def de(pdbfile1="IL1B.atm",
pdbfile2="MIM_tor.atm",
charges=True,
logscale=True,
dielectric=80.,
eps=0.1,
handle=False):
# extract names, and create the 'object' name in the pymol menu window
print('22 apr 2020 add ability to save/restore poses')
#pdbobj1 = pdbfile1[:-4]
pdbobj1 = 'dockeye_prt'
cmd.load(pdbfile1, pdbobj1)
#pdbobj2 = pdbfile2[:-4]
#cmd.load(pdbfile2, pdbobj2)
#
# Dockeye class reads pdb file upon init
pdbobj2 = 'dockeye_lig'
obj = Dockeye(pdbfile1, pdbfile2, pdbobj1, pdbobj2, charges, logscale,
dielectric, eps, handle)
#
# but pymol also loads first ligand model for display
cmd.load('dockeye_lig.pdb', pdbobj2)
os.system('/bin/rm -f dockeye_lig.pdb')
# remove any previous temporary files
os.system('/bin/rm -f dockeye_mark.*')
os.system('/bin/rm -f dockeye_action')
cmd.zoom()
cmd.do("set auto_zoom, off", echo=0)
name = 'dockeye'
cmd.load_callback(obj, name)
return obj
def testPseSupport(self):
cmd.load_callback(callback.Callback(), 'c1')
with testing.mktemp('tmp.pse') as session_filename:
cmd.save(session_filename)
cmd.delete('*')
cmd.load(session_filename)
self.assertTrue('c1' in cmd.get_names())
def de(pdbfile1="IL1B.atm",
pdbfile2="MIM_tor.atm",
charges=True,
logscale=True,
dielectric=80.,
eps=0.1):
# extract names, and create the 'object' name in the pymol menu window
#pdbobj1 = pdbfile1[:-4]
pdbobj1 = 'dockeye_prt'
cmd.load(pdbfile1, pdbobj1)
#pdbobj2 = pdbfile2[:-4]
#cmd.load(pdbfile2, pdbobj2)
#
# Dockeye class reads pdb file upon init
pdbobj2 = 'dockeye_lig'
obj = Dockeye(pdbfile1, pdbfile2, pdbobj1, pdbobj2, charges, logscale,
dielectric, eps)
#
# but pymol also loads first ligand model for display
cmd.load('dockeye_lig.pdb', pdbobj2)
os.system('rm -f dockeye_lig.pdb')
cmd.zoom()
cmd.do("set auto_zoom, off", echo=0)
name = 'dockeye'
cmd.load_callback(obj, name)
return obj
def __init__(self, selection=None, name=None, symbols='', state=-1):
try:
from pymol.plugins import get_pmgapp
pmgapp = get_pmgapp()
except ImportError:
pmgapp = None
if pmgapp is not None:
rootframe = Tkinter.Toplevel(pmgapp.root)
parent = rootframe
else:
rootframe = Tkinter.Tk()
parent = rootframe
rootframe.title(' Dynamic Angle Plotting ')
rootframe.protocol("WM_DELETE_WINDOW", self.close_callback)
canvas = SimplePlot(parent, width=320, height=320)
canvas.bind("<Button-2>", canvas.pickWhich)
canvas.bind("<Button-3>", canvas.pickWhich)
canvas.pack(side=Tkinter.LEFT, fill="both", expand=1)
canvas.axis(xint=150,
xlabels=[-180, -120, -60, 0, 60, 120, 180],
ylabels=[
-180, -150, -120, -90, -60, -30, 0, 30, 60, 90, 120,
150, 180
])
if symbols == 'ss':
canvas.symbols = 1
if name is None:
try:
name = cmd.get_unused_name('DynoRama')
except AttributeError:
name = 'DynoRamaObject'
self.rootframe = rootframe
self.canvas = canvas
self.name = name
self.lock = 0
self.state = state
if name != 'none':
auto_zoom = cmd.get('auto_zoom')
cmd.set('auto_zoom', 0)
cmd.load_callback(self, name)
cmd.set('auto_zoom', auto_zoom)
canvas.bind("<ButtonPress-1>", canvas.down)
canvas.bind("<ButtonRelease-1>", canvas.up)
canvas.bind("<Motion>", canvas.drag)
if selection is not None:
self.start(selection)
if with_mainloop and pmgapp is None:
rootframe.mainloop()
def __init__(self, selection=None, name=None, symbols='', state=-1):
try:
from pymol.plugins import get_pmgapp
pmgapp = get_pmgapp()
except ImportError:
pmgapp = None
if pmgapp is not None:
rootframe = Tkinter.Toplevel(pmgapp.root)
parent = rootframe
else:
rootframe = Tkinter.Tk()
parent = rootframe
rootframe.title(' Dynamic Angle Plotting ')
rootframe.protocol("WM_DELETE_WINDOW", self.close_callback)
canvas = SimplePlot(parent, width=320, height=320)
canvas.bind("<Button-2>", canvas.pickWhich)
canvas.bind("<Button-3>", canvas.pickWhich)
canvas.pack(side=Tkinter.LEFT, fill="both", expand=1)
canvas.axis(xint=150,
xlabels=[-180, -120, -60, 0, 60, 120, 180],
ylabels=[-180, -150, -120, -90, -60, -30, 0, 30, 60, 90, 120, 150, 180])
if symbols == 'ss':
canvas.symbols = 1
if name is None:
try:
name = cmd.get_unused_name('DynoRama')
except AttributeError:
name = 'DynoRamaObject'
self.rootframe = rootframe
self.canvas = canvas
self.name = name
self.lock = 0
self.state = state
if name != 'none':
auto_zoom = cmd.get('auto_zoom')
cmd.set('auto_zoom', 0)
cmd.load_callback(self, name)
cmd.set('auto_zoom', auto_zoom)
canvas.bind("<ButtonPress-1>", canvas.down)
canvas.bind("<ButtonRelease-1>", canvas.up)
canvas.bind("<Motion>", canvas.drag)
if selection is not None:
self.start(selection)
if with_mainloop and pmgapp is None:
rootframe.mainloop()
x -= x.mean(axis=0)
return 5 * x / x.std()
class myCallback(Callback):
"""Creates a simple vertex shader..."""
def __init__(self):
self.rebuild(100000000)
def rebuild(self, nlines):
self.nlines = nlines
mygeom = random_walk(nlines) * 5
self.vbo = vbo.VBO(mygeom)
def __call__(self):
try:
self.vbo.bind()
try:
glEnableClientState(GL_VERTEX_ARRAY)
glVertexPointerf(self.vbo)
glDrawArrays(GL_LINE_STRIP, 0, self.nlines + 1)
finally:
self.vbo.unbind()
glDisableClientState(GL_VERTEX_ARRAY)
finally:
pass
walker = myCallback()
cmd.load_callback(walker, 'gl01')
self.norm[2 * a + 1][0] = self.norm[2 * a][0]
self.norm[2 * a + 1][1] = self.norm[2 * a][1]
self.norm[2 * a + 1][2] = self.norm[2 * a][2]
def __call__(self):
glColor3f(1.0, 1.0, 1.0)
glVertexPointer(3, GL_FLOAT, 0, self.vert)
glNormalPointer(GL_FLOAT, 0, self.norm)
glEnableClientState(GL_VERTEX_ARRAY)
glEnableClientState(GL_NORMAL_ARRAY)
glDisableClientState(GL_COLOR_ARRAY)
glDrawArrays(GL_TRIANGLE_STRIP, 0, 126)
def get_extent(self):
return [[0.0, 0.0, -1.0], [6.3, 1.0, 1.0]]
# load it into PyMOL
for b in range(0, 63):
cmd.load_callback(myCallback(b), 'gl03', b + 1)
# give us a nice view
cmd.turn('z', 20)
cmd.turn('y', 20)
cmd.turn('x', 20)
cmd.mplay()
def createWFObj(file, name, translate=[0, 0, 0], flip=0):
obj = WFMesh(file, translate, flip)
cmd.load_callback(obj, name)
def createWFObj(file, name,translate=[0,0,0],flip=0):
obj = WFMesh(file,translate,flip)
cmd.load_callback(obj,name)
def load(self):
cmd.load_callback(self, self.cb_name)
def rama(sel):
rama = DynoRamaObject()
rama.start(sel)
cmd.load_callback(rama, "DynoRamaObject")
cmd.zoom("all")
class myCallback(Callback):
def __call__(self):
glBegin(GL_LINES)
glColor3f(1.0,1.0,1.0)
glVertex3f(0.0,0.0,0.0)
glVertex3f(1.0,0.0,0.0)
glVertex3f(0.0,0.0,0.0)
glVertex3f(0.0,2.0,0.0)
glVertex3f(0.0,0.0,0.0)
glVertex3f(0.0,0.0,3.0)
glEnd()
def get_extent(self):
return [[0.0,0.0,0.0],[1.0,2.0,3.0]]
# load it into PyMOL
cmd.load_callback(myCallback(),'gl01')
return [
self.vert.min(0).tolist(),
self.vert.max(0).tolist(),
]
class myCallbackDynamic(myCallback):
'''
Dynamic object which updates vertex coordinates every frame
'''
def __call__(self):
self.update(cmd.get_frame() * 2)
myCallback.__call__(self)
# load it into PyMOL
for b in range(0, 63):
cmd.load_callback(myCallback(b), 'gl03', b + 1)
cmd.load_callback(myCallbackDynamic(), 'gl03dyn', 1)
# give us a nice view
cmd.turn('z', 20)
cmd.turn('y', 20)
cmd.turn('x', 20)
cmd.mset('1-62')
cmd.mplay()
def get_extent(self):
return [
self.vert.min(0).tolist(),
self.vert.max(0).tolist(),
]
class myCallbackDynamic(myCallback):
'''
Dynamic object which updates vertex coordinates every frame
'''
def __call__(self):
self.update(cmd.get_frame() * 2)
myCallback.__call__(self)
# load it into PyMOL
for b in range(0, 63):
cmd.load_callback(myCallback(b), 'gl03', b + 1)
cmd.load_callback(myCallbackDynamic(), 'gl03dyn', 1)
# give us a nice view
cmd.turn('z',20)
cmd.turn('y',20)
cmd.turn('x',20)
cmd.mset('1-62')
cmd.mplay()
return 0.5 * x / x.std()
class myCallback(Callback):
"""Creates a simple vertex shader..."""
def __init__(self):
self.rebuild(10 * 1000 * 1000)
def rebuild(self, nlines):
self.nlines = nlines
mygeom = random_walk(nlines) * 10
self.vbo = vbo.VBO(mygeom)
def __call__(self):
try:
self.vbo.bind()
try:
glEnableClientState(GL_VERTEX_ARRAY)
glVertexPointerf(self.vbo)
glDrawArrays(GL_LINE_STRIP, 0, self.nlines + 1)
finally:
self.vbo.unbind()
glDisableClientState(GL_VERTEX_ARRAY)
finally:
pass
walker = myCallback()
cmd.load_callback(walker, 'gl01')
self.norm[2 * a][2] = 0.0
self.norm[2 * a + 1][0] = self.norm[2 * a][0]
self.norm[2 * a + 1][1] = self.norm[2 * a][1]
self.norm[2 * a + 1][2] = self.norm[2 * a][2]
def __call__(self):
glColor3f(1.0, 1.0, 1.0)
glVertexPointer(3, GL_FLOAT, 0, self.vert)
glNormalPointer(GL_FLOAT, 0, self.norm)
glEnableClientState(GL_VERTEX_ARRAY)
glEnableClientState(GL_NORMAL_ARRAY)
glDisableClientState(GL_COLOR_ARRAY)
glDrawArrays(GL_TRIANGLE_STRIP, 0, 126)
def get_extent(self):
return [[0.0, 0.0, -1.0], [6.3, 1.0, 1.0]]
# load it into PyMOL
cmd.load_callback(myCallback(), "gl02")
# give us a nice view
cmd.turn("z", 20)
cmd.turn("y", 20)
cmd.turn("x", 20)
self.norm[2 * a][1] = math.sqrt(1.0 - dydx * dydx)
self.norm[2 * a][2] = 0.0
self.norm[2 * a + 1][0] = self.norm[2 * a][0]
self.norm[2 * a + 1][1] = self.norm[2 * a][1]
self.norm[2 * a + 1][2] = self.norm[2 * a][2]
def __call__(self):
glColor3f(1.0, 1.0, 1.0)
glVertexPointer(3, GL_FLOAT, 0, self.vert)
glNormalPointer(GL_FLOAT, 0, self.norm)
glEnableClientState(GL_VERTEX_ARRAY)
glEnableClientState(GL_NORMAL_ARRAY)
glDisableClientState(GL_COLOR_ARRAY)
glDrawArrays(GL_TRIANGLE_STRIP, 0, 126)
def get_extent(self):
return [[0.0, 0.0, -1.0], [6.3, 1.0, 1.0]]
# load it into PyMOL
cmd.load_callback(myCallback(), 'gl02')
# give us a nice view
cmd.turn('z', 20)
cmd.turn('y', 20)
cmd.turn('x', 20)
self.norm[2*a+1][1]=self.norm[2*a][1]
self.norm[2*a+1][2]=self.norm[2*a][2]
def __call__(self):
glColor3f(1.0,1.0,1.0)
glVertexPointer(3,GL_FLOAT, 0,self.vert)
glNormalPointer(GL_FLOAT,0,self.norm)
glEnableClientState(GL_VERTEX_ARRAY)
glEnableClientState(GL_NORMAL_ARRAY)
glDisableClientState(GL_COLOR_ARRAY)
glDrawArrays(GL_TRIANGLE_STRIP,0,126)
def get_extent(self):
return [[0.0,0.0,-1.0],
[6.3,1.0,1.0]]
# load it into PyMOL
for b in range(0,63):
cmd.load_callback(myCallback(b),'gl03',b+1)
# give us a nice view
cmd.turn('z',20)
cmd.turn('y',20)
cmd.turn('x',20)
cmd.mplay()
def load(self):
cmd.load_callback(self, self.cb_name)
def runSurfStamp_(self):
import tempfile
tmpdir = tempfile.TemporaryDirectory()
tmp_outfile = tmpdir.name + "/tmpout.obj"
if len(re.sub("[\s]*", "", self.text_outprefix.text())) > 0:
tmp_outfile = self.text_outprefix.text()
my_view = cmd.get_view()
modelname = self.combo_model.currentText()
output_modelname = re.sub("[^A-Za-z0-9\\.\\-]", "_",
modelname) + "_obj"
output_modelname = cmd.get_unused_name(output_modelname)
surf_args = ["java", "-jar", surfstamp_jar]
surf_args.extend(["-out", tmp_outfile])
tmpmodel_created = ""
if self.check_cartoon.isChecked() or (
not self.check_builtin.isChecked()):
#Use .obj generated by PyMOL. If this step is skipped, built-in generator is used.
tmpmodel_created = cmd.get_unused_name("tmpmodel_")
cmd.load_model(cmd.get_model(modelname), tmpmodel_created)
cmd.set_view((0.9999905824661255, -0.00367919635027647,
-0.002306032460182905, 0.003680833615362644,
0.9999929666519165, 0.0007080769282765687,
0.0023034177720546722, -0.0007165365968830884,
0.999997079372406, 0.0, 0.0, -50.0, 0.0, 0.0, 0.0,
40.0, 100.0, -20.0))
activeobjects = cmd.get_names('public_objects', enabled_only=1)
for aa in list(activeobjects):
cmd.disable(aa)
cmd.enable(tmpmodel_created)
modelname = tmpmodel_created
cmd.hide("everything", modelname)
if self.check_cartoon.isChecked():
cmd.show("cartoon", modelname)
surf_args.extend(["-use_ca", "-force", "-sep_block"])
else:
cmd.show("surface", modelname)
surf_args.extend(["-force"])
cmd.reset()
cmd.origin(position=[0.0, 0.0, 0.0])
cmd.center(origin=0)
unusedname = cmd.get_unused_name("pseudo_")
unused_selectionname = cmd.get_unused_name("pseudo_sel_")
cmd.pseudoatom(unusedname, pos=[0, 0, 0])
cmd.select(unused_selectionname, "/pseudo_//P/PSD`1/PS1")
cmd.center(selection=unused_selectionname)
cmd.save(tmpdir.name + "/tmpin.obj", modelname)
cmd.delete(unusedname)
cmd.delete(unused_selectionname)
for aa in list(activeobjects):
cmd.enable(aa)
surf_args.extend(["-obj", tmpdir.name + "/tmpin.obj"])
cmd.hide("everything", modelname)
if self.check_mmcif.isChecked():
tmp_infile = tmpdir.name + "/tmpin.cif"
surf_args.extend(["-mmcif_use_label", "-mmcif", tmp_infile])
cmd.save(tmp_infile, modelname)
else:
tmp_infile = tmpdir.name + "/tmpin.pdb"
cmd.save(tmp_infile, modelname)
surf_args.extend(["-pdb", tmp_infile])
if len(tmpmodel_created) > 0:
cmd.delete(tmpmodel_created)
surf_args.extend(["-surface_resolution",
str(self.spin_reso.value())])
surf_args.extend(["-image_size",
str(self.spin_imagesize.value())])
if not self.check_outline.isChecked():
surf_args.extend(["-nooutline"])
if self.check_nowater.isChecked():
surf_args.extend(["-nowater"])
if self.check_oneletter.isChecked():
surf_args.extend(["-residue_oneletter"])
if self.check_nochainname.isChecked():
surf_args.extend(["-nochainname"])
if self.check_tile.isChecked():
if self.check_cartoon.isChecked():
surf_args.extend(
["-tile", "-font_size",
str(self.spin_fontsize.value())])
else:
surf_args.extend([
"-tile", "-no_sep", "-font_size",
str(self.spin_fontsize.value())
])
if self.check_colorall.isChecked():
surf_args.extend(["-color_missing", "-color_chainbreak"])
if self.check_ignore_occupancy.isChecked():
surf_args.extend(["-ignore_occupancy"])
surf_args.extend(["-quiet", "1"])
import subprocess
process = subprocess.run(surf_args,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
#process = subprocess.run(surf_args, stdout=None, stderr=subprocess.PIPE);
print(process.stdout.decode("utf-8"))
#os.system(" ".join(surf_args)+" >&2 ");
self.label_message.setText("Finished.")
print("Finished.")
self.text_outprefix.setText("")
self.button_ok.setEnabled(True)
self.update()
if not re.search("\.obj$", tmp_outfile):
tmp_outfile = tmp_outfile + ".obj"
cmd.load_callback(pymol_obj_loader.myOBJCallback(tmp_outfile),
output_modelname)
cmd.set_view(my_view)
