 8 may reduce the dynamic range of the image.
.. warning:: Setting clip_on_percentiles to True reduces the dynamic range of the image.
"""
if not self.fits:
raise ValueError, "AstroPNG was not initialized with a FITS image"
hdu = pyfits.open(self.fits)
header, fluxes = hdu[0].header, hdu[0].data
height, width = fluxes.shape
# Prepare data
fluxes = numpy.flipud(fluxes)
fluxes = fluxes.flatten()
if header['BITPIX'] == 16:
fluxes = fluxes.astype(numpy.uint16)
# Determine the minimum pixel and maximum pixel value
min_pix, max_pix = numpy.nanmin(fluxes), numpy.nanmax(fluxes)
# Clip data
if clip_on_percentiles:
min_pix, max_pix = self.__compute_percentile(fluxes)
fluxes = self.__clip(fluxes, min_pix, max_pix)
# Scale down to zero
if header['BITPIX'] == -64:
fluxes = fluxes - min_pix
# Scale image to 8 bit integer space
if bit_depth == 8:
range_of_pixels = max_pix - min_pix
fluxes = 255 * ( (data - min_pix) / range_of_pixels )
min_pix, max_pix = 0, 255
# Reshape the data to its original dimensions
fluxes = fluxes.reshape(height, width)
# If non-integer data type then quantize pixels
if header['BITPIX'] in (-32, -64):
nan_indices = self.__find_nans(fluxes)
z_zeros, z_scales, fluxes = self.__quantize(fluxes)
fluxes[nan_indices] = 0
# Create a PNG writer object with the appropriate settings
png_writer = AstroPNGWriter(
width = width,
height = height,
greyscale = True,
alpha = False,
bitdepth = bit_depth,
)
# Set various metadata in PNG
png_writer.set_header(header)
if self.quantized:
png_writer.set_quantization_parameters(z_zeros, z_scales)
png_writer.set_nans(nan_indices)
f = open(out_file, 'wb')
png_writer.write(f, fluxes)
f.close()
# Crush
if crush:
pngcrush = which('pngcrush')
if pngcrush:
path, extension = os.path.splitext(out_file)
filename = "%s_crushed%s" % (path, extension)
os.system("%s -save %s %s" % (pngcrush, out_file, filename))
shutil.move(filename, out_file)
