/
browse_fragmax_structures_in_coot.py
executable file
·208 lines (166 loc) · 7 KB
/
browse_fragmax_structures_in_coot.py
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import os
import glob
import pygtk, gtk, pango
import coot
class GUI(object):
def __init__(self):
self.projectDir = None
self.index = -1
self.Todo = []
self.autoproc_software = [
'autoproc',
'fastdp',
'edna',
'dials',
'xdsapp',
'xdsxcale'
]
self.refine_software = [
'dimple',
'pipedream'
]
self.autoproc = self.autoproc_software[0]
self.autorefine = self.refine_software[0]
def StartGUI(self):
self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
self.window.connect("delete_event", gtk.main_quit)
self.window.set_border_width(10)
self.window.set_default_size(400, 600)
self.window.set_title("browse structures")
self.vbox = gtk.VBox() # this is the main container
self.vbox.add(gtk.Label('project directory (paste absolute path below)'))
projectDir_entry = gtk.Entry()
projectDir_entry.add_events(gtk.gdk.KEY_RELEASE_MASK)
projectDir_entry.connect("key-release-event", self.on_key_release_projectDir)
projectDir_entry.set_text('')
self.vbox.add(projectDir_entry)
self.vbox.add(gtk.Label())
frame = gtk.Frame()
frame.add(gtk.Label('current project directory'))
self.vbox.add(frame)
frame = gtk.Frame()
self.current_project_directory_label = gtk.Label()
frame.add(self.current_project_directory_label)
self.vbox.add(frame)
parseProjectDirbutton = gtk.Button(label="read project directory")
parseProjectDirbutton.connect("clicked", self.parseProjectDir)
self.vbox.add(parseProjectDirbutton)
self.vbox.add(gtk.Label())
outer_frame = gtk.Frame()
hbox = gtk.HBox()
frame = gtk.Frame(label='auto-processing')
vbox = gtk.VBox()
for n, button in enumerate(self.autoproc_software):
if n == 0:
new_button = gtk.RadioButton(None, button)
else:
new_button = gtk.RadioButton(new_button, button)
new_button.connect("toggled", self.selected_autoprocessing)
vbox.pack_start(new_button,False,False,0)
frame.add(vbox)
hbox.pack_start(frame)
frame = gtk.Frame(label='auto-refinement')
vbox = gtk.VBox()
for n, button in enumerate(self.refine_software):
if n == 0:
new_button = gtk.RadioButton(None, button)
else:
new_button = gtk.RadioButton(new_button, button)
new_button.connect("toggled", self.selected_autorefinement)
vbox.pack_start(new_button,False,False,0)
frame.add(vbox)
hbox.pack_start(frame)
outer_frame.add(hbox)
self.vbox.pack_start(outer_frame)
frame = gtk.Frame()
self.number_pdb_files_found = gtk.Label()
frame.add(self.number_pdb_files_found)
self.vbox.add(frame)
self.vbox.add(gtk.Label())
self.PREVbutton = gtk.Button(label="<<<")
self.NEXTbutton = gtk.Button(label=">>>")
self.PREVbutton.connect("clicked", self.backward)
self.NEXTbutton.connect("clicked", self.forward)
hbox = gtk.HBox()
hbox.pack_start(self.PREVbutton)
hbox.pack_start(self.NEXTbutton)
self.vbox.add(hbox)
self.vbox.add(gtk.Label())
frame = gtk.Frame()
frame.add(gtk.Label('current folder'))
self.vbox.add(frame)
frame = gtk.Frame()
self.current_folder_label = gtk.Label()
frame.add(self.current_folder_label)
self.vbox.add(frame)
self.vbox.add(gtk.Label())
frame = gtk.Frame()
frame.add(gtk.Label('current PDB file'))
self.vbox.add(frame)
frame = gtk.Frame()
self.current_pdb_label = gtk.Label()
frame.add(self.current_pdb_label)
self.vbox.add(frame)
self.vbox.add(gtk.Label())
frame = gtk.Frame()
frame.add(gtk.Label('current MTZ file'))
self.vbox.add(frame)
frame = gtk.Frame()
self.current_mtz_label = gtk.Label()
frame.add(self.current_mtz_label)
self.vbox.add(frame)
self.window.add(self.vbox)
self.window.show_all()
def selected_autoprocessing(self, widget):
self.autoproc = widget.get_label()
print('selected auto-processing program: {0!s}'.format(self.autoproc))
def selected_autorefinement(self, widget):
self.autorefine = widget.get_label()
print('selected auto-refinement program: {0!s}'.format(self.autorefine))
def RefreshData(self):
if self.index < 0:
self.index = 0
if self.index > len(self.Todo) - 1:
self.index = len(self.Todo) - 1
if len(molecule_number_list()) > 0:
for item in molecule_number_list():
coot.close_molecule(item)
coot.set_nomenclature_errors_on_read("ignore")
coot.handle_read_draw_molecule_with_recentre(self.Todo[self.index][1], 0)
coot.auto_read_make_and_draw_maps(self.Todo[self.index][2])
self.current_folder_label.set_label(self.Todo[self.index][0])
self.current_pdb_label.set_label(self.Todo[self.index][3])
self.current_mtz_label.set_label(self.Todo[self.index][4])
def backward(self, widget):
self.index -= 1
self.RefreshData()
def forward(self, widget):
self.index += 1
self.RefreshData()
def parseProjectDir(self, widget):
typical_names = ['refine', 'dimple','final']
for pdbFile in sorted(glob.glob(os.path.join(self.projectDir,'*',self.autoproc,self.autorefine,'*.pdb'))):
pdb = pdbFile.split('/')[len(pdbFile.split('/'))-1]
pdbRoot = pdb.replace('.pdb','')
folderName = pdbFile.split('/')[len(pdbFile.split('/'))-4]
print('checking folder {0!s}'.format(folderName))
if pdbRoot in typical_names:
if os.path.isfile(pdbFile.replace('.pdb','.mtz')):
mtzFile = pdbFile.replace('.pdb','.mtz')
mtz = pdb.replace('.pdb','.mtz')
self.Todo.append([folderName,pdbFile,mtzFile,pdb,mtz])
print('folder: {0!s} PDB: {1!s} MTZ: {2!s}'.format(folderName,pdbFile,mtzFile))
continue
self.number_pdb_files_found.set_label('found {0!s} PDB files'.format(len(self.Todo)))
def on_key_release_projectDir(self, widget, event):
self.projectDir = widget.get_text()
# if os.path.isdir(self.projectDir)
self.current_project_directory_label.set_label(self.projectDir)
if os.path.isdir(self.projectDir):
self.current_project_directory_label.modify_fg(gtk.STATE_NORMAL, gtk.gdk.color_parse("darkgreen"))
else:
self.current_project_directory_label.modify_fg(gtk.STATE_NORMAL, gtk.gdk.color_parse("red"))
def CANCEL(self, widget):
self.window.destroy()
if __name__ == '__main__':
GUI().StartGUI()