def testIsomesh(self):
cmd.viewport(100, 100)
cmd.fragment('gly', 'm1')
cmd.set('gaussian_b_floor', 30)
cmd.set('mesh_width', 5)
cmd.map_new('map')
cmd.delete('m1')
# make mesh
cmd.isomesh('mesh', 'map')
cmd.isomesh('mesh', 'map', source_state=1, state=-2)
## check mesh presence by color
meshcolor = 'red'
cmd.color(meshcolor, 'mesh')
self.ambientOnly()
self.assertImageHasColor(meshcolor)
cmd.frame(2)
self.assertEqual(cmd.get_state(), 2)
self.assertImageHasColor(meshcolor)
with testing.mktemp('.pse') as filename:
cmd.save(filename)
cmd.delete('*')
self.assertImageHasNotColor(meshcolor)
cmd.load(filename)
self.assertImageHasColor(meshcolor)
cmd.frame(2)
self.assertEqual(cmd.get_state(), 2)
self.assertImageHasColor(meshcolor)
def test(self):
cmd.viewport(100, 100)
# make map
cmd.fragment('gly', 'm1')
cmd.set('gaussian_b_floor', 30)
cmd.set('mesh_width', 5)
cmd.map_new('map')
cmd.delete('m1')
# make mesh
cmd.isomesh('mesh', 'map')
# check mesh presence by color
meshcolor = 'red'
cmd.color(meshcolor, 'mesh')
self.ambientOnly()
self.assertImageHasColor(meshcolor)
# continue without map
cmd.delete('map')
with testing.mktemp('.pse') as filename:
cmd.save(filename)
cmd.delete('*')
self.assertImageHasNotColor(meshcolor)
cmd.load(filename)
self.assertImageHasColor(meshcolor)
def mesh_ribbon():
cmd.hide('everything')
glb.update()
cmd.map_new('map', "gaussian", "0.75", 'all')
glb.procolor(None,show_all=('lines','ribbon'),color_all='red')
cmd.isomesh('map1', 'map', '1')
cmd.color('purple','map1')
def mesh_ribbon():
cmd.hide('everything')
glb.update()
cmd.map_new('map', "gaussian", "0.75", 'all')
glb.procolor(None, show_all=('lines', 'ribbon'), color_all='red')
cmd.isomesh('map1', 'map', '1')
cmd.color('purple', 'map1')
def test(self):
cmd.viewport(100, 100)
# make map
cmd.fragment('gly', 'm1')
cmd.set('gaussian_b_floor', 30)
cmd.set('mesh_width', 5)
cmd.map_new('map')
cmd.delete('m1')
# make mesh
cmd.isomesh('mesh', 'map')
# check mesh presence by color
meshcolor = 'red'
cmd.color(meshcolor, 'mesh')
self.ambientOnly()
self.assertImageHasColor(meshcolor)
# continue without map
cmd.delete('map')
with testing.mktemp('.pse') as filename:
cmd.save(filename)
cmd.delete('*')
self.assertImageHasNotColor(meshcolor)
cmd.load(filename)
self.assertImageHasColor(meshcolor)
def test(self):
cmd.viewport(100,100)
cmd.set('gaussian_b_floor', 20)
cmd.set('ambient', 1)
cmd.set('specular', 0)
cmd.set('mesh_color', 'blue')
cmd.set('dot_color', 'green')
cmd.fragment('gly')
cmd.map_new('map1')
cmd.disable('*')
cmd.isomesh('o1', 'map1')
cmd.color('red', 'o1')
cmd.show('cell')
self._check_colors('red', 'blue')
cmd.delete('o1')
cmd.isodot('o1', 'map1')
cmd.color('red', 'o1')
self._check_colors('green')
cmd.delete('o1')
cmd.gradient('o1', 'map1')
cmd.color('yellow', 'o1')
self._check_colors('yellow')
cmd.delete('o1')
def update(self):
self.center = cmd.get_position()
cmd.alter_state(0,
self.center_name,
"(x, y, z) = p",
space={'p': self.center})
cmd.isomesh(self.name,
self.map_name,
self.level,
self.center_name,
carve=self.radius)
def emesh(event):
delcrea()
try:
if len(nameit.get()) < 1:
showinfo("Error", 'Enter a name for the object')
interior.mainloop()
elif len(pdbname.get()) < 1:
showinfo('Error', "Enter the Map Filename")
interior.mainloop()
else:
cmd.isomesh(nameit.get(), pdbname.get(), contour1.get())
except:
showinfo("Error", 'No map is present')
interior.mainloop()
def roving_density(self, cleanup=0):
if not cleanup:
try:
cmd.load("$PYMOL_DATA/demo/il2.pdb")
cmd.set("suspend_updates", 1, quiet=1)
cmd.remove("hydro")
cmd.disable()
cmd.enable("il2")
cmd.map_new("map", "gaussian", "0.75", "il2")
cmd.feedback("disable", "objectmesh", "actions")
cmd.set("ribbon_color", "purple", "il2")
cmd.set("roving_detail", 1)
cmd.set("roving_origin", 1)
cmd.set("stick_radius", 0.12, "il2")
cmd.set("roving_sticks", 0)
cmd.set("roving_polar_contacts", 0)
cmd.set("line_width", "3")
cmd.set("roving_map1_name", "map")
cmd.isomesh("rov_m1", "map", 9999.0, "il2")
cmd.color("density", "rov_m1")
cmd.set_view ((\
0.132852688, -0.729740858, 0.670686543,\
-0.228543565, 0.635894477, 0.737154961,\
-0.964425683, -0.251212329, -0.082298420,\
0.000062190, 0.000183226, -58.861488342,\
13.349151611, -1.565427899, 22.383148193,\
55.259441376, 63.259449005, 0.000000000 ))
finally:
cmd.set("suspend_updates", 0, quiet=1)
cmd.refresh()
else:
cmd.set("roving_detail", 0)
cmd.set("roving_map1_name", "")
cmd.set("roving_polar_contacts", 7)
cmd.set("roving_sticks", 6)
cmd.delete("il2")
cmd.delete("map")
cmd.set("line_width", 1.5)
cmd.refresh()
cmd.set("roving_detail", 0)
cmd.delete("rov_*")
cmd.sync()
def emesh1(event):
delcrea()
try:
cmd.isomesh('map1','map', contour1.get(), 'sele')
except:
try:
cmd.remove("hydro")
cmd.enable('all')
cmd.map_new('map',"gaussian","0.75", 'all')
cmd.isomesh('map1','map', contour1.get(), 'sele')
except:
cmd.orient('all')
showinfo("Error", 'No PDB is present\nOr there is no selection ('"sele"')')
interior.mainloop()
def roving_density(self,cleanup=0):
if not cleanup:
try:
cmd.load("$PYMOL_DATA/demo/il2.pdb")
cmd.set("suspend_updates",1,quiet=1)
cmd.remove("hydro")
cmd.disable()
cmd.enable("il2")
cmd.map_new("map","gaussian","0.75","il2")
cmd.feedback("disable","objectmesh","actions")
cmd.set("ribbon_color","purple","il2")
cmd.set("roving_detail",1)
cmd.set("roving_origin",1)
cmd.set("stick_radius",0.12,"il2")
cmd.set("roving_sticks",0)
cmd.set("roving_polar_contacts",0)
cmd.set("line_width","3")
cmd.set("roving_map1_name","map")
cmd.isomesh("rov_m1","map",9999.0,"il2")
cmd.color("density","rov_m1")
cmd.set_view ((\
0.132852688, -0.729740858, 0.670686543,\
-0.228543565, 0.635894477, 0.737154961,\
-0.964425683, -0.251212329, -0.082298420,\
0.000062190, 0.000183226, -58.861488342,\
13.349151611, -1.565427899, 22.383148193,\
55.259441376, 63.259449005, 0.000000000 ))
finally:
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
else:
cmd.set("roving_detail",0)
cmd.set("roving_map1_name","")
cmd.set("roving_polar_contacts",7)
cmd.set("roving_sticks",6)
cmd.delete("il2")
cmd.delete("map")
cmd.set("line_width",1.5)
cmd.refresh()
cmd.set("roving_detail",0)
cmd.delete("rov_*")
cmd.sync()
def emesh(event):
delcrea()
try:
if len(nameit.get()) < 1:
showinfo("Error", 'Enter a name for the object')
interior.mainloop()
elif len(pdbname.get()) < 1:
showinfo('Error', "Enter the Map Filename")
interior.mainloop()
else:
cmd.isomesh(nameit.get(),pdbname.get(), contour1.get())
except:
showinfo("Error", 'No map is present')
interior.mainloop()
def emesh1(*args):
delcrea()
try:
if len(nameit.get()) < 1:
showinfo("Error", 'Enter a name for the object')
interior.mainloop()
elif len(pdbname.get()) < 1:
showinfo('Error', "Enter the Map Filename")
interior.mainloop()
else:
cmd.isomesh(nameit.get(), pdbname.get(), contour1.get(),
('sele'))
except:
cmd.orient('all')
showinfo("Error",
'No map is present\n Or there is no selection ("sele")')
interior.mainloop()
def emesh1(event):
delcrea()
try:
cmd.isomesh('map1', 'map', contour1.get(), 'sele')
except:
try:
cmd.remove("hydro")
cmd.enable('all')
cmd.map_new('map', "gaussian", "0.75", 'all')
cmd.isomesh('map1', 'map', contour1.get(), 'sele')
except:
cmd.orient('all')
showinfo(
"Error", 'No PDB is present\nOr there is no selection ('
"sele"
')')
interior.mainloop()
def show_map(unit_cell, map_covering_unit_cell, label, level):
map_grid = map_covering_unit_cell.focus()
print "map_grid:", map_grid
ucell_params = unit_cell.parameters()
first = [0, 0, 0]
last = [map_grid[i] + 1 for i in xrange(3)]
c_obj_map = maptbx.as_CObjectZYX(map_unit_cell=map_covering_unit_cell,
first=first,
last=last,
apply_sigma_scaling=True)
map = Map()
map.from_c_object(c_obj_map, 'CObjectZYXfloat', ucell_params[0:3],
ucell_params[3:6], list(map_grid), first, last)
cmd.load_map(map, label + "_cell")
print "map loaded into PyMol"
cmd.isomesh(label + "_con", label + "_cell", level) # create mesh
cmd.color('gray', label + "_cell") # color wire frame
cmd.set('auto_zoom', '0') # disable zooming
cmd.set('ortho', '1') # orthoscopic projects
cmd.enable(label + "_cell") # put box around map object
cmd.color('cyan', label + "_con") # color mesh
def emesh1(*args):
delcrea()
try:
if len(nameit.get()) < 1:
showinfo("Error", 'Enter a name for the object')
interior.mainloop()
elif len(pdbname.get()) < 1:
showinfo('Error', "Enter the Map Filename")
interior.mainloop()
else:
cmd.isomesh(nameit.get(),pdbname.get(), contour1.get(), ('sele'))
except:
cmd.orient('all')
showinfo("Error", 'No map is present\n Or there is no selection ("sele")')
interior.mainloop()
def show_map(unit_cell, map_covering_unit_cell, label, level):
map_grid = map_covering_unit_cell.focus()
print "map_grid:", map_grid
ucell_params = unit_cell.parameters()
first = [0,0,0]
last = [map_grid[i] + 1 for i in xrange(3)]
c_obj_map = maptbx.as_CObjectZYX(
map_unit_cell=map_covering_unit_cell,
first=first,
last=last,
apply_sigma_scaling=True)
map=Map()
map.from_c_object(c_obj_map,'CObjectZYXfloat',
ucell_params[0:3], ucell_params[3:6],
list(map_grid), first, last)
cmd.load_map(map, label+"_cell")
print "map loaded into PyMol"
cmd.isomesh(label+"_con", label+"_cell", level) # create mesh
cmd.color('gray', label+"_cell") # color wire frame
cmd.set('auto_zoom', '0') # disable zooming
cmd.set('ortho', '1') # orthoscopic projects
cmd.enable(label+"_cell") # put box around map object
cmd.color('cyan', label+"_con") # color mesh
def roving_density():
delcrea()
try:
cmd.set("suspend_updates", 1, quiet=1)
cmd.remove("hydro")
cmd.disable()
cmd.enable('all')
cmd.map_new('map', "gaussian", "0.75", 'all')
cmd.set('roving_isomesh', rovingradius1.get())
cmd.set("roving_detail", 1)
cmd.set("stick_radius", 0.5)
cmd.set("roving_sticks", 0)
cmd.set('roving_lines', rovingradius1.get())
cmd.set("roving_polar_contacts", 0)
cmd.set("line_width", "3")
cmd.set("roving_map1_name", 'map')
cmd.isomesh("map1", "map", 9999.0, 'all')
cmd.set("suspend_updates", 0, quiet=1)
cmd.refresh()
cmd.delete('rov_s1')
cmd.set('roving_isosurface', 0)
except:
showinfo("Error", 'No PDB is present')
interior.mainloop()
def roving_density():
delcrea()
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.remove("hydro")
cmd.disable()
cmd.enable('all')
cmd.map_new('map',"gaussian","0.75", 'all')
cmd.set('roving_isomesh', rovingradius1.get())
cmd.set("roving_detail",1)
cmd.set("stick_radius",0.5)
cmd.set("roving_sticks",0)
cmd.set('roving_lines', rovingradius1.get())
cmd.set("roving_polar_contacts",0)
cmd.set("line_width","3")
cmd.set("roving_map1_name",'map')
cmd.isomesh("map1", "map", 9999.0, 'all')
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.delete('rov_s1')
cmd.set('roving_isosurface',0)
except:
showinfo("Error", 'No PDB is present')
interior.mainloop()
def emesh(*args):
delcrea()
try:
cmd.isomesh('map1', 'map', contour1.get())
except:
try:
cmd.set("suspend_updates", 1, quiet=1)
cmd.remove("hydro")
cmd.enable('all')
cmd.map_new('map', "gaussian", "0.75", 'all')
cmd.isomesh("map1", "map", 9999.0, 'all')
cmd.set("suspend_updates", 0, quiet=1)
cmd.isomesh('map1', 'map', contour1.get())
cmd.refresh()
except:
showinfo("Error", 'No PDB is present')
interior.mainloop()
def emesh(*args):
delcrea()
try:
cmd.isomesh('map1','map', contour1.get())
except:
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.remove("hydro")
cmd.enable('all')
cmd.map_new('map',"gaussian","0.75", 'all')
cmd.isomesh("map1", "map", 9999.0, 'all')
cmd.set("suspend_updates",0,quiet=1)
cmd.isomesh('map1','map', contour1.get())
cmd.refresh()
except:
showinfo("Error", 'No PDB is present')
interior.mainloop()
cmd.load(f, 'label_threshold_8.35000038147')
cmd.hide('everything', 'label_threshold_8.35000038147')
cmd.label("label_threshold_8.35000038147", "name")
cmd.set("label_font_id", 7)
cmd.set("label_size", -0.4)
cmd.group('Pharmacophore_8.35000038147',
members='label_threshold_8.35000038147')
if dirpath:
f = join(dirpath, '0/mesh.grd')
else:
f = '0/mesh.grd'
cmd.load(f, 'mesh_0')
cmd.isomesh("isomesh_0", "mesh_0", 0.9)
cmd.color("grey80", "isomesh_0")
cmd.set('transparency', 0.4, "isomesh_0")
cmd.group('hotspot_0', "isomesh_0")
cmd.group('hotspot_0', "mesh_0")
if dirpath:
f = join(dirpath, "1/label_threshold_13.1.mol2")
else:
f = "1/label_threshold_13.1.mol2"
cmd.load(f, 'label_threshold_13.1')
cmd.hide('everything', 'label_threshold_13.1')
cmd.label("label_threshold_13.1", "name")
cmd.set("label_font_id", 7)
def _make_mesh(self, oname):
mapname = oname + '_map'
self._make_map(mapname)
cmd.isomesh(oname, mapname)
def update(self):
self.center = cmd.get_position()
cmd.alter_state(0, self.center_name, "(x, y, z) = p", space={'p': self.center})
cmd.isomesh(self.name, self.map_name, self.level, self.center_name, carve=self.radius)
def _make_mesh(self, oname):
mapname = oname + '_map'
self._make_map(mapname)
cmd.isomesh(oname, mapname)
cmd.load_mtz(reflectionFile, prefix='my_map'
) #, amplitudes = 'unknown/unknown291019/REFM_FWT',
#phases = 'unknown/unknown291019/REFM_PHWT',reso_low = 23.96, reso_high = 1.9)
#cmd.map_double("my_map")
cmd.map_double("my_map.2fofc")
print("upload finished")
cmd.hide("everything")
cmd.show("sticks")
cmd.set_bond('stick_radius', '0.1', 'overall_best')
cmd.center()
cmd.select('site',
'br. all within ' + str(radius_check) + ' of center')
cmd.isomesh('map', 'my_map.2fofc', 1.0, 'site', carve=1.6)
cmd.color('gray40', 'map')
cmd.set('mesh_width', '0.1')
cmd.bg_color('white')
cmd.set("ray_trace_fog", "0")
cmd.set("depth_cue", "0")
cmd.set("ray_shadows", "off")
cmd.ray(1024, 1024)
cmd.show("mesh", "map")
cmd.zoom('site')
f = "0\label_threshold_rank_1.mol2"
cmd.load(f, 'label_threshold_rank_1')
cmd.hide('everything', 'label_threshold_rank_1')
cmd.label("label_threshold_rank_1", "name")
cmd.set("label_font_id", 7)
cmd.set("label_size", -0.4)
cmd.group('Pharmacophore_rank_1', members='label_threshold_rank_1')
if dirpath:
f = join(dirpath, '0\mesh.grd')
else:
f = '0\mesh.grd'
cmd.load(f, 'mesh_0')
cmd.isomesh("isomesh_0", "mesh_0", 0.9)
cmd.color("grey80", "isomesh_0")
cmd.set('transparency', 0.4, "isomesh_0")
cmd.group('hotspot_0', "isomesh_0")
cmd.group('hotspot_0', "mesh_0")
if dirpath:
f = join(dirpath, "1\label_threshold_15.2.mol2")
else:
f = "1\label_threshold_15.2.mol2"
cmd.load(f, 'label_threshold_15.2')
cmd.hide('everything', 'label_threshold_15.2')
cmd.label("label_threshold_15.2", "name")
cmd.set("label_font_id", 7)
