def surfinglines():
cmd.hide('everything')
glb.update()
cmd.map_new('map', "gaussian", "0.75", 'all')
glb.procolor(None,show_all='lines')
cmd.isosurface('map1', 'map', '1')
cmd.color('orange', "map1")
cmd.set('transparency', '0.4')
cmd.set('ambient', '0.45')
def nci( arg1 ):
densf=arg1+"-dens"
gradf=arg1+"-grad"
# gdens=open(densf+".cube","r")
# grad=open(gradf+".cube","r")
cmd.isosurface("grad",gradf, 0.5)
cmd.ramp_new("ramp", densf, [-5,5], "rainbow")
cmd.set("surface_color", "ramp", "grad")
cmd.set('two_sided_lighting',value=1)
def testSurfaceAction(self):
sele = 'surf1'
mapname = 'map1'
self._make_map(mapname)
cmd.isosurface(sele, mapname)
m = menu.surface_action(cmd, sele)
self._eval_first(m)
m = menu.surface_hide(cmd, sele)
self._eval_first(m)
m = menu.surface_show(cmd, sele)
self._eval_first(m)
def rpcLoadSurface(fileName, objName, format='', surfaceLevel=1.0):
""" loads surface data from a file and adds an isosurface
Arguments:
fileName: the file to load
objName: (OPTIONAL) name of the object to create
format: (OPTIONAL) the format of the input file
surfaceLevel: (OPTIONAL) the isosurface level
"""
if not objName:
objName = fileName.split('.')[0]
gridName = 'grid-%s' % objName
res = cmd.load(fileName, gridName, format='')
cmd.isosurface(objName, gridName, level=surfaceLevel)
if res is not None:
return res
else:
return ''
def esurf(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.isosurface(nameit.get(), pdbname.get(), contour1.get())
except:
showinfo("Error", 'No map is present')
interior.mainloop()
def esurf1(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.isosurface(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 esurf(*args):
delcrea()
try:
cmd.isosurface('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.isosurface("map1", "map", 9999.0, 'all')
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.isosurface('map1','map', contour1.get())
except:
showinfo("Error", 'No PDB is present')
interior.mainloop()
def esurf1(event):
delcrea()
try:
cmd.isosurface('map1','map', contour1.get(), 'sele')
except:
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.remove("hydro")
cmd.enable('all')
cmd.map_new('map',"gaussian","0.75", 'all')
cmd.isosurface("map1", "map", 9999.0, 'all')
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.isosurface('map1','map', contour1.get(), 'sele')
except:
cmd.orient('all')
showinfo("Error", 'No PDB is present\nOr there is no selection ('"sele"')')
interior.mainloop()
from os.path import join
import tempfile
import zipfile
import math
from pymol import cmd, finish_launching
from pymol.cgo import *
finish_launching()
cmd.set_color("pomegranate",
(0.9411764705882353, 0.20392156862745098, 0.20392156862745098))
cmd.load("test_grid.grd", "mygrid", state=1)
cmd.isosurface(name="mysurface", map="mygrid", level="4")
cmd.color("pomegranate", "mysurface")
def genAV(obstacles,
attachment,
linker_length=20.0,
linker_diameter=2.0,
dye_radius=3.5,
disc_step=0.9,
name=None,
state=1,
stripsc=True,
allowed_sphere_radius=0.0,
smoothSurf=True):
source = np.array(cmd.get_model(attachment, state).get_coord_list())
if (source.shape[0] != 1):
print(
'attachment selection must contain exactly one atom, selected: {}'.
format(source.shape[0]))
return
source = source.reshape(3)
srcAt = cmd.get_model(attachment, state).atom[0]
srcModelName = cmd.get_names('objects', 0, attachment)[0]
obstacles = '(' + obstacles + ') and not (' + attachment + ')'
if stripsc and isAA(srcAt.resn):
obstacles += ' and not (' + srcModelName
if len(srcAt.chain) > 0:
obstacles += ' and chain ' + srcAt.chain
obstacles += ' and resi ' + srcAt.resi + ' and sidechain' + ')'
if allowed_sphere_radius > 0.0:
obstacles += ' and not (({}) around {})'.format(
attachment, allowed_sphere_radius)
xyzRT = np.zeros((1, 4))
nAtoms = cmd.count_atoms(obstacles)
if nAtoms > 0:
atoms = cmd.get_model(obstacles, state).atom
nAtoms = len(atoms)
xyzRT = np.zeros((nAtoms, 4))
for i, at in enumerate(atoms):
xyzRT[i] = [at.coord[0], at.coord[1], at.coord[2], at.vdw]
av1 = ll.dyeDensityAV1(xyzRT.T, source, linker_length, linker_diameter,
dye_radius, disc_step)
m = avToModel(av1)
if len(m.atom) == 0:
print('Failed: Empty AV. Is attachment position buried?')
return
if name is None:
name = srcModelName + '_'
if len(srcAt.chain) > 0:
name += srcAt.chain + '-'
name += srcAt.resi + '-' + srcAt.name
cmd.load_model(m, name)
if smoothSurf:
surfName = name + '_surf'
mapName = name + '_map'
gRes = cmd.get('gaussian_resolution')
cmd.set('gaussian_resolution', 3.0)
cmd.map_new(mapName, 'gaussian', 1.0, name, 6)
cmd.isosurface(surfName, mapName, 0.9)
cmd.set('gaussian_resolution', gRes)
cmd.disable(name)
colour_dict = {'acceptor':'red', 'donor':'blue', 'apolar':'yellow', 'negative':'purple', 'positive':'cyan'}
threshold_list = [10, 14, 17]
gfiles = ['donor.grd', 'apolar.grd', 'acceptor.grd']
grids = ['donor', 'apolar', 'acceptor']
num = 0
surf_transparency = 0.2
if dirpath:
gfiles = [join(dirpath, g) for g in gfiles]
for t in threshold_list:
for i in range(len(grids)):
try:
cmd.load(r'%s'%(gfiles[i]), '%s_%s'%(grids[i], str(num)))
cmd.isosurface('surface_%s_%s_%s'%(grids[i], t, num), '%s_%s'%(grids[i], num), t)
cmd.set('transparency', surf_transparency, 'surface_%s_%s_%s'%(grids[i], t, num))
cmd.color(colour_dict['%s'%(grids[i])], 'surface_%s_%s_%s'%(grids[i], t, num))
cmd.group('threshold_%s'%(t), members = 'surface_%s_%s_%s'%(grids[i],t, num))
cmd.group('threshold_%s' % (t), members='label_threshold_%s' % (t))
except:
continue
try:
cmd.group('hotspot_%s' % (num), members='threshold_%s' % (t))
except:
continue
for g in grids:
cmd.group("ligand_pharmacophore", members="CYS_pts")
cmd.group("ligand_pharmacophore", members="PHE_pts")
cmd.group("ligand_pharmacophore", members="LEU_pts")
cmd.group("ligand_pharmacophore", members="LYS_pts")
cmd.group("ligand_pharmacophore", members="ILE_pts")
cmd.group("ligand_pharmacophore", members="THR_pts")
cmd.group("ligand_pharmacophore", members="TRP_pts")
cmd.group("ligand_pharmacophore", members="ASN_pts")
cmd.group("ligand_pharmacophore", members="VAL_pts")
cmd.group("ligand_pharmacophore", members="HIS_pts")
cmd.group("ligand_pharmacophore", members="MET_pts")
cmd.group("ligand_pharmacophore", members="ARG_pts")
cmd.group("ligand_pharmacophore", members="GLU_pts")
cmd.set_color("ring_color", (0.33, 1.0, 0.0))
cmd.load("ring.grd", "ring_grid")
cmd.isosurface(name="surface_ring", map="ring_grid", level="1")
cmd.color("ring_color", "surface_ring")
cmd.set_color("acceptor_projected_color", (1.0, 0.0, 0.0))
cmd.load("acceptor_projected.grd", "acceptor_projected_grid")
cmd.isosurface(name="surface_acceptor_projected",
map="acceptor_projected_grid",
level="1")
cmd.color("acceptor_projected_color", "surface_acceptor_projected")
cmd.set_color("donor_projected_color", (0.0, 0.0, 1.0))
cmd.load("donor_projected.grd", "donor_projected_grid")
cmd.isosurface(name="surface_donor_projected",
map="donor_projected_grid",
level="1")
def set_atom_level(level,
selection='*',
state=None,
rec_map=None,
lig_map=None):
if rec_map is None:
rec_channels = atom_types.get_default_rec_channels()
else:
rec_channels = atom_types.get_channels_from_file(
rec_map, name_prefix='Receptor')
if lig_map is None:
lig_channels = atom_types.get_default_lig_channels()
else:
lig_channels = atom_types.get_channels_from_file(lig_map,
name_prefix='Ligand')
channels = rec_channels + lig_channels
channels_by_name = dict((c.name, c) for c in channels)
for c in channels:
cmd.set_color(c.name + '$', atom_types.get_channel_color(c))
dx_regex = re.compile(r'(.*)_(\d+)_({})\.dx'.format(
'|'.join(channels_by_name)))
surface_groups = OrderedDict()
for dx_object in sorted(cmd.get_names('objects')):
if not fnmatch.fnmatch(dx_object, selection):
continue
m = dx_regex.match(dx_object)
if not m:
continue
grid_prefix = m.group(1)
sample_idx = int(m.group(2))
channel = channels_by_name[m.group(3)]
if state is None:
surface_state = sample_idx + 1
else:
surface_state = state
surface_object = '{}_{}_surface'.format(grid_prefix, channel.name)
cmd.isosurface(surface_object,
dx_object,
level=level,
state=surface_state)
cmd.color(channel.name + '$', surface_object)
if grid_prefix not in surface_groups:
surface_groups[grid_prefix] = []
if surface_object not in surface_groups[grid_prefix]:
surface_groups[grid_prefix].append(surface_object)
for grid_prefix, surface_objects in surface_groups.items():
surface_group = '{}_surfaces'.format(grid_prefix)
cmd.group(surface_group, ' '.join(surface_objects))
import zipfile
import math
from pymol import cmd, finish_launching, plugins
from pymol.cgo import *
finish_launching()
dirpath = tempfile.mkdtemp()
zip_dir = "out.zip"
wd = os.getcwd()
with zipfile.ZipFile(zip_dir) as hs_zip:
hs_zip.extractall(dirpath)
os.chdir(dirpath)
cmd.load("hotspot/apolar.grd", "apolar_hotspot")
cmd.isosurface(name="surface_apolar_hotspot", map="apolar_hotspot", level="5")
cmd.color("yellow", "surface_apolar_hotspot")
cmd.set("transparency", 0.2, "surface_apolar_hotspot")
cmd.load("hotspot/donor.grd", "donor_hotspot")
cmd.isosurface(name="surface_donor_hotspot", map="donor_hotspot", level="5")
cmd.color("blue", "surface_donor_hotspot")
cmd.set("transparency", 0.2, "surface_donor_hotspot")
cmd.load("hotspot/acceptor.grd", "acceptor_hotspot")
cmd.isosurface(name="surface_acceptor_hotspot",
map="acceptor_hotspot",
level="5")
cmd.color("red", "surface_acceptor_hotspot")
cmd.set("transparency", 0.2, "surface_acceptor_hotspot")
def set_atom_level(level, selection='*', state=None):
channels = atom_types.get_default_channels(True)
channel_names = [c.name for c in channels]
channels_by_name = {n: channels[i] for i, n in enumerate(channel_names)}
for channel in channels:
cmd.set_color(channel.name + '$',
atom_types.get_channel_color(channel))
# first identify .dx atom density grids
dx_pattern = r'(.*)_({})\.dx'.format('|'.join(channel_names))
dx_groups = OrderedDict()
for obj in sorted(cmd.get_names('objects')):
match = re.match(dx_pattern, obj)
if match:
dx_prefix = match.group(1)
if dx_prefix not in dx_groups:
dx_groups[dx_prefix] = []
dx_groups[dx_prefix].append(obj)
surface_groups = OrderedDict()
for dx_prefix in dx_groups:
match = re.match(r'^(.*)_(\d+)$', dx_prefix)
if match:
surface_prefix = match.group(1)
if state is None:
state_ = int(match.group(2)) + 1
else:
state_ = state
else:
surface_prefix = dx_prefix
state_ = state or 0
for dx_object in dx_groups[dx_prefix]:
if fnmatch.fnmatch(dx_object, selection):
match = re.match(dx_pattern, dx_object)
channel_name = match.group(2)
channel = channels_by_name[channel_name]
element = atom_types.get_name(channel.atomic_num)
surface_object = '{}_{}_surface'.format(
surface_prefix, channel_name)
cmd.isosurface(surface_object,
dx_object,
level=level,
state=state_)
cmd.color(channel.name + '$', surface_object)
if surface_prefix not in surface_groups:
surface_groups[surface_prefix] = []
if surface_object not in surface_groups[surface_prefix]:
surface_groups[surface_prefix].append(surface_object)
for surface_prefix in surface_groups:
surface_group = '{}_surface'.format(surface_prefix)
cmd.group(surface_group, ' '.join(surface_groups[surface_prefix]))
def show_iso(dname, iso, color="white"):
sname = "%s%.4f" % (dname, iso)
cmd.isosurface(sname, dname, iso)
cmd.set("surface_color", color, sname)
cmd.rebuild()
cmd.load_cgo(obj, 'axes')
cmd.bg_color('white')
#cmd.set_bond ('stick_color', 'white', 'clauc2h2', 'clauc2h2')
#cmd.set_bond ('stick_radius', -0.14, 'clauc2h2', 'clauc2h2')
#cmd.set ('stick_ball', 1)
#cmd.set ('stick_ball_ratio', -0.5)
#cmd.set ('stick_ball_color', 'atomic')
#cmd.show ('sticks', 'clauc2h2')
##cmd.set ('sphere_scale', 0.25, 'clauc2h2')
##cmd.show ('spheres', 'clauc2h2')
cmd.load('this.cube')
cmd.isosurface('sp', 'this', _iso)
cmd.color('green', 'sp')
cmd.isosurface('sm', 'this', -_iso)
cmd.color('_colorm', 'sm')
#cmd.load('dif_B1.cube')
#cmd.isosurface('spp', 'dif_B1', 0.00008)
#cmd.color('blue', 'spp')
#cmd.isosurface('smp', 'dif_B1', -0.00008)
#cmd.color('red', 'smp')
#cmd.set ('label_font_id', 16)
#cmd.set ('label_size', 24)
#cmd.pseudoatom('xatom', pos=[1,0,0], label="x")
#cmd.pseudoatom('yatom', pos=[0,1,0], label="y")
#cmd.pseudoatom('zatom', pos=[0,0,2], label="z")
cmd.load_cgo(obj, 'axes')
cmd.bg_color('white')
#cmd.set_bond ('stick_color', 'white', 'clauc2h2', 'clauc2h2')
#cmd.set_bond ('stick_radius', -0.14, 'clauc2h2', 'clauc2h2')
#cmd.set ('stick_ball', 1)
#cmd.set ('stick_ball_ratio', -0.5)
#cmd.set ('stick_ball_color', 'atomic')
#cmd.show ('sticks', 'clauc2h2')
##cmd.set ('sphere_scale', 0.25, 'clauc2h2')
##cmd.show ('spheres', 'clauc2h2')
cmd.load('this.cube')
cmd.isosurface('sp', 'this', 0.005)
cmd.color('gray90', 'sp')
cmd.isosurface('sm', 'this', -0.005)
cmd.color('red', 'sm')
#cmd.set ('label_font_id', 16)
#cmd.set ('label_size', 24)
#cmd.pseudoatom('xatom', pos=[1,0,0], label="x")
#cmd.pseudoatom('yatom', pos=[0,1,0], label="y")
#cmd.pseudoatom('zatom', pos=[0,0,2], label="z")
cmd.set('label_font_id', 16)
cmd.set('label_size', 20)
cmd.pseudoatom('xatom', pos=[2.5, 0, 0], label="x")
cmd.pseudoatom('yatom', pos=[0, 2.5, 0], label="y")
cmd.pseudoatom('zatom', pos=[0, 0, 5.5], label="z")
def set_atom_level(
level,
selection='*',
state=None,
rec_map=None,
lig_map=None,
interp=False,
job_name=None,
array_job=False,
):
interp = as_bool(interp)
array_job = as_bool(array_job)
# get atom type channel info and set custom colors
try:
rec_channels = atom_types.get_channels_from_file(rec_map)
except:
rec_channels = atom_types.get_default_rec_channels()
try:
lig_channels = atom_types.get_channels_from_file(lig_map)
except:
lig_channels = atom_types.get_default_lig_channels()
channels = rec_channels + lig_channels
channels_by_name = {ch.name: ch for ch in channels}
channel_names = channels_by_name.keys()
for ch in channels:
for grid_type in ['rec', 'lig', 'lig_gen', 'lig_fit', 'lig_gen_fit']:
color_name = grid_type + '_' + ch.name
cmd.set_color(color_name+'$', get_color(grid_type, ch.atomic_num))
# We sort grids based on two different criteria before creating surfaces
# for each grid. The first criteria determines what STATE to put the
# surface in, the second determines what GROUP to put it in.
# We expect grid names to store info in the following basic format:
# {job_name}_{lig_name}_{grid_type}_{sample_idx}_{channel_name}
# By default,
# group=(job_name, lig_name, grid_type)
# state=(sample_idx,)
# With interp=True,
# group=(job_name, grid_type)
# state=(lig_name, sample_idx)
# get list of selected grid objects
grids = []
for obj in cmd.get_names('objects'):
m = re.match(r'^(.*)(\.dx|_grid)$', obj)
if m and fnmatch.fnmatch(obj, selection):
grids.append(obj)
# try to infer the job_name from working directory
if job_name is None:
job_name = os.path.basename(os.getcwd())
# create a regex for parsing grid names
grid_re_fields = [r'(?P<job_name>{})'.format(job_name)]
if array_job:
grid_re_fields += [r'(?P<array_idx>\d+)']
grid_re_fields += [
r'(?P<lig_name>.+)',
r'(?P<grid_type>rec|lig(_gen)?(_conv|_fit)?)',
r'(?P<sample_idx>\d+)',
r'(?P<channel_name>{})'.format('|'.join(channel_names)),
]
grid_re = re.compile('^' + '_'.join(grid_re_fields) + r'(\.dx|_grid)$')
# assign grids to groups and states
grouped_surfaces = OrderedDict()
grouped_lig_names = OrderedDict()
state_counter = OrderedDict()
for i, grid in enumerate(grids):
m = grid_re.match(grid)
try:
lig_name = m.group('lig_name')
grid_type = m.group('grid_type')
sample_idx = int(m.group('sample_idx'))
channel_name = m.group('channel_name')
except:
print(grid_re)
print(grid)
raise
if interp:
group_criteria = (job_name, grid_type)
state_criteria = (lig_name, sample_idx)
surface_format = '{job_name}_{grid_type}_{channel_name}_surface'
else:
group_criteria = (job_name, lig_name, grid_type)
state_criteria = sample_idx
surface_format = '{job_name}_{lig_name}_{grid_type}_{channel_name}_surface'
surface = surface_format.format(**m.groupdict())
if state_criteria not in state_counter:
state_counter[state_criteria] = len(state_counter) + 1
s = state_counter[state_criteria]
if group_criteria not in grouped_surfaces:
grouped_surfaces[group_criteria] = []
grouped_lig_names[group_criteria] = []
if surface not in grouped_surfaces[group_criteria]:
grouped_surfaces[group_criteria].append(surface)
if lig_name not in grouped_lig_names[group_criteria]:
grouped_lig_names[group_criteria].append(lig_name)
channel = channels_by_name[channel_name]
cmd.isosurface(surface, grid, level=level, state=s)
cmd.color(grid_type + '_' + channel.name+'$', surface)
print('[{}/{}] {}'.format(i+1, len(grids), surface, group_criteria, s))
for group_criteria, surfaces in grouped_surfaces.items():
if interp:
job_name, grid_type = group_criteria
lig_names = grouped_lig_names[group_criteria]
surface_group = '_'.join(
(job_name, '_to_'.join(lig_names), grid_type)
) + '_surfaces'
else:
surface_group = '_'.join(group_criteria) + '_surfaces'
cmd.group(surface_group, ' '.join(surfaces))
print('Done')