def __parse_score_weights_penalties(self, line, param_name):
values = [line.split()[1], line.split()[2]]
if len(values) != 2 : raise ConfigError(str(param_name).upper()+" parameter you must provide 2 values")
if values[0].upper() == "X" or values[1].upper() == "X": return 1
if values[0].isalpha() or values[1].isalpha(): raise ConfigError(str(param_name).upper()+"must be DIGID not alfanumeric value")
elif float(values[0]) >= 0 and float(values[1]) >=0 : setattr(self, param_name, [float(values[0]), float(values[1])])
else: raise ConfigError(str(param_name).upper()+"value must be positive value!")
if param_name == "freespace_penalty":
if float(values[0]) == 0. and float(values[1]) == 0:
self.is_freespace_defined = False
else:
self.is_freespace_defined = True
if param_name == "density_penalty":
if float(values[0]) == 0. and float(values[1]) == 0:
self.is_density_defined = False
else:
self.is_density_defined = True
if param_name == "chi2_penalty":
if float(values[0]) == 0. and float(values[1]) == 0:
self.is_chi2_defined = False
else:
self.is_chi2_defined = True
if param_name == "rg_penalty":
if float(values[0]) == 0. and float(values[1]) == 0:
self.is_rg_penalty_defined = False
else:
self.is_rg_penalty_defined = True
def __parse_rot_angle(self, line):
"""
"""
maxrot = line.split()[1]
if maxrot.upper() == "X": return 1
if maxrot.isalpha() : raise ConfigError("MAXROT must be DIGID not alfanumeric value")
if -360.0 > float(maxrot) > 360.: raise ConfigError("Rotation angle cannot be larger than 360 degrees or smaller than -360")
else: self.max_rot_angle = float(maxrot)
def __parse_kvol(self, line):
"""
"""
kvol = line.split()[1]
if kvol.isalpha() : raise ConfigError("KVOL must be DIGIDS not alfanumeric value")
if kvol.upper() == "X": return 1
else:
if (float(kvol) > 10 or float(kvol) < 0):
raise ConfigError("Volume you provided is not in the range from 0 to 10!%s "%(kvol))
elif float(kvol) == 0:
raise ConfigError("Volume must be larger than 0!")
self.kvol = float(kvol)
def __parse_reheating_param(self, line):
line = line.split()
reheat = line[1]
reheat_rejections = line[2]
if reheat.upper() not in ["TRUE", "FALSE"]: raise ConfigError("Reheat is of value True or False")
if reheat_rejections.isalpha(): raise ConfigError("Rejection must be float value")
elif reheat.upper() == "TRUE" and float(reheat_rejections) > self.simul_steps : raise ConfigError ("Rejection frequency cannot be larger than number of simulation steps")
elif float(reheat_rejections) <= 0 : raise ConfigError ("Rejection frequency cannot be lower than 0")
if reheat.upper() == "TRUE": self.reheat = True
else: self.reheat = False
self.reheat_rejections = float(reheat_rejections)
def __parse_outsteps(self, line):
"""
"""
out_steps = [line.split()[1], line.split()[2]]
if len(out_steps) != 2 : raise ConfigError("for OUTSTEPS parameter you must provide 2 values")
if (out_steps[0].upper() == "X" and out_steps[1].upper() == "X") \
or (out_steps[0].upper() == "FIRST" and out_steps[1].upper() == "LAST"):
self.out_steps.append(1)
self.out_steps.append(self.simul_steps-1)
elif float(out_steps[1]) > self.simul_steps:
raise ConfigError("Steps value cannot be larger than number of simulations!")
elif (out_steps[0] > 0 and out_steps[1] > 0): self.out_steps = [int(line.split()[1]), int(line.split()[2])]
else: raise ConfigError("OutSteps value must be positive value!")
def __parse_mutation_frequencies(self, line, param_name):
value = line.split()[1]
floatValue = float(value)
if value.upper() == "X": return 1
#mutation_name = param_name.split("_")[0]
mutation_name = param_name.replace("_freq","")
if mutation_name == "simul_dd": mutation_name = "SimulateDisorder"
if floatValue == 0: self.disabled_mutations.append(mutation_name)
if value.isalpha() : raise ConfigError(str(param_name)+"must be DIGID not alfanumeric value")
elif 0. <= floatValue <= 1. : setattr(self, param_name, floatValue)
else: raise ConfigError("Frequency of"+str(param_name).upper()+"must be defined in range from 0 to 1")
return {mutation_name: floatValue}
def __set_outsave_mode(self):
"""
"""
if self.simul_steps == 0: pass
elif self.niter > self.simul_steps:
raise ConfigError("Steps to write cannot be larger than number of simulation steps!")
#self.out_steps = []
if self.out_steps and self.niter and self.write_eachbetter:
raise ConfigError("You can select only one of output save methods either WRITE_N_ITER or or WRITE_EACHBETTER or OUT_STEPS")
if self.out_steps : self.save_res_mode = "outsteps"
elif self.write_eachbetter : self.save_res_mode = "eachbetter"
elif self.niter : self.save_res_mode = "niter"
def __parse_positive_params(self, line, param_name, type = "float"):
"""
"""
value = line.split()[1]
if value.upper() == "X": return 1
if value.isalpha() : raise ConfigError(str(param_name)+"must be DIGID not alfanumeric value")
if not param_name == "threshold":
try:
float(value) < 0
except:
raise ConfigError(str(param_name).upper()+"must be positive value! Use dots for float numbers.")
if type == "float":
setattr(self, param_name, float(value))
if type == "int":
setattr(self, param_name, int(value))
def __parse_param_value(self, line, param_name, list_of_values):
"""
"""
value = line.split()[1]
found = False
if value.upper() == "X" : return 1
if value.isdigit() : raise ConfigError(str(param_name).upper()+"must be alfanumeric not DIGIT value")
for val in list_of_values:
if value.lower() == val.lower():
found = True
break
if found == False:
raise ConfigError(str(param_name).upper()+" has only possible values "+"".join(list_of_values) )
if param_name == "simmethod" and value.upper() == "X": setattr(self,param_name, "simulatedannealing")
else: setattr(self,param_name, value.lower())
def __parse_scaling(self, line, param_name, counter):
"""
"""
if counter == 3:
values = [float(line.split()[1]), float(line.split()[2]), float(line.split()[3])]
elif counter == 2:
values = [float(line.split()[1]), float(line.split()[2])]
percentValues = []
for val in values:
if str(val).isalpha(): raise ConfigError(param_name.upper()+"must be DIGITS not alfanumeric value")
elif 100 < val < 0: raise ConfigError(param_name.upper()+"must be from range 0 to 100")
percentValues.append(val/100.0)
setattr(self, param_name, percentValues)
return percentValues
def __check_shape_descriptors(self):
"""
"""
if self.shapedesc:
if self.kvol_given == False and self.threshold_given == False and self.shapedesc == "map":
raise ConfigError("You must provide kvol or threshold value when you provide density map as input")
if self.kvol_given and self.threshold_given:
raise ConfigError("Please provide only one of these two parameters: KVOL or THRESHOLD!")
if self.threshold != None:
self.kvol = None
if self.is_freespace_defined == False:
self.freespace_penalty = [0.,0.]
if self.is_density_defined == False:
self.density_penalty = [0.,0.]
if self.density_penalty[0] != 0. and self.freespace_penalty[0] != 0.:
print ConfigError("Scoring function will penalyze shape filling twice since you defined two parameters: DENSITY and MAP_FREESPACE!")
logfile.write_file("Scoring function will penalyze shape filling twice since you defined two parameters: DENSITY and MAP_FREESPACE!\n")
if self.simbox > 10:
raise ConfigError("The size of the system you want to use is very large. Max simbox value is 10")
#when no file with density map or ab initio model was provided but density filling or mapspace weights were provided
if self.shapedesc == False and self.is_density_defined == True: #and (self.density_penalty[0] != 0):
raise ConfigError("Map filling cannot be calculated when no shape descriptor was provided!\n")
logfile.write_file("Map filling cannot be calculated when no shape descriptor was provided!")
#print "@@@@@@", self.shapedesc, self.is_freespace_defined
if self.shapedesc == False and self.is_freespace_defined == True: #(self.freespace_penalty[0] != 0):
#print "****", self.shapedesc, self.is_freespace_defined
raise ConfigError("Map filling cannot be calculated when no shape descriptor was provided!")
logfile.write_file("Map filling cannot be calculated when no shape descriptor was provided!\n")
if self.shapedesc == "map" or self.shapedesc == "saxs": self.shapedesc = True
if self.is_chi2_defined == True or self.is_rg_penalty_defined == True:
if not self.curve:
raise ConfigError("To verify discrepancy with SAXS/SANS curves you must provide .dat file!")
else:
self.crysol_outfile = open("crysol_summary.txt", "w")
if self.representation == "sphere" and self.restraints_penalty[0] == 0 and self.restraints_penalty[1] == 0:
raise ConfigError ("To validate clashes between spheres PyRy3D calculates violation of distances betweeen\
spheres centres. To allow this option penalty for RESTRAINTS must be different than 0 0")
if self.identify_disorders == False and self.simul_dd_freq != 0.:
raise ConfigError ("You must allow PyRy3D to identify disorders to use simulate disorder mutation. Please set IDENTIFY_DISORDER parameter into True or disable simulate disorder mutation by setting SIMUL_DD_FREQ to 0 0 values")
def __check_save_structnr(self, params):
"""
"""
for param in params:
if self.simul_steps == 0: pass
elif getattr(self, param) > self.simul_steps:
print getattr(self, param)
raise ConfigError(str(param).upper()+" value cannot be larger than number of simulations!")
def __parse_bool_param(self,line, param_name):
val = line.split()[1]
if val.upper() not in ["TRUE", "FALSE"]:
raise ConfigError('%s can be "True" or "False"'%(param_name.upper()))
else:
if val.upper() == "TRUE": val = True
else: val=False
setattr(self, param_name, val)
def __parse_trans_vector(self, line):
"""
"""
trans_vec = [line.split()[1], line.split()[2], line.split()[3]]
if len(trans_vec) != 3 : raise ConfigError("for MAXTRANS parameter you must provide 3 values")
if trans_vec[0].upper() == "X" or trans_vec[1].upper() == "X" or trans_vec[2].upper() == "X": return 1
elif trans_vec[0].isalpha() or trans_vec[1].isalpha() or trans_vec[2].isalpha() : raise ConfigError("MAXTRANS must be DIGIDS not alfanumeric value")
self.max_trans_vec = [float(trans_vec[0]), float(trans_vec[1]), float(trans_vec[2])]
def __parse_movestate(self, line):
"""
"""
chain_name = line.split()[1]
move_state = line.split()[2]
if move_state.lower() == "fixed" or move_state.lower() == "movable": pass
else: raise ConfigError("unknown state %s"%(move_state))
move_state = Movable(chain_name, line)
#print "@@@@@@@@@@2", move_state
self.movable.append(move_state)
def __check_mut_freq_correctness(self):
"""
"""
sumpar = float(self.rotation_freq + self.rotation_cov_freq + self.translation_freq + self.exchange_freq + self.exchangeandsample_freq\
+ self.simul_dd_freq + self.translation_all_freq + self.rotation_all_freq \
+ self.rotation_whole_freq)
if round(sumpar,1) > float(1.0):
raise ConfigError("Frequencies of mutations must sum up to 1. You provided %s"%(sumpar))
if round(sumpar,1) < float(1.0):
self.rotation_freq = self.rotation_freq/sumpar *1.0
self.rotation_cov_freq = self.rotation_cov_freq/sumpar *1.0
self.translation_freq = self.translation_freq/sumpar *1.0
self.exchange_freq = self.exchange_freq/sumpar *1.0
self.exchangesample_freq = self.exchangeandsample_freq/sumpar *1.0
self.simul_dd_freq = self.simul_dd_freq/sumpar *1.0
self.translation_all_freq = self.translation_all_freq/sumpar *1.0
self.rotation_all_freq = self.rotation_all_freq/sumpar *1.0
self.rotation_whole_freq = self.rotation_whole_freq/sumpar *1.0
def __parse_covalent_links(self, line):
try: linked_components = eval(line.split()[2]) #.replace("[","").replace("]","").replace(",",""))
except ConfigError: print "Please provide correct format for COVALENT_BONDS parameter in configuration file"
#linked_components = line.split()[2].replace("[","").replace("]","").replace(",","")
component = line.split()[1]
if component not in self.linked_components.keys():
for el in linked_components:
if el == component:
raise ConfigError("Component %s cannot be bound with %s "%(component, el))
#self.linked_components[component] = linked_components
at1 = eval(line.split()[3])
at2 = eval(line.split()[4])
covbond = CovalentBond(linked_components, at1, at2)
if self.linked_components.has_key(component):
self.linked_components[component].append(covbond)
else:
self.linked_components[component] = [covbond]
def __check_atoms(self, atom):
if len(atom) != 2: raise ConfigError("You haven't provided enough information about covalent bonds atoms")
if not str(atom[0]).isdigit(): raise ConfigError ("Residue number should be number not string")
if not str(atom[1]).isalpha(): raise ConfigError ("Atom name must be string, not number")
def __check_mutual_clashes_options(self):
if self.required_clashes_penalty == True and self.required_clashes_penalty_allatoms == True:
raise ConfigError("Only one option can be applied CLASHES or CLASHES_ALLATOMS. \
Please change values into 0 for one of the parameters or comment one option in configuarion file")