def setup_alignment_contexts(context_info): # Author: Warren DeLano
(list,dict) = context_info[0:2]
doc_list = ['\888Legend:']
obj_name_dict = {}
for a in list:
sf = string.find(a,"_")
if sf>=0:
object_name = a[0:sf]
if not obj_name_dict.has_key(object_name):
obj_name_dict[object_name] = 1
col_index = cmd.get_object_color_index(object_name)
if col_index>=0:
col_tup = cmd.get_color_tuple(col_index)
if is_tuple(col_tup):
col_int = map(lambda x:int(x*9+0.49999),col_tup)
col_str = string.join(map(lambda x:chr(ord('0')+x),col_int),'')
doc_list.append("\\"+col_str+object_name+"\\---")
key_list = [
'F1','F2','F3','F4','F5','F6','F7','F8','F9','F10', #,'F11','F12',
'SHFT-F1','SHFT-F2','SHFT-F3','SHFT-F4','SHFT-F5','SHFT-F6','SHFT-F7',
'SHFT-F8','SHFT-F9','SHFT-F10']# ,'SHFT-F11','SHFT-F12']
doc_list.append("")
doc_list.append("\\888Toggles:")
zoom_context = 1
global labels,ligands,waters,sites,cgos,zooms,dashes
labels = 1
ligands = 1
waters = 1
sites = 1
cgos = 0
zooms = 0
dashes = 1
global m4x_sites,m4x_ligands,m4x_waters
m4x_sites = "m4x_sites"
m4x_ligands = "m4x_ligands"
m4x_waters = "m4x_waters"
cmd.select(m4x_sites,"none")
cmd.select(m4x_ligands,"none")
cmd.select(m4x_waters,"none")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_zooms)
doc_list.append(key+": Zoom")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_sites)
doc_list.append(key+": Sites")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_waters)
doc_list.append(key+": Waters")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_dashes)
doc_list.append(key+": H-Bonds")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_cgos)
doc_list.append(key+": Fits")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_ligands)
doc_list.append(key+": Ligands")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_labels)
doc_list.append(key+": HB-Dists")
for a in list:
include_flag = 0
water = a+"_water"
ligand = a+"_ligand"
site = a+"_site"
hbond = a+"_hbond"
if cmd.count_atoms(site):
if cmd.count_atoms(site+" & m4x_aligned"):
include_flag = 1
if cmd.count_atoms(ligand):
if cmd.count_atoms(ligand+" & m4x_nearby"):
include_flag = 1
if include_flag:
name_list = dict[a]
if water in name_list:
cmd.select(m4x_waters,m4x_waters+"|"+water)
if ligand in name_list:
cmd.select(m4x_ligands,m4x_ligands+"|"+ligand)
if site in name_list:
cmd.select(m4x_sites,m4x_sites+"|"+site+
"|((byres (neighbor ("+site+" and name c))) and name n+ca)"+
"|((byres (neighbor ("+site+" and name n))) and name c+ca+o)")
cmd.wizard("fedora",doc_list)
toggle_cgos(1)
toggle_labels(0)
toggle_dashes(0)
toggle_ligands(1)
toggle_sites(0)
toggle_waters(0)
toggle_cgos(1)
cmd.deselect()
# cmd.feedback("enable","python","output")
cmd.feedback("enable","objectmolecule","results")
cmd.set("internal_feedback",1)
cmd.set("internal_prompt",0)
cmd.feedback("disable","selector","actions")
cmd.feedback("disable","scene","actions")
def setup_alignment_contexts(context_info): # Author: Warren DeLano
(list, dict) = context_info[0:2]
doc_list = ['\888Legend:']
obj_name_dict = {}
for a in list:
sf = string.find(a, "_")
if sf >= 0:
object_name = a[0:sf]
if not obj_name_dict.has_key(object_name):
obj_name_dict[object_name] = 1
col_index = cmd.get_object_color_index(object_name)
if col_index >= 0:
col_tup = cmd.get_color_tuple(col_index)
if is_tuple(col_tup):
col_int = map(lambda x: int(x * 9 + 0.49999), col_tup)
col_str = string.join(
map(lambda x: chr(ord('0') + x), col_int), '')
doc_list.append("\\" + col_str + object_name + "\\---")
key_list = [
'F1',
'F2',
'F3',
'F4',
'F5',
'F6',
'F7',
'F8',
'F9',
'F10', #,'F11','F12',
'SHFT-F1',
'SHFT-F2',
'SHFT-F3',
'SHFT-F4',
'SHFT-F5',
'SHFT-F6',
'SHFT-F7',
'SHFT-F8',
'SHFT-F9',
'SHFT-F10'
] # ,'SHFT-F11','SHFT-F12']
doc_list.append("")
doc_list.append("\\888Toggles:")
zoom_context = 1
global labels, ligands, waters, sites, cgos, zooms, dashes
labels = 1
ligands = 1
waters = 1
sites = 1
cgos = 0
zooms = 0
dashes = 1
global m4x_sites, m4x_ligands, m4x_waters
m4x_sites = "m4x_sites"
m4x_ligands = "m4x_ligands"
m4x_waters = "m4x_waters"
cmd.select(m4x_sites, "none")
cmd.select(m4x_ligands, "none")
cmd.select(m4x_waters, "none")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_zooms)
doc_list.append(key + ": Zoom")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_sites)
doc_list.append(key + ": Sites")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_waters)
doc_list.append(key + ": Waters")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_dashes)
doc_list.append(key + ": H-Bonds")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_cgos)
doc_list.append(key + ": Fits")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_ligands)
doc_list.append(key + ": Ligands")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_labels)
doc_list.append(key + ": HB-Dists")
for a in list:
include_flag = 0
water = a + "_water"
ligand = a + "_ligand"
site = a + "_site"
hbond = a + "_hbond"
if cmd.count_atoms(site):
if cmd.count_atoms(site + " & m4x_aligned"):
include_flag = 1
if cmd.count_atoms(ligand):
if cmd.count_atoms(ligand + " & m4x_nearby"):
include_flag = 1
if include_flag:
name_list = dict[a]
if water in name_list:
cmd.select(m4x_waters, m4x_waters + "|" + water)
if ligand in name_list:
cmd.select(m4x_ligands, m4x_ligands + "|" + ligand)
if site in name_list:
cmd.select(
m4x_sites,
m4x_sites + "|" + site + "|((byres (neighbor (" + site +
" and name c))) and name n+ca)" + "|((byres (neighbor (" +
site + " and name n))) and name c+ca+o)")
cmd.wizard("fedora", doc_list)
toggle_cgos(1)
toggle_labels(0)
toggle_dashes(0)
toggle_ligands(1)
toggle_sites(0)
toggle_waters(0)
toggle_cgos(1)
cmd.deselect()
# cmd.feedback("enable","python","output")
cmd.feedback("enable", "objectmolecule", "results")
cmd.set("internal_feedback", 1)
cmd.set("internal_prompt", 0)
cmd.feedback("disable", "selector", "actions")
cmd.feedback("disable", "scene", "actions")
def setup_contexts(context_info): # Author: Warren DeLano
(list,dict) = context_info[0:2]
key_list = [
'F1','F2','F3','F4','F5','F6','F7','F8','F9','F10', #,'F11','F12',
'SHFT-F1','SHFT-F2','SHFT-F3','SHFT-F4','SHFT-F5','SHFT-F6','SHFT-F7',
'SHFT-F8','SHFT-F9','SHFT-F10']# ,'SHFT-F11','SHFT-F12']
doc_list = ["Keys"]
zoom_context = 1
global labels
labels = 1
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_labels)
doc_list.append(key+": Toggle Dist")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,lambda :(cmd.zoom(),toggle_labels(0)))
doc_list.append(key+": Zoom All")
for a in list:
water = a+"_water"
ligand = a+"_ligand"
site = a+"_site"
hbond = a+"_hbond"
name_list = dict[a]
zoom_list = []
if water in name_list:
cmd.show("nonbonded",water)
util.cbac(water)
zoom_list.append(water)
if ligand in name_list:
cmd.show("sticks",ligand)
cmd.hide("cartoon",ligand)
util.cbag(ligand)
zoom_list.append(ligand)
if site in name_list:
cmd.show("sticks",site)
util.cbac(site)
zoom_list.append(site)
# replace cartoon with explicit atoms for "site" atoms
cmd.hide("cartoon",site)
cmd.show("sticks","(byres (neighbor ("+site+" and name c))) and name n+ca")
cmd.show("sticks","(byres (neighbor ("+site+" and name n))) and name c+ca+o")
if len(zoom_list):
if len(key_list):
key = key_list.pop(0)
zoom_str = string.join(zoom_list,' or ')
if zoom_context == 1:
zoom_context = zoom_str
elif zoom_context not in (0,1):
zoom_context = 0
cmd.set_key(key,lambda x=zoom_str:(cmd.zoom(x)))
mo = re.search("_([^_]+)$",a)
if mo:
cont_name = mo.groups()[0]
else:
cont_name = a
doc_list.append(key+": Zoom "+cont_name)
if hbond in name_list:
cmd.show("dashes",hbond)
cmd.show("labels",hbond)
cmd.wizard("fedora",doc_list)
if zoom_context not in (0,1):
cmd.zoom(zoom_context)
toggle_labels(0)
# cmd.feedback("enable","python","output")
cmd.feedback("enable","objectmolecule","results")
cmd.feedback("disable","selector","actions")
cmd.feedback("disable","scene","actions")
cmd.set("internal_feedback",1)
cmd.set("internal_prompt",0)
def setup_contexts(context_info): # Author: Warren DeLano
(list, dict) = context_info[0:2]
key_list = [
'F1',
'F2',
'F3',
'F4',
'F5',
'F6',
'F7',
'F8',
'F9',
'F10', #,'F11','F12',
'SHFT-F1',
'SHFT-F2',
'SHFT-F3',
'SHFT-F4',
'SHFT-F5',
'SHFT-F6',
'SHFT-F7',
'SHFT-F8',
'SHFT-F9',
'SHFT-F10'
] # ,'SHFT-F11','SHFT-F12']
doc_list = ["Keys"]
zoom_context = 1
global labels
labels = 1
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_labels)
doc_list.append(key + ": Toggle Dist")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, lambda: (cmd.zoom(), toggle_labels(0)))
doc_list.append(key + ": Zoom All")
for a in list:
water = a + "_water"
ligand = a + "_ligand"
site = a + "_site"
hbond = a + "_hbond"
name_list = dict[a]
zoom_list = []
if water in name_list:
cmd.show("nonbonded", water)
util.cbac(water)
zoom_list.append(water)
if ligand in name_list:
cmd.show("sticks", ligand)
cmd.hide("cartoon", ligand)
util.cbag(ligand)
zoom_list.append(ligand)
if site in name_list:
cmd.show("sticks", site)
util.cbac(site)
zoom_list.append(site)
# replace cartoon with explicit atoms for "site" atoms
cmd.hide("cartoon", site)
cmd.show(
"sticks",
"(byres (neighbor (" + site + " and name c))) and name n+ca")
cmd.show(
"sticks",
"(byres (neighbor (" + site + " and name n))) and name c+ca+o")
if len(zoom_list):
if len(key_list):
key = key_list.pop(0)
zoom_str = string.join(zoom_list, ' or ')
if zoom_context == 1:
zoom_context = zoom_str
elif zoom_context not in (0, 1):
zoom_context = 0
cmd.set_key(key, lambda x=zoom_str: (cmd.zoom(x)))
mo = re.search("_([^_]+)$", a)
if mo:
cont_name = mo.groups()[0]
else:
cont_name = a
doc_list.append(key + ": Zoom " + cont_name)
if hbond in name_list:
cmd.show("dashes", hbond)
cmd.show("labels", hbond)
cmd.wizard("fedora", doc_list)
if zoom_context not in (0, 1):
cmd.zoom(zoom_context)
toggle_labels(0)
# cmd.feedback("enable","python","output")
cmd.feedback("enable", "objectmolecule", "results")
cmd.feedback("disable", "selector", "actions")
cmd.feedback("disable", "scene", "actions")
cmd.set("internal_feedback", 1)
cmd.set("internal_prompt", 0)
