def main():
#Check settings file exist?
dataController = DataController()
dataController.checkExist()
ViLASApp().run()
class RemoveDialog(Popup):
gromacsRun = GromacsRun()
thread = ObjectProperty(None)
dataController = DataController()
def cancel(self):
self.dismiss()
self.thread = Process(target=self.gromacsRun.main)
self.thread.start()
pass
def remove(self):
self.dismiss()
call('rm -r ' + self.dataController.getdata('path ') + '/run/*',
shell=True)
call('rm -r ' + self.dataController.getdata('path ') +
'/output/ligand/*',
shell=True)
call('rm -r ' + self.dataController.getdata('path ') +
'/output/receptor/*',
shell=True)
self.thread = Process(target=self.gromacsRun.main)
self.thread.start()
pass
pass
class FinishDialog(Popup):
dialogText = ObjectProperty(None)
def setText(self, dialog_text):
self.dialogText.text = dialog_text
gromacsRun = GromacsRun()
thread = ObjectProperty(None)
dataController = DataController()
def cancel(self):
self.dismiss()
pass
# def remove(self):
# self.dismiss()
# App().stop()
# # App.get_running_app().stop()
# pass
pass
class ConfigurationScreen(Screen):
root_path = os.path.dirname(__file__)
dataController = DataController()
optimizedButton = ObjectProperty(None)
customButton = ObjectProperty(None)
OptimizedButton = ObjectProperty(None)
optimizedTick = ObjectProperty(None)
configLayout = ObjectProperty(None)
boxGromacs = ObjectProperty(None)
versionButton = ObjectProperty(None)
is_optimized = True
pathText = ObjectProperty(None)
caverBox = ObjectProperty(None)
icstBox = ObjectProperty(None)
ligandAutoBox = ObjectProperty(None)
repeatTimesText = ObjectProperty(None)
nohupBox = ObjectProperty(None)
configpBox = ObjectProperty(None)
normalBox = ObjectProperty(None)
maximumCoresText = ObjectProperty(None)
gpuAutoBox = ObjectProperty(None)
def setupView(self):
dropdown = DropDown()
#Check gromacs version
try:
command_version = check_output("compgen -ac | grep mdrun", shell=True, executable='/bin/bash').splitlines()
for x in range(0, len(command_version)):
print command_version[x]
try:
versions = check_output(str(command_version[x])+" -version", shell=True, executable='/bin/bash').splitlines()
if not any("Gromacs version" in s for s in versions):
continue
version = [s for s in versions if "Gromacs version" in s][0].split(":")[1]
btn = Button(text=str(command_version[x]) + version, size_hint_y=None, height=35)
btn.bind(on_release=lambda btn: dropdown.select(btn.text))
# then add the button inside the dropdown
dropdown.add_widget(btn)
#Set first gromacs found
if x == 0 and self.dataController.getdata('gromacs_version ') == '':
self.versionButton.text = str(command_version[x]) + version
self.dataController.setdata('gromacs_version ', str(command_version[x] + version))
if self.dataController.getdata('gromacs_version ') == str(command_version[x]) + version:
self.versionButton.text = str(command_version[x]) + version
except subprocess.CalledProcessError as e:
print e
except subprocess.CalledProcessError as e:
print e
try:
gmx_version = check_output("compgen -ac | grep gmx", shell=True, executable='/bin/bash').splitlines()
for x in range(0, len(gmx_version)):
print gmx_version[x]
try:
versions = check_output(str(gmx_version[x])+" -version", shell=True, executable='/bin/bash').splitlines()
if not any("GROMACS version" in s for s in versions):
continue
version = [s for s in versions if "GROMACS version" in s][0].split(":")[1]
numVers = version.split('VERSION')[1].replace(' ','').split('.')
# If version >= 5.1
if int(numVers[0]) == 5 and int(numVers[1])>0:
btn = Button(text=str(gmx_version[x]) + version, size_hint_y=None, height=35)
btn.bind(on_release=lambda btn: dropdown.select(btn.text))
# then add the button inside the dropdown
dropdown.add_widget(btn)
#Set first gromacs found
if self.dataController.getdata('gromacs_version ') == '':
self.versionButton.text = str(gmx_version[x]) + version
self.dataController.setdata('gromacs_version ', str(gmx_version[x] + version))
if self.dataController.getdata('gromacs_version ') == str(gmx_version[x]) + version:
self.versionButton.text = str(gmx_version[x]) + version
except subprocess.CalledProcessError as e:
print e
except subprocess.CalledProcessError as e:
print e
self.versionButton.bind(on_release=dropdown.open)
dropdown.bind(on_select=self.gromacs_version_check)
#Check number of cores
command_cores = check_output("nproc", shell=True, executable='/bin/bash').splitlines()
if(len(command_cores) > 0):
self.dataController.setdata('maximum_cores ', command_cores[0])
self.maximumCoresText.text = command_cores[0]
def __init__(self, *args, **kwargs):
super(ConfigurationScreen, self).__init__(*args, **kwargs)
if ( self.dataController.getdata('config_auto ') == 'True' ):
self.configLayout.disabled = True
else:
# Disable touch = false
self.configLayout.disabled = False
# Set color of button
self.is_optimized = False
self.optimizedTick.color = [1,1,1,0]
self.customTick.color = [1,1,1,1]
self.optimizedButton.background_color = [0.62, 0.62, 0.62, 1]
self.customButton.background_color = [0, 0.588, 0.533, 1]
# Set init value for config
self.pathText.text = self.dataController.getdata('path ')
if (self.dataController.getdata('caver') == 'True'):
self.caverBox.active = True
else:
self.caverBox.active = False
if (self.dataController.getdata('icst') == 'True'):
self.icstBox.active = True
else:
self.icstBox.active = False
if (self.dataController.getdata('ligand_auto') == 'True'):
self.ligandAutoBox.active = True
else:
self.ligandAutoBox.active = False
self.repeatTimesText.text = self.dataController.getdata('repeat_times')
self.nohupBox.active = False
self.configBox.active = False
self.normalBox.active = False
if (self.dataController.getdata('mode') == 'nohup'):
self.nohupBox.active = True
elif(self.dataController.getdata('mode') == 'config'):
self.configBox.active = True
else:
self.normalBox.active = True
# self.dataController.setdata('mode', 'normal')
self.maximumCoresText.text = self.dataController.getdata('maximum_cores')
if (self.dataController.getdata('gpu_auto') == 'True'):
self.gpuAutoBox.active = True
else:
self.gpuAutoBox.active = False
# set listener
self.pathText.bind(text = self.path_change)
self.caverBox.bind(active = self.caver_check)
self.icstBox.bind(active = self.icst_check)
self.ligandAutoBox.bind(active = self.ligand_auto_check)
self.repeatTimesText.bind(text = self.repeat_times)
self.nohupBox.bind(active = self.nohup_check)
self.configBox.bind(active = self.config_check)
self.normalBox.bind(active = self.normal_check)
self.maximumCoresText.bind(text = self.maximum_cores)
self.gpuAutoBox.bind(active = self.gpu_auto_check)
def path_change(self, instance, value):
self.dataController.setdata('path ', value)
def caver_check(self, checkbox, value):
self.dataController.setdata('caver', str(value))
#self.dataController.setdata('icst', str(not value))
def icst_check(self, checkbox, value):
self.dataController.setdata('icst', str(value))
#self.dataController.setdata('caver', str(not value))
def ligand_auto_check(self, checkbox, value):
self.dataController.setdata('ligand_auto', str(value))
def repeat_times(self, instance, value):
self.dataController.setdata('repeat_times ', value)
def nohup_check(self, checkbox, value):
if value == True:
self.dataController.setdata('mode ', 'nohup')
def config_check(self, checkbox, value):
if value == True:
self.dataController.setdata('mode ', 'config')
def normal_check(self, checkbox, value):
if value == True:
self.dataController.setdata('mode ', 'normal')
def maximum_cores(self, instance, value):
self.dataController.setdata('maximum_cores ', value)
def gpu_auto_check(self, checkbox, value):
self.dataController.setdata('gpu_auto ', str(value))
def gromacs_version_check(self, instance, value):
self.dataController.setdata('gromacs_version ', str(value))
self.versionButton.text = value
# For 2 button
def optimizedConfig(self):
if (self.is_optimized == True):
pass
else:
self.is_optimized = True
self.optimizedTick.color = [1,1,1,1]
self.customTick.color = [1,1,1,0]
self.optimizedButton.background_color = [0, 0.588, 0.533, 1]
self.customButton.background_color = [0.62, 0.62, 0.62, 1]
self.configLayout.disabled = True
self.dataController.setdata('config_auto ', 'True')
def customConfig(self):
if (self.is_optimized == True):
self.is_optimized = False
self.optimizedTick.color = [1,1,1,0]
self.customTick.color = [1,1,1,1]
self.optimizedButton.background_color = [0.62, 0.62, 0.62, 1]
self.customButton.background_color = [0, 0.588, 0.533, 1]
self.configLayout.disabled = False
self.dataController.setdata('config_auto ', 'False')
else:
pass
pass
class RunningScreen(Screen):
root_path = os.path.dirname(__file__)
dataController = DataController()
pymol = ObjectProperty(None)
progressBar = ObjectProperty(None)
checkFile = ObjectProperty(None)
emImg = ObjectProperty(None)
nvtImg = ObjectProperty(None)
nptImg = ObjectProperty(None)
mdImg = ObjectProperty(None)
smdImg = ObjectProperty(None)
smdLog = ObjectProperty(None)
progressText = ObjectProperty(None)
progressLayout = ObjectProperty(None)
progressImage = ObjectProperty(None)
progressUnit = 0
progressPoint = 0
checkPOINT = ''
checkEM = False
checkNVT = False
checkNPT = False
checkMD = False
checkSMD = False
lastSMD = 0
angle = 0
firstFinish = True
lastFinish = False
GroLeft = ''
GroRight = ''
GroVersion = ''
#Create thread to run background
gromacsRun = GromacsRun()
thread = ObjectProperty(None)
def __init__(self, *args, **kwargs):
super(RunningScreen, self).__init__(*args, **kwargs)
# init progress image
self.progressImage = ProgressImage()
self.progressLayout.add_widget(self.progressImage)
pass
def set_pymol(self, pym):
self.pymol = pym
def setupView(self):
# Check gromacs version
self.checkGromacVersion()
#Check if folder is exits
call('mkdir ' + self.dataController.getdata('path '), shell=True)
call('mkdir ' + self.dataController.getdata('path ') + '/run',
shell=True)
call('mkdir ' + self.dataController.getdata('path ') + '/output',
shell=True)
call('mkdir ' + self.dataController.getdata('path ') +
'/output/receptor',
shell=True)
call('mkdir ' + self.dataController.getdata('path ') +
'/output/ligand',
shell=True)
call('mkdir ' + self.dataController.getdata('path ') + '/analyse',
shell=True)
runfolders = check_output(
'ls ' + self.dataController.getdata('path ') + '/run/',
shell=True).splitlines()
if len(runfolders) > 0:
popup = RemoveDialog()
popup.open()
else:
call('rm -r ' + self.dataController.getdata('path ') + '/run/*',
shell=True)
call('rm -r ' + self.dataController.getdata('path ') +
'/output/ligand/*',
shell=True)
call('rm -r ' + self.dataController.getdata('path ') +
'/output/receptor/*',
shell=True)
self.thread = Process(target=self.gromacsRun.main)
self.thread.start()
#Check log
repeat_times = int(self.dataController.getdata('repeat_times '))
self.progressUnit = 1000 / (4.5 + repeat_times) / len(
Variable.parsepdb.Ligands)
self.progressPoint = 0
self.dataController.setdata('status', '')
Clock.schedule_interval(self.check_log, 5)
Clock.schedule_interval(self.spin_progress, 0.05)
# Clock.schedule_interval(self.pymol_log, 300)
#close pymol
self.pymol.cmd.window('hide')
def spin_progress(self, dt):
if self.dataController.getdata('status') != 'finished':
if (self.angle == 360):
self.angle = 0
self.angle += 10
self.progressImage.rot.angle = self.angle
self.progressImage.rot.origin = self.progressImage.center
self.progressImage.rot.axis = (0, 0, 1)
# self.progressImage.canvas.add(Rotate(angle=(self.angle), origin=(self.progressImage.center)))
def check_log(self, dt):
if self.dataController.getdata('status') == 'finished':
if self.lastFinish == False:
self.lastFinish = True
popup = FinishDialog()
popup.setText(
'Your job is finished. \n \nNow, you can close the interface. '
)
popup.open()
self.progressText.text = 'Labpi finished your jobs! now you can close app.'
self.checkFile.text = str(
self.dataController.getdata('status'))
elif self.dataController.getdata('status') != '':
# Check run nohup finish app
if (self.dataController.getdata('mode ') == 'nohup'
and self.firstFinish == True):
self.firstFinish = False
popup = FinishDialog()
popup.setText(
'Your job is running in background. \n \nNow, you can close the interface. '
)
popup.open()
run_path = str(
self.dataController.getdata('path ')) + '/run/' + str(
self.dataController.getdata('status'))
repeat_times = int(self.dataController.getdata('repeat_times '))
if self.checkPOINT == '':
self.checkPOINT = str(self.dataController.getdata('status'))
elif self.checkPOINT != str(self.dataController.getdata('status')):
self.checkEM = checkNVT = checkNPT = checkMD = checkSMD = True
self.lastSMD = 0
self.checkPOINT = str(self.dataController.getdata('status'))
em_path = run_path + '/em.gro'
if os.path.isfile(em_path) == True:
self.emImg.source = self.root_path + '/img/tick_select.png'
if self.checkEM == False:
self.checkEM = True
self.progressPoint += self.progressUnit * 0.5
self.progressText.text = 'Labpi is running at NVT step'
else:
self.emImg.source = self.root_path + '/img/tick_normal.png'
self.progressText.text = 'Labpi is running at Energy minimization step'
# self.emImg.reload()
nvt_path = run_path + '/nvt.gro'
if os.path.isfile(nvt_path) == True:
self.nvtImg.source = self.root_path + '/img/tick_select.png'
if self.checkNVT == False:
self.checkNVT = True
self.progressPoint += self.progressUnit * 0.5
self.progressText.text = 'Labpi is running at NPT step'
else:
self.nvtImg.source = self.root_path + '/img/tick_normal.png'
# self.nvtImg.reload()
npt_path = run_path + '/npt.gro'
if os.path.isfile(npt_path) == True:
self.nptImg.source = self.root_path + '/img/tick_select.png'
if self.checkNPT == False:
self.checkNPT = True
self.progressPoint += self.progressUnit * 0.5
self.progressText.text = 'Labpi is running at MD step'
else:
self.nptImg.source = self.root_path + '/img/tick_normal.png'
# self.nptImg.reload()
md_path = run_path + '/md.gro'
if os.path.isfile(md_path) == True:
self.mdImg.source = self.root_path + '/img/tick_select.png'
if self.checkMD == False:
self.checkMD = True
self.progressPoint += self.progressUnit
self.progressText.text = 'Labpi is running at SMD step'
else:
self.mdImg.source = self.root_path + '/img/tick_normal.png'
# self.mdImg.reload()
# TODO: check percent import signal
smd_log = 0
for x in range(0, int(repeat_times)):
smd_path_x = run_path + '/md_st_' + str(x) + '.gro'
if os.path.isfile(smd_path_x) == True:
smd_log += 1
if self.lastSMD < x:
self.lastSMD = x
self.checkSMD = False
if self.checkSMD == False:
self.checkSMD = True
self.progressPoint += self.progressUnit
self.smdLog.text = str(smd_log) + '/' + str(repeat_times)
smd_path_last = run_path + '/md_st_' + str(repeat_times -
1) + '.gro'
if os.path.isfile(smd_path_last) == True:
self.smdImg.source = self.root_path + '/img/tick_select.png'
else:
self.smdImg.source = self.root_path + '/img/tick_normal.png'
# self.smdImg.reload()
self.progressBar.value = self.progressPoint
self.checkFile.text = str(self.dataController.getdata('status'))
def pymol_log(self, dt):
if self.dataController.getdata(
'status') == '' or self.dataController.getdata(
'status') == 'finished':
return
run_folder = self.dataController.getdata('status')
run_path = str(
self.dataController.getdata('path ')) + '/run/' + run_folder
ligand_name = run_folder.split('run_')[1]
repeat_times = int(self.dataController.getdata('repeat_times '))
# Check point for pymol
check_path = ''
if os.path.isfile(run_path + '/em.gro') == False and os.path.isfile(
run_path +
'/em.cpt') == True and os.path.isfile(run_path +
'/em.tpr') == True:
check_path = run_path + '/em'
if os.path.isfile(run_path + '/nvt.gro') == False and os.path.isfile(
run_path +
'/nvt.cpt') == True and os.path.isfile(run_path +
'/nvt.tpr') == True:
check_path = run_path + '/nvt'
if os.path.isfile(run_path + '/npt.gro') == False and os.path.isfile(
run_path +
'/npt.cpt') == True and os.path.isfile(run_path +
'/npt.tpr') == True:
check_path = run_path + '/npt'
if os.path.isfile(run_path + '/md.gro') == False and os.path.isfile(
run_path +
'/md.cpt') == True and os.path.isfile(run_path +
'/md.tpr') == True:
check_path = run_path + '/md'
if os.path.isfile(run_path + '/md_st.gro') == False and os.path.isfile(
run_path +
'/md_st.cpt') == True and os.path.isfile(run_path +
'/md_st.tpr') == True:
check_path = run_path + '/md_st'
for x in range(0, int(repeat_times)):
if os.path.isfile(run_path + '/md_st_' + str(x) +
'.gro') == False and os.path.isfile(
run_path + '/md_st_' + str(x) +
'.cpt') == True and os.path.isfile(
run_path + '/md_st_' + str(x) +
'.tpr') == True:
check_path = run_path + '/md_st_' + str(x)
if (check_path != ''):
call('echo \"non-Water\"|' + self.GroLeft + 'trjconv' +
self.GroRight + '-f ' + check_path + '.cpt -s ' + check_path +
'.tpr -o ' + check_path + '.pdb',
shell=True)
self.pymol.cmd.reinitialize()
self.pymol.cmd.load(check_path + '.pdb')
chains = ParsePdb().listChain(check_path + '.pdb')
for chain in chains:
if chain.chain_type == 'protein':
self.pymol.cmd.show_as('cartoon', str(chain.chain_view))
self.pymol.cmd.cartoon('automatic', str(chain.chain_view))
else:
self.pymol.cmd.show_as(
'sticks',
'resname ' + str(chain.chain_view.getResnames()[0]))
# self.pymol.cmd.set('stick_color', 'red')
self.pymol.util.cbc()
pass
def checkGromacVersion(self):
gromacs_version = self.dataController.getdata('gromacs_version ')
version_array = gromacs_version.split(' VERSION ')[1].split('.')
print version_array
# If version >= 5
if int(version_array[0]) == 5:
# If version >= 5.1
if int(version_array[1]) > 0:
self.GroLeft = gromacs_version.split(' VERSION ')[0]
self.GroRight = ''
else:
# Check gmx
mdrun_array = gromacs_version.split(' VERSION ')[0].split(
'mdrun')
self.GroLeft = 'gmx '
self.GroRight = mdrun_array[1]
self.GroVersion = 5
# If version = 4
else:
mdrun_array = gromacs_version.split(' VERSION ')[0].split('mdrun')
self.GroLeft = mdrun_array[0]
self.GroRight = mdrun_array[1]
self.GroVersion = 4
class GromacsMD(object):
dataController = DataController()
# Get version of gromacs
GroLeft = ''
GroRight = ''
GroVersion = ''
GroOption = ''
repeat_times = 0
def mdrun(self):
main_path = self.dataController.getdata('path ')
runfolders = check_output('ls ' + main_path + '/run',
shell=True).splitlines()
call('rm -r ' + main_path + '/analyse/*/', shell=True)
for x in range(0, len(runfolders)):
run_path = main_path + '/run/' + runfolders[x]
if not os.path.isdir(main_path + '/run/' + runfolders[x]):
continue
if os.path.isfile(run_path + '/solv_ions.gro') is False:
continue
#create folder for analyse
call('mkdir ' + self.dataController.getdata('path ') +
'/analyse/' + runfolders[x].split('_')[1],
shell=True)
# Check point to show log
self.dataController.setdata('status', runfolders[x])
run_path = main_path + '/run/' + runfolders[x]
ligandCurrent = runfolders[x].split('_')[1] #A01
print self.GroLeft + 'mdrun' + self.GroRight + ' ' + self.GroOption
groCmd = ''
#Run em
call('mkdir ' + run_path + '/em', shell=True)
if os.path.isfile(run_path + '/em/em.gro') is False:
groCmd += self.GroLeft + 'grompp' + self.GroRight + ' -maxwarn 20 -f mdp/minim.mdp -c solv_ions.gro -p topol.top -o em/em.tpr \n'
groCmd += self.GroLeft + 'mdrun' + self.GroRight + ' ' + self.GroOption + ' -v -deffnm em/em -cpt 5\n'
#Run nvt
call('mkdir ' + run_path + '/nvt', shell=True)
if os.path.isfile(run_path + '/nvt/nvt.gro') is False:
groCmd += self.GroLeft + 'grompp' + self.GroRight + ' -maxwarn 20 -f mdp/nvt.mdp -c em/em.gro -p topol.top -n index.ndx -o nvt/nvt.tpr \n'
groCmd += self.GroLeft + 'mdrun' + self.GroRight + ' ' + self.GroOption + ' -deffnm nvt/nvt -v -cpt 5\n'
#Run npt
call('mkdir ' + run_path + '/npt', shell=True)
if os.path.isfile(run_path + '/npt/npt.gro') is False:
groCmd += self.GroLeft + 'grompp' + self.GroRight + ' -maxwarn 20 -f mdp/npt.mdp -c nvt/nvt.gro -t nvt/nvt.cpt -p topol.top -n index.ndx -o npt/npt.tpr \n'
groCmd += self.GroLeft + 'mdrun' + self.GroRight + ' ' + self.GroOption + ' -deffnm npt/npt -v -cpt 5\n'
#Run md
call('mkdir ' + run_path + '/md', shell=True)
if os.path.isfile(run_path + '/md/md.gro') is False:
groCmd += self.GroLeft + 'grompp' + self.GroRight + ' -maxwarn 20 -f mdp/md.mdp -c npt/npt.gro -t npt/npt.cpt -p topol.top -n index.ndx -o md/md.tpr \n'
groCmd += self.GroLeft + 'mdrun' + self.GroRight + ' ' + self.GroOption + ' -deffnm md/md -v -cpt 5\n'
groCmd += 'echo -e \"System\"|' + self.GroLeft + 'trjconv' + self.GroRight + ' -s md/md.tpr -f md/md.xtc -o md/md_noPBC.xtc -pbc mol -ur compact\n'
if (self.GroVersion >= 5):
groCmd += 'echo -e \"Backbone\\nBackbone\"|' + self.GroLeft + 'rms' + self.GroRight + ' -s md/md.tpr -f md/md_noPBC.xtc -o md/rmsd.xvg -tu ns\n'
else:
groCmd += 'echo -e \"Backbone\\nBackbone\"|' + 'g_rms' + self.GroRight + ' -s md/md.tpr -f md/md_noPBC.xtc -o md/rmsd.xvg -tu ns\n'
# if int(Method) == 1:
# if (int(self.repeat_times) == 1 or int(self.repeat_times) == 0 ):
# if(self.GroVersion >= 5):
# self.replaceLine('pull-group2-name', 'pull-group2-name = '+ligandCurrent+'\n', run_path+'/mdp/md_pull_5.mdp')
# groCmd += self.GroLeft+'grompp'+self.GroRight+ ' -maxwarn 20 -f mdp/md_pull_5.mdp -c md.gro -t md.cpt -p topol.top -n index.ndx -o md_st.tpr \n'
# else:
# self.replaceLine('pull_group1', 'pull_group1 = '+ligandCurrent+'\n', run_path+'/mdp/md_pull.mdp')
# groCmd += self.GroLeft+'grompp'+self.GroRight+ ' -maxwarn 20 -f mdp/md_pull.mdp -c md.gro -t md.cpt -p topol.top -n index.ndx -o md_st.tpr \n'
# groCmd += self.GroLeft+'mdrun'+self.GroRight+ ' '+self.GroOption+ ' -px pullx.xvg -pf pullf.xvg -deffnm md_1 -v -cpt 5\n'
# groCmd += 'python2.7 parse_pull.py -x pullx.xvg -f pullf.xvg -o pullfx.xvg\n'
# else:
# Repeat the steered for times
analyse_path = main_path + '/analyse/' + runfolders[x].split(
'_')[1]
pull_vec = self.dataController.getdata('smd-vel ')
pullx_path = ''
pullf_path = ''
call('mkdir ' + run_path + '/smd', shell=True)
for k in range(1, int(self.repeat_times) + 1):
if os.path.isfile(run_path + '/smd/md_st_' + str(k) +
'.gro') is False:
groCmd += self.GroLeft + 'grompp' + self.GroRight + ' -maxwarn 20 -f mdp/md_pull_repeat.mdp -c md/md.gro -t md/md.cpt -p topol.top -n index.ndx -o smd/md_st_' + str(
k) + '.tpr \n'
groCmd += self.GroLeft + 'mdrun' + self.GroRight + ' ' + self.GroOption + ' -px smd/pullx_' + str(
k) + '.xvg -pf smd/pullf_' + str(
k) + '.xvg -deffnm smd/md_st_' + str(
k) + ' -v -cpt 5\n'
groCmd += 'python2.7 parse_pull.py -x smd/pullx_' + str(
k) + '.xvg -f smd/pullf_' + str(
k) + '.xvg -o smd/pullfx_' + str(k) + '.xvg\n'
pullx_path += ' smd/pullx_' + str(k) + '.xvg'
pullf_path += ' smd/pullf_' + str(k) + '.xvg'
groCmd += 'python2.7 pullana.py -px ' + pullx_path + ' -pf ' + pullf_path + ' -plot ' + analyse_path + '/pull_force_time.png ' + analyse_path + '/pull_force_distance.png -log ' + analyse_path + '/pull_data.csv -v ' + pull_vec + '\n'
groCmd += 'python2.7 mathplot.py -i md/rmsd.xvg -o ' + analyse_path + '/rmsd.png\n'
# analyze cmd
cmd_analyze = 'python2.7 LabpiAnalyzer.py --gro ' + run_path + '/md/md.gro --trj ' + run_path + '/md/md.xtc --mdp ' + run_path + '/mdp/md.mdp --tpr ' + run_path + '/md/md.tpr --start 0 --end 20 --receptor Receptor --ligand ' + ligandCurrent + ' --run ' + run_path + ' --analyze ' + main_path + '/analyse '
if self.GroLeft.replace(' ', '') != '':
cmd_analyze += ' --gleft ' + self.GroLeft
if self.GroRight.replace(' ', '') != '':
cmd_analyze += ' --gright ' + self.GroRight
groCmd += cmd_analyze + ' -i False\n'
# elif int(Method) == 2:
# if os.path.isfile(run_path+'/md_2.gro') is False:
# groCmd += GroLeft+'grompp'+GroRight+ ' -maxwarn 20 -f mdp/md_md.mdp -c md.gro -t md.cpt -p topol.top -n index.ndx -o md_2.tpr \n'
# groCmd += GroLeft+'mdrun'+GroRight+ ' '+GroOption+ ' -deffnm md_2 -v \n'
# groCmd += 'export OMP_NUM_THREADS=4\n'
# groCmd += 'echo -e \"Receptor\\n'+ligandCurrent+'\\n\" | g_mmpbsa -f md_2.trr -b 100 -dt 20 -s md_2.tpr -n index.ndx -pdie 2 -decomp \n'
# groCmd += 'echo -e \"Receptor\\n'+ligandCurrent+'\\n\" | g_mmpbsa -f md_2.trr -b 100 -dt 20 -s md_2.tpr -n index.ndx -i mdp/polar.mdp -nomme -pbsa -decomp \n'
# groCmd += 'echo -e \"Receptor\\n'+ligandCurrent+'\\n\" | g_mmpbsa -f md_2.trr -b 100 -dt 20 -s md_2.tpr -n index.ndx -i mdp/apolar_sasa.mdp -nomme -pbsa -decomp -apol sasa.xvg -apcon sasa_contrib.dat \n'
# groCmd += 'python2.7 MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a sasa.xvg \n'
self.CallCommand(run_path, groCmd)
# print groCmd
call('rm -r ' + run_path + '/#*', shell=True)
self.dataController.setdata('status', 'finished')
self.CallCommand(main_path, 'rm -r caver')
self.CallCommand(main_path + '/analyse', 'python2.7 top_pull.py')
self.CallCommand(main_path + '/analyse', 'rm top_pull.py')
def setupOptions(self):
gromacs_version = self.dataController.getdata('gromacs_version ')
version_array = gromacs_version.split(' VERSION ')[1].split('.')
print version_array
# If version >= 5
if int(version_array[0]) == 5:
# If version >= 5.1
if int(version_array[1]) > 0:
self.GroLeft = gromacs_version.split(' VERSION ')[0]
self.GroRight = ''
else:
# Check gmx
mdrun_array = gromacs_version.split(' VERSION ')[0].split(
'mdrun')
self.GroLeft = 'gmx '
self.GroRight = mdrun_array[1]
self.GroVersion = 5
# If version = 4
else:
mdrun_array = gromacs_version.split(' VERSION ')[0].split('mdrun')
self.GroLeft = mdrun_array[0]
self.GroRight = mdrun_array[1]
self.GroVersion = 4
# Set number of core or gpu
number_cores = self.dataController.getdata('maximum_cores ')
if int(number_cores) > 0:
self.GroOption = ' -ntomp ' + number_cores
else:
self.GroOption = ''
check_gpu = check_output(gromacs_version.split(' VERSION ')[0] +
" -version",
shell=True,
executable='/bin/bash').splitlines()
if ([s for s in check_gpu if "GPU support:" in s
][0].split(":")[1].replace(' ', '') == 'enabled'):
self.GroOption += ' -gpu_id 0'
#Repeat times
self.repeat_times = int(self.dataController.getdata('repeat_times '))
def CallCommand(self, patch, command):
call('cd ' + patch + '; ' + command,
shell=True,
executable='/bin/bash')
class SettingScreen(Screen):
root_path = os.path.dirname(__file__)
dataController = DataController()
nvtNsteps = ObjectProperty(None)
nvtNst = ObjectProperty(None)
nptNsteps = ObjectProperty(None)
nptNst = ObjectProperty(None)
mdNsteps = ObjectProperty(None)
mdNst = ObjectProperty(None)
smdNsteps = ObjectProperty(None)
smdNst = ObjectProperty(None)
smdVel = ObjectProperty(None)
smdK = ObjectProperty(None)
smdDirection = ObjectProperty(None)
smdDistance = ObjectProperty(None)
def __init__(self, *args, **kwargs):
super(SettingScreen, self).__init__(*args, **kwargs)
self.nvtNsteps.text = self.dataController.getdata('nvt-nsteps ')
self.nvtNst.text = self.dataController.getdata('nvt-nst ')
self.nptNsteps.text = self.dataController.getdata('npt-nsteps ')
self.nptNst.text = self.dataController.getdata('npt-nst ')
self.mdNsteps.text = self.dataController.getdata('md-nsteps ')
self.mdNst.text = self.dataController.getdata('md-nst ')
self.smdNsteps.text = self.dataController.getdata('smd-nsteps ')
self.smdNst.text = self.dataController.getdata('smd-nst ')
self.smdVel.text = self.dataController.getdata('smd-vel ')
self.smdK.text = self.dataController.getdata('smd-k ')
if (self.dataController.getdata('smd-direction') == 'True'):
self.smdDirection.active = True
else:
self.smdDirection.active = False
if (self.dataController.getdata('smd-distance') == 'True'):
self.smdDistance.active = True
else:
self.smdDistance.active = False
self.nvtNsteps.bind(text=self.on_nvt_nsteps)
self.nvtNst.bind(text=self.on_nvt_nst)
self.nptNsteps.bind(text=self.on_npt_nsteps)
self.nptNst.bind(text=self.on_npt_nst)
self.mdNsteps.bind(text=self.on_md_nsteps)
self.mdNst.bind(text=self.on_md_nst)
self.smdNsteps.bind(text=self.on_smd_nsteps)
self.smdNst.bind(text=self.on_smd_nst)
self.smdVel.bind(text=self.on_smd_vel)
self.smdK.bind(text=self.on_smd_k)
self.smdDirection.bind(active=self.smd_direction)
self.smdDistance.bind(active=self.smd_distance)
pass
def on_nvt_nsteps(self, instance, value):
self.dataController.setdata('nvt-nsteps ', value)
def on_nvt_nst(self, instance, value):
self.dataController.setdata('nvt-nst ', value)
def on_npt_nsteps(self, instance, value):
self.dataController.setdata('npt-nsteps ', value)
def on_npt_nst(self, instance, value):
self.dataController.setdata('npt-nst ', value)
def on_md_nsteps(self, instance, value):
self.dataController.setdata('md-nsteps ', value)
def on_md_nst(self, instance, value):
self.dataController.setdata('md-nst ', value)
def on_smd_nsteps(self, instance, value):
self.dataController.setdata('smd-nsteps ', value)
def on_smd_nst(self, instance, value):
self.dataController.setdata('smd-nst ', value)
def on_smd_vel(self, instance, value):
self.dataController.setdata('smd-vel ', value)
def on_smd_k(self, instance, value):
self.dataController.setdata('smd-k ', value)
def smd_direction(self, checkbox, value):
self.dataController.setdata('smd-direction', str(value))
#self.dataController.setdata('smd-distance', str(not value))
def smd_distance(self, checkbox, value):
self.dataController.setdata('smd-distance', str(value))