def __init__(self, parent, selections_list, *args, **configs):
self.selections_list = selections_list
PyMod_tool_window_qt.__init__(self, parent, *args, **configs)
# Builds a combobox for each PyMOL object to import.
self.sele_checkbox_list = []
for sele in selections_list:
checkbox = QtWidgets.QCheckBox(sele)
self.sele_checkbox_list.append(checkbox)
self.middle_formlayout.addRow(checkbox)
def build_protocol_middle_frame(self):
"""
Allow to choose between plotting all amino acids types or only a subset
of them.
"""
# Radioselect.
aa_select_choices = ("Use all amino acids", "Select amino acids types")
aa_select_choices_values = ["all", "single"]
self.aa_select_choices_dict = dict([
(k, v)
for (k, v) in zip(aa_select_choices, aa_select_choices_values)
])
self.aa_select_rds = PyMod_radioselect_qt(
label_text="Select Amino Acids", buttons=aa_select_choices)
self.aa_select_rds.setvalue(aa_select_choices[0])
self.aa_select_rds.buttons_dict[aa_select_choices[0]].clicked.connect(
self.hide_select_single_aa_frame)
self.aa_select_rds.buttons_dict[aa_select_choices[1]].clicked.connect(
self.show_select_single_aa_frame)
self.middle_formlayout.add_widget_to_align(self.aa_select_rds)
# Checkboxes for selecting single amino acids.
self.aa_select_grid_layout = QtWidgets.QGridLayout()
self.aa_select_rds.input.addLayout(self.aa_select_grid_layout)
self.aa_checkbutton = {}
self.aa_freq_dict = {}
self.aa_checkbutton_list = []
for i, aa in enumerate(prot_standard_one_letter):
# Get the number of aa in the sequence.
aa_freq = str(self.protocol.target_sequence.my_sequence).count(aa)
self.aa_freq_dict[aa] = aa_freq
# Build a checkbox for the aa.
checkbox = QtWidgets.QCheckBox(
pmsm.one2three(aa) + " (" + str(aa_freq) + ")")
checkbox.setEnabled(False)
self.aa_select_grid_layout.addWidget(checkbox, int(i % 10),
int(i / 10))
self.aa_checkbutton[aa] = checkbox
self.aa_checkbutton_list.append(checkbox)
self.aa_select_grid_layout.setAlignment(QtCore.Qt.AlignLeft)
self.middle_formlayout.set_input_widgets_width("auto", padding=40)
def __init__(self, widget, window=None, name='', _self=None):
if window:
window.setWindowTitle(name + ' - Volume Color Map Editor')
cmd = _self
layout = QtWidgets.QVBoxLayout()
widget.setLayout(layout)
widget.editor = VolumeEditorWidget(widget, name, _self)
layout.addWidget(widget.editor)
layout.setContentsMargins(5, 5, 5, 5)
get_colors_btn = QtWidgets.QPushButton("Get colors as script")
get_colors_btn.setAutoDefault(False)
get_colors_btn.clicked.connect(widget.editor.displayScript)
help_btn = QtWidgets.QPushButton("Help")
help_btn.setAutoDefault(False)
help_btn.clicked.connect(widget.editor.displayHelp)
reset_btn = QtWidgets.QPushButton("Reset Data Range")
reset_btn.setAutoDefault(False)
reset_btn.clicked.connect(widget.editor.reset)
widget.editor.update_cb = QtWidgets.QCheckBox(
"Update volume colors in real-time")
widget.editor.update_cb.setObjectName("volume_checkbox")
widget.editor.update_cb.setChecked(True)
widget.editor.update_cb.setMinimumWidth(30)
widget.editor.update_cb.toggled.connect(
widget.editor.toggleRealTimeUpdates)
button_layout = QtWidgets.QHBoxLayout()
button_layout.addWidget(get_colors_btn)
button_layout.addWidget(reset_btn)
button_layout.addWidget(help_btn)
button_layout.addStretch()
button_layout.addWidget(widget.editor.update_cb)
layout.addLayout(button_layout)
histogram = cmd.get_volume_histogram(name)
widget.editor.setHistogram(histogram)
colors = cmd.volume_color(name)
widget.editor.setColors(colors)
def add_plot(self, x_data, y_data,
label=None,
additional_data=None):
"""
Adds a plot to the pyqtgraph PlotWidget.
"""
# Check and prepare the data.
if len(x_data) != len(y_data):
raise ValueError(("The x series and the y series do not have the same"
" number of elements (%s and %s respectively)" % (len(x_data), len(y_data))))
if additional_data:
if not len(x_data) == len(additional_data):
raise ValueError(("The 'additional_data' series does not have the"
" same number of elements of the data to plot"
" (%s and %s respectively)" % (len(x_data), len(additional_data))))
_x_data, _y_data = self.remove_none(x_data, y_data)
# Add the plot to the PlotWidget.
plot_color = self.plot_colors[self.plot_color_index]
self.change_plot_color_index()
curve_pen = pyqtgraph.mkPen(width=2, color=plot_color) # Color and width of the curve.
plot_item = self.graphWidget.plot(_x_data, _y_data,
name=label,
connect="finite",
pen=curve_pen,
clickable=True)
plot_item._pymod_id = self.plot_count
plot_item.curve._pymod_id = self.plot_count
plot_item.curve.setClickable(True)
# plot_item.curve.sigClicked.connect(self.on_curve_click)
plot_item.sigClicked.connect(self.on_curve_click)
# Store information about the plot.
self.plot_items[self.plot_count] = {}
# The 'plot' key will store the pyqtgraph object for the plot.
self.plot_items[self.plot_count]["plot"] = plot_item
# The 'state' will be 1 if the plot is shown, and 0 it is hidden.
self.plot_items[self.plot_count]["state"] = 1
# Add a label.
if label is None:
label = "Plot %s" % self.plot_count
self.plot_items[self.plot_count]["label"] = label
# Data.
self.plot_items[self.plot_count]["x_data"] = x_data
self.plot_items[self.plot_count]["y_data"] = y_data
# Additional data.
self.plot_items[self.plot_count]["additional_data"] = additional_data
# Stores all the data in a single list.
for idx, (xi, yi) in enumerate(zip(x_data, y_data)):
if yi is not None:
self.all_points.append((xi, yi))
self.all_points_info.append((self.plot_count, idx))
# Add a checkbox in the controls frame. Used for showing/hiding the plot.
if self.use_controls:
plot_checkbox = QtWidgets.QCheckBox(label)
plot_checkbox.setStyleSheet(small_font_style)
plot_checkbox.setChecked(True)
plot_checkbox.clicked.connect(lambda a=None, i=self.plot_count: self.toggle_plot(i))
plot_color_label = QtWidgets.QLabel("---") # \u2796") # "\u25CF"
plot_color_label.setStyleSheet("color: %s; font-weight: bold" % plot_color)
self.controls_frame_layout.addWidget(plot_color_label, self.plot_count+1, 0, 1, 1)
self.controls_frame_layout.addWidget(plot_checkbox, self.plot_count+1, 1, 1, 1)
self.plot_items[self.plot_count]["checkbox"] = plot_checkbox
# Increase the plot counter.
self.plot_count += 1
def qtdialog():
dialog = QtWidgets.QDialog()
uifile = os.path.join(os.path.dirname(__file__), 'excelexporter.ui')
form = pymolqtutils.loadUi(uifile, dialog)
form._dialog = dialog
# pre-fill form with likely data
names = pymol.cmd.get_object_list()
names += ['(' + n + ')' for n in pymol.cmd.get_names('public_selections')]
form.input_sele.addItems(names)
checkboxes = {
'x': form.check_x,
'y': form.check_y,
'z': form.check_z,
}
prop_names = [
'model', 'segi', 'chain', 'resi', 'resv', 'resn', 'name', 'alt', 'b',
'q', 'elem', 'type', 'formal_charge', 'partial_charge', 'numeric_type',
'text_type', 'stereo', 'ID', 'rank', 'index', 'vdw', 'ss', 'color',
'reps', 'protons', 'state'
]
# user properties
p_set = set()
pymol.cmd.iterate('all',
'p_set_update(p)',
space={'p_set_update': p_set.update})
prop_names.extend('p.' + prop for prop in sorted(p_set))
ncols = 3
for i, prop in enumerate(prop_names):
check = QtWidgets.QCheckBox(prop, form.groupBox)
form.gridLayout.addWidget(check, i // ncols, i % ncols, 1, 1)
checkboxes[prop] = check
# add state properties to list
prop_names.extend('xyz')
for prop in ['chain', 'resi', 'resn', 'name']:
checkboxes[prop].setChecked(True)
@form.button_ok.clicked.connect
def _(*args):
props = [p for p in prop_names if checkboxes[p].isChecked()]
sele = form.input_sele.currentText()
statetext = form.input_state.checkedButton().text()
if statetext.startswith('current'):
state = -1
elif statetext.startswith('all'):
state = 0
else:
state = STATELESS
props = [p for p in props if p not in ['x', 'y', 'z']]
if not _check_xlwings():
return
with pymolqtutils.PopupOnException():
dumpexcel(sele, props, state)
form._dialog.show()
def display_blast_hits(self):
"""
This is used to display in the BLAST results window information for each
hit and a checkbutton to select it for importing it inside PyMod.
"""
# Shows the headers of the columns.
headers_font_style = "%s; color: %s; font-weight: bold" % (small_font_style, highlight_color)
self.blast_seq_label = QtWidgets.QLabel("Name")
self.blast_seq_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.blast_seq_label, 0, 0)
if not self.protocol.blast_version in hmmer_protocols_names:
evalue_header_text = "E-Value"
else:
evalue_header_text = "E-Value (c-Evalue)"
self.blast_e_val_label = QtWidgets.QLabel(evalue_header_text)
self.blast_e_val_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.blast_e_val_label, 0, 1)
if self.protocol.protocol_name != "hmmsearch":
self.blast_iden_label = QtWidgets.QLabel("Identity")
self.blast_iden_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.blast_iden_label, 0, 2)
self.query_span_label = QtWidgets.QLabel("Query span")
self.query_span_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.query_span_label, 0, 3)
self.subject_span_label = QtWidgets.QLabel("Subject span")
self.subject_span_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.subject_span_label, 0, 4)
# Displays in the results window the hsps found in the output file of the
# similarity search program.
self.blast_output_row = 1
self.sbjct_checkbuttons_list = [] # List containing the checkbutton widgets.
for hsp in self.protocol.hsp_list:
# Hit name and checkbox.
subject_name = self.protocol.get_subject_name(hsp)
hsp_checkbox = QtWidgets.QCheckBox(subject_name)
hsp_checkbox.setStyleSheet(small_font_style)
self.sbjct_checkbuttons_list.append(hsp_checkbox)
self.results_grid.addWidget(hsp_checkbox, self.blast_output_row, 0)
# E-value info.
if not self.protocol.blast_version in hmmer_protocols_names:
evalue_label_text = "%.2e" % (self.protocol.get_hsp_evalue(hsp))
else:
evalue_tuple = self.protocol.get_hsp_evalue(hsp)
evalue_label_text = "%.1e (%.1e)" % (evalue_tuple[0], evalue_tuple[1])
# evalue_label_text = "%.1e" % (evalue_tuple[0])
evalue_label = QtWidgets.QLabel(evalue_label_text)
evalue_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(evalue_label, self.blast_output_row, 1)
# HSP seqid info.
if self.protocol.protocol_name != "hmmsearch":
id_text = "%s/%s (%.1f%%)" % (hsp.pymod_info["identities"], int(hsp.pymod_info["matches"]), hsp.pymod_info["seqid"]*100)
identities_label = QtWidgets.QLabel(id_text)
identities_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(identities_label, self.blast_output_row, 2)
# Query span info.
span_info_text = "%s-%s (%.1f%%)" % (hsp.pymod_info["query_start"], hsp.pymod_info["query_end"], hsp.pymod_info["query_span"]*100)
span_info_label = QtWidgets.QLabel(span_info_text)
span_info_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(span_info_label, self.blast_output_row, 3)
# Subject span info.
hspan_info_text = "%s-%s" % (hsp.pymod_info["sbjct_start"], hsp.pymod_info["sbjct_end"])
hspan_info_label = QtWidgets.QLabel(hspan_info_text)
hspan_info_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(hspan_info_label, self.blast_output_row, 4)
self.blast_output_row += 1
def __init__(self, parent=None, app=None):
super(_BuilderPanel, self).__init__(parent)
self.setWindowTitle("Builder")
self.setObjectName("builder")
self.cmd = app.pymol.cmd
self.layout = QtWidgets.QVBoxLayout()
self.setLayout(self.layout)
self.buttons_layout = QtWidgets.QVBoxLayout()
self.tabs = QtWidgets.QTabWidget(self)
self.layout.setContentsMargins(5, 5, 5, 5);
self.layout.setSpacing(5);
self.layout.addWidget(self.tabs)
self.layout.addLayout(self.buttons_layout)
self.layout.addStretch()
self.fragments_layout = QtWidgets.QGridLayout()
self.fragments_layout.setContentsMargins(5, 5, 5, 5);
self.fragments_layout.setSpacing(5);
self.fragments_tab = QtWidgets.QWidget()
self.fragments_tab.setLayout(self.fragments_layout)
self.protein_layout = QtWidgets.QGridLayout()
self.protein_layout.setContentsMargins(5, 5, 5, 5);
self.protein_layout.setSpacing(5);
self.protein_tab = QtWidgets.QWidget()
self.protein_tab.setLayout(self.protein_layout)
self.tabs.addTab(self.fragments_tab, "Chemical")
self.tabs.addTab(self.protein_tab, "Protein")
self.getIcons()
buttons = [
[ ("H", "Hydrogen", lambda: self.replace("H", 1, 1, "Hydrogen")),
("C", "Carbon", lambda: self.replace("C", 4, 4, "Carbon")),
("N", "Nitrogen", lambda: self.replace("N", 4, 3, "Nitrogen")),
("O", "Oxygen", lambda: self.replace("O", 4, 2, "Oxygen")),
("P", "Phosphorus", lambda: self.replace("P",4,3, "Phosphorous")),
("S", "Sulfur", lambda: self.replace("S",2,2, "Sulfur")),
("F", "Fluorine", lambda: self.replace("F",1,1, "Fluorine")),
("Cl", "Chlorrine", lambda: self.replace("Cl",1,1, "Chlorine")),
("Br", "Bromine", lambda: self.replace("Br",1,1, "Bromine")),
("I", "Iodine", lambda: self.replace("I",1,1, "Iodine")),
("-CF3", "Trifluoromethane", lambda: self.replace("trifluoromethane",4,0, "trifluoro")),
("-OMe", "Methanol", lambda: self.replace("methanol",5,0, "methoxy")),
],
[ ("CH4", "Methyl", lambda: self.grow("methane",1,0,"methyl")),
("C=C", "Ethylene", lambda: self.grow("ethylene",4,0,"vinyl")),
("C#C", "Acetylene", lambda: self.grow("acetylene",2,0,"alkynl")),
("C#N", "Cyanide", lambda: self.grow("cyanide",2,0,"cyano")),
("C=O", "Aldehyde", lambda: self.grow("formaldehyde",2,0,"carbonyl",)),
("C=OO", "Formic Acid", lambda: self.grow("formic",4,0,"carboxyl")),
("C=ON", "C->N amide", lambda: self.grow("formamide",5,0,"C->N amide")),
("NC=O", "N->C amide", lambda: self.grow("formamide",3,1,"N->C amide")),
("S=O2", "Sulfone", lambda: self.grow("sulfone",3,1,"sulfonyl")),
("P=O3", "Phosphite", lambda: self.grow("phosphite",4,0,"phosphoryl")),
("N=O2", "Nitro", lambda: self.grow("nitro",3,0,"nitro")),
],
[
("#cyc3", "Cyclopropane", lambda: self.grow("cyclopropane",4,0,"cyclopropyl")),
("#cyc4", "Cyclobutane", lambda: self.grow("cyclobutane",4,0,"cyclobutyl")),
("#cyc5", "Cyclopentane", lambda: self.grow("cyclopentane",5,0,"cyclopentyl")),
("#cyc6", "Cyclohexane", lambda: self.grow("cyclohexane",7,0,"cyclohexyl")),
("#cyc7", "Cycloheptane", lambda: self.grow("cycloheptane",8,0,"cycloheptyl")),
("#aro5", "Cyclopentadiene", lambda: self.grow("cyclopentadiene",5,0,"cyclopentadienyl")),
("#aro6", "Benzene", lambda: self.grow("benzene",6,0,"phenyl")),
("#aro65", "Indane", lambda: self.grow("indane",12,0,"indanyl")),
("#aro66", "Napthylene", lambda: self.grow("napthylene",13,0,"napthyl")),
("#aro67", "Benzocycloheptane", lambda: self.grow("benzocycloheptane",13,0, "benzocycloheptyl")),
]
]
self.btn_icons = {}
requestsize = QtCore.QSize(48, 48)
for row, btn_row in enumerate(buttons):
for col, bb in enumerate(btn_row):
btn_label, btn_tooltip, btn_command = bb
btn = makeFragmentButton()
if btn_label.startswith('#'):
icons = self.icons[btn_label[1:]]
btn.setIcon(icons[0])
btn.setIconSize(icons[1].actualSize(requestsize))
self.btn_icons[btn] = icons
else:
btn.setText(btn_label)
btn.setToolTip(btn_tooltip)
btn.clicked.connect(btn_command)
self.fragments_layout.addWidget(btn, row, col)
buttons = [
[ 'Ace', 'Ala', 'Arg', 'Asn', 'Asp', 'Cys', 'Gln', 'Glu', 'Gly', 'His', 'Ile', 'Leu' ],
[ 'Lys', 'Met', 'Phe', 'Pro', 'Ser', 'Thr', 'Trp', 'Tyr', 'Val', 'NMe', 'NHH' ]
]
for row, btn_row in enumerate(buttons):
for col, btn_label in enumerate(btn_row):
btn = makeFragmentButton()
btn.setText(btn_label)
btn.setToolTip("Build %s residue" % btn_label)
res = btn_label.lower()
slot = lambda val=None, s=self,r=res: s.attach(r)
btn.clicked.connect(slot)
self.protein_layout.addWidget(btn, row, col)
lab = QtWidgets.QLabel('Secondary Structure:')
lab_cols = 3
self.ss_cbox = QtWidgets.QComboBox()
self.ss_cbox.addItem("Alpha Helix")
self.ss_cbox.addItem("Beta Sheet (Anti-Parallel)")
self.ss_cbox.addItem("Beta Sheet (Parallel)")
self.protein_layout.addWidget(lab, 2, 0, 1, lab_cols)
self.protein_layout.addWidget(self.ss_cbox, 2, lab_cols, 1, 4)
self.ss_cbox.currentIndexChanged[int].connect(self.ssIndexChanged)
buttons = [
[
( "@Atoms:", None, None),
( "Fix H", "Fix hydrogens on picked atoms", self.fixH),
( "Add H", "Add hydrogens to entire molecule", self.addH),
( "Invert", "Invert stereochemistry around pk1 (pk2 and pk3 will remain fixed)", self.invert),
( "Delete", "Remove atoms", self.removeAtom),
( "Clear", "Delete everything", self.clear),
( "@ Charge:", None, None),
( " +1 ", "Positive Charge", lambda: self.setCharge(1,"+1")),
( " 0 ", "Neutral Charge", lambda: self.setCharge(0,"neutral")),
( " -1 ", "Negative Charge", lambda: self.setCharge(-1,"-1")),
],
[
( "@Bonds:", None, None),
( "Create", "Create bond between pk1 and pk2", self.createBond),
( "Delete", "Delete bond between pk1 and pk2", self.deleteBond),
( "Cycle", "Cycle bond valence", self.cycleBond),
( " | ", "Create single bond", lambda: self.setOrder("1", "single")),
( " || ", "Create double bond", lambda: self.setOrder("2", "double")),
( " ||| ", "Create triple bond", lambda: self.setOrder("3", "triple")),
( "Arom", "Create aromatic bond", lambda: self.setOrder("4", "aromatic")),
( "@ Model:", None, None),
( "Clean", "Cleanup structure", self.clean),
( "Sculpt", "Molecular sculpting", self.sculpt),
( "Fix", "Fix atom positions", self.fix),
( "Rest", "Restrain atom positions", self.rest),
],
[
( "$El-stat", "Electrostatics term for 'Clean' action", "clean_electro_mode"),
( "@ ", None, None),
( "$Bumps", "Show VDW contacts during sculpting", "sculpt_vdw_vis_mode"),
( "@ ", None, None),
( "#Undo Enabled", "", "suspend_undo"),
( "Undo", "Undo last change", self.undo),
( "Redo", "Redo last change", self.redo),
]
]
for row, btn_row in enumerate(buttons):
btn_row_layout = QtWidgets.QHBoxLayout()
self.buttons_layout.addLayout(btn_row_layout)
for col, bb in enumerate(btn_row):
btn_label, btn_tooltip, btn_command = bb
if btn_label[0] == '@':
btn = QtWidgets.QLabel(btn_label[1:])
elif btn_label[0] in ('#', '$'):
btn = QtWidgets.QCheckBox(btn_label[1:])
setting = btn_command
value = self.cmd.get_setting_int(setting)
if btn_label[0] == '$':
btn.setChecked(bool(value))
@btn.toggled.connect
def _(checked, n=setting):
self.cmd.set(n, checked, quiet=0)
else:
btn.setChecked(not value)
@btn.toggled.connect
def _(checked, n=setting):
self.cmd.set(n, not checked, quiet=0)
else:
btn = makeFragmentButton()
btn.setText(btn_label)
btn.clicked.connect(btn_command)
if btn_tooltip:
btn.setToolTip(btn_tooltip)
btn_row_layout.addWidget(btn)
btn_row_layout.addStretch()
def display_hmmscan_hits(self):
"""
This is used to display in the HMMSCAN results window information for
each hit and a checkbutton to select it for importing it inside PyMod.
"""
#------------------------------------
# Shows the headers of the columns. -
#------------------------------------
headers_font_style = "%s; color: %s" % (small_font_style,
highlight_color)
headers_font_style = "%s; font-weight: bold" % (small_font_style)
self.hmmscan_seq_label = QtWidgets.QLabel("Name")
self.hmmscan_seq_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.hmmscan_seq_label, 0, 0)
self.description_label = QtWidgets.QLabel("Description")
self.description_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.description_label, 0, 1)
self.hmmscan_e_val_label = QtWidgets.QLabel("E-Value")
self.hmmscan_e_val_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.hmmscan_e_val_label, 0, 2)
self.query_span_label = QtWidgets.QLabel("Query span")
self.query_span_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.query_span_label, 0, 3)
self.hmm_span_label = QtWidgets.QLabel("HMM span")
self.hmm_span_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.hmm_span_label, 0, 4)
#----------------------
# Prepare the colors. -
#----------------------
self.color_palette_dec = domain_colors_ordered
# self.color_palette = [[j*255 for j in i[1]] for i in self.color_palette_dec]
self.color_palette_hex = [
convert_rgb_to_hex(i[1]) for i in self.color_palette_dec
]
color_idx = 0
for hit in self.protocol.parsed_res:
hit.update({
'dom_color': self.color_palette_dec[color_idx],
'dom_color_hex': self.color_palette_hex[color_idx]
})
color_idx += 1
if color_idx == len(self.color_palette_dec):
color_idx = 0
#---------------------------------------
# Show the hits in the results window. -
#---------------------------------------
# Keep track of the rows in the grid.
hmmscan_output_row = 1
# This is going to contain the list of values of each checkbutton.
self.color_square_lst = [] # all in a row
self.domain_check_states = [] # clustered
self.domain_widgets_dict = {}
domain_counter = 0
# Process all the hits. Eeach hit is a different HMM profile, that is, a
# different domain type.
for hit in self.protocol.parsed_res:
# Hit name.
hit_name_label = QtWidgets.QLabel(hit['id'])
hit_name_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(hit_name_label, hmmscan_output_row, 0)
# Hit description.
if 'desc' in hit:
descr_text = hit['desc'][:40] + '...' if len(
hit['desc']) > 41 else hit['desc']
else:
descr_text = '-'
hit_descr_label = QtWidgets.QLabel(descr_text)
hit_descr_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(hit_descr_label, hmmscan_output_row, 1)
# E-value info.
evalue_label = QtWidgets.QLabel(str(hit['evalue']))
evalue_label.setStyleSheet(
"%s; color: %s" %
(small_font_style,
hit['dom_color_hex'])) # results_row_options
self.results_grid.addWidget(evalue_label, hmmscan_output_row, 2)
hmmscan_output_row += 1
self.domain_check_states.append([])
for domain_hit in hit['location']:
domain_widgets = {"checkbox": None, "rect": None}
# Domain rectangle shown in the upper frame of the window.
domain_rect = self.add_domain_representation(hit, domain_hit)
domain_widgets["rect"] = domain_rect
# Checkbox for selection.
color_square = QtWidgets.QCheckBox(" ")
self.color_square_lst.append(color_square)
self.domain_check_states[-1].append(color_square)
color_square.clicked.connect(
lambda a=None, x=domain_counter: self.toggle_domain(x))
self.results_grid.addWidget(color_square, hmmscan_output_row,
0)
domain_widgets["checkbox"] = color_square
# Grahical representation of the domain in the query sequence.
graphics_view = self.create_little_canvas(hit, domain_hit)
self.results_grid.addWidget(graphics_view, hmmscan_output_row,
1)
# Individual E-value info.
hsp_ievalue_label = QtWidgets.QLabel(str(domain_hit['evalue']))
hsp_ievalue_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(hsp_ievalue_label,
hmmscan_output_row, 2)
# Query span info.
span_info_label = QtWidgets.QLabel(
str(domain_hit['start']) + ' - ' + str(domain_hit['end']))
span_info_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(span_info_label,
hmmscan_output_row, 3)
# HMM span info.
hspan_info_text = str(domain_hit['hmm_start']) + ' - ' + str(
domain_hit['hmm_end'])
hspan_info_label = QtWidgets.QLabel(hspan_info_text)
hspan_info_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(hspan_info_label,
hmmscan_output_row, 4)
hmmscan_output_row += 1
self.domain_widgets_dict[domain_counter] = domain_widgets
domain_counter += 1
def display_blast_hits(self):
"""
This is used to display in the BLAST results window information for each
hit and a checkbutton to select it for importing it inside PyMod.
"""
# Shows the headers of the columns.
headers_font_style = "%s; color: %s; font-weight: bold" % (
small_font_style, highlight_color)
self.blast_seq_label = QtWidgets.QLabel("Name")
self.blast_seq_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.blast_seq_label, 0, 0)
self.blast_e_val_label = QtWidgets.QLabel("E-Value")
self.blast_e_val_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.blast_e_val_label, 0, 1)
self.prob_val_label = QtWidgets.QLabel("Probability")
self.prob_val_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.prob_val_label, 0, 2)
self.blast_iden_label = QtWidgets.QLabel("Identity")
self.blast_iden_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.blast_iden_label, 0, 3)
self.query_span_label = QtWidgets.QLabel("Query span")
self.query_span_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.query_span_label, 0, 4)
self.subject_span_label = QtWidgets.QLabel("Template span")
self.subject_span_label.setStyleSheet(headers_font_style)
self.results_grid.addWidget(self.subject_span_label, 0, 5)
# Displays in the results window the hsps found in the output file of the
# similarity search program.
self.blast_output_row = 1
self.sbjct_checkbuttons_list = [
] # List containing the checkbutton widgets.
for hsp in self.protocol.hhr_results:
# Hit name and checkbox.
hsp_checkbox = QtWidgets.QCheckBox(
self.protocol.get_subject_name(hsp))
hsp_checkbox.setStyleSheet(small_font_style)
self.sbjct_checkbuttons_list.append(hsp_checkbox)
self.results_grid.addWidget(hsp_checkbox, self.blast_output_row, 0)
# E-value info.
evalue_label = QtWidgets.QLabel(
"%.2e" % (self.protocol.get_hsp_evalue(hsp)))
evalue_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(evalue_label, self.blast_output_row, 1)
# Probability.
probability_label = QtWidgets.QLabel(
str(self.protocol.get_prob_value(hsp)))
probability_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(probability_label,
self.blast_output_row, 2)
# Get alignment stats.
matches_count, identities_count = self.protocol.get_hsp_matches(
hsp)
seqid = identities_count / matches_count
# Sequence identity.
identities_label = QtWidgets.QLabel("{}/{} ({:.1f}%)".format(
identities_count, matches_count, seqid * 100))
identities_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(identities_label,
self.blast_output_row, 3)
# Query span info.
query_span_val = (hsp.end[0] - hsp.start[0]) / hsp.query_length
query_span_info_text = "{}-{} ({:.1f}%)".format(
hsp.start[0], hsp.end[0], query_span_val * 100)
span_info_label = QtWidgets.QLabel(query_span_info_text)
span_info_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(span_info_label, self.blast_output_row,
4)
# Subject span info.
tem_span_val = (hsp.end[1] - hsp.start[1]) / hsp.template_length
tem_span_info_text = "{}-{} ({:.1f}%)".format(
hsp.start[1], hsp.end[1], tem_span_val * 100)
hspan_info_label = QtWidgets.QLabel(tem_span_info_text)
hspan_info_label.setStyleSheet(small_font_style)
self.results_grid.addWidget(hspan_info_label,
self.blast_output_row, 5)
self.blast_output_row += 1
def __init__(self, parent=None):
super(SurfStampFrame, self).__init__(parent)
self.layout = QtWidgets.QVBoxLayout()
self.setLayout(self.layout)
glayout1 = QtWidgets.QGridLayout()
self.label_message = QtWidgets.QLabel(self)
self.label_message.setText("SurfStamp PyMOL plugin")
self.layout.addWidget(self.label_message)
self.combo_model = QtWidgets.QComboBox()
self.combo_model.addItems([])
self.layout.addWidget(self.combo_model)
self.label_reso = QtWidgets.QLabel(self)
self.label_reso.setText("Surface Resolution")
glayout1.addWidget(self.label_reso, 1, 0)
self.spin_reso = QtWidgets.QDoubleSpinBox(self)
self.spin_reso.setRange(0.1, 1.0)
self.spin_reso.setSingleStep(0.05)
self.spin_reso.setValue(0.7)
glayout1.addWidget(self.spin_reso, 1, 1)
self.label_imagesize = QtWidgets.QLabel(self)
self.label_imagesize.setText("Image Size")
glayout1.addWidget(self.label_imagesize, 2, 0)
self.spin_imagesize = QtWidgets.QSpinBox(self)
self.spin_imagesize.setRange(1000, 10000)
#PILLOW？は 13000 くらいが Max っぽい
self.spin_imagesize.setSingleStep(100)
self.spin_imagesize.setValue(4000)
glayout1.addWidget(self.spin_imagesize, 2, 1)
self.label_fontsize = QtWidgets.QLabel(self)
self.label_fontsize.setText("Font Size")
glayout1.addWidget(self.label_fontsize, 3, 0)
self.spin_fontsize = QtWidgets.QSpinBox(self)
self.spin_fontsize.setRange(3, 100)
self.spin_fontsize.setSingleStep(1)
self.spin_fontsize.setValue(20)
glayout1.addWidget(self.spin_fontsize, 3, 1)
glayout2 = QtWidgets.QGridLayout()
self.check_outline = QtWidgets.QCheckBox('Outline')
self.check_outline.setChecked(True)
glayout2.addWidget(self.check_outline, 0, 0)
self.check_nowater = QtWidgets.QCheckBox('Remove Waters')
self.check_nowater.setChecked(True)
glayout2.addWidget(self.check_nowater, 0, 1)
self.check_colorall = QtWidgets.QCheckBox('Color All')
self.check_colorall.setChecked(False)
glayout2.addWidget(self.check_colorall, 1, 0)
self.check_tile = QtWidgets.QCheckBox('Repeating Tile')
self.check_tile.clicked.connect(self.checkTileOn)
self.check_tile.setChecked(False)
glayout2.addWidget(self.check_tile, 1, 1)
self.check_oneletter = QtWidgets.QCheckBox('One Letter')
glayout2.addWidget(self.check_oneletter, 2, 0)
self.check_nochainname = QtWidgets.QCheckBox('No Chain Name')
glayout2.addWidget(self.check_nochainname, 2, 1)
self.check_ignore_occupancy = QtWidgets.QCheckBox('Ignore Occupancy')
glayout2.addWidget(self.check_ignore_occupancy, 3, 0)
self.check_cartoon = QtWidgets.QCheckBox('Cartoon')
self.check_cartoon.clicked.connect(self.checkCartoonOn)
glayout2.addWidget(self.check_cartoon, 3, 1)
self.check_mmcif = QtWidgets.QCheckBox('Use MMCIF')
glayout2.addWidget(self.check_mmcif, 4, 0)
self.check_builtin = QtWidgets.QCheckBox('Built-in Surface Generator')
glayout2.addWidget(self.check_builtin, 4, 1)
self.check_builtin.clicked.connect(self.checkBuiltinOn)
#MMCIF は AUTH が不完全だ！
#self.check_label = QtWidgets.QCheckBox('ID Label');
#self.layout.addWidget(self.check_label);
# Text field for output file
glayout4 = QtWidgets.QVBoxLayout()
self.label_outprefix = QtWidgets.QLabel(
'Output Prefix (Prefix+<something> will be overwritten.)')
glayout4.addWidget(self.label_outprefix)
glayout4b = QtWidgets.QGridLayout()
self.text_outprefix = QtWidgets.QLineEdit(self)
self.text_outprefix.setReadOnly(True)
glayout4b.addWidget(self.text_outprefix, 0, 0)
self.button_outprefix = QtWidgets.QPushButton(self)
self.button_outprefix.setText("Save As")
self.button_outprefix.clicked.connect(self.getFile)
self.text_outprefix.setStyleSheet("background-color: lightgray;")
glayout4b.addWidget(self.button_outprefix, 0, 1)
glayout4.addLayout(glayout4b)
glayout3 = QtWidgets.QGridLayout()
self.button_ok = QtWidgets.QPushButton('Create')
self.button_ok.clicked.connect(self.runSurfStamp)
glayout3.addWidget(self.button_ok, 0, 0)
self.button_close = QtWidgets.QPushButton('Close')
self.button_close.clicked.connect(self.hide)
glayout3.addWidget(self.button_close, 0, 1)
self.layout.addLayout(glayout1)
self.layout.addLayout(glayout2)
self.layout.addLayout(glayout4)
self.layout.addLayout(glayout3)
screengeom = QtWidgets.qApp.desktop().screenGeometry()
wwidth = 300
hheight = 200
self.setGeometry(screengeom.width() / 2 - wwidth / 2,
screengeom.height() / 2 - hheight / 2, wwidth,
hheight)
self.setWindowTitle('SurfStamp')
self.checkTileOn()
self.checkBuiltinOn()
self.checkCartoonOn()
self.show()