def __init__(self, parent):
self.gui = parent
self.fb_scale = 1.0
# OpenGL context setup
if USE_QOPENGLWIDGET:
f = QtGui.QSurfaceFormat()
else:
f = QtOpenGL.QGLFormat()
from pymol.invocation import options
# logic equivalent to layer5/main.cpp:launch
if options.multisample:
f.setSamples(4)
if options.force_stereo != -1:
# See layer1/Setting.h for stereo modes
if options.stereo_mode in (1, 12) or (
options.stereo_mode == 0 and AUTO_DETECT_STEREO):
f.setStereo(True)
if options.stereo_mode in (11, 12) and not USE_QOPENGLWIDGET:
f.setAccum(True)
if USE_QOPENGLWIDGET:
super(PyMOLGLWidget, self).__init__(parent=parent)
self.setFormat(f)
self.setUpdateBehavior(QtWidgets.QOpenGLWidget.PartialUpdate)
else:
super(PyMOLGLWidget, self).__init__(f, parent=parent)
# pymol instance
self.pymol = PyMOL()
self.pymol.start()
self.cmd = self.pymol.cmd
# capture python output for feedback
import pcatch
pcatch._install()
# for passive move drag
self.setMouseTracking(True)
# for accepting keyboard input (command line, shortcuts)
self.setFocusPolicy(Qt.ClickFocus)
# for idle rendering
self._timer = QtCore.QTimer()
self._timer.setSingleShot(True)
self._timer.timeout.connect(self._pymolProcess)
# drag n drop
self.setAcceptDrops(True)
# pinch-zoom
self.grabGesture(Qt.PinchGesture)
def __init__(self, parent):
self.gui = parent
self.fb_scale = 1.0
# OpenGL context setup
if USE_QOPENGLWIDGET:
f = QtGui.QSurfaceFormat()
else:
f = QtOpenGL.QGLFormat()
from pymol.invocation import options
# logic equivalent to layer5/main.cpp:launch
if options.multisample:
f.setSamples(4)
if options.force_stereo != -1:
# See layer1/Setting.h for stereo modes
if options.stereo_mode in (1, 12) or (
options.stereo_mode == 0 and AUTO_DETECT_STEREO):
f.setStereo(True)
if options.stereo_mode in (11, 12) and not USE_QOPENGLWIDGET:
f.setAccum(True)
if USE_QOPENGLWIDGET:
super(PyMOLGLWidget, self).__init__(parent=parent)
self.setFormat(f)
else:
super(PyMOLGLWidget, self).__init__(f, parent=parent)
# pymol instance
self.pymol = PyMOL()
self.pymol.start()
self.cmd = self.pymol.cmd
# capture python output for feedback
import pcatch
pcatch._install()
# for passive move drag
self.setMouseTracking(True)
# for accepting keyboard input (command line, shortcuts)
self.setFocusPolicy(Qt.ClickFocus)
# for idle rendering
self._timer = QtCore.QTimer()
self._timer.setSingleShot(True)
self._timer.timeout.connect(self._pymolProcess)
# drag n drop
self.setAcceptDrops(True)
# pinch-zoom
self.grabGesture(Qt.PinchGesture)
class PyMOLGLWidget(BaseGLWidget):
'''
PyMOL OpenGL Widget
'''
# mouse button map
_buttonMap = {
Qt.LeftButton: 0,
Qt.MidButton: 1,
Qt.RightButton: 2,
}
def __init__(self, parent):
self.gui = parent
# OpenGL context setup
if USE_QOPENGLWIDGET:
f = QtGui.QSurfaceFormat()
else:
f = QtOpenGL.QGLFormat()
from pymol.invocation import options
# logic equivalent to layer5/main.cpp:launch
if options.multisample:
f.setSamples(4)
if options.force_stereo != -1:
# See layer1/Setting.h for stereo modes
if options.stereo_mode in (1, 12) or (
options.stereo_mode == 0 and AUTO_DETECT_STEREO):
f.setStereo(True)
if options.stereo_mode in (11, 12) and not USE_QOPENGLWIDGET:
f.setAccum(True)
if USE_QOPENGLWIDGET:
super(PyMOLGLWidget, self).__init__(parent=parent)
self.setFormat(f)
else:
super(PyMOLGLWidget, self).__init__(f, parent=parent)
# pymol instance
self.pymol = PyMOL()
self.pymol.start()
self.cmd = self.pymol.cmd
# capture python output for feedback
import pcatch
pcatch._install()
# for passive move drag
self.setMouseTracking(True)
# for accepting keyboard input (command line, shortcuts)
self.setFocusPolicy(Qt.ClickFocus)
# for idle rendering
self._timer = QtCore.QTimer()
self._timer.setSingleShot(True)
self._timer.timeout.connect(self._pymolProcess)
# drag n drop
self.setAcceptDrops(True)
# pinch-zoom
self.grabGesture(Qt.PinchGesture)
def sizeHint(self):
# default 640 + internal_gui, 480 + internal_feedback
return QtCore.QSize(860, 498)
##########################
# Input Events
##########################
def event(self, ev):
if ev.type() == Gesture:
return self.gestureEvent(ev)
return super(PyMOLGLWidget, self).event(ev)
def gestureEvent(self, ev):
gesture = ev.gesture(Qt.PinchGesture)
if gesture is None:
return False
if gesture.state() == Qt.GestureStarted:
self.pinch_start_z = self.cmd.get_view()[11]
changeFlags = gesture.changeFlags()
if changeFlags & QtWidgets.QPinchGesture.RotationAngleChanged:
delta = gesture.lastRotationAngle() - gesture.rotationAngle()
self.cmd.turn('z', delta)
if changeFlags & QtWidgets.QPinchGesture.ScaleFactorChanged:
view = list(self.cmd.get_view())
# best guess for https://bugreports.qt.io/browse/QTBUG-48138
totalscalefactor = gesture.totalScaleFactor()
if totalscalefactor == 1.0:
totalscalefactor = gesture.scaleFactor()
z = self.pinch_start_z / totalscalefactor
delta = z - view[11]
view[11] = z
view[15] -= delta
view[16] -= delta
self.cmd.set_view(view)
return True
def mouseMoveEvent(self, ev):
self.pymol.drag(int(self.fb_scale * ev.x()),
int(self.fb_scale * (self.height() - ev.y())),
get_modifiers(ev))
def mousePressEvent(self, ev, state=0):
if ev.button() not in self._buttonMap:
return
self.pymol.button(self._buttonMap[ev.button()], state,
int(self.fb_scale * ev.x()),
int(self.fb_scale * (self.height() - ev.y())),
get_modifiers(ev))
def mouseReleaseEvent(self, ev):
self.mousePressEvent(ev, 1)
def wheelEvent(self, ev):
pymolmod = get_modifiers(ev)
try:
delta = ev.delta()
except AttributeError:
# Qt5
angledelta = ev.angleDelta()
delta = angledelta.y()
if abs(delta) < abs(angledelta.x()):
# Shift+Wheel emulates horizontal scrolling
if not (ev.modifiers() & Qt.ShiftModifier):
return
delta = angledelta.x()
if not delta:
return
button = 3 if delta > 0 else 4
args = (int(self.fb_scale * ev.x()),
int(self.fb_scale * (self.height() - ev.y())),
pymolmod)
self.pymol.button(button, 0, *args)
self.pymol.button(button, 1, *args)
##########################
# OpenGL
##########################
def paintGL(self):
if not USE_QOPENGLWIDGET:
glViewport(0, 0, int(self.fb_scale * self.width()),
int(self.fb_scale * self.height()))
self.pymol.draw()
self._timer.start(0)
def resizeGL(self, w, h):
if USE_QOPENGLWIDGET:
w = int(w * self.fb_scale)
h = int(h * self.fb_scale)
self.pymol.reshape(w, h, True)
def updateFbScale(self, context):
'''Update PyMOL's display scale factor from the window or screen context
@type context: QWindow or QScreen
'''
self.fb_scale = context.devicePixelRatio()
try:
self.cmd.set('display_scale_factor', int(self.fb_scale))
except BaseException as e:
# fails with modal draw (mpng ..., modal=1)
print(e)
def initializeGL(self):
# Scale framebuffer for Retina displays
try:
window = self.windowHandle()
# QOpenGLWidget workaround
if window is None:
window = self.parent().windowHandle()
self.updateFbScale(window)
window.screenChanged.connect(self.updateFbScale)
except AttributeError:
# Fallback for Qt4
self.fb_scale = 1.0
def _pymolProcess(self):
idle = self.pymol.idle()
if idle or self.pymol.getRedisplay():
self.update()
self._timer.start(20)
##########################
# drag n drop
##########################
def dragEnterEvent(self, event):
if event.mimeData().hasUrls:
event.accept()
else:
event.ignore()
def dropEvent(self, event):
if event.mimeData().hasUrls:
for url in event.mimeData().urls():
if url.isLocalFile():
url = url.toLocalFile()
else:
url = url.toString()
self.gui.load_dialog(url)
event.accept()
class PyMOLGLWidget(BaseGLWidget):
'''
PyMOL OpenGL Widget
'''
# mouse button map
_buttonMap = {
Qt.LeftButton: 0,
Qt.MidButton: 1,
Qt.RightButton: 2,
}
def __init__(self, parent):
self.gui = parent
self.fb_scale = 1.0
# OpenGL context setup
if USE_QOPENGLWIDGET:
f = QtGui.QSurfaceFormat()
else:
f = QtOpenGL.QGLFormat()
from pymol.invocation import options
# logic equivalent to layer5/main.cpp:launch
if options.multisample:
f.setSamples(4)
if options.force_stereo != -1:
# See layer1/Setting.h for stereo modes
if options.stereo_mode in (1, 12) or (
options.stereo_mode == 0 and AUTO_DETECT_STEREO):
f.setStereo(True)
if options.stereo_mode in (11, 12) and not USE_QOPENGLWIDGET:
f.setAccum(True)
if USE_QOPENGLWIDGET:
super(PyMOLGLWidget, self).__init__(parent=parent)
self.setFormat(f)
else:
super(PyMOLGLWidget, self).__init__(f, parent=parent)
# pymol instance
self.pymol = PyMOL()
self.pymol.start()
self.cmd = self.pymol.cmd
# capture python output for feedback
import pcatch
pcatch._install()
# for passive move drag
self.setMouseTracking(True)
# for accepting keyboard input (command line, shortcuts)
self.setFocusPolicy(Qt.ClickFocus)
# for idle rendering
self._timer = QtCore.QTimer()
self._timer.setSingleShot(True)
self._timer.timeout.connect(self._pymolProcess)
# drag n drop
self.setAcceptDrops(True)
# pinch-zoom
self.grabGesture(Qt.PinchGesture)
def sizeHint(self):
# default 640 + internal_gui, 480 + internal_feedback
return QtCore.QSize(860, 498)
##########################
# Input Events
##########################
def event(self, ev):
if ev.type() == Gesture:
return self.gestureEvent(ev)
return super(PyMOLGLWidget, self).event(ev)
def gestureEvent(self, ev):
gesture = ev.gesture(Qt.PinchGesture)
if gesture is None:
return False
if gesture.state() == Qt.GestureStarted:
self.pinch_start_z = self.cmd.get_view()[11]
changeFlags = gesture.changeFlags()
if changeFlags & QtWidgets.QPinchGesture.RotationAngleChanged:
delta = gesture.lastRotationAngle() - gesture.rotationAngle()
self.cmd.turn('z', delta)
if changeFlags & QtWidgets.QPinchGesture.ScaleFactorChanged:
view = list(self.cmd.get_view())
# best guess for https://bugreports.qt.io/browse/QTBUG-48138
totalscalefactor = gesture.totalScaleFactor()
if totalscalefactor == 1.0:
totalscalefactor = gesture.scaleFactor()
z = self.pinch_start_z / totalscalefactor
delta = z - view[11]
view[11] = z
view[15] -= delta
view[16] -= delta
self.cmd.set_view(view)
return True
def mouseMoveEvent(self, ev):
self.pymol.drag(int(self.fb_scale * ev.x()),
int(self.fb_scale * (self.height() - ev.y())),
get_modifiers(ev))
def mousePressEvent(self, ev, state=0):
if ev.button() not in self._buttonMap:
return
self.pymol.button(self._buttonMap[ev.button()], state,
int(self.fb_scale * ev.x()),
int(self.fb_scale * (self.height() - ev.y())),
get_modifiers(ev))
def mouseReleaseEvent(self, ev):
self.mousePressEvent(ev, 1)
def wheelEvent(self, ev):
pymolmod = get_modifiers(ev)
try:
delta = ev.delta()
except AttributeError:
# Qt5
angledelta = ev.angleDelta()
delta = angledelta.y()
if abs(delta) < abs(angledelta.x()):
# Shift+Wheel emulates horizontal scrolling
if not (ev.modifiers() & Qt.ShiftModifier):
return
delta = angledelta.x()
if not delta:
return
button = 3 if delta > 0 else 4
args = (int(self.fb_scale * ev.x()),
int(self.fb_scale * (self.height() - ev.y())),
pymolmod)
self.pymol.button(button, 0, *args)
self.pymol.button(button, 1, *args)
##########################
# OpenGL
##########################
def paintGL(self):
if not USE_QOPENGLWIDGET:
glViewport(0, 0, int(self.fb_scale * self.width()),
int(self.fb_scale * self.height()))
self.pymol.draw()
self._timer.start(0)
def resizeGL(self, w, h):
if USE_QOPENGLWIDGET:
w = int(w * self.fb_scale)
h = int(h * self.fb_scale)
self.pymol.reshape(w, h, True)
def updateFbScale(self, context):
'''Update PyMOL's display scale factor from the window or screen context
@type context: QWindow or QScreen
'''
self.fb_scale = context.devicePixelRatio()
try:
self.cmd.set('display_scale_factor', int(self.fb_scale))
except BaseException as e:
# fails with modal draw (mpng ..., modal=1)
print(e)
def initializeGL(self):
# Scale framebuffer for Retina displays
try:
window = self.windowHandle()
# QOpenGLWidget workaround
if window is None:
window = self.parent().windowHandle()
self.updateFbScale(window)
window.screenChanged.connect(self.updateFbScale)
window.screen().physicalDotsPerInchChanged.connect(
lambda dpi: self.updateFbScale(window))
except AttributeError:
# Fallback for Qt4
pass
def _pymolProcess(self):
idle = self.pymol.idle()
if idle or self.pymol.getRedisplay():
self.update()
self._timer.start(20)
##########################
# drag n drop
##########################
def dragEnterEvent(self, event):
if event.mimeData().hasUrls:
event.accept()
else:
event.ignore()
def dropEvent(self, event):
if event.mimeData().hasUrls:
for url in event.mimeData().urls():
if url.isLocalFile():
url = url.toLocalFile()
else:
url = url.toString()
self.gui.load_dialog(url)
event.accept()
3ALA CA 22 2.863 2.764 1.192
3ALA C 23 3.013 2.747 1.191
3ALA O 24 3.066 2.635 1.188
3ALA CB 25 2.813 2.842 1.316
3ALA H 26 2.848 2.549 1.189
3ALA HA 27 2.835 2.820 1.100
3ALA 1HB 28 2.703 2.857 1.313
3ALA 2HB 29 2.836 2.789 1.410
3ALA 3HB 30 2.858 2.942 1.322
3.41363 3.41363 2.41380 0.00000 0.00000 0.00000 0.00000 1.70681 1.70681
"""
with open(GRO_PATH, "wt") as f:
f.write(grodata)
pymol = SingletonPyMOL()
pymol.start()
cmd = pymol.cmd
cmd.load(CIF_PATH)
# Test rendering
cmd.png(PNG_PATH, ray=1)
assert isfile(PNG_PATH)
# Test correct integration of NumPy
assert cmd.get_coordset(PDB_ID).shape == (304, 3)
# Test if we can load a .gro file
cmd.load(GRO_PATH, 'grodata')
assert cmd.get_coordset('grodata').shape == (30, 3)
def __init__(self, parent):
self.gui = parent
# OpenGL context setup
f = QtOpenGL.QGLFormat()
f.setRgba(True)
f.setDepth(True)
f.setDoubleBuffer(True)
from pymol.invocation import options
# logic equivalent to layer5/main.cpp:launch
if options.multisample:
f.setSampleBuffers(True)
if options.force_stereo != -1:
# See layer1/Setting.h for stereo modes
if options.stereo_mode in (0, 1, 12):
# this effectively disables stereo detection
# on Linux that is faulty in QGLWidget / PyQt5
if not (options.stereo_mode == 0
and sys.platform.startswith("linux")):
f.setStereo(True)
if options.stereo_mode in (11, 12):
f.setAccum(True)
if options.stereo_mode in (0, 6, 7, 8, 9):
f.setStencil(True)
QtOpenGL.QGLWidget.__init__(self, f, parent=parent)
if not self.isValid():
raise RuntimeError('OpenGL initialization failed')
f_actual = self.format()
# report if quad buffer available
options.stereo_capable = int(f_actual.stereo()
or (options.force_stereo == 1))
# feedback if stereo request failed
if options.stereo_mode and (
# QTBUG-59636 f.stereo() and not f_actual.stereo() or
f.accum() and not f_actual.accum()
or f.stencil() and not f_actual.stencil()):
# cPyMOLGlobals_LaunchStatus_StereoFailed
options.launch_status |= 0x1
# feedback if multisample request failed
if options.multisample and not f_actual.sampleBuffers():
# cPyMOLGlobals_LaunchStatus_MultisampleFailed
options.launch_status |= 0x2
# pymol instance
self.pymol = PyMOL()
self.pymol.start()
self.cmd = self.pymol.cmd
# capture python output for feedback
import pcatch
pcatch._install()
# for passive move drag
self.setMouseTracking(True)
# for accepting keyboard input (command line, shortcuts)
self.setFocusPolicy(Qt.ClickFocus)
# for idle rendering
self._timer = QtCore.QTimer()
self._timer.setSingleShot(True)
self._timer.timeout.connect(self._pymolProcess)
# drag n drop
self.setAcceptDrops(True)
# pinch-zoom
self.grabGesture(Qt.PinchGesture)