def __init__(self, session, tool_name):
# Standard template stuff for intializing tool
super().__init__(session, tool_name)
from chimerax.core.ui.gui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.tool_window.manage(placement="side")
parent = self.tool_window.ui_area
# Create an HTML viewer for our user interface.
# We can include other Qt widgets if we want to.
from PyQt5.QtWidgets import QGridLayout
from chimerax.core.ui.widgets import HtmlView
layout = QGridLayout()
self.html_view = HtmlView(parent, size_hint=(575, 200),
interceptor=self._navigate,
schemes=[self.CUSTOM_SCHEME])
layout.addWidget(self.html_view, 0, 0) # row 0, column 0
parent.setLayout(layout)
# Register for model addition/removal so we can update model list
from chimerax.core.models import ADD_MODELS, REMOVE_MODELS
t = session.triggers
self._add_handler = t.add_handler(ADD_MODELS, self._update_models)
self._remove_handler = t.add_handler(REMOVE_MODELS, self._update_models)
# Go!
self._update_models()
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
# FIXME: display_name' defaults to class name with spaces inserted
# between lower-then-upper-case characters (therefore "Tool UI"
# in this case), so only override if different name desired
self.display_name = "custom name for running tool"
from chimerax.core.ui.gui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.tool_window.manage(placement="side")
parent = self.tool_window.ui_area
class ToolUI(ToolInstance):
SESSION_ENDURING = False
# if SESSION_ENDURING is True, tool instance not deleted at session closure
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
# FIXME: display_name' defaults to class name with spaces inserted
# between lower-then-upper-case characters (therefore "Tool UI"
# in this case), so only override if different name desired
self.display_name = "Xlink Analyzer"
from chimerax.core.ui.gui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.tool_window.manage(placement="side")
parent = self.tool_window.ui_area
def layout_main(tool):
# Standard template stuff
tool.display_name = "Tempy"
tool.tool_window = MainToolWindow(tool)
tool.tool_window.manage(placement="side")
parent = tool.tool_window.ui_area
policy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
parent.setSizePolicy(policy)
layout = QVBoxLayout()
tool.top_layout = layout
# Create some tabs
tab_widget = QTabWidget(parent)
tab_widget.setMinimumHeight(210)
tab_widget.setMinimumWidth(400)
tab_widget.setSizePolicy(policy)
tab_smoc = QWidget()
tab_smoc.setMinimumHeight(210)
tab_smoc.setMinimumWidth(400)
tab_smoc.setSizePolicy(policy)
tab_widget.addTab(tab_smoc, "SMOC")
tab_sccc = QWidget()
tab_sccc.setMinimumHeight(210)
tab_sccc.setMinimumWidth(400)
tab_sccc.setSizePolicy(policy)
tab_widget.addTab(tab_sccc, "SCCC")
tab_ccc = QWidget()
tab_ccc.setMinimumHeight(210)
tab_ccc.setMinimumWidth(400)
tab_ccc.setSizePolicy(policy)
tab_widget.addTab(tab_ccc, "CCC")
tab_nmi = QWidget()
tab_nmi.setMinimumHeight(210)
tab_nmi.setMinimumWidth(400)
tab_nmi.setSizePolicy(policy)
tab_widget.addTab(tab_nmi, "NMI")
tab_dif = QWidget()
tab_dif.setMinimumHeight(210)
tab_dif.setMinimumWidth(400)
tab_dif.setSizePolicy(policy)
tab_widget.addTab(tab_dif, "DIFMAP")
# Now layout each tab
layout_nmi(tool, tab_nmi)
layout_sccc(tool, tab_sccc)
layout_smoc(tool, tab_smoc)
layout_ccc(tool, tab_ccc)
layout_dif(tool, tab_dif)
parent.setLayout(layout)
layout.addWidget(tab_widget)
# Figures for SMOC
tool._figure = None
tool._canvas = None
class SampleTool(ToolInstance):
SESSION_ENDURING = False
SESSION_SKIP = True # No session saving for now
CUSTOM_SCHEME = "sample" # HTML scheme for custom links
display_name = "Sample Tool"
def __init__(self, session, tool_name):
# Standard template stuff for intializing tool
super().__init__(session, tool_name)
from chimerax.core.ui.gui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.tool_window.manage(placement="side")
parent = self.tool_window.ui_area
# Create an HTML viewer for our user interface.
# We can include other Qt widgets if we want to.
from PyQt5.QtWidgets import QGridLayout
from chimerax.core.ui.widgets import HtmlView
layout = QGridLayout()
self.html_view = HtmlView(parent, size_hint=(575, 200),
interceptor=self._navigate,
schemes=[self.CUSTOM_SCHEME])
layout.addWidget(self.html_view, 0, 0) # row 0, column 0
parent.setLayout(layout)
# Register for model addition/removal so we can update model list
from chimerax.core.models import ADD_MODELS, REMOVE_MODELS
t = session.triggers
self._add_handler = t.add_handler(ADD_MODELS, self._update_models)
self._remove_handler = t.add_handler(REMOVE_MODELS, self._update_models)
# Go!
self._update_models()
def _update_models(self, trigger=None, trigger_data=None):
# Called to update page with current list of models
from chimerax.core.atomic import AtomicStructure
html = ["<h2>Sample Tool</h2>", "<ul>"]
from urllib.parse import quote
for m in self.session.models.list(type=AtomicStructure):
html.append("<li><a href=\"%s:%s\">%s - %s</a></li>" %
(self.CUSTOM_SCHEME, quote(m.atomspec()),
m.id_string(), m.name))
html.extend(["</ul>",
"<h3>Output:</h3>",
'<div id="output">Counts appear here</div>'])
self.html_view.setHtml('\n'.join(html))
def _navigate(self, info):
# Called when link is clicked.
# "info" is an instance of QWebEngineUrlRequestInfo
url = info.requestUrl()
scheme = url.scheme()
if scheme == self.CUSTOM_SCHEME:
# Intercept our custom scheme.
# Method may be invoked in a different thread than
# the main thread where Qt calls may be made.
self.session.ui.thread_safe(self._run, url.path())
def _run(self, atomspec):
# Execute "sample count" command for given atomspec
from chimerax.core.commands import run
from chimerax.core.logger import StringPlainTextLog
with StringPlainTextLog(self.session.logger) as log:
try:
run(self.session, "sample count " + atomspec)
finally:
html = "<pre>\n%s</pre>" % log.getvalue()
js = ('document.getElementById("output").innerHTML = %s'
% repr(html))
self.html_view.page().runJavaScript(js)
class ViewDockTool(ToolInstance):
SESSION_ENDURING = False
SESSION_SKIP = True # No session saving for now
CUSTOM_SCHEME = "viewdockx" # HTML scheme for custom links
display_name = "ViewDockX"
def __init__(self, session, tool_name, structures=None):
# Standard template stuff for intializing tool
super().__init__(session, tool_name)
from chimerax.core.ui.gui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.tool_window.manage(placement="side")
if structures is None:
structures = session.models.list(type=AtomicStructure)
self.structures = structures
parent = self.tool_window.ui_area
# Create an HTML viewer for our user interface.
# We can include other Qt widgets if we want to.
from PyQt5.QtWidgets import QGridLayout
from chimerax.core.ui.widgets import HtmlView
layout = QGridLayout()
self.html_view = HtmlView(parent,
size_hint=(575, 200),
interceptor=self._navigate,
schemes=[self.CUSTOM_SCHEME])
layout.addWidget(self.html_view, 0, 0) # row 0, column 0
parent.setLayout(layout)
# Register for model addition/removal so we can update model list
from chimerax.core.models import REMOVE_MODELS
t = session.triggers
# self._add_handler = t.add_handler(ADD_MODELS, self._update_models)
self._remove_handler = t.add_handler(REMOVE_MODELS,
self._update_models)
# Go!
self._update_models()
def delete(self):
t = self.session.triggers
if self._remove_handler:
t.remove_handler(self._remove_handler)
self._remove_handler = None
super().delete()
def _update_models(self, trigger=None, trigger_data=None):
""" Called to update page with current list of models"""
from urllib.parse import urlunparse, urlencode
if trigger_data is not None:
for struct in self.structures:
if struct in trigger_data:
self.structures.remove(struct)
if not self.structures:
self.delete()
return
# TRANSFERS ALL KEYS INTO A SET, THEN A LIST
category_set = set()
for struct in self.structures:
try:
category_set.update({key for key in struct.viewdock_comment})
except AttributeError:
pass
category_list = sorted(list(category_set), key=str.lower)
####################
#### TABLE ####
####################
table = []
table.append(
'<table id="viewdockx_table" class="tablesorter" style="width:100%">'
)
###########################
### COLUMN HEADERS ###
###########################
# COLUMN HEADER | ID |
table.append('<thead><tr>')
table.append('<th class="id">ID</th>')
# COLUMN HEADERS | NAME |...|...|...
table.append('<th>NAME</th>')
for category in category_list:
if category.upper() == "NAME":
pass
else:
table.append('<th>{}</th>'.format(category.upper()))
table.append("</tr></thead>")
########################
### COLUMN DATA ###
########################
table.append('<tbody>')
for struct in self.structures:
try:
comment_dict = struct.viewdock_comment
except AttributeError: # for files with empty comment sections
comment_dict = {}
# MAKES THE URL FOR EACH STRUCTURE
args = [("atomspec", struct.atomspec())]
query = urlencode(args)
#url = urlunparse((self.CUSTOM_SCHEME, "", "", "", query, ""))
checkbox_url = urlunparse(
(self.CUSTOM_SCHEME, "", "checkbox", "", query, ""))
link_url = urlunparse(
(self.CUSTOM_SCHEME, "", "link", "", query, ""))
# ADDING ID VALUE
table.append("<tr>")
table.extend([
'<td class="id">',
# for checkbox + atomspec string
'<span class="checkbox">'
'<input class="checkbox, struct" type="checkbox" href="{}"/>'
'{}</span>'.format(checkbox_url,
struct.atomspec()[1:]),
# for atomspec links only
'<span class="link"><a href="{}">{}</a></span>'.format(
link_url,
struct.atomspec()[1:]),
'</td>'
])
# ADDING VALUE FOR NAME
for category in category_list:
if category.upper() == "NAME":
try:
table.append('<td>{}</td>'.format(
comment_dict[category]))
except KeyError:
table.append('<td>missing</td>')
# ADDING THE REST
for category in category_list:
try:
if category.upper() != "NAME":
table.append('<td>{}</td>'.format(
comment_dict[category]))
except KeyError:
table.append('<td>missing</td>')
table.append("</tr>")
table.append("</tbody>")
table.append("</table>")
import os
from PyQt5.QtCore import QUrl
# os.path.join()
dir_path = os.path.dirname(os.path.abspath(__file__))
# lib_path = os.path.join(dir_path, "lib")
qurl = QUrl.fromLocalFile(os.path.join(dir_path, "viewdockx.html"))
with open(os.path.join(dir_path, "viewdockx_frame.html"), "r") as file:
template = file.read()
output = template.replace("TABLE", ('\n'.join(table)))\
.replace("urlbase", qurl.url())
self.html_view.setHtml(output, qurl)
# output_file = os.path.join(
# "C:/Users/hannahku/Desktop/RBVIInternship/GitHub/UCSF-RBVI-Internship/ViewDockX/src/output-test.html")
# print(output_file)
# with open(output_file, "w") as file2:
# file2.write(output)
# print("TEST SUCCESS")
def _navigate(self, info):
# Called when link is clicked.
# "info" is an instance of QWebEngineUrlRequestInfo
from urllib.parse import parse_qs
url = info.requestUrl()
scheme = url.scheme()
if scheme == self.CUSTOM_SCHEME:
# Intercept our custom scheme.
# Method may be invoked in a different thread than
# the main thread where Qt calls may be made.
query = parse_qs(url.query())
path = url.path()
function_map = {
"check_all": self.check_all,
"checkbox": self.checkbox,
"link": self.link,
"graph": self.graph
}
function_map[path](query)
# self.session.ui.thread_safe(function_map[path](query))
def check_all(self, query):
"""shows or hides all structures"""
show_all = query["show_all"][0]
self.session.ui.thread_safe(self._run_checkall, show_all)
def checkbox(self, query):
"""shows or hides individual structure"""
from chimerax.core.commands.cli import StructuresArg
print(query)
try:
atomspec = query["atomspec"][0]
disp = query["display"][0]
except (KeyError, ValueError):
atomspec = "missing"
structures = StructuresArg.parse(atomspec, self.session)[0]
self.session.ui.thread_safe(self._run_cb, structures, disp)
def link(self, query):
"""shows only selected structure"""
from chimerax.core.commands.cli import StructuresArg
try:
atomspec = query["atomspec"][0]
except (KeyError, ValueError):
atomspec = "missing"
structures = StructuresArg.parse(atomspec, self.session)[0]
self.session.ui.thread_safe(self._run_link, structures)
def graph(self, query):
"""open new window to render graph"""
pass
def _run_cb(self, structures, disp):
if disp == "0":
for struct in self.structures:
if structures[0] == struct:
struct.display = False
else:
for struct in self.structures:
if structures[0] == struct:
struct.display = True
def _run_link(self, structures):
for struct in self.structures:
struct.display = struct in structures
def _run_checkall(self, show_all):
if show_all == "true":
for struct in self.structures:
struct.display = True
else:
for struct in self.structures:
struct.display = False