def surfdist(self):
if not self.vol_file:
self.select_first_message(".vol file")
return
self.get_options()
self.options['reportmode']='both'
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
text,html = Voronoia.process_command('surfdist',self.vol_dataset,self.vol_dataset,self.options)
else:
text,html = Voronoia.process_command('surfdist',self.vol_file,self.out_path,self.options)
self.text_dialog('Surface distance','Surface distance values for data from %s'%(self.vol_file),text,html)
def write_avgpd(self):
if not self.vol_file:
self.select_first_message(".vol file")
return
self.get_options()
self.options['reportmode']='both'
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
text,html = Voronoia.process_command('average',self.vol_dataset,self.vol_dataset,self.options)
else:
text,html = Voronoia.process_command('average',self.vol_file,self.out_path,self.options)
self.text_dialog('Average packing','Average packing values for data from %s'%(self.vol_file),text,html)
def packing_report(self):
if not self.vol_file:
self.select_first_message(".vol file")
return
self.get_options()
self.options['reportmode']='both'
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
text,html = Voronoia.process_command('report',self.vol_dataset,self.vol_dataset,self.options)
else:
text,html = Voronoia.process_command('report',self.vol_file,self.out_path,self.options)
self.text_dialog('Packing report','Packing report for %s'%(self.vol_file),text,html)
def write_cav(self,response=1):
if not self.vol_file:
self.select_first_message(".vol file")
return
self.get_options()
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
message = Voronoia.process_command('cavities',self.vol_dataset,self.vol_dataset,self.options)
else:
message = Voronoia.process_command('cavities',self.vol_file,self.out_path,self.options)
if response:
ms = Pmw.MessageDialog(self.parent,title="Cavities written as PDB file",message_text=message[0])
ms.activate()
ms.withdraw()
return message[1]
def compare_ref(self):
if not self.vol_file:
self.select_first_message(".vol file")
return
if not self.options['reference_file']:
self.select_first_message("reference file")
return
self.get_options()
self.options['reportmode']='both'
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
text,html = Voronoia.process_command('compare',self.vol_dataset,self.vol_dataset,self.options)
else:
text,html = Voronoia.process_command('compare',self.vol_file,self.out_path,self.options)
self.text_dialog('Packing compared to reference','Packing compared to reference values in\n%s'%(self.options['reference_file']),text,html)
def calc_packing(self,show_message=1):
# check for complete data
self.get_options()
if not self.input_file:
self.select_first_message("PDB file")
return
if not self.out_path:
self.select_first_message("output directory")
return
result = []
for in_file in self.get_vol_files():
# show calculation message
ms = Pmw.MessageDialog(title="Calculation running",buttons=[],message_text="""Packing data for the structure
%s
is being calculated. Please wait.
The calculation takes 1-15 minutes per file, depending on the size of the structure
and your hardware."""%in_file)
ms.show()
self.approot.update()
# calculate
message = Voronoia.process_command('calc',in_file,self.out_path,self.options)
result.append(message)
# destroy old message
ms.withdraw()
ms.destroy()
self.approot.update()
# set vol file variable
if self.pdb_dataset:
text = "%i packing files were calculated:\n"%len(result)
text += string.join(['\t'+name[1] for name in result],'\n')
if show_message:
ms = Pmw.MessageDialog(title=".vol files calculated",message_text=text)
self.vol_dataset = self.out_path
self.vol_file = result[0][1]
self.vol_file_var.set(self.vol_dataset)
self.vol_dataset_radio.setvalue(['Process all .vol files in this directory'])
return [name[1] for name in result]
else:
message = result[0]
if show_message:
ms = Pmw.MessageDialog(title=".vol file calculated",message_text=message[0])
self.vol_file = message[1]
self.vol_file_var.set(self._short_name(message[1]))
return message[1]
