def generate(self, component=None):
"""
"""
# self.grapes[0] = self.findBallPoint(self.masterPoint, self.masterRadius-self.radius)
self.grapes[0] = self.masterPoint
if (self.generationMethod == "anchored_chain"):
if (not self.checkChainDistance()):
self.generationMethod = "chain"
print "Warning! Anchored chain distance too big, switching to regular chain"
logfile.write_file(
"Warning! Anchored chain distance too big, switching to regular chain\n"
)
else:
self.startAnchoredChain()
for i in range(1, self.grapeCount):
lIterCount = 0
if (self.generationMethod == "anchored_chain"):
self.anchoredReposition(i - 1)
while (
lIterCount < 100
): #Try a hundred times before going ahead (last generated grape is left there, even if it collides)
lIterCount += 1
if (self.generationMethod == "random"):
n = randint(0, i - 1) #attach to a random one
elif self.generationMethod == "chain":
n = i - 1 #attach new grape to the last one
elif self.generationMethod == "anchored_chain":
#attention! i-2 can be equal -1
n = i - 2 #attach new grape to the previous to last one
if (self.generationMethod == "anchored_chain"):
if (i == 1
): #skip first step, we have the anchor point there
continue
angle = self.getMaxAngle(self.grapes[n],
self.grapes[n + 1], i)
self.grapes[i] = self.findChainPoint(
self.grapes[n], 2 * self.radius, 0.75 * angle,
0.75 * min(angle, pi / 4), i == self.grapeCount - 1)
else:
self.grapes[i] = self.findSpherePoint(
self.grapes[n], 2 * self.radius)
if (self.collides(i) == 0):
if (self.detectCollisions != None):
if component:
if (self.detectCollisions(component,
self.grapes[i],
self.radius) == 0):
break
else:
break
#print "new grape", self.grapes[i]
if (self.generationMethod == "anchored_chain"):
self.endAnchoredChain()
return self.grapes
def save_logfile(self):
"""
saves all alphabetically sorted config attributes to logfile
"""
attribs = self.__dict__
for a in sorted(attribs.keys()):
logfile.write_file(str(a).upper()+"."*20+" "+str(attribs[a])+"\n")
def save_simulation_results(self, i, lBestScoreComplex, fname=False):
"""
Saves results of simulation to trafl file (if requested by the user) and
to pdb files
results are saved every N steps (defined by the user) and best scored
complex in last N iterations is saved
start/stop number of iterations to save (requested by the user)
"""
if self.traflfile and not self.server: # and (i not in self.saved_iterations):
for cx in lBestScoreComplex:
cx.add_trajectory(i, cx.temp)
for replica in lBestScoreComplex:
if replica == None:
continue
if replica.simulation_score not in self.scores:
self.scores.append(replica.simulation_score)
if self.mReplicaTemperatures:
replica.save_pdb(i, replica.reptemp,
fname) #self.mReplicaTemperatures[j])
else:
replica.save_pdb(i, replica.temp, fname)
if not self.server:
logfile.write_file(\
"cx score for iteration "+str(i+1)+" is\t"+str(round(replica.simulation_score,3))\
+"\tcomponents: restraints: "+str(round(replica.restraints,3) * replica.restraints_penalty)+" "+\
"collisions: "+str(round(replica.clashes,3) * replica.clashes_penalty)+" "+\
"map filling: "+str(round(replica.freespace,3) * replica.freespace_penalty)+" "+\
"outbox atoms: "+str(round(replica.outbox,3) * replica.outbox_penalty)+" "+\
"density filling: "+str(round(replica.density,3) * replica.density_penalty)+" "+\
"\tACTUAL WEIGHTS are respectively: "+str(replica.restraints_penalty)+", "+\
str(replica.clashes_penalty)+", "+str(replica.freespace_penalty)+", "+\
str(replica.outbox_penalty)+", "+str(replica.density_penalty)+"\n")
if self.plot == True:
plot_cx = PlotComplex(replica, i)
self.saved_complexes.append(plot_cx)
else:
logfile.write_file("Rejected\t" +
str(replica.simulation_score) +
"\titer_nr\t" + str(i + 1) + "\n")
##@TODO: put into separate function
#if self.simul_params.movehistory:
# for replica in lBestScoreComplex:
# movehist.write_message("COMPLEX \t"+str(i)+ "\t"+str(replica.simulation_score)+"\t"+str(replica.temp))
# for component in replica.components:
# movehist.write_message(str(component.pyrystruct.chain)+"\tROTATIONS\t"+str(component.rot_history)\
# +"\tTRANSLATIONS\t"+str(list(component.trans_history)))
self.saved_iterations.append(i)
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 get_map(self, saxsfile, mapfile, simul_params, first_complex):
"""
sets Density_map object and assigns attributes
Parameters:
-----------
mapfile : file with density map
cx_volume : volume of entire complex
simul_params : user defined simulation parameters
vollist : list of all complex' residues MWs
Returns:
--------
mapcomponent : Complex_map object
"""
mapcomponent = Complex_map()
#no shape descriptor
if saxsfile == None and mapfile == None:
mapcomponent.set_simbox_with_no_shape_descriptor(
first_complex, simul_params.start_orient,
simul_params.simboxradius, simul_params.simgridtype)
simul_params.freespace_penalty = [0.0, 0.0]
#return mapcomponent
if saxsfile:
mapcomponent.saxsfile = saxsfile
#if 0. in simul_params.density_penalty: raise ConfigError ("To score complex compatibility with SAXS shape please use MAP_FREESPACE parameter in a configuration file")
if simul_params.is_freespace_defined == False:
print "WARNING! You have not provided penalty value to score a compatibility with complex shape, \
default weight has been assigned of 1 1"
logfile.write_file(
"WARNING! You have not provided penalty value to score a compatibility with complex shape, \
default weight has been assigned of 1 1\n")
if 0. in simul_params.freespace_penalty:
print "WARNING! Bear in mind that a compatibility with complex shape will not be calculated at least \
in some parts of the simulations. Check MAP_FREESPACE value in configuration file"
logfile.write_file(
"WARNING! Bear in mind that a compatibility with complex shape will not be calculated at least \
in some parts of the simulations. Check MAP_FREESPACE value in configuration file\n"
)
mapcomponent.set_mapgrid_by_saxs_data(simul_params.simboxradius,
simul_params.saxsradius,
simul_params.simgridtype)
#get data when kmax is defined!
elif simul_params.threshold == None: #if threshold
if mapfile:
mapcomponent.mapfile = mapfile
mapcomponent.set_mapgrid_by_volume(simul_params.simboxradius,
first_complex,
simul_params.kvol,
simul_params.simgridtype)
elif simul_params.kvol == None:
if mapfile:
if 0. in simul_params.freespace_penalty and 0. in simul_params.density_penalty:
print "WARNING! Bear in mind that a compatibility with complex shape will not be calculated at least in some parts of the simulations.\
Check MAP_FREESPACE and DENSITY values in configuration file"
logfile.write_file(
"WARNING! Bear in mind that a compatibility with complex shape will not be calculated at least in some parts of the simulations.\
Check MAP_FREESPACE and DENSITY values in configuration file")
if simul_params.is_freespace_defined == False and simul_params.is_density_defined == False:
print "WARNING! You have not provided penalty value to score a compatibility with complex shape, default weights have been assigned of 1 1 to MAP_FREESPACE and DENSITY parametrs. \
Please check whether these values are defined in a configuration file"
mapcomponent.mapfile = mapfile
mapcomponent.set_mapgrid_by_threshold(
simul_params.simboxradius, simul_params.threshold,
simul_params.simgridtype)
mapcomponent.set_map_obj(simul_params.simbox, simul_params.simgridtype,
simul_params.simboxradius)
return mapcomponent
# ---------- create first complex --------------------------
first_complex = create_first_complex(trans.components, con, inp.traflfile)
#------------generate interactions between complex components
density_map = trans.get_map(inp.saxsfile, inp.mapfile, con, first_complex)
trans.get_interactions(inp.restraints, inp.symrestraints, trans.components,
density_map)
#first_complex.interactions = trans.interactions
#------------locate components randomly inside the density map----------
calculate_simulbox_statistics(first_complex, density_map, inp, trans, con)
arrange_components_inside_simulbox(first_complex, density_map, trans, con)
#------------perform simulation!-----------------------------------------------
#import cProfile
if con.simul_steps != 0:
best_complex, sim, last_complex = run_simulation(
first_complex, con, trans.interactions, density_map, inp.traflfile)
# best_complex, sim, last_complex = cProfile.run('run_simulation(first_complex, con, trans.interactions, density_map, inp.traflfile)')
if inp.fullatom_file: save_fullatom_bestmodel(best_complex)
# ---------- save log messages -------------------------------------------
logfile.write_file()
#if inp.movehistory_file: save_movehistory(best_complex, movehist) #movehist.write_file()
if inp.movehistory_file:
save_movehistory(last_complex, movehist) #movehist.write_file()
if inp.scoreplot: draw_scores_plot(inp.scoreplot, sim)