def load_refinement(self, ref, stats):
hkl = hklf.reader(open(ref.replace('.dat', '.hkl')))
pdbf = pdb.input(file_name=ref.replace('.dat', '.pdb'))
pdbt = PDBTools(file_name=ref.replace('.dat', '.pdb'))
cs = crystal_symmetry_from_ins.extract_from(ref.replace('.dat', '.ins'))
ma = hkl.as_miller_arrays(crystal_symmetry=cs)
mp = pdbf.xray_structure_simple().scatterers()[0].multiplicity()
s = pdbt.get_s()
vm = cs.unit_cell().volume() / (pdbt.get_rmm() * mp)
c = ma[0].completeness(d_max=stats['res'])
dmin = stats['res']
r = stats['r']
rfree = stats['rfree']
self._mv.SetLabel('%.2f' % vm)
self._s.SetLabel('%.2f' % s)
self._dmin.SetLabel('%.2f' % dmin)
self._c.SetLabel('%.1f' % (c*100))
self._r.SetLabel('%.3f' % r)
self._rfree.SetLabel('%.3f' % rfree)
sigxr = self._sigx_r(s, vm, c, r, dmin)
self._sigxr.SetLabel('%.4f' % sigxr)
sigxrf = self._sigx_rfree(s, vm, c, rfree, dmin)
self._sigxrf.SetLabel('%.4f' % sigxrf)
x = np.linspace(dmin+0.5,dmin-0.5, 20)
ys = [[],[],[],[],[],[]]
for i in x:
sr = self._sigx_r(s, vm, c, r, i)
ys[0].append(sr)
ys[1].append(sr*1.15)
ys[2].append(sr*0.85)
sr = self._sigx_rfree(s, vm, c, rfree, i)
ys[3].append(sr)
ys[4].append(sr*1.15)
ys[5].append(sr*0.85)
self.ax1.plot(x, ys[0], 'b-', label='R')
self.ax1.fill_between(x, ys[1], ys[2], alpha=0.1, facecolor='blue')
self.ax1.plot(x, ys[3], 'g-', label='Rfree')
self.ax1.fill_between(x, ys[4], ys[5], alpha=0.1, facecolor='green')
al = self.ax1.axis()
yam = al[3]-al[2]
xam = al[1]-al[0]
self.ax1.axhline(y=0.0236, color='purple', label='3sig (ASP)')
self.ax1.axvline(x=dmin, ymin=0, ymax=(sigxr-al[2])/yam, color='0.7', label='Actual')
self.ax1.axhline(y=sigxr, xmin=0, xmax=(dmin-al[0])/xam, color='0.7')
self.ax1.legend(prop={'size':8}, numpoints=1, loc='best', fancybox=True)
def analyse(self):
pdbt = PDBTools()
self._bond_lengths = []
for f in self._pdbs:
om, res = pdbt.get_bond_lengths(str(f))
self._bond_lengths.append(res)
combined = {}
for ty in self._bond_lengths[0].keys():
combined[ty] = {}
for pid,p in enumerate(self._bond_lengths):
for rid,r in p[ty].iteritems():
if not rid in combined[ty]:
combined[ty][rid] = {}
if type(r) == type({}):
for bl,v in r.iteritems():
#print pid, ty, rid, bl, v
if not bl in combined[ty][rid]:
combined[ty][rid][bl] = [[v[0]], [v[1]], [v[2]]]
else:
for i in range(3):
combined[ty][rid][bl][i].append(v[i])
self._all_data = dict(combined)
self._averaged = {}
for tid,res in combined.iteritems():
self._averaged[tid] = {}
for rid,r in res.iteritems():
if not rid in self._averaged[tid]:
self._averaged[tid][rid] = {}
for n,bl in r.iteritems():
tmp = []
for i in range(3):
tmp.append(self._stat(bl[i]))
self._averaged[tid][rid][n] = tmp
self._residue_types = []
self.res_type.Clear()
for k in sorted(self._averaged.keys()):
if k != 'avg' and len(self._averaged[k]) > 0:
self.res_type.Append(self._rtypes[[ x.lower() for x in self._rtypess].index(k)])
self._residue_types.append(k)
def __init__(self, nb):
Tab.__init__(self, nb)
self._pdbt = PDBTools()
self._res_size = (200,170)
self._to_save = []
self.fig = Figure((5.0, 4.0), dpi=100)
col = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BACKGROUND)
self.fig.patch.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.canvas = FigCanvas(self, -1, self.fig)
self.res = wx.StaticBitmap(self, size=self._res_size)
self.res.SetBitmap(wx.EmptyImage(self._res_size[0], self._res_size[1]).ConvertToBitmap())
self._rtypes = ['Aspartate', 'Glutamate', 'Histidine', 'Arginine']
self._rtypess = ['Asp', 'Glu', 'His', 'Arg']
self.ax1 = self.fig.add_subplot(111)
self.ax1.set_position([0.10,0.153,0.80,0.81])
#self.ax1.set_frame_on(False)
[i.set_linewidth(0.5) for i in self.ax1.spines.itervalues()]
self.ax2 = self.ax1.twinx()
self.ax2.set_position([0.10,0.153,0.80,0.81])
self.ax1.tick_params(labelsize=8)
self.ax2.tick_params(labelsize=8)
self._highlight = -2
self._bond_lengths = ''
self._std_devs = ''
self._residue_selection = []
self._chain_lookup = {}
self._residue_type = 0
self._residues = {'asp': {}, 'glu': {}, 'his': {}, 'arg': {}}
self._omitted = {'asp': [], 'glu': [], 'his': [], 'arg': []}
self.omitted_title = wx.StaticBox( self, -1, "Omitted" )
self.omitted_sizer = wx.StaticBoxSizer( self.omitted_title, wx.HORIZONTAL)
self.selected_title = wx.StaticBox( self, -1, "Displayed" )
self.selected_sizer = wx.StaticBoxSizer( self.selected_title, wx.HORIZONTAL)
self.residue_info_title = wx.StaticBox( self, -1, "Residue Info: " )
self.residue_info_sizer = wx.StaticBoxSizer( self.residue_info_title, wx.VERTICAL)
#self.residue_info = wx.FlexGridSizer(rows=0, cols=2, vgap=5, hgap=5)
#self.residue_info.Add(wx.StaticText(self, -1, 'D(C-O)'))
#self._dco = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._dco)
#self.residue_info.Add(wx.StaticText(self, -1, 'S(D(C-O))'))
#self._sdco = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._sdco)
#self.residue_info.Add(wx.StaticText(self, -1, 'Level'))
#self._lev = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._lev)
#self.residue_info_sizer.Add(self.residue_info, 0)
self.residue_info_sizer.Add(self.res, 0)
self.residue_sel = wx.ListBox(self, 26, wx.DefaultPosition, (70, 80), [], wx.LB_MULTIPLE)
self.residue_sel.Bind(wx.EVT_LISTBOX, self._update_sel)
self.omitted_res = wx.ListBox(self, 26, wx.DefaultPosition, (70, 80), [], wx.LB_SINGLE)
self.omitted_res.Bind(wx.EVT_LISTBOX, self._goto_omitted)
self.data_box = wx.BoxSizer(wx.HORIZONTAL)
self.data_box.Add(wx.StaticText(self, -1, 'Residue Type'), 0, wx.EXPAND|wx.ALL, 5)
self.res_type = wx.ComboBox(self, -1, choices=[], style=wx.CB_READONLY)
self.res_type.Bind(wx.EVT_COMBOBOX, self._set_residue_type)
self.data_box.Add(self.res_type, 0, wx.EXPAND|wx.ALL, 5)
self.omitted_sizer.Add(self.omitted_res, 1, wx.EXPAND|wx.ALL, 0)
self.selected_sizer.Add(self.residue_sel, 1, wx.EXPAND|wx.ALL, 0)
self.ressel_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.ressel_sizer.Add(self.omitted_sizer, 1, wx.EXPAND|wx.ALL, 5)
self.ressel_sizer.Add(self.selected_sizer, 1, wx.EXPAND|wx.ALL, 5)
lig = metallicbutton.MetallicButton(self, -1, 'Ligands', '', bitmaps.fetch_icon_bitmap('actions', 'viewmag', scale=(16,16)), size=(75, 25))
save = metallicbutton.MetallicButton(self, -1, 'Figure', '', bitmaps.fetch_icon_bitmap('actions', 'save_all', scale=(16,16)), size=(65, 25))
tab = metallicbutton.MetallicButton(self, -1, 'Data', '', bitmaps.fetch_icon_bitmap('actions', 'save_all', scale=(16,16)), size=(65, 25))
self.Bind(wx.EVT_BUTTON, self._view_ligands, lig)
self.Bind(wx.EVT_BUTTON, self._save_figure, save)
self.Bind(wx.EVT_BUTTON, self._save_data, tab)
self.button_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.button_sizer.Add(save, 0, wx.LEFT, 5)
self.button_sizer.Add(tab, 0, wx.LEFT, 5)
self.button_sizer.Add(lig, 0, wx.LEFT, 5)
self.residue_box = wx.BoxSizer(wx.VERTICAL)
self.residue_box.Add(self.data_box, 0)
self.residue_box.Add(self.residue_info_sizer, 0, wx.EXPAND, 10)
self.residue_box.Add(self.ressel_sizer, 0)
self.residue_box.Add(self.button_sizer, 0)
self.main = wx.BoxSizer(wx.HORIZONTAL)
self.main.Add(self.residue_box, 1, wx.EXPAND|wx.ALL, 5)
self.averages = wx.StaticText(self, -1, '', style=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.bottom_sizer = wx.BoxSizer(wx.HORIZONTAL)
#self.bottom_sizer.Add(self.button_sizer, 0)
self.bottom_sizer.Add(self.averages, 1, wx.EXPAND)
self.canvas_sizer = wx.BoxSizer(wx.VERTICAL)
self.canvas_sizer.Add(self.canvas, 1, wx.EXPAND|wx.ALL)
self.canvas_sizer.Add(self.bottom_sizer, 0, wx.EXPAND)
self.main.Add(self.canvas_sizer, 3, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self.main)
self.main.Fit(self)
self.canvas.mpl_connect('button_press_event', self._on_click)
self.canvas.mpl_connect('pick_event', self._show_series)
class BondLengths(Tab):
def __init__(self, nb):
Tab.__init__(self, nb)
self._pdbt = PDBTools()
self._res_size = (200,170)
self._to_save = []
self.fig = Figure((5.0, 4.0), dpi=100)
col = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BACKGROUND)
self.fig.patch.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.canvas = FigCanvas(self, -1, self.fig)
self.res = wx.StaticBitmap(self, size=self._res_size)
self.res.SetBitmap(wx.EmptyImage(self._res_size[0], self._res_size[1]).ConvertToBitmap())
self._rtypes = ['Aspartate', 'Glutamate', 'Histidine', 'Arginine']
self._rtypess = ['Asp', 'Glu', 'His', 'Arg']
self.ax1 = self.fig.add_subplot(111)
self.ax1.set_position([0.10,0.153,0.80,0.81])
#self.ax1.set_frame_on(False)
[i.set_linewidth(0.5) for i in self.ax1.spines.itervalues()]
self.ax2 = self.ax1.twinx()
self.ax2.set_position([0.10,0.153,0.80,0.81])
self.ax1.tick_params(labelsize=8)
self.ax2.tick_params(labelsize=8)
self._highlight = -2
self._bond_lengths = ''
self._std_devs = ''
self._residue_selection = []
self._chain_lookup = {}
self._residue_type = 0
self._residues = {'asp': {}, 'glu': {}, 'his': {}, 'arg': {}}
self._omitted = {'asp': [], 'glu': [], 'his': [], 'arg': []}
self.omitted_title = wx.StaticBox( self, -1, "Omitted" )
self.omitted_sizer = wx.StaticBoxSizer( self.omitted_title, wx.HORIZONTAL)
self.selected_title = wx.StaticBox( self, -1, "Displayed" )
self.selected_sizer = wx.StaticBoxSizer( self.selected_title, wx.HORIZONTAL)
self.residue_info_title = wx.StaticBox( self, -1, "Residue Info: " )
self.residue_info_sizer = wx.StaticBoxSizer( self.residue_info_title, wx.VERTICAL)
#self.residue_info = wx.FlexGridSizer(rows=0, cols=2, vgap=5, hgap=5)
#self.residue_info.Add(wx.StaticText(self, -1, 'D(C-O)'))
#self._dco = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._dco)
#self.residue_info.Add(wx.StaticText(self, -1, 'S(D(C-O))'))
#self._sdco = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._sdco)
#self.residue_info.Add(wx.StaticText(self, -1, 'Level'))
#self._lev = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._lev)
#self.residue_info_sizer.Add(self.residue_info, 0)
self.residue_info_sizer.Add(self.res, 0)
self.residue_sel = wx.ListBox(self, 26, wx.DefaultPosition, (70, 80), [], wx.LB_MULTIPLE)
self.residue_sel.Bind(wx.EVT_LISTBOX, self._update_sel)
self.omitted_res = wx.ListBox(self, 26, wx.DefaultPosition, (70, 80), [], wx.LB_SINGLE)
self.omitted_res.Bind(wx.EVT_LISTBOX, self._goto_omitted)
self.data_box = wx.BoxSizer(wx.HORIZONTAL)
self.data_box.Add(wx.StaticText(self, -1, 'Residue Type'), 0, wx.EXPAND|wx.ALL, 5)
self.res_type = wx.ComboBox(self, -1, choices=[], style=wx.CB_READONLY)
self.res_type.Bind(wx.EVT_COMBOBOX, self._set_residue_type)
self.data_box.Add(self.res_type, 0, wx.EXPAND|wx.ALL, 5)
self.omitted_sizer.Add(self.omitted_res, 1, wx.EXPAND|wx.ALL, 0)
self.selected_sizer.Add(self.residue_sel, 1, wx.EXPAND|wx.ALL, 0)
self.ressel_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.ressel_sizer.Add(self.omitted_sizer, 1, wx.EXPAND|wx.ALL, 5)
self.ressel_sizer.Add(self.selected_sizer, 1, wx.EXPAND|wx.ALL, 5)
lig = metallicbutton.MetallicButton(self, -1, 'Ligands', '', bitmaps.fetch_icon_bitmap('actions', 'viewmag', scale=(16,16)), size=(75, 25))
save = metallicbutton.MetallicButton(self, -1, 'Figure', '', bitmaps.fetch_icon_bitmap('actions', 'save_all', scale=(16,16)), size=(65, 25))
tab = metallicbutton.MetallicButton(self, -1, 'Data', '', bitmaps.fetch_icon_bitmap('actions', 'save_all', scale=(16,16)), size=(65, 25))
self.Bind(wx.EVT_BUTTON, self._view_ligands, lig)
self.Bind(wx.EVT_BUTTON, self._save_figure, save)
self.Bind(wx.EVT_BUTTON, self._save_data, tab)
self.button_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.button_sizer.Add(save, 0, wx.LEFT, 5)
self.button_sizer.Add(tab, 0, wx.LEFT, 5)
self.button_sizer.Add(lig, 0, wx.LEFT, 5)
self.residue_box = wx.BoxSizer(wx.VERTICAL)
self.residue_box.Add(self.data_box, 0)
self.residue_box.Add(self.residue_info_sizer, 0, wx.EXPAND, 10)
self.residue_box.Add(self.ressel_sizer, 0)
self.residue_box.Add(self.button_sizer, 0)
self.main = wx.BoxSizer(wx.HORIZONTAL)
self.main.Add(self.residue_box, 1, wx.EXPAND|wx.ALL, 5)
self.averages = wx.StaticText(self, -1, '', style=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.bottom_sizer = wx.BoxSizer(wx.HORIZONTAL)
#self.bottom_sizer.Add(self.button_sizer, 0)
self.bottom_sizer.Add(self.averages, 1, wx.EXPAND)
self.canvas_sizer = wx.BoxSizer(wx.VERTICAL)
self.canvas_sizer.Add(self.canvas, 1, wx.EXPAND|wx.ALL)
self.canvas_sizer.Add(self.bottom_sizer, 0, wx.EXPAND)
self.main.Add(self.canvas_sizer, 3, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self.main)
self.main.Fit(self)
self.canvas.mpl_connect('button_press_event', self._on_click)
self.canvas.mpl_connect('pick_event', self._show_series)
def residues(self):
return self._residues
def _save_data(self, e):
dlg = wx.FileDialog(self, "Save Data as CSV", os.getcwd(), "", "*.csv", wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
out = open(path, 'w')
for l in self._to_save:
print >> out, ','.join(map(str, l))
out.close()
dlg.Destroy()
def _view_ligands(self, event):
if self._bond_lengths is not None:
frame = Ligand(self._bond_lengths, self._bond_lengths.replace('_start.pdb', '').replace(self._project.root(), ''), stdevs=self._std_devs)
frame.Show(True)
def load_refinement(self, ref, type):
if type == FULL_MATRIX:
self._bond_lengths = ref.replace('.dat', '_start.pdb')
self._std_devs = ref.replace('.dat', '.cif')
else:
self._bond_lengths = ref.replace('.dat', '.pdb')
self.analyse()
if os.path.exists(self._bond_lengths):
self._chain_lookup = self._pdbt.get_chains(self._bond_lengths)
self.res_type.Clear()
for t in sorted(self._residues.keys()):
if t != 'avg':
if len(self._residues[t].keys()) > 0:
self.res_type.Append(self._rtypes[[x.lower() for x in self._rtypess].index(t)])
self.res_type.SetSelection(0)
self._set_residue_type('')
self.draw()
def refresh(self):
pass
def _save_figure(self, event):
dlg = wx.FileDialog(self, "Save Image", os.getcwd(), "", "*.png", wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
self.fig.savefig(path, dpi=300, transparent=True)
dlg.Destroy()
def _update_sel(self, event):
t = self._rtypess[self._residue_type].lower()
x = self._residues[t].keys()
x.sort()
n = list(self.residue_sel.GetSelections())
n.sort()
self._residue_selection = [ x[i] for i in n ]
self.draw()
def _set_data(self, new = False):
#t, stdevs = self._get_inputs('cif')
#std = self._data_widgets[1].GetCurrentSelection()
#if std < len(stdevs) and std > -1:
# if stdevs[std] != self._std_devs:
# self._std_devs = stdevs[std]
# new = True
if new:
self.analyse()
self.res_type.Clear()
for t in sorted(self._residues.keys()):
if t != 'avg':
if len(self._residues[t].keys()) > 0:
self.res_type.Append(self._rtypes[[x.lower() for x in self._rtypess].index(t)])
self.res_type.SetSelection(0)
self._set_residue_type('')
self.draw()
def _set_residue_type(self, event):
self._residue_type = self._rtypes.index(self.res_type.GetValue())
self._update_lists()
self._highlight = -2
self.draw()
self.res_im = wx.Image(self.s.proot + 'Resources/gui_resources/'+self._rtypess[self._residue_type].lower()+'.png', wx.BITMAP_TYPE_PNG).Scale(self._res_size[0], self._res_size[1]).ConvertToBitmap()
self.res.SetBitmap(self.res_im)
#if 'avg' in self._residues:
#sn = self._rtypess[self._residue_type].lower()
#if sn in self._residues['avg']:
# s = self._residues['avg'][sn]
# self._values[3].SetLabel(str(round(s, 2)))
#self._values[4].SetLabel(str(round(self._residues['avg']['b'], 2)))
def _show_residue(self):
if self._highlight == -2:
return
t = self._rtypess[self._residue_type].lower()
tu = self._rtypess[self._residue_type]
r = self._residues[t][self._residue_selection[self._highlight]]
rid = self._residue_selection[self._highlight]
self.residue_info_title.SetLabel('Residue Info: ' + tu + '-' + str(rid))
self.res_im = wx.Image(self.s.proot + 'Resources/gui_resources/'+self._rtypess[self._residue_type].lower()+'.png', wx.BITMAP_TYPE_PNG).Scale(self._res_size[0], self._res_size[1]).ConvertToBitmap()
memDC = wx.MemoryDC()
#memDC.SetTextForeground((0,0,0));
memDC.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.NORMAL) )
memDC.SelectObject(self.res_im)
labels = {0: [[1,115,10,20],[2,5,85,95]],
1: [[1,115,10,20],[2,5,85,95]],
2: [[1,80,8,20],[2,0,132,142],[3,5,40,50],[4,130,138,148],[5,147,90,100]],
3: [[1,115,135,145],[2,42,65,75],[3,70,2,12]]}
temp1 = '%.1f' if self._residue_type == 2 else '%.3f'
temp2 = '%.1f+%.1f' if self._residue_type == 2 else '%.3f+%.3f'
for l in labels[self._residue_type]:
if len(r[l[0]]) > 3:
str1 = temp2 % (r[l[0]][0], r[l[0]][3])
else:
str1 = temp1 % r[l[0]][0]
memDC.DrawText(str1, l[1], l[2])
memDC.DrawText('(' + '%.1f' % r[l[0]][2] + ')', l[1], l[3])
if 'r' in r.keys():
memDC.DrawText('Level: %.2f' % r['r'][2], 5, 155)
memDC.SelectObject(wx.NullBitmap)
self.res.SetBitmap(self.res_im)
#if 'r' in r.keys():
#self._dco.SetLabel(str(round(r['r'][0],3)))
#self._sdco.SetLabel(str(round(r['r'][1],3)))
#self._lev.SetLabel(str(round(r['r'][2],2)))
#else:
#self._dco.SetLabel('')
#self._sdco.SetLabel('')
#self._lev.SetLabel('')
atoms = ['CG', 'CD', 'CG', 'CZ']
self._coot_client.centre_residue(self._chain_lookup[rid], rid, atoms[self._residue_type])
def _goto_omitted(self, event):
selected = self._omitted[self._rtypess[self._residue_type].lower()][self.omitted_res.GetSelections()[0]]
self._coot_client.centre_residue(selected, 'CA')
def _on_click(self,event):
if event.xdata:
id = int(round(event.xdata, 0))
if id < len(self._residue_selection) and id > -1:
self._highlight = id
else:
self._highlight = -2
else:
self._highlight = -2
h = self._highlight
self._highlight_span.set_xy(([h-0.5, 0],[h-0.5, 1],[h+0.5, 1],[h+0.5, 0],[h-0.5, 0]))
self.canvas.draw()
self._show_residue()
def _get_inputs(self, type='res'):
inputs = []
files = []
for f in os.listdir(self._project.root()):
m = re.match('(\d+)_', f)
if m:
res = glob.glob(self._project.root() + '/' + f + '/*.' + type)
if len(res) > 0:
if res[0].find('.fcf.cif') == -1:
inputs.append(f)
files.append(res[0])
return inputs, files
def analyse(self):
self._highlight = -2
self._omitted, self._residues = self._pdbt.get_bond_lengths(self._bond_lengths)
if os.path.exists(self._std_devs):
devs = open(self._std_devs)
asp_re = re.compile(r'CG_(\d+) OD(1|2)_\1 (\d+\.?\d+)\((\d+)\)')
glu_re = re.compile(r'CD_(\d+) OE(1|2)_\1 (\d+\.?\d+)\((\d+)\)')
his_re = [re.compile(r'CG_(\d+) CD2_\1 NE2_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'ND1_(\d+) CE1_\1 NE2_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'CE1_(\d+) NE2_\1 CD2_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'CG_(\d+) ND1_\1 CE1_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'CD2_(\d+) CG_\1 ND1_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'NE2_(\d+) CD2_\1 CG_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'NE2_(\d+) CE1_\1 ND1_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'CD2_(\d+) NE2_\1 CE1_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'CE1_(\d+) ND1_\1 CG_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'ND1_(\d+) CG_\1 CD2_\1 (\d+\.?\d+)\((\d+)\)'),
]
arg_re = [re.compile(r'CZ_(\d+) NH2_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'CZ_(\d+) NE_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'CZ_(\d+) NH1_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'NH2_(\d+) CZ_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'NE_(\d+) CZ_\1 (\d+\.?\d+)\((\d+)\)'),
re.compile(r'NH1_(\d+) CZ_\1 (\d+\.?\d+)\((\d+)\)')
]
for s in devs:
for t,rex in {'asp': asp_re, 'glu': glu_re}.items():
a = rex.match(s)
if a:
if int(a.group(1)) in self._residues[t]:
if len(self._residues[t][int(a.group(1))][int(a.group(2))]) < 4:
d = pow(10, len((a.group(3).split('.'))[1]))
self._residues[t][int(a.group(1))][int(a.group(2))].append(float(a.group(4))/d)
for id,rex in enumerate(his_re):
a = rex.match(s)
if a:
if int(a.group(1)) in self._residues['his']:
if len(a.group(2).split('.')) > 1:
d = pow(10, len((a.group(2).split('.'))[1]))
else:
d = 1
self._residues['his'][int(a.group(1))][(id%5)+1].append(float(a.group(3))/d)
for id,rex in enumerate(arg_re):
a = rex.match(s)
if a:
if int(a.group(1)) in self._residues['arg']:
d = pow(10, len((a.group(2).split('.'))[1]))
self._residues['arg'][int(a.group(1))][(id%3)+1].append(float(a.group(3))/d)
devs.close()
for type in self._residues.keys():
std_arr = []
for res in self._residues[type]:
if type == 'asp'or type == 'glu' or type == 'his':
r = self._residues[type][res]
if len(r[1]) == 4 and len(r[2]) == 4:
std_arr.append(r[1][3])
std_arr.append(r[2][3])
delta = abs(r[1][0] - r[2][0])
sigdel = math.sqrt(pow(r[1][3],2)+pow(r[2][3],2))
siglev = delta/sigdel
bavg = (r[1][2]+r[2][2])/2
self._residues[type][res]['r'] = [delta, sigdel, siglev, r[1][1], bavg]
if len(std_arr) > 0:
self._residues['avg'][type] = sum(std_arr)/len(std_arr)
else:
self._residues['avg'][type] = 0
self._update_lists()
self._show_residue()
def _update_lists(self):
t = self._rtypess[self._residue_type].lower()
tu = self._rtypess[self._residue_type]
x = self._residues[t].keys()
x.sort()
self._residue_selection = [ k for k in x ]
self.omitted_res.Clear()
for i in range(len(self._omitted[t])):
self.omitted_res.Append(tu + '-' + str(self._omitted[t][i]))
self.residue_sel.Clear()
all = self._residues[t].keys()
all.sort()
for id,i in enumerate(all):
self.residue_sel.Append(tu + '-' + str(i))
self.residue_sel.SetSelection(id, True)
def _show_series(self, event):
legline = event.artist
ol = self.seried[legline]
if type(ol) == type(()):
for o in ol:
o.set_visible(not o.get_visible())
else:
ol.set_visible(not ol.get_visible())
self.canvas.draw()
def draw(self):
self.ax1.cla()
self.ax2.cla()
self.series = []
self.ax2.set_ylabel('B Factor $(\AA^2)$', fontsize=9)
t = self._rtypess[self._residue_type].lower()
tu = self._rtypess[self._residue_type]
x = self._residue_selection
xs = [ tu + '-' + str(k) for k in x ]
xa = range(len(self._residue_selection))
l1 = [self._residues[t][k][1][0] for k in x ]
l2 = [self._residues[t][k][2][0] for k in x ]
if len(x) > 0:
if len(self._residues[t][k][1]) == 4:
el1 = [self._residues[t][k][1][3] for k in x ]
else:
el1 = [ 0 for k in x ]
if len(self._residues[t][k][2]) == 4:
el2 = [self._residues[t][k][2][3] for k in x ]
else:
el2 = [ 0 for k in x ]
b1 = [self._residues[t][k][1][2] for k in x ]
b2 = [self._residues[t][k][2][2] for k in x ]
if self._residue_type == 0 or self._residue_type == 1:
dg = 'C-O$\gamma$' if self._residue_type == 0 else 'C-O$\delta$'
self.ax1.errorbar(xa, l1, yerr=el1, fmt='ro', label=dg+'1')
self.ax1.errorbar(xa, l2, yerr=el2, fmt='bo', label=dg+'2')
self.ax2.plot(xa, b1, '^', label='B('+dg+'1)', color='#FF6666'),
self.ax2.plot(xa, b2, '^', label='B('+dg+'2)', color='#3399FF')
self.ax1.axhline(y=1.21, color='0.7')
self.ax1.axhline(y=1.31, color='0.7')
self.ax1.axhspan(1.327, 1.293, alpha=0.6, color='0.9')
self.ax1.axhspan(1.194, 1.226, alpha=0.6, color='0.9')
self.ax1.set_ylim(min(l1+l2+[1.2])-0.2, max(l1+l2+[1.32])+0.05)
self.ax1.set_ylabel('C-O $(\AA)$', fontsize=9)
self._to_save = [['Residue', 'C-OD1', 'ESDS(C-OD1)', 'B(C-OD1)', 'C-OD2', 'ESDS(C-OD2)', 'B(C-OD2)', 'D(C-O)', 'S(D(C-O)', 'Level']]
for i,k in enumerate(x):
diff = abs(l2[i]-l1[i])
sig = math.sqrt(math.pow(el1[i],2) + math.pow(el1[i],2))
if sum(el1) == 0 and sum(el2) == 0:
self._to_save.append([k, l1[i], 'N/A', b1[i], l2[i], 'N/A', b2[i], diff, 'N/A', 'N/A'])
else:
self._to_save.append([k, l1[i], el1[i], b1[i], l2[i], el2[i], b2[i], diff, sig, diff/sig])
# his CG CD2 NE2, ND1 CE1 NE2
elif self._residue_type == 2:
self.ax1.errorbar(xa, l1, yerr=el1, fmt='ro', label='CG-CD2-NE2')
self.ax1.errorbar(xa, l2, yerr=el2, fmt='bo', label='ND1-CE1-NE2')
l3 = [self._residues[t][k][3][0] for k in x ]
b3 = [self._residues[t][k][3][2] for k in x ]
l4 = [self._residues[t][k][4][0] for k in x ]
b4 = [self._residues[t][k][4][2] for k in x ]
l5 = [self._residues[t][k][5][0] for k in x ]
b5 = [self._residues[t][k][5][2] for k in x ]
if len(self._residues[t][k][3]) == 4:
el3 = [self._residues[t][k][3][3] for k in x ]
else:
el3 = [ 0 for k in x ]
if len(self._residues[t][k][4]) == 4:
el4 = [self._residues[t][k][5][3] for k in x ]
else:
el4 = [ 0 for k in x ]
if len(self._residues[t][k][5]) == 4:
el5 = [self._residues[t][k][5][3] for k in x ]
else:
el5 = [ 0 for k in x ]
self.ax1.errorbar(xa, l3, yerr=el3, fmt='go', label='CD2-NE2-CE1')
self.ax1.errorbar(xa, l4, yerr=el4, fmt='co', label='CE1-ND1-CG')
self.ax1.errorbar(xa, l5, yerr=el5, fmt='mo', label='CD2-CG-ND1')
self.ax2.plot(xa, b1, '^', label='B(CG-CD2-NE2)', color='#FF6666')
self.ax2.plot(xa, b2, '^', label='B(ND1-CE1-NE2)', color='#3399FF')
self.ax2.plot(xa, b3, '^', label='B(CD2-NE2-CE2)', color='#99FF99')
self.ax2.plot(xa, b4, 'c^', label='B(CE1-ND1-CG')
self.ax2.plot(xa, b5, 'm^', label='B(CD2-CG-ND1)')
self.ax1.axhline(y=111.2, color='0.7')
self.ax1.axhline(y=109.3, color='0.7')
self.ax1.axhline(y=107.5, color='0.7')
self.ax1.axhline(y=107.2, color='0.7')
self.ax1.set_ylim(95, 115)
self.ax1.set_ylabel('Angle $(^\circ)$', fontsize=9)
angles = ['CG-CD2-NE2', 'ND1-CE1-NE2', 'CD2-NE2-CE1', 'CE1-ND1-CG', 'CD2-CG-ND1']
cols = [ [ n, 'ESDS('+n+')', 'B('+n+')'] for n in angles ]
self._to_save = [['Residue', 'D(ang)', 'S(D(ang))', 'Level']]
self._to_save[0][1:1] = cols
for i,k in enumerate(xs):
diff = abs(l2[i]-l1[i])
sig = math.sqrt(math.pow(el1[i],2) + math.pow(el1[i],2))
if sum(el1) == 0 and sum(el2) == 0:
self._to_save.append([k, l1[i], 'N/A', b1[i], l2[i], 'N/A', b2[i], l3[i], 'N/A', b3[i], l4[i], 'N/A', b4[i], l5[i], 'N/A', b5[i], diff, 'N/A', 'N/A'])
else:
self._to_save.append([k, l1[i], el1[i], b1[i], l2[i], el2[i], b2[i], l3[i], el3[i], b3[i], l4[i], el4[i], b4[i], l5[i], el5[i], b5[i], diff, sig, diff/sig])
# arg CZ NH2, CZ NE, CZ NH1, CD NE?
elif self._residue_type == 3:
l3 = [self._residues[t][k][3][0] for k in x ]
b3 = [self._residues[t][k][3][2] for k in x ]
if len(self._residues[t][k][3]) == 4:
el3 = [self._residues[t][k][3][3] for k in x ]
else:
el3 = [ 0 for k in x ]
self.ax1.errorbar(xa, l1, yerr=el1, fmt='bo', label='CZ-NH2')
self.ax1.errorbar(xa, l2, yerr=el2, fmt='ro', label='CZ-NE')
self.ax1.errorbar(xa, l3, yerr=el3, fmt='go', label='CZ-NH1')
self.ax2.plot(xa, b1, '^', label='B(CZ-NH2)', color='#3399FF')
self.ax2.plot(xa, b2, '^', label='B(CZ-NE)', color='#FF6666')
self.ax2.plot(xa, b3, '^', label='B(CZ-NH1)', color='#99FF99')
self.ax1.set_ylim(min(l1+l2)-0.2, max(l1+l2)+0.05)
self.ax1.set_ylabel('CZ-X $(\AA)$', fontsize=9)
self.ax1.axhline(y=1.326, color='0.7')
self.ax1.axhline(y=1.41, color='0.7')
self._to_save = [['Residue', 'CZ-NH2', 'ESDS(CZ-NH2)', 'B(CZ-NH2)', 'CZ-NE', 'ESDS(CZ-NE)', 'B(CZ-NE)', 'CZ-NH1', 'ESDS(CCZ-NH1)', 'B(CZ-NH1)', 'D(CZ-NH2 - CZ-NE)', 'S(D(CZ-NH2 - CZ-NE))', 'Level']]
for i,k in enumerate(xs):
diff = abs(l2[i]-l1[i])
sig = math.sqrt(math.pow(el1[i],2) + math.pow(el1[i],2))
if sum(el1) == 0 and sum(el2) == 0:
self._to_save.append([k, l1[i], 'N/A', b1[i], l2[i], 'N/A', b2[i], l3[i], 'N/A', b3[i], diff, 'N/A', 'N/A'])
else:
self._to_save.append([k, l1[i], el1[i], b1[i], l2[i], el2[i], b2[i], l3[i], el3[i], b3[i], diff, sig, diff/sig])
if sum(el1) == 0 and sum(el2) == 0:
txt = 'Average B factor: %.1f' % (self._residues['avg']['pro'])
else:
txt = 'Average B factor: %.1f, Average sigma: %.3f' % (self._residues['avg']['pro'],sum(el1+el2)/(len(el1)+len(el2)))
self.averages.SetLabel(txt)
self.ax2.axhline(y=self._residues['avg']['pro'], color=(0.5,0.5,0), ls='--', label='B(avg)')
self.ax2.set_ylim(min(b1+b2)-2, max(b1+b2)+20)
self.ax2.set_xlim(-1, len(x))
self.ax1.set_xlim(-1, len(x))
self.ax1.set_xticks(xa)
self.ax1.set_xticklabels(xs, rotation='vertical', size=8)
self.ax1.tick_params(labelsize=8)
self.ax2.tick_params(labelsize=8)
#if self._highlight > -1:
self._highlight_span = self.ax1.axvspan(self._highlight-0.5, self._highlight+0.5, alpha=0.3, color='0.9')
handles, labels = self.ax1.get_legend_handles_labels()
handl = [ h[0] for h in handles ]
handt = [ (h[0],h[1][0], h[1][1], h[2][0]) for h in handles ]
handles2, labels2 = self.ax2.get_legend_handles_labels()
leg = self.ax2.legend(handl+handles2, labels+labels2, prop={'size':8}, numpoints=1, loc='best', fancybox=True)
leg.get_frame().set_alpha(0.5)
self.seried = {}
for legline, origline in zip(leg.get_lines(), handt+handles2):
legline.set_picker(5)
self.seried[legline] = origline
self.canvas.draw()