def update_settings(self):
idxs = self.inp_box.ctr.GetItemCount()
items = [self.inp_box.ctr.GetItemData(i) for i in range(idxs)]
inputs = []
reference = None
sequence = None
for i in items:
inp_type = i.type.type.GetString(i.type_selection)
if inp_type in ('processed pickle list', 'processed pickle folder',
'processed pickle'):
inputs.append(i.path)
elif inp_type == 'reference MTZ':
reference = i.path
elif inp_type == 'sequence':
sequence = i.path
self.pparams.data = inputs
if reference is not None:
self.pparams.hklisoin = reference
if self.opt_chk_useref.GetValue():
self.pparams.hklrefin = reference
self.out_dir = self.out_box.ctr.GetValue()
self.pparams.run_no = misc.set_base_dir(
out_dir=self.out_dir) # Need to change
self.pparams.title = self.project_title.ctr.GetValue()
self.pparams.n_residues = self.opt_spc_nres.ctr.GetValue()
self.pparams.n_processors = self.opt_spc_nproc.ctr.GetValue()
update_phil = master_phil.format(python_object=self.pparams)
self.regenerate_params(update_phil)
def onRun(self, e):
# Run full processing
self.init_settings()
prime_phil = master_phil.format(python_object=self.pparams)
with misc.Capturing() as output:
prime_phil.show()
txt_out = ''
for one_output in output:
txt_out += one_output + '\n'
prime_file = os.path.join(self.out_dir, self.prime_filename)
out_file = os.path.join(self.out_dir, 'stdout.log')
with open(prime_file, 'w') as pf:
pf.write(txt_out)
self.prime_run_window = PRIMERunWindow(self, -1,
title='PRIME Output',
params=self.pparams,
prime_file=prime_file,
out_file=out_file)
self.prime_run_window.prev_pids = easy_run.fully_buffered('pgrep -u {} {}'
''.format(user, python)).stdout_lines
self.prime_run_window.Show(True)
def onRun(self, e):
# Run full processing
self.init_settings()
if self.sanity_check():
prime_phil = master_phil.format(python_object=self.pparams)
with misc.Capturing() as output:
prime_phil.show()
txt_out = ''
for one_output in output:
txt_out += one_output + '\n'
source_dir = os.path.dirname(self.out_dir)
prime_file = os.path.join(source_dir, self.prime_filename)
out_file = os.path.join(self.out_dir, 'stdout.log')
with open(prime_file, 'w') as pf:
pf.write(txt_out)
self.prime_run_window = frm.PRIMERunWindow(self, -1,
title='PRIME Output',
params=self.pparams,
prime_file=prime_file)
self.prime_run_window.prev_pids = easy_run.fully_buffered('pgrep -u {} {}'
''.format(user, python)).stdout_lines
self.prime_run_window.Show(True)
def regenerate_params(self, phil=None):
if phil is not None:
current_phil = master_phil.format(python_object=phil)
else:
current_phil = master_phil
# Generate Python object and text of parameters
self.generate_phil_string(current_phil)
self.pparams = current_phil.extract()
def regenerate_params(self, phil=None):
if phil is not None:
current_phil = master_phil.format(python_object=phil)
else:
current_phil = master_phil
# Generate Python object and text of parameters
self.pparams = current_phil.extract()
with misc.Capturing() as txt_output:
current_phil.show()
self.phil_string = ''
for one_output in txt_output:
self.phil_string += one_output + '\n'
def regenerate_params(self, phil=None):
if phil is not None:
current_phil = master_phil.format(python_object=phil)
else:
current_phil = master_phil
# Generate Python object and text of parameters
self.pparams = current_phil.extract()
with misc.Capturing() as txt_output:
current_phil.show()
self.phil_string = ''
for one_output in txt_output:
self.phil_string += one_output + '\n'
def onSaveScript(self, e):
self.init_settings()
# Generate text of params
final_phil = master_phil.format(python_object=self.pparams)
with misc.Capturing() as txt_output:
final_phil.show()
txt_out = ''
for one_output in txt_output:
txt_out += one_output + '\n'
# Save param file
save_dlg = wx.FileDialog(self,
message="Save PRIME Script",
defaultDir=os.curdir,
defaultFile="*.phil",
wildcard="*.phil",
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
if save_dlg.ShowModal() == wx.ID_OK:
with open(save_dlg.GetPath(), 'w') as savefile:
savefile.write(txt_out)
save_dlg.Destroy()
def onSaveScript(self, e):
self.init_settings()
# Generate text of params
final_phil = master_phil.format(python_object=self.pparams)
with misc.Capturing() as txt_output:
final_phil.show()
txt_out = ''
for one_output in txt_output:
txt_out += one_output + '\n'
# Save param file
save_dlg = wx.FileDialog(self,
message="Save PRIME Script",
defaultDir=os.curdir,
defaultFile="*.phil",
wildcard="*.phil",
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT
)
if save_dlg.ShowModal() == wx.ID_OK:
with open(save_dlg.GetPath(), 'w') as savefile:
savefile.write(txt_out)
save_dlg.Destroy()
def __init__(self, parent, phil=None):
self.parent = parent
super(PRIMEInputWindow, self).__init__(self.parent)
#Generate default parameters
if phil is not None:
self.pparams = master_phil.format(python_object=phil).extract()
else:
self.pparams = master_phil.extract()
main_box = wx.StaticBox(self, label='Main Settings')
vbox = wx.StaticBoxSizer(main_box, wx.VERTICAL)
# Input file box
self.inp_box = ct.InputCtrl(self, label='Input: ',
label_size=(120, -1),
label_style='bold',
button=True)
vbox.Add(self.inp_box,
flag=wx.LEFT | wx.TOP | wx.RIGHT| wx.EXPAND,
border=15)
# Output file box
self.out_box = ct.InputCtrl(self, label='Output: ',
label_size=(120, -1),
label_style='bold',
button=True)
vbox.Add(self.out_box,
flag=wx.LEFT | wx.TOP | wx.RIGHT| wx.EXPAND,
border=15)
# # Sequence file box
# self.seq_box = ct.InputCtrl(self, label='Sequence: ',
# label_size=(120, -1),
# button=True)
# vbox.Add(self.seq_box,
# flag=wx.LEFT | wx.TOP | wx.RIGHT| wx.EXPAND,
# border=15)
# Isomorphous reference file box
self.ref_box = ct.InputCtrl(self, label='Reference: ',
label_size=(120, -1),
button=True)
vbox.Add(self.ref_box,
flag=wx.LEFT | wx.TOP | wx.RIGHT| wx.EXPAND,
border=15)
# Title box
self.title_box = ct.InputCtrl(self, label='Job Title: ',
label_size=(120, -1))
vbox.Add(self.title_box,
flag=wx.LEFT | wx.TOP | wx.RIGHT| wx.EXPAND,
border=15)
# Options and number of processors
opt_box = wx.FlexGridSizer(2, 4, 15, 10)
self.opt_chk_useref = wx.CheckBox(self, label='Use reference in refinement')
self.opt_chk_useref.SetValue(False)
self.opt_chk_useref.Disable()
self.opt_txt_nres = wx.StaticText(self, label='No. of Residues: ')
self.opt_spc_nres = wx.SpinCtrl(self, value='500',
max=(15000), size=(80,-1))
self.opt_txt_nproc = wx.StaticText(self, label='No. of Processors: ')
self.opt_spc_nproc = wx.SpinCtrl(self, value='8', size=(80, -1))
self.opt_btn = wx.Button(self, label='Advanced Options...')
opt_box.Add((120, -1))
opt_box.Add(self.opt_chk_useref)
opt_box.Add(self.opt_txt_nres, flag=wx.ALIGN_RIGHT)
opt_box.Add(self.opt_spc_nres, flag=wx.ALIGN_RIGHT)
opt_box.Add((120, -1))
opt_box.Add(self.opt_btn)
opt_box.Add(self.opt_txt_nproc, flag=wx.ALIGN_RIGHT)
opt_box.Add(self.opt_spc_nproc, flag=wx.ALIGN_RIGHT)
opt_box.AddGrowableCol(1, 1)
vbox.Add(opt_box,
flag=wx.LEFT | wx.TOP | wx.RIGHT| wx.EXPAND,
border=15)
vbox.Add((-1, 15))
self.SetSizer(vbox)
# Button bindings
self.inp_box.btn_browse.Bind(wx.EVT_BUTTON, self.onInputBrowse)
self.out_box.btn_browse.Bind(wx.EVT_BUTTON, self.onOutputBrowse)
# self.seq_box.btn_browse.Bind(wx.EVT_BUTTON, self.onSequenceBrowse)
self.ref_box.btn_browse.Bind(wx.EVT_BUTTON, self.onIsoRefBrowse)
self.opt_btn.Bind(wx.EVT_BUTTON, self.onAdvancedOptions)
def onAdvancedOptions(self, e):
advanced = dlg.PRIMEAdvancedOptions(
self,
title='Advanced PRIME Options',
style=wx.DEFAULT_DIALOG_STYLE | wx.STAY_ON_TOP | wx.RESIZE_BORDER)
advanced.SetMinSize((600, -1))
advanced.Fit()
# Populate the PHIL textbox
current_phil = master_phil.format(python_object=self.pparams)
self.generate_phil_string(current_phil=current_phil)
advanced.phil.ctr.SetValue(self.phil_string)
# Set values to default parameters
advanced.res.high.SetValue('{:4.2f}'.format(
self.pparams.postref.allparams.d_max))
advanced.res.low.SetValue('{:4.2f}'.format(
self.pparams.postref.allparams.d_min))
advanced.sg.spacegroup.SetValue(str(self.pparams.target_space_group))
if str(self.pparams.target_unit_cell).lower() != 'none':
uc = ' '.join(
list(map(str, self.pparams.target_unit_cell.parameters())))
advanced.uc.unit_cell.SetValue(uc)
else:
advanced.uc.unit_cell.SetValue(str(self.pparams.target_unit_cell))
advanced.anom.SetValue(self.pparams.target_anomalous_flag)
advanced.cc.cc_cutoff.SetValue(str(self.pparams.frame_accept_min_cc))
advanced.pix.pixel_size.SetValue(str(self.pparams.pixel_size_mm))
advanced.cycles.ctr.SetValue(int(self.pparams.n_postref_cycle))
if advanced.ShowModal() == wx.ID_OK:
# Read PHIL string from window, convert to params
self.phil_string = advanced.phil.ctr.GetValue()
new_phil = ip.parse(self.phil_string)
self.pparams = master_phil.fetch(sources=[new_phil]).extract()
# Param controls will override the PHIL string (clunky, but for now)
if advanced.res_override.GetValue():
self.pparams.scale.d_max = float(advanced.res.high.GetValue())
self.pparams.scale.d_min = float(advanced.res.low.GetValue())
self.pparams.merge.d_max = float(advanced.res.high.GetValue())
self.pparams.merge.d_min = float(advanced.res.low.GetValue())
self.pparams.postref.scale.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.scale.d_min = float(
advanced.res.low.GetValue())
self.pparams.postref.crystal_orientation.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.crystal_orientation.d_min = float(
advanced.res.low.GetValue())
self.pparams.postref.reflecting_range.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.reflecting_range.d_min = float(
advanced.res.low.GetValue())
self.pparams.postref.unit_cell.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.unit_cell.d_min = float(
advanced.res.low.GetValue())
self.pparams.postref.allparams.d_max = float(
advanced.res.high.GetValue())
self.pparams.postref.allparams.d_min = float(
advanced.res.low.GetValue())
self.pparams.target_space_group = advanced.sg.spacegroup.GetValue()
if advanced.uc.unit_cell.GetValue().lower() != 'none':
uc = str_split(advanced.uc.unit_cell.GetValue())
self.pparams.target_unit_cell = unit_cell(list(map(float, uc)))
else:
self.pparams.target_unit_cell = None
self.pparams.target_anomalous_flag = advanced.anom.GetValue()
if advanced.cc.cc_cutoff.GetValue().lower() != 'none':
self.pparams.frame_accept_min_cc = float(
advanced.cc.cc_cutoff.GetValue())
else:
self.pparams.frame_accept_min_cc = None
if advanced.pix.pixel_size.GetValue().lower() != 'none':
self.pparams.pixel_size_mm = float(
advanced.pix.pixel_size.GetValue())
else:
self.pparams.pixel_size_mm = None
self.pparams.n_postref_cycle = int(advanced.cycles.ctr.GetValue())
self.regenerate_params(self.pparams)
advanced.Destroy()
e.Skip()
