def __init__(self, filename, quality, parent=None, name=None):
QGLWidget.__init__(self, parent, name)
# load molecule and read from xyz file
self.mol = Molecule()
self.mol.readxyz(filename)
self.mol.genbonds()
# adjust quality to sanity
# set display quality
if self.mol.natoms > 10000:
self.quality = min(2, quality)
else:
self.quality = quality
print(quality)
self.atom_size = 0.4
self.bond_size = 0.1
self.offset = -self.mol.box[0] - self.mol.box[1]
# set initial coordinates
self.x, self.y = self.lastx, self.lasty = [0, 0]
def __init__(self, filename, quality, parent=None, name=None):
QGLWidget.__init__(self,parent,name)
# load molecule and read from xyz file
self.mol = Molecule()
self.mol.readxyz(filename)
self.mol.genbonds()
# adjust quality to sanity
# set display quality
if self.mol.natoms > 10000:
self.quality = min(2,quality)
else:
self.quality = quality
print(quality)
self.atom_size = 0.4
self.bond_size = 0.1
self.offset = -self.mol.box[0]-self.mol.box[1]
# set initial coordinates
self.x,self.y = self.lastx,self.lasty = [0,0]
class OpenGLCanvas(QGLWidget):
def __init__(self, filename, quality, parent=None, name=None):
QGLWidget.__init__(self, parent, name)
# load molecule and read from xyz file
self.mol = Molecule()
self.mol.readxyz(filename)
self.mol.genbonds()
# adjust quality to sanity
# set display quality
if self.mol.natoms > 10000:
self.quality = min(2, quality)
else:
self.quality = quality
print(quality)
self.atom_size = 0.4
self.bond_size = 0.1
self.offset = -self.mol.box[0] - self.mol.box[1]
# set initial coordinates
self.x, self.y = self.lastx, self.lasty = [0, 0]
def initializeGL(self):
# set OpenGL global states
glEnable(GL_LIGHTING)
glEnable(GL_LIGHT0)
glEnable(GL_LIGHT1)
glEnable(GL_COLOR_MATERIAL)
glClearColor(0., 0., 0., 1.)
glClearDepth(1.0)
glDepthFunc(GL_LESS)
glEnable(GL_DEPTH_TEST)
glCullFace(GL_BACK)
glEnable(GL_CULL_FACE)
glEnable(GL_BLEND)
# load identity matrix and zoom out
glLoadIdentity()
glTranslate(0., 0., self.offset)
# draw the elements, set up paint callback
if self.quality > 0:
self.drawBallAndStick(self.atom_size, self.bond_size)
self.paintScene = self.paintBallAndStick
else:
self.drawWireFrame()
self.paintScene = self.paintWireFrame
def paintGL(self):
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
# rotation matrix adopted from molcas gv, needs improvement!!
w = max(self.w, 1.0)
h = max(self.h, 1.0)
xScale = 2.0 / w
yScale = 2.0 / h
x = (self.y - self.lasty) * yScale
y = (self.x - self.lastx) * xScale
z = (self.x * self.lasty - self.y * self.lastx) * xScale * yScale
a = numpy.sqrt((x**2 + y**2 + z**2) * (self.lastx**2 + self.lasty**2) /
(self.x**2 + self.y**2 + 1)) * 180.
glRotatef(a, x, y, z)
# paint the scene
self.paintScene()
def resizeGL(self, w, h):
self.w = w
self.h = h
glViewport(0, 0, w, h)
glMatrixMode(GL_PROJECTION)
glLoadIdentity()
gluPerspective(45.0, float(w) / float(h), 0.1, 1000.0)
glMatrixMode(GL_MODELVIEW)
def drawBallAndStick(self, r_ball=0.4, r_stick=0.1):
res = self.quality * 6
quad = gluNewQuadric()
glNewList(1, GL_COMPILE)
for i in range(self.mol.natoms):
glPushMatrix()
# set atom color
r, g, b = self.mol.col[i]
glColor3f(r, g, b)
# translate to atom position
x, y, z = self.mol.pos[i]
glTranslatef(x, y, z)
# draw the atom
gluSphere(quad, r_ball * self.mol.rad[i], res, res)
glPopMatrix()
for i, c in enumerate(self.mol.con):
m = c[0]
n = c[1]
glPushMatrix()
# set bond color
r, g, b = self.mol.col[m]
glColor3f(r, g, b)
# translate to atom position
x, y, z = self.mol.pos[m]
glTranslatef(x, y, z)
# draw the bond
v = self.mol.pos[n] - self.mol.pos[m]
angle = math.acos(
numpy.dot([0.0, 0.0, 1.0], v) /
self.mol.dist[i]) * 180. / math.pi
x, y, z = numpy.cross([0.0, 0.0, 1.0], v)
glRotatef(angle, x, y, z)
h = self.mol.dist[i] * self.mol.rad[m] / (self.mol.rad[m] +
self.mol.rad[n])
gluCylinder(quad, r_stick, r_stick, h, res, res)
glPopMatrix()
glEndList()
def paintBallAndStick(self):
glCallList(1)
def drawWireFrame(self):
glEnableClientState(GL_VERTEX_ARRAY)
glEnableClientState(GL_COLOR_ARRAY)
glVertexPointer(3, GL_FLOAT, 0, self.mol.pos)
glColorPointer(3, GL_FLOAT, 0, self.mol.col)
# experimental VBO usage, currently not working
#glGenBuffers(2, vboID)
#glBindBuffer(GL_ARRAY_BUFFER, vboID[0])
#glBufferData(GL_ARRAY_BUFFER, len(self.mol.pos)*4, self.mol.pos, GL_STATIC_DRAW)
#glBindBuffer(GL_ARRAY_ELEMENTS_BUFFER, vboID[1])
#glBufferData(GL_ARRAY_ELEMENTS_BUFFER, len(self.mol.con)*4, self.mol.con, GL_STATIC_DRAW)
def paintWireFrame(self):
glDrawElements(GL_POINTS, self.mol.natoms, GL_UNSIGNED_INT,
numpy.arange(self.mol.natoms))
glDrawElements(GL_LINES, 2 * self.mol.nbonds, GL_UNSIGNED_INT,
self.mol.con)
def drawSurface(self):
pass
def paintSurface(self):
pass
def translateModel(self, zoom):
mat = glGetFloatv(GL_MODELVIEW_MATRIX)
glLoadIdentity()
glTranslatef(0., 0., zoom * abs(self.offset))
glMultMatrixf(mat)
mat = glGetFloatv(GL_MODELVIEW_MATRIX)
self.updateGL()
def zoomModel(self, zoom):
self.translateModel(zoom)
class OpenGLCanvas(QGLWidget):
def __init__(self, filename, quality, parent=None, name=None):
QGLWidget.__init__(self,parent,name)
# load molecule and read from xyz file
self.mol = Molecule()
self.mol.readxyz(filename)
self.mol.genbonds()
# adjust quality to sanity
# set display quality
if self.mol.natoms > 10000:
self.quality = min(2,quality)
else:
self.quality = quality
print(quality)
self.atom_size = 0.4
self.bond_size = 0.1
self.offset = -self.mol.box[0]-self.mol.box[1]
# set initial coordinates
self.x,self.y = self.lastx,self.lasty = [0,0]
def initializeGL(self):
# set OpenGL global states
glEnable(GL_LIGHTING)
glEnable(GL_LIGHT0)
glEnable(GL_LIGHT1)
glEnable(GL_COLOR_MATERIAL)
glClearColor(0., 0., 0., 1.)
glClearDepth(1.0)
glDepthFunc(GL_LESS)
glEnable(GL_DEPTH_TEST)
glCullFace(GL_BACK)
glEnable(GL_CULL_FACE)
glEnable(GL_BLEND)
# load identity matrix and zoom out
glLoadIdentity()
glTranslate(0.,0.,self.offset)
# draw the elements, set up paint callback
if self.quality > 0:
self.drawBallAndStick(self.atom_size, self.bond_size)
self.paintScene = self.paintBallAndStick
else:
self.drawWireFrame()
self.paintScene = self.paintWireFrame
def paintGL(self):
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
# rotation matrix adopted from molcas gv, needs improvement!!
w = max(self.w, 1.0)
h = max(self.h, 1.0)
xScale = 2.0 / w
yScale = 2.0 / h
x = (self.y - self.lasty) * yScale
y = (self.x - self.lastx) * xScale
z = (self.x * self.lasty - self.y * self.lastx) * xScale * yScale
a = numpy.sqrt((x**2+y**2+z**2) * (self.lastx**2+self.lasty**2) / (self.x**2+self.y**2+1)) * 180.
glRotatef(a, x, y, z)
# paint the scene
self.paintScene()
def resizeGL(self, w, h):
self.w = w
self.h = h
glViewport(0, 0, w, h)
glMatrixMode(GL_PROJECTION)
glLoadIdentity()
gluPerspective(45.0, float(w)/float(h), 0.1, 1000.0)
glMatrixMode(GL_MODELVIEW)
def drawBallAndStick(self, r_ball = 0.4, r_stick = 0.1):
res = self.quality * 6
quad = gluNewQuadric()
glNewList(1,GL_COMPILE)
for i in range(self.mol.natoms):
glPushMatrix()
# set atom color
r,g,b = self.mol.col[i]
glColor3f(r,g,b)
# translate to atom position
x,y,z = self.mol.pos[i]
glTranslatef(x,y,z)
# draw the atom
gluSphere(quad, r_ball*self.mol.rad[i], res, res)
glPopMatrix()
for i,c in enumerate(self.mol.con):
m = c[0]
n = c[1]
glPushMatrix()
# set bond color
r,g,b = self.mol.col[m]
glColor3f(r,g,b)
# translate to atom position
x,y,z = self.mol.pos[m]
glTranslatef(x,y,z)
# draw the bond
v = self.mol.pos[n] - self.mol.pos[m]
angle = math.acos(numpy.dot([0.0,0.0,1.0], v)/self.mol.dist[i])*180./math.pi
x,y,z = numpy.cross([0.0,0.0,1.0], v)
glRotatef(angle,x,y,z)
h = self.mol.dist[i] * self.mol.rad[m] / (self.mol.rad[m] + self.mol.rad[n])
gluCylinder(quad, r_stick, r_stick, h, res, res)
glPopMatrix()
glEndList()
def paintBallAndStick(self):
glCallList(1)
def drawWireFrame(self):
glEnableClientState(GL_VERTEX_ARRAY)
glEnableClientState(GL_COLOR_ARRAY)
glVertexPointer(3, GL_FLOAT, 0, self.mol.pos)
glColorPointer(3, GL_FLOAT, 0, self.mol.col)
# experimental VBO usage, currently not working
#glGenBuffers(2, vboID)
#glBindBuffer(GL_ARRAY_BUFFER, vboID[0])
#glBufferData(GL_ARRAY_BUFFER, len(self.mol.pos)*4, self.mol.pos, GL_STATIC_DRAW)
#glBindBuffer(GL_ARRAY_ELEMENTS_BUFFER, vboID[1])
#glBufferData(GL_ARRAY_ELEMENTS_BUFFER, len(self.mol.con)*4, self.mol.con, GL_STATIC_DRAW)
def paintWireFrame(self):
glDrawElements(GL_POINTS, self.mol.natoms, GL_UNSIGNED_INT, numpy.arange(self.mol.natoms))
glDrawElements(GL_LINES, 2*self.mol.nbonds, GL_UNSIGNED_INT, self.mol.con)
def drawSurface(self):
pass
def paintSurface(self):
pass
def translateModel(self, zoom):
mat = glGetFloatv(GL_MODELVIEW_MATRIX)
glLoadIdentity()
glTranslatef(0.,0.,zoom*abs(self.offset))
glMultMatrixf(mat)
mat = glGetFloatv(GL_MODELVIEW_MATRIX)
self.updateGL()
def zoomModel(self, zoom):
self.translateModel(zoom)