def pseudoatom(object='', selection='', name='PS1', resn='PSD', resi='1', chain='P',
segi='PSDO', elem='PS', vdw=-1.0, hetatm=1, b=0.0, q=0.0, color='',
label='', pos=None, state=0, mode='rms', quiet=1,_self=cmd):
'''
DESCRIPTION
"pseudoatom" adds a pseudoatom to a molecular object, and will
creating the molecular object if it does not yet exist.
USAGE
pseudoatom object [, selection [, name [, resn [, resi [, chain
[, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label
[, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
NOTES
"pseudoatom" can be used for a wide variety of random tasks where
on must place an atom or a label in 3D space.
'''
r = DEFAULT_ERROR
# preprocess selection
if len(color):
color = _self.get_color_index(str(color))
else:
color = -1 # default
object = str(object)
if not len(object):
object = _self.get_unused_name(prefix="pseudo")
selection = selector.process(selection)
mode = pseudoatom_mode_dict[pseudoatom_mode_sc.auto_err(str(mode),'pseudoatom mode')]
(name,resn,resi,chain,segi,elem,label) = map(unquote,(name,resn,resi,chain,segi,elem,label))
#
try:
_self.lock(_self)
if pos!=None:
if not (is_list(pos) or is_tuple(pos)):
pos = safe_list_eval(pos)
pos = (float(pos[0]), # tuple-ize
float(pos[1]),
float(pos[2]))
if len(selection.split())>1:
selection = "("+str(selection)+")"
r = _cmd.pseudoatom(_self._COb,str(object), str(selection),
str(name), str(resn), str(resi), str(chain),
str(segi), str(elem), float(vdw), int(hetatm),
float(b), float(q), str(label), pos, int(color),
int(state)-1, int(mode), int(quiet))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def _get_dump_str(obj):
if is_list(obj):
list = map(_get_dump_str,obj)
result = "[ "+string.join(list,",\n")+" ] "
elif is_dict(obj):
list = []
for key in obj.keys():
list.append( _get_dump_str(key)+" : "+_get_dump_str(obj[key]) )
result = "{ "+string.join(list,",\n")+" } "
elif is_tuple(obj):
list = map(_get_dump_str,obj)
result = "( "+string.join(list,",\n")+" ) "
else:
result = str(obj)
return result
def _get_dump_str(obj):
if is_list(obj):
list = map(_get_dump_str,obj)
result = "[ "+string.join(list,",\n")+" ] "
elif is_dict(obj):
list = []
for key in obj.keys():
list.append( _get_dump_str(key)+" : "+_get_dump_str(obj[key]) )
result = "{ "+string.join(list,",\n")+" } "
elif is_tuple(obj):
list = map(_get_dump_str,obj)
result = "( "+string.join(list,",\n")+" ) "
else:
result = str(obj)
return result
def volume_color(name, colors, _self=cmd):
"""
DESCRIPTION -- untested do not use
ALSO -- this belongs in a different module
"""
if not (is_list(colors) or is_tuple(colors)):
colors = safe_list_eval(colors)
# tuple of tuples to list of float
cList = []
map(lambda x: cList.extend(x), colors)
cList = map(lambda x: float(x), cList)
try:
_self.lock(_self)
r = _cmd.volume_color(_self._COb, str(name), cList)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
# unlock and then use this to differentiate our viz
return r
def volume_color(name, colors, _self=cmd):
"""
DESCRIPTION -- untested do not use
ALSO -- this belongs in a different module
"""
if not (is_list(colors) or is_tuple(colors)):
colors = safe_list_eval(colors)
# tuple of tuples to list of float
cList = []
map(lambda x: cList.extend(x), colors)
cList = map(lambda x: float(x), cList)
try:
_self.lock(_self)
r = _cmd.volume_color(_self._COb, str(name), cList)
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
# unlock and then use this to differentiate our viz
return r
def pseudoatom(object='',
selection='',
name='PS1',
resn='PSD',
resi='1',
chain='P',
segi='PSDO',
elem='PS',
vdw=-1.0,
hetatm=1,
b=0.0,
q=0.0,
color='',
label='',
pos=None,
state=0,
mode='rms',
quiet=1,
_self=cmd):
'''
DESCRIPTION
"pseudoatom" adds a pseudoatom to a molecular object, and will
creating the molecular object if it does not yet exist.
USAGE
pseudoatom object [, selection [, name [, resn [, resi [, chain
[, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label
[, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]
NOTES
"pseudoatom" can be used for a wide variety of random tasks where
on must place an atom or a label in 3D space.
'''
r = DEFAULT_ERROR
# preprocess selection
if len(color):
color = _self.get_color_index(str(color))
else:
color = -1 # default
object = str(object)
if not len(object):
object = _self.get_unused_name(prefix="pseudo")
selection = selector.process(selection)
mode = pseudoatom_mode_dict[pseudoatom_mode_sc.auto_err(
str(mode), 'pseudoatom mode')]
(name, resn, resi, chain, segi, elem,
label) = map(unquote, (name, resn, resi, chain, segi, elem, label))
#
try:
_self.lock(_self)
if pos != None:
if not (is_list(pos) or is_tuple(pos)):
pos = safe_list_eval(pos)
pos = (
float(pos[0]), # tuple-ize
float(pos[1]),
float(pos[2]))
if len(selection.split()) > 1:
selection = "(" + str(selection) + ")"
r = _cmd.pseudoatom(_self._COb, str(object), str(selection),
str(name), str(resn), str(resi), str(chain),
str(segi), str(elem), float(vdw), int(hetatm),
float(b), float(q), str(label), pos,
int(color),
int(state) - 1, int(mode), int(quiet))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
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")