def UIBased(categoryList, cmdList, undo_steps):
os.system('clear') # CLEAR SCREEN
UIBasedHelp()
while True:
userInput = raw_input("Please enter a command: ") # Reading the user input
step_count = len(undo_steps)
os.system('clear') # CLEAR SCREEN
userCommand = cmd.getCommand(userInput) # Extracting the COMMAND from the user input
remainderAfterCommand = cmd.getRemainder(userInput) # Extracting the remainder after the command
files.checkIntegrityOfTheFiles(categoryList) # Checking that the files are in good condition
if userCommand == "exit": # In case the user wants to terminate the program, this allows him to do so
return
elif userCommand == "add":
sum, category = UIAdd(categoryList)
userInput = str(userCommand) + " " + str(sum) + " " + str(category)
print cmd.add(userInput, categoryList, undo_steps, step_count)
elif userCommand == "insert":
day, sum, category = UIInsert(categoryList)
userInput = str(userCommand) + " " + str(day) + " " + str(sum) + " " + str(category)
print cmd.insert(userInput, categoryList, undo_steps, 1, step_count)
elif userCommand == "remove":
userInput = str(userCommand) + " " + UIRemove(categoryList)
print cmd.remove(userInput, categoryList, undo_steps, step_count)
elif userCommand == "list":
userInput = str(userCommand) + " " + UIList(categoryList)
cmd.printFunc(cmd.list(userInput, categoryList))
elif userCommand == "sum":
userInput = str(userCommand) + " " + UISum(categoryList)
print cmd.suma(userInput, categoryList)
elif userCommand == "max":
userInput = str(userCommand) + " " + UIMax()
print cmd.maxi(userInput, categoryList)
elif userCommand == "sort":
userInput = str(userCommand) + " " + UISort(categoryList)
cmd.printFunc(cmd.sort(userInput, categoryList))
elif userCommand == "filter":
userInput = str(userCommand) + " " + UIFilter(categoryList)
print cmd.filter(userInput, categoryList, undo_steps, step_count)
elif userCommand == "undo":
print cmd.undo(userInput, categoryList, undo_steps, step_count)
elif userCommand == "help":
cmd.userHelp(cmdList)
elif userCommand == "clear":
os.system('clear')
else:
print(" '" + userInput + "' not recognized. \"~:help\"")
def protein_assign_charges_and_radii(obj_name,_self=cmd):
pymol=_self._pymol
cmd=_self
from chempy.champ import assign
# apply a few kludges
# convent Seleno-methionine to methionine
cmd.alter(obj_name+"///MSE/SE","elem='S';name='SD'",quiet=1)
cmd.alter(obj_name+"///MSE/","resn='MET'",quiet=1)
cmd.flag("ignore",obj_name,"clear")
# remove alternate conformers
cmd.remove(obj_name+" and not alt ''+A")
cmd.alter(obj_name,"alt=''")
cmd.sort(obj_name)
cmd.fix_chemistry(obj_name,obj_name,1)
# make sure all atoms are included...
cmd.alter(obj_name,"q=1.0",quiet=1)
print " Util: Fixing termini and assigning formal charges..."
assign.missing_c_termini(obj_name,quiet=1,_self=_self)
while not assign.formal_charges(obj_name,quiet=1,_self=_self):
print " WARNING: unrecognized or incomplete residues are being deleted:"
cmd.iterate("(byres ("+obj_name+" and flag 23)) and flag 31",
'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/"',quiet=1)
cmd.remove("byres ("+obj_name+" and flag 23)") # get rid of residues that weren't assigned
assign.missing_c_termini(obj_name,quiet=1,_self=_self)
print " Util: Assigning Amber 99 charges and radii..."
cmd.h_add(obj_name)
if not assign.amber99(obj_name,quiet=1,_self=_self):
print " WARNING: some unassigned atoms are being deleted:"
cmd.iterate("byres ("+obj_name+" and flag 23)",
'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/"+name+"? ["+elem+"]"',quiet=1)
cmd.remove(obj_name+" and flag 23") # get rid of any atoms that weren't assigned
# show the user what the net charges are...
formal = sum_formal_charges(obj_name,quiet=0,_self=_self)
partial = sum_partial_charges(obj_name,quiet=0,_self=_self)
if round(formal)!=round(partial):
print " WARNING: formal and partial charge sums don't match -- there is a problem!"
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 _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
