def _special(k,x,y,m=0,_self=cmd): # INTERNAL (invoked when special key is pressed)
pymol=_self._pymol
# WARNING: internal routine, subject to change
k=int(k)
m=int(m)
my_special = _self.special
if(m>0) and (m<5):
my_special = (_self.special,
_self.shft_special,
_self.ctrl_special,
_self.ctsh_special,
_self.alt_special)[m]
if my_special.has_key(k):
if my_special[k][1]:
apply(my_special[k][1],my_special[k][2],my_special[k][3])
else:
key = my_special[k][0]
if(m>0) and (m<5):
key = ('','SHFT-','CTRL-','CTSH-','ALT-')[m] + key
if pymol._scene_dict.has_key(key):
_self.scene(key)
elif is_string(pymol._scene_dict_sc.interpret(key+"-")):
_self.scene(pymol._scene_dict_sc[key+"-"])
elif pymol._view_dict.has_key(key):
_self.view(key)
elif is_string(pymol._view_dict_sc.interpret(key+"-")):
_self.view(pymol._view_dict_sc[key+"-"])
return None
def _special(k,
x,
y,
m=0,
_self=cmd): # INTERNAL (invoked when special key is pressed)
pymol = _self._pymol
# WARNING: internal routine, subject to change
k = int(k)
m = int(m)
my_special = _self.special
if (m > 0) and (m < 5):
my_special = (_self.special, _self.shft_special, _self.ctrl_special,
_self.ctsh_special, _self.alt_special)[m]
if my_special.has_key(k):
if my_special[k][1]:
apply(my_special[k][1], my_special[k][2], my_special[k][3])
else:
key = my_special[k][0]
if (m > 0) and (m < 5):
key = ('', 'SHFT-', 'CTRL-', 'CTSH-', 'ALT-')[m] + key
if pymol._scene_dict.has_key(key):
_self.scene(key)
elif is_string(pymol._scene_dict_sc.interpret(key + "-")):
_self.scene(pymol._scene_dict_sc[key + "-"])
elif pymol._view_dict.has_key(key):
_self.view(key)
elif is_string(pymol._view_dict_sc.interpret(key + "-")):
_self.view(pymol._view_dict_sc[key + "-"])
return None
def edit_mode(active=1,quiet=1,_self=cmd):
'''
DESCRIPTION
"edit_mode" switches the mouse into editing mode, if such a mode
is available in the current mouse ring.
'''
# legacy function
if is_string(active):
active=boolean_dict[boolean_sc.auto_err(active,'active')]
active = int(active)
if len(mouse_ring):
bm = int(_cmd.get_setting(_self._COb,"button_mode"))
mouse_mode = mouse_ring[bm]
if active:
if mouse_mode[0:10]=='two_button':
if mouse_mode!='two_button_editing':
mouse(action='two_button_editing',quiet=quiet,_self=_self)
elif mouse_mode[0:12] == 'three_button':
if mouse_mode!='three_button_editing':
mouse(action='three_button_editing',quiet=quiet,_self=_self)
else:
if mouse_mode[0:10]=='two_button':
if mouse_mode!='two_button_viewing':
mouse(action='two_button_viewing',quiet=quiet,_self=_self)
elif mouse_mode[0:12] == 'three_button':
if mouse_mode!='three_button_viewing':
mouse(action='three_button_viewing',quiet=quiet,_self=_self)
return DEFAULT_SUCCESS
def _interpret_color(_self,color):
# WARNING: internal routine, subject to change
_validate_color_sc(_self)
new_color = _self.color_sc.interpret(color)
if new_color:
if is_string(new_color):
return new_color
else:
_self.color_sc.auto_err(color,'color')
else:
return color
def _interpret_color(_self, color):
# WARNING: internal routine, subject to change
_validate_color_sc(_self)
new_color = _self.color_sc.interpret(color)
if new_color:
if is_string(new_color):
return new_color
else:
_self.color_sc.auto_err(color, 'color')
else:
return color
def order(names, sort=0, location='current', _self=cmd):
'''
DESCRIPTION
"order" changes the ordering of names in the control panel.
USAGE
order names, sort, location
ARGUMENTS
names = string: a space-separated list of names
sort = yes or no {default: no}
location = top, current, or bottom {default: current}
EXAMPLES
order 1dn2 1fgh 1rnd # sets the order of these three objects
order *,yes # sorts all names
order 1dn2_*, yes # sorts all names beginning with 1dn2_
order 1frg, location=top # puts 1frg at the top of the list
PYMOL API
cmd.order(string names, string sort, string location)
NOTES
"order" can also be used to reorder objects within a group.
SEE ALSO
set_name, group
'''
r = DEFAULT_ERROR
location = location_code[location_sc.auto_err(location, 'location')]
if is_string(sort):
sort = boolean_dict[boolean_sc.auto_err(sort, 'sort option')]
try:
_self.lock(_self)
r = _cmd.order(_self._COb, str(names), int(sort), int(location))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
def order(names,sort=0,location='current',_self=cmd):
'''
DESCRIPTION
"order" changes the ordering of names in the control panel.
USAGE
order names, sort, location
ARGUMENTS
names = string: a space-separated list of names
sort = yes or no {default: no}
location = top, current, or bottom {default: current}
EXAMPLES
order 1dn2 1fgh 1rnd # sets the order of these three objects
order *,yes # sorts all names
order 1dn2_*, yes # sorts all names beginning with 1dn2_
order 1frg, location=top # puts 1frg at the top of the list
PYMOL API
cmd.order(string names, string sort, string location)
NOTES
"order" can also be used to reorder objects within a group.
SEE ALSO
set_name, group
'''
r = DEFAULT_ERROR
location=location_code[location_sc.auto_err(location,'location')]
if is_string(sort):
sort=boolean_dict[boolean_sc.auto_err(sort,'sort option')]
try:
_self.lock(_self)
r = _cmd.order(_self._COb,str(names),int(sort),int(location))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def log_open(filename='log.pml', mode='w', _self=cmd):
'''
DESCRIPTION
"log_open" opens a log file for writing.
USAGE
log_open filename
SEE ALSO
log, log_close
'''
pymol = _self._pymol
if not is_string(filename): # we're logging to Queue, not a file.
pymol._log_file = QueueFile(filename)
_self.set("logging", 1, quiet=1)
else:
try:
try:
if hasattr(pymol, "_log_file"):
if pymol._log_file != None:
pymol._log_file.close()
del pymol._log_file
except:
pass
pymol._log_file = open(filename, mode)
if _self._feedback(fb_module.cmd,
fb_mask.details): # redundant
if mode != 'a':
print " Cmd: logging to '%s'." % filename
else:
print " Cmd: appending to '%s'." % filename
if mode == 'a':
pymol._log_file.write("\n") # always start on a new line
if (re.search(r"\.py$|\.PY$|\.pym$|\.PYM$", filename)):
_self.set("logging", 2, quiet=1)
else:
_self.set("logging", 1, quiet=1)
except:
print "Error: unable to open log file '%s'" % filename
pymol._log_file = None
_self.set("logging", 0, quiet=1)
traceback.print_exc()
raise QuietException
def log_open(filename='log.pml', mode='w', _self=cmd):
'''
DESCRIPTION
"log_open" opens a log file for writing.
USAGE
log_open filename
SEE ALSO
log, log_close
'''
pymol=_self._pymol
if not is_string(filename): # we're logging to Queue, not a file.
pymol._log_file = QueueFile(filename)
_self.set("logging",1,quiet=1)
else:
try:
try:
if hasattr(pymol,"_log_file"):
if pymol._log_file!=None:
pymol._log_file.close()
del pymol._log_file
except:
pass
pymol._log_file = open(filename,mode)
if _self._feedback(fb_module.cmd,fb_mask.details): # redundant
if mode!='a':
print " Cmd: logging to '%s'."%filename
else:
print " Cmd: appending to '%s'."%filename
if mode=='a':
pymol._log_file.write("\n") # always start on a new line
if(re.search(r"\.py$|\.PY$|\.pym$|\.PYM$",filename)):
_self.set("logging",2,quiet=1)
else:
_self.set("logging",1,quiet=1)
except:
print"Error: unable to open log file '%s'"%filename
pymol._log_file = None
_self.set("logging",0,quiet=1)
traceback.print_exc()
raise QuietException
def alignto(target=None,method="cealign",quiet=1,_self=cmd, **kwargs):
"""
DESCRIPTION
"alignto" aligns all other loaded objects to the target
using the specified alignment algorithm.
USAGE
alignto target [, method [, quiet ]]
NOTES
Available alignment methods are "align", "super" and "cealign".
EXAMPLE
# fetch some calmodulins
fetch 1cll 1sra 1ggz 1k95, async=0
# align them to 1cll using cealign
alignto 1cll, method=cealign
alignto 1cll, object=all_to_1cll
SEE ALSO
align, super, cealign, fit, rms, rms_cur, intra_fit
"""
if cmd.is_string(method):
if method in cmd.keyword:
method = cmd.keyword[method][0]
else:
raise CmdException('Unknown method: ' + method)
names = cmd.get_names("public_objects", 1)
if not target:
target = names[0]
for x in names:
if x == target:
continue
if not quiet:
print "Aligning %s to %s" % (x, target)
method(mobile=x, target=target, **kwargs)
def alignto(target=None, method="cealign", quiet=1, _self=cmd, **kwargs):
"""
DESCRIPTION
"alignto" aligns all other loaded objects to the target
using the specified alignment algorithm.
USAGE
alignto target [, method [, quiet ]]
NOTES
Available alignment methods are "align", "super" and "cealign".
EXAMPLE
# fetch some calmodulins
fetch 1cll 1sra 1ggz 1k95, async=0
# align them to 1cll using cealign
alignto 1cll, method=cealign
alignto 1cll, object=all_to_1cll
SEE ALSO
align, super, cealign, fit, rms, rms_cur, intra_fit
"""
if cmd.is_string(method):
if method in cmd.keyword:
method = cmd.keyword[method][0]
else:
raise CmdException('Unknown method: ' + method)
names = cmd.get_names("public_objects", 1)
if not target:
target = names[0]
for x in names:
if x == target:
continue
if not quiet:
print "Aligning %s to %s" % (x, target)
method(mobile=x, target=target, **kwargs)
def edit_mode(active=1, quiet=1, _self=cmd):
'''
DESCRIPTION
"edit_mode" switches the mouse into editing mode, if such a mode
is available in the current mouse ring.
'''
# legacy function
if is_string(active):
active = boolean_dict[boolean_sc.auto_err(active, 'active')]
active = int(active)
bm = _self.get_setting_int("button_mode")
if 0 <= bm < len(mouse_ring):
mouse_mode = mouse_ring[bm]
if active:
if mouse_mode[0:10] == 'two_button':
if mouse_mode != 'two_button_editing':
mouse(action='two_button_editing',
quiet=quiet,
_self=_self)
elif mouse_mode[0:12] == 'three_button':
if mouse_mode != 'three_button_editing':
mouse(action='three_button_editing',
quiet=quiet,
_self=_self)
else:
if mouse_mode[0:10] == 'two_button':
if mouse_mode != 'two_button_viewing':
mouse(action='two_button_viewing',
quiet=quiet,
_self=_self)
elif mouse_mode[0:12] == 'three_button':
if mouse_mode != 'three_button_viewing':
mouse(action='three_button_viewing',
quiet=quiet,
_self=_self)
return DEFAULT_SUCCESS
def ramp_new(name,
map_name,
range=[-1.0, 0.0, 1.0],
color=['red', [1.0, 1.0, 1.0], 'blue'],
state=1,
selection='',
beyond=2.0,
within=6.0,
sigma=2.0,
zero=1,
quiet=1,
_self=cmd):
'''
DESCRIPTION
"ramp_new" creates a color ramp based on a map potential value or
based on proximity to a molecular object.
USAGE
ramp_new name, map_name [, range [, color [, state [, selection [,
beyond [, within [, sigma [, zero ]]]]]]]]
ARGUMENTS
name = string: name of the ramp object
map_name = string: name of the map (for potential) or molecular
object (for proximity)
range = list: values corresponding to slots in the ramp
color = list: colors corresponding to slots in the ramp
state = integer: state identifier
selection = selection: for automatic ranging
beyond = number: with automatic ranging, are we excluding
values beyond a certain distance from the selection?
within = number: with automatic ranging, are we only including
valuess within a certain distance from the selection?
sigma = number: with automatic ranging, how many standard
deviations from the mean do we go?
zero = integer: with automatic ranging, do we force the central
value to be zero?
EXAMPLES
ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
NOTES
Color ramps are extremely powerful but complicated to use.
In the simplest case, they can be used to color representations
based on the potential values found in a map object at the
corresponding positions in space.
In another simple case, representations can be colored based on
proximity to a target. Note that since ramp targets must
themselves be real objects (not merely selections), the "create"
command may be needed in order to generate an appropriate target.
In more complicated cases, they can be used to color
representations on one object based atoms found in another.
Ramps can operate recursively. In other words, the output color
from one ramp can be used as the input color for another. For
example, you could color by map potential within a certain
distance of the target object, beyond which, a uniform color is applied.
PYMOL API
def ramp_new(string name, string map_name, list range, list color,
int state, string selection, float beyond, float
within, float sigma, int zero, int quiet)
SEE ALSO
load, color, create, slice, gradient
'''
r = DEFAULT_ERROR
safe_color = string.strip(str(color))
if (safe_color[0:1] == "["): # looks like a list
color = safe_alpha_list_eval(str(safe_color))
else: # looks like a literal
color = str(color)
new_color = []
# preprocess selection
if selection != '':
selection = selector.process(selection)
# coerce range
try:
if isinstance(range, str):
range = safe_list_eval(range)
range = map(float, range)
except:
raise pymol.CmdException('invalid range')
if is_list(color):
for a in color:
if not is_list(a):
new_color.append(list(_self.get_color_tuple(
a, 4))) # incl negative RGB special colors
else:
new_color.append(a)
elif is_string(color):
new_color = ramp_spectrum_dict[ramp_spectrum_sc.auto_err(
str(color), 'ramp color spectrum')]
else:
new_color = int(color)
try:
_self.lock(_self)
r = _cmd.ramp_new(_self._COb, str(name), str(map_name), range,
new_color,
int(state) - 1, str(selection), float(beyond),
float(within), float(sigma), int(zero),
int(quiet))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
def _fab(input,name,mode,resi,chain,segi,state,dir,hydro,ss,quiet,_self=cmd):
r = DEFAULT_ERROR
code = _fab_codes.get(mode,None)
quiet = int(quiet)
resi = int(resi)
state = int(state)
dir = int(dir)
hydro = int(hydro)
if hydro < 0:
hydro = not _self.get_setting_boolean("auto_remove_hydrogens")
seq_len = 0
if (mode == 'peptide') and is_string(input):
# '123/ ADC B/234/ AFCD' to [ '123/','A','D','C','B/234/','F','C','D' ]
frags = input.split()
input = []
for frag in frags:
if '/' in frag:
input.append(frag)
else:
seq_len = seq_len + len(frag)
input.extend(list(frag))
input.append("/") # breaks chain
if name == None:
name = _self.get_unused_name("obj")
# if mode in [ 'smiles' ]: # small molecule (FUTURE)
# from chempy.champ import Champ
# ch = Champ()
# ch.insert_pattern_string(input)
if mode in [ 'peptide' ]: # polymers
if (seq_len>99) and not quiet:
print " Generating a %d residue peptide from sequence..."%seq_len
input.reverse()
sequence = input
if code != None:
while len(sequence):
while len(sequence) and '/' in sequence[-1]:
part = sequence.pop().split('/')
if len(part)>1:
if len(part[-2]):
resi = int(part[-2])
if len(part)>2:
chain = part[-3]
if len(part)>3:
segi = part[-4]
if len(sequence) and not _self.count_atoms("?pk1"): # new polymer segment
tmp_obj = _self.get_unused_name()
first = sequence.pop()
_self.fragment(code[first], tmp_obj)
if not hydro:
cmd.remove(tmp_obj + ' and hydro')
_self.alter(tmp_obj,'resi="""%s""";chain="""%s""";segi="""%s"""'%(resi,chain,segi))
_self.create(name,tmp_obj+" or ?"+name,1,state,zoom=0)
tmp_sel = _self.get_unused_name()
if mode == 'peptide':
if dir>0:
_self.select(tmp_sel,"name c and "+tmp_obj)
resi = resi + 1
else:
_self.select(tmp_sel,"name n and "+tmp_obj)
resi = resi - 1
_self.edit(name+" in "+tmp_sel) # set the editor's pk1 selection
_self.delete(tmp_sel+" "+tmp_obj)
if mode == 'peptide':
while len(sequence):
if '/' in sequence[-1]:
_self.unpick() # break chain at this point
break
if not _self.count_atoms("?pk1"):
break
else:
attach_amino_acid("pk1",code[sequence.pop()],animate=0,ss=ss,hydro=hydro,_self=_self)
if dir>0:
resi = resi + 1
else:
resi = resi - 1
if not len(sequence):
r = DEFAULT_SUCCESS
def feedback(action="?", module="?", mask="?", _self=cmd):
'''
DESCRIPTION
"feedback" changes the amount of information output by pymol.
USAGE
feedback action, module, mask
ARGUMENTS
action = set, enable, or disable
module = string: a space-separated list of modules or simply "all"
mask = string: a space-separated list of output categories or simply "everything"
NOTES
"feedback" alone will print a list of the available module choices
PYMOL API
cmd.feedback(string action,string module,string mask)
EXAMPLES
feedback enable, all , debugging
feedback disable, selector, warnings actions
feedback enable, main, blather
'''
r = None
# validate action
if not hasattr(_self,'_fb_dict'):
_self._fb_dict = copy.deepcopy(_fb_dict)
if action=="?":
print " feedback: possible actions: \nset, enable, disable"
act_int = 0
else:
act_kee = fb_action_sc.interpret(action)
if act_kee == None:
print "Error: invalid feedback action '%s'."%action
if _raising(_self=_self):
raise QuietException
else:
return None
elif not is_string(act_kee):
print "Error: ambiguous feedback action '%s'."%action
print action_amb
if _raising(_self=_self):
raise QuietException
else:
return None
act_int = int(getattr(fb_action,act_kee))
if (act_int<3) and ("?" in [action,module,mask]):
if module=="?":
print " feedback: Please specify module names:"
lst = fb_module.__dict__.keys()
lst.sort()
for a in lst:
if a[0]!='_':
print " ",a
if mask=="?":
print " feedback: Please specify masks:"
lst = fb_mask.__dict__.keys()
lst.sort()
for a in lst:
if a[0]!='_':
print " ",a
else:
if (act_int>=3):
module='all'
mask='everything'
# validate and combine masks
mask_int = 0
mask_lst = string.split(mask)
for mask in mask_lst:
mask_kee = fb_mask_sc.interpret(mask)
if mask_kee == None:
print "Error: invalid feedback mask '%s'."%mask
if _raising(_self=_self): raise QuietException
else: return None
elif not is_string(mask_kee):
print "Error: ambiguous feedback mask '%s'."%mask
if _raising(_self=_self): raise QuietException
else: return None
mask_int = int(getattr(fb_mask,mask_kee))
# validate and iterate modules
mod_lst = string.split(module)
for module in mod_lst:
mod_kee = fb_module_sc.interpret(module)
if mod_kee == None:
print "Error: invalid feedback module '%s'."%module
if _raising(_self=_self): raise QuietException
else: return None
elif not is_string(mod_kee):
print "Error: ambiguous feedback module '%s'."%module
if _raising(_self=_self): raise QuietException
else: return None
mod_int = int(getattr(fb_module,mod_kee))
if mod_int>=0:
try:
_self.lock(_self)
r = _cmd.set_feedback(_self._COb,act_int,mod_int,mask_int)
finally:
_self.unlock(r,_self)
if mod_int<=0:
if mod_int:
if act_int==0:
_self._fb_dict[mod_int] = mask_int
elif act_int==1:
_self._fb_dict[mod_int] = _self._fb_dict[mod_int] | mask_int
elif act_int==2:
_self._fb_dict[mod_int] = _self._fb_dict[mod_int] & ( 0xFF - mask_int )
else:
for mod_int in _self._fb_dict.keys():
if act_int==0:
_self._fb_dict[mod_int] = mask_int
elif act_int==1:
_self._fb_dict[mod_int] = _self._fb_dict[mod_int] | mask_int
elif act_int==2:
_self._fb_dict[mod_int] = _self._fb_dict[mod_int] & ( 0xFF - mask_int )
if _feedback(fb_module.feedback,fb_mask.debugging,_self):
sys.stderr.write(" feedback: mode %d on %d mask %d\n"%(
act_int,mod_int,mask_int))
return r
def feedback(action="?", module="?", mask="?", _self=cmd):
'''
DESCRIPTION
"feedback" changes the amount of information output by pymol.
USAGE
feedback action, module, mask
ARGUMENTS
action = set, enable, or disable
module = string: a space-separated list of modules or simply "all"
mask = string: a space-separated list of output categories or simply "everything"
NOTES
"feedback" alone will print a list of the available module choices
PYMOL API
cmd.feedback(string action,string module,string mask)
EXAMPLES
feedback enable, all , debugging
feedback disable, selector, warnings actions
feedback enable, main, blather
'''
r = None
# validate action
if not hasattr(_self,'_fb_dict'):
_self._fb_dict = copy.deepcopy(_fb_dict)
if action=="?":
print " feedback: possible actions: \nset, enable, disable"
act_int = 0
else:
act_kee = fb_action_sc.interpret(action)
if act_kee == None:
print "Error: invalid feedback action '%s'."%action
if _raising(_self=_self):
raise QuietException
else:
return None
elif not is_string(act_kee):
print "Error: ambiguous feedback action '%s'."%action
print action_amb
if _raising(_self=_self):
raise QuietException
else:
return None
act_int = int(getattr(fb_action,act_kee))
if (act_int<3) and ("?" in [action,module,mask]):
if module=="?":
print " feedback: Please specify module names:"
lst = fb_module.__dict__.keys()
lst.sort()
for a in lst:
if a[0]!='_':
print " ",a
if mask=="?":
print " feedback: Please specify masks:"
lst = fb_mask.__dict__.keys()
lst.sort()
for a in lst:
if a[0]!='_':
print " ",a
else:
if (act_int>=3):
module='all'
mask='everything'
# validate and combine masks
mask_int = 0
mask_lst = string.split(mask)
for mask in mask_lst:
mask_kee = fb_mask_sc.interpret(mask)
if mask_kee == None:
print "Error: invalid feedback mask '%s'."%mask
if _raising(_self=_self): raise QuietException
else: return None
elif not is_string(mask_kee):
print "Error: ambiguous feedback mask '%s'."%mask
if _raising(_self=_self): raise QuietException
else: return None
mask_int |= int(getattr(fb_mask,mask_kee))
# validate and iterate modules
mod_lst = string.split(module)
for module in mod_lst:
mod_kee = fb_module_sc.interpret(module)
if mod_kee == None:
print "Error: invalid feedback module '%s'."%module
if _raising(_self=_self): raise QuietException
else: return None
elif not is_string(mod_kee):
print "Error: ambiguous feedback module '%s'."%module
if _raising(_self=_self): raise QuietException
else: return None
mod_int = int(getattr(fb_module,mod_kee))
if mod_int>=0:
try:
_self.lock(_self)
r = _cmd.set_feedback(_self._COb,act_int,mod_int,mask_int)
finally:
_self.unlock(r,_self)
if mod_int<=0:
if mod_int:
if act_int==0:
_self._fb_dict[mod_int] = mask_int
elif act_int==1:
_self._fb_dict[mod_int] = _self._fb_dict[mod_int] | mask_int
elif act_int==2:
_self._fb_dict[mod_int] = _self._fb_dict[mod_int] & ( 0xFF - mask_int )
else:
for mod_int in _self._fb_dict.keys():
if act_int==0:
_self._fb_dict[mod_int] = mask_int
elif act_int==1:
_self._fb_dict[mod_int] = _self._fb_dict[mod_int] | mask_int
elif act_int==2:
_self._fb_dict[mod_int] = _self._fb_dict[mod_int] & ( 0xFF - mask_int )
if _feedback(fb_module.feedback,fb_mask.debugging,_self):
sys.stderr.write(" feedback: mode %d on %d mask %d\n"%(
act_int,mod_int,mask_int))
return r
def _fab(input,name,mode,resi,chain,segi,state,dir,hydro,ss,quiet,_self=cmd):
r = DEFAULT_ERROR
code = _fab_codes.get(mode,None)
quiet = int(quiet)
resi = int(resi)
state = int(state)
dir = int(dir)
hydro = int(hydro)
if hydro < 0:
hydro = not _self.get_setting_boolean("auto_remove_hydrogens")
seq_len = 0
if (mode == 'peptide') and is_string(input):
# '123/ ADC B/234/ AFCD' to [ '123/','A','D','C','B/234/','F','C','D' ]
frags = input.split()
input = []
for frag in frags:
if '/' in frag:
input.append(frag)
else:
seq_len = seq_len + len(frag)
input.extend(list(frag))
input.append("/") # breaks chain
if name == None:
name = _self.get_unused_name("obj")
# if mode in [ 'smiles' ]: # small molecule (FUTURE)
# from chempy.champ import Champ
# ch = Champ()
# ch.insert_pattern_string(input)
if mode in [ 'peptide' ]: # polymers
if (seq_len>99) and not quiet:
print " Generating a %d residue peptide from sequence..."%seq_len
input.reverse()
sequence = input
if code != None:
while len(sequence):
while len(sequence) and '/' in sequence[-1]:
part = sequence.pop().split('/')
if len(part)>1:
if len(part[-2]):
resi = int(part[-2])
if len(part)>2:
chain = part[-3]
if len(part)>3:
segi = part[-4]
if len(sequence) and not _self.count_atoms("?pk1"): # new polymer segment
tmp_obj = _self.get_unused_name()
first = sequence.pop()
_self.fragment(code[first], tmp_obj)
if not hydro:
cmd.remove(tmp_obj + ' and hydro')
_self.alter(tmp_obj,'resi="""%s""";chain="""%s""";segi="""%s"""'%(resi,chain,segi))
_self.create(name,tmp_obj+" or ?"+name,1,1,zoom=0)
tmp_sel = _self.get_unused_name()
if mode == 'peptide':
if dir>0:
_self.select(tmp_sel,"name c and "+tmp_obj)
resi = resi + 1
else:
_self.select(tmp_sel,"name n and "+tmp_obj)
resi = resi - 1
_self.edit(name+" in "+tmp_sel) # set the editor's pk1 selection
_self.delete(tmp_sel+" "+tmp_obj)
if mode == 'peptide':
while len(sequence):
if '/' in sequence[-1]:
_self.unpick() # break chain at this point
break
if not _self.count_atoms("?pk1"):
break
else:
attach_amino_acid("pk1",code[sequence.pop()],animate=0,ss=ss,hydro=hydro,_self=_self)
if dir>0:
resi = resi + 1
else:
resi = resi - 1
if not len(sequence):
r = DEFAULT_SUCCESS
def ramp_new(name, map_name, range=[-1.0,0.0,1.0],
color=['red',[1.0,1.0,1.0],'blue'], state=1,
selection='', beyond=2.0, within=6.0, sigma=2.0,
zero=1, quiet=1, _self=cmd):
'''
DESCRIPTION
"ramp_new" creates a color ramp based on a map potential value or
based on proximity to a molecular object.
USAGE
ramp_new name, map_name [, range [, color [, state [, selection [,
beyond [, within [, sigma [, zero ]]]]]]]]
ARGUMENTS
name = string: name of the ramp object
map_name = string: name of the map (for potential) or molecular
object (for proximity)
range = list: values corresponding to slots in the ramp
color = list: colors corresponding to slots in the ramp
state = integer: state identifier
selection = selection: for automatic ranging
beyond = number: with automatic ranging, are we excluding
values beyond a certain distance from the selection?
within = number: with automatic ranging, are we only including
valuess within a certain distance from the selection?
sigma = number: with automatic ranging, how many standard
deviations from the mean do we go?
zero = integer: with automatic ranging, do we force the central
value to be zero?
EXAMPLES
ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
NOTES
Color ramps are extremely powerful but complicated to use.
In the simplest case, they can be used to color representations
based on the potential values found in a map object at the
corresponding positions in space.
In another simple case, representations can be colored based on
proximity to a target. Note that since ramp targets must
themselves be real objects (not merely selections), the "create"
command may be needed in order to generate an appropriate target.
In more complicated cases, they can be used to color
representations on one object based atoms found in another.
Ramps can operate recursively. In other words, the output color
from one ramp can be used as the input color for another. For
example, you could color by map potential within a certain
distance of the target object, beyond which, a uniform color is applied.
PYMOL API
def ramp_new(string name, string map_name, list range, list color,
int state, string selection, float beyond, float
within, float sigma, int zero, int quiet)
SEE ALSO
load, color, create, slice, gradient
'''
r = DEFAULT_ERROR
safe_color = string.strip(str(color))
if(safe_color[0:1]=="["): # looks like a list
color = safe_alpha_list_eval(str(safe_color))
else: # looks like a literal
color = str(color)
new_color = []
# preprocess selection
if selection!='':
selection = selector.process(selection)
# coerce range
try:
if isinstance(range, str):
range = safe_list_eval(range)
range = map(float, range)
except:
raise pymol.CmdException('invalid range')
if is_list(color):
for a in color:
if not is_list(a):
new_color.append(list(_self.get_color_tuple(a,4))) # incl negative RGB special colors
else:
new_color.append(a)
elif is_string(color):
new_color = ramp_spectrum_dict[ramp_spectrum_sc.auto_err(str(color),'ramp color spectrum')]
else:
new_color=int(color)
try:
_self.lock(_self)
r = _cmd.ramp_new(_self._COb,str(name),str(map_name),range,new_color,
int(state)-1,str(selection),float(beyond),float(within),
float(sigma),int(zero),int(quiet))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
