def autoimage_traj(parm_name,
trajin_name,
trajout_name,
box_info,
cpptraj_script_location,
cpptraj_exe='cpptraj',
writing_frames=()):
'''Runs the CPPTRAJ autoimage command for a triclinic box simulation.
Input:
- parm_name: a string representing the filename of a .prmtop or .parm7 AMBER
parameter/topology file
- trajin_name: a non-imaged trajectory to load for imaging
- box_info: a string representing the triclinic box in x,y,z,alpha,beta,gamma
format
- cpptraj_script_location: string for the location to write the cpptraj script
- cpptraj_exe: an optional string representing the OS command to run CPPTRAJ
Output:
- None
'''
cpptraj_template = '''parm $PARMFILE
box $BOX_INFO
trajin $TRAJIN
autoimage
trajout $TRAJOUT $FRAME_STR
go
quit
'''
assert len(
writing_frames
) < 4, 'When writing the autoimaged trajectory, the format of the writing_frames variable must be: (start, stop, offset)'
if len(writing_frames) == 0: # then write all frames
frame_str = ''
elif len(writing_frames) == 1:
frame_str = 'start %d' % writing_frames[0] # only include the start
elif len(writing_frames) == 2:
frame_str = 'start %d stop %d' % (writing_frames[0], writing_frames[1])
else: # the length is 3
frame_str = 'start %d stop %d offset %d' % (
writing_frames[0], writing_frames[1], writing_frames[2])
cpptraj_dict = {
'PARMFILE': parm_name,
'TRAJIN': trajin_name,
'TRAJOUT': trajout_name,
'BOX_INFO': box_info,
'FRAME_STR': frame_str
} # define template dictionary
cpptraj_script = Adv_template(
cpptraj_template, cpptraj_dict
) # fill in the values into the template from the dictionary
extract_file = open(cpptraj_script_location,
'w') # open the script for writing
extract_file.write(cpptraj_script.get_output()) # write a cpptraj script
extract_file.close()
os.system("%s < %s" %
(cpptraj_exe, cpptraj_script_location)) # run cpptraj
return
def tclforces(settings):
'''generates the string that will be included in the NAMD file for the tclforces script'''
tcltemplatestring = """
set SCRIPT_INTERVAL $script_interval ;# number of timesteps before script should be evaluated. Examples: 1=script evaluated every timestep. 5=script eval'd every 5th timestep, ...
set LIGROT $ligrot ;# whether we care about ligand rotation
set RECROT $recrot ;# whether we care about receptor rotation
set ABORT_ON_CROSSING $abort_on_crossing ;# whether a job should be aborted right after crossing a milestone
set PHASE $phase ;# can be 'forward' or 'reverse'
set CARE_ABOUT_SELF $care_about_self ;# whether we care about the milestone's self in this simulation
set whoami_const $whoami ;# the index of the milestone we started from
set whoami $whoami_const
set whoami_rot_const $whoami_rot ;# the index of the rotational milestone we started from
set whoami_rot $whoami_rot_const
set GRID_EDGE_RAD $grid_edge_rad ;# radius to the edge of the grid from the center
set LIGRANGE {$ligrange} ;# the indeces of the atoms that define the ligand
set RECRANGE {$recrange} ;# the indeces of the atoms that define the receptor
#set RECPA1_LIST {$recpa1_list} ;# the list of relatively immobile atoms that define the receptor's 1st PA. MARKED FOR REMOVAL
#set RECPA3_LIST {$recpa3_list} ;# the list of relatively immobile atoms that define the receptor's 3rd PA. MARKED FOR REMOVAL
set MILESTONE_LIST $milestone_string ;# a list of milestones to be converted to arrays
set SITEID $siteid ;# the ID if the current site
set MAX_NUM_STEPS $max_num_steps ;# the maximum number of steps before starting a new crossing phase
"""
tcltemplate = Adv_template(tcltemplatestring,
settings) # fill in the missing values
return tcltemplate
def submit(self, my_params, my_template):
# make the submission files
params = fill_params(self, my_params) #{ 'job_name' : self.name+str(self.number), 'queue':queue,'procs':self.procs, 'time_str':self.time_str, 'acct':acct, 'sys_name':self.system, 'stage':self.name, 'namd_script': self.name+str(self.number)+'.namd', 'namd_output':self.name+str(self.number)+'.out' }
script_name = '%s%d_%d.submit' % (self.name, self.procs, self.number)
submit_filename = os.path.join(self.dir, script_name)
print " writing submit script to location:", submit_filename
#BRJ 4/4 _0_ should be changed to rotational milestone number
if self.name == "ens_equil":
params['job_name']=self.name+"_0_"+str(self.number)
else:
params['job_name']=self.name+str(self.number)
#BRJ4/4
params['curdir']=os.path.join(os.getcwd(), self.dir)
submit = Adv_template(my_template, params)
submit_file = open(submit_filename,'w')
submit_file.write(submit.get_output())
submit_file.close()
# submit the files
cmd = '%s %s' % (submit_cmd, submit_filename)
submit_stdout = self.command(cmd)
# print " executing command:", cmd
self.status = "submitted"
def quat_tclforces(settings):
'''generates the string that will be included in the NAMD file for the quaternion tclforces script for rotational colvars'''
tcltemplatestring = """
set FORCE_CONSTANT {$force_constant}
set RECROT $recrot
set REC_INDECES {$rec_indeces}
set REC_PA1_INDECES {$rec_pa1_indeces}
set REC_PA3_INDECES {$rec_pa3_indeces}
set LIG_PA1_INDECES {$lig_pa1_indeces}
set LIG_PA3_INDECES {$lig_pa3_indeces}
set LIG_INDECES {$lig_indeces}
set ANCHOR_QUAT $anchor_quat
set MAIN_NEIGHBOR $main_neighbor
set NEIGHBOR_QUATS {
"""
#for neighbor_quat in settings['neighbor_quats']:
neighbor_quat_string = ' '.join(settings['neighbor_quats'])
tcltemplatestring += neighbor_quat_string + '}'
quat_tcltemplate = Adv_template(tcltemplatestring,
settings) # fill in the missing values
return quat_tcltemplate
def prep(
settings,
holo,
stage,
inpname,
outname='',
temperatures=[],
write_freq='1000',
):
if verbose: print "creating %s files" % stage
i = settings['index']
path = settings['md_file_paths'][i][stage]
ff = settings['ff'] # forcefield
pos_milestone = settings['milestone_pos_rot_list'][i][0]
rot_milestone = settings['milestone_pos_rot_list'][i][1]
temperature = settings['master_temperature']
absolute_mode = settings['absolute_mode']
if not outname: outname = stage # provide the default outname
get_cell = False
if len(temperatures) == 0:
temperatures = [settings['master_temperature']]
if stage == 'min':
stage_settings = settings['min_settings']
if not stage_settings['namd_settings'][
'extendedsystem']: # if they didn't define a starting XSC file
get_cell = settings[
'cell_shape'] # create the periodic boundary conditions
if stage == 'temp_equil':
stage_settings = settings['temp_equil_settings']
if stage == 'ens_equil':
stage_settings = settings['ensemble_equil_settings']
if stage == 'prod':
stage_settings = settings['prod_settings']
if stage == 'fwd_rev':
stage_settings = settings['fwd_rev_settings']
ensemble = stage_settings['ensemble']
namd_settings = stage_settings[
'namd_settings'] # extra settings to send to the NAMD input file
if 'constrained' in stage_settings.keys() and stage_settings[
'constrained']: # if the settings exists and not empty/False
fixed = True
occ_pdb = deepcopy(
holo) # copy the holo structure so we can change the occupancy
constrained = stage_settings['constrained']
constraints(occ_pdb, constrained,
settings) # constrain the selected atoms
fxd_name = os.path.join(path, 'fxd1.pdb')
namd_settings['fixedAtoms'] = 'on'
namd_settings['fixedAtomsFile'] = 'fxd1.pdb'
namd_settings['fixedAtomsCol'] = 'O'
occ_pdb.save(fxd_name, amber=True,
standard=False) # save the constraint file
else:
fixed = False
if 'restrained' in stage_settings.keys() and stage_settings[
'restrained']: # if the settings exists and not empty/False
const = True
occ_pdb = deepcopy(
holo) # copy the holo structure so we can change the occupancy
restrained = stage_settings['restrained']
restrained_force = stage_settings['restrained_force']
restraints(occ_pdb, restrained, restrained_force,
settings) # constrain the selected atoms
rest_name = os.path.join(path, 'restrained1.pdb')
occ_pdb.save(rest_name, amber=True, standard=False)
#ens_namd_settings['fixedatoms'] = 'off' # we may not necessarily want to turn off fixed atoms
namd_settings['constraints'] = 'on'
namd_settings['consref'] = 'restrained1.pdb'
namd_settings['conskfile'] = 'restrained1.pdb'
namd_settings['conskcol'] = 'O'
else:
const = False
settings['whoami'] = str(pos_milestone.index)
settings['whoami_rot'] = str(rot_milestone.index)
settings['siteid'] = str(pos_milestone.siteid)
settings[
'grid_edge_rad'] = '0.0' # temporary value until this can be more effectively predicted; will speed up TCL script evaluation
if ff == 'amber':
namd_settings['parmfile'] = make_relative_path(
settings['prmtop'], path
) # Find the relative location of the prmtop/inpcrd to be used in the mins
namd_settings['ambercoor'] = make_relative_path(
settings['inpcrd'], path)
elif ff == 'charmm':
namd_settings['amber'] = 'no'
namd_settings['coordinates'] = '../holo_wet.pdb'
namd_settings['structure'] = '../building/holo_wet.psf'
namd_settings['paratypecharmm'] = 'on'
counter = 1
for parameter in settings['charmm_settings']['parameters']:
if counter == 1: # we need to make sure the namd input file can get more than one parameter file
i = ""
else:
i = str(counter)
namd_settings['parameters%s' % i] = parameter
counter += 1
#namd_settings['parameters2'] = '/extra/moana/rswift1/Permeability/Colvar/A/1F/par_all36_lipid.prm'
#fhpd_file = 'fhpd.txt'
namd_settings['watermodel'] = settings['watermodel']
if stage == 'ens_equil':
namd_settings['outfilename'] = outname + "_0_1"
if settings['lig_rot']:
hedron = positions_orient.get_hedron(settings['quat_hedron'])
quat_tclforces_settings = {}
quat_tclforces_settings['force_constant'] = settings[
'quat_force_constant']
quat_tclforces_settings['recrot'] = settings['recrot']
quat_tclforces_settings['rec_indeces'] = settings[
'quat_rec_indeces']
quat_tclforces_settings['lig_indeces'] = settings[
'quat_lig_indeces']
#quat_tclforces_settings['lig_pa1_indeces'] = settings['ligpa1_list'] # MARKED FOR REMOVAL
#quat_tclforces_settings['lig_pa3_indeces'] = settings['ligpa3_list'] # MARKED FOR REMOVAL
#quat_tclforces_settings['rec_pa1_indeces'] = settings['recpa1_list'] # MARKED FOR REMOVAL
#quat_tclforces_settings['rec_pa3_indeces'] = settings['recpa3_list'] # MARKED FOR REMOVAL
allquats = make_quat_list_in_tcl(hedron)
#for i in range(len(allquats)):
quat = rot_milestone.rotation
tcl_quat = make_quat_list_in_tcl(quat)
quat_tclforces_settings['anchor_quat'] = tcl_quat
quat_tclforces_settings['neighbor_quats'] = allquats
closest_neighbors = make_closest_neighbors(ref_quat=quat,
hedron=hedron,
tcl_output=False)
if len(closest_neighbors) == 0: closest_neighbors = ["None"]
number_of_neighbors = len(closest_neighbors)
#closest_neighbors = make_quat_list_in_tcl(closest_neighbors)
for f in range(number_of_neighbors):
quat_tclforces_settings[
'main_neighbor'] = make_quat_list_in_tcl(
closest_neighbors[f])
namd_settings['tclforces'] = 'on'
namd_settings['tclforcesscript'] = settings[
'quatforcesscript'] # the script to be evaluated to keep the ligand forced to the rotational milestone
namd_settings['tclforces_vars'] = quat_tclforces(
quat_tclforces_settings).get_output()
# write namd file here
namd_settings['inpfilename'] = inpname
namd_settings[
'outfilename'] = outname + "_neighbor_%d_1" % f # 1st number: number of the neighbor, 2nd number: number of ens_equil simulation
inp, namd_params = namd_inputs.make_input(
holo,
ff,
stage,
temperature,
write_freq,
receptor_type=settings['receptor_type'],
ensemble=ensemble,
fixed=fixed,
get_cell=get_cell,
constraints=const,
settings=namd_settings) #...
input_name = os.path.join(path, '%s_%d_1.namd' % (stage, f))
inp.save(input_name)
param_filename = (os.path.join(path, 'namd_parameters.pkl'))
param_file = open(param_filename, 'wb')
pickle.dump(namd_params, param_file)
param_file.close()
return os.path.join(
stage, namd_settings['outfilename']) # return ens_equil
else: # then lig_rot is False
namd_settings['inpfilename'] = inpname
namd_settings['outfilename'] = outname + "_0_1"
inp, namd_params = namd_inputs.make_input(
holo,
ff,
stage,
temperature,
write_freq,
receptor_type=settings['receptor_type'],
ensemble=ensemble,
fixed=fixed,
get_cell=get_cell,
constraints=const,
settings=namd_settings) #...
input_name = os.path.join(path, '%s_%d_1.namd' % (stage, 0))
inp.save(input_name)
param_filename = (os.path.join(path, 'namd_parameters.pkl'))
param_file = open(param_filename, 'wb')
pickle.dump(namd_params, param_file)
param_file.close()
return os.path.join(
stage, namd_settings['outfilename']) # return ens_equil
hedron = positions_orient.get_hedron(settings['quat_hedron'])
allquats = make_quat_list_in_tcl(hedron)
quat = rot_milestone.rotation
closest_neighbors = make_closest_neighbors(ref_quat=quat,
hedron=hedron,
tcl_output=False)
if len(closest_neighbors) == 0: closest_neighbors = ["None"]
number_of_neighbors = len(closest_neighbors)
if stage == 'fwd_rev':
prelim_string_template = '''set TEMP $temperature
set NUM_REVERSALS $num_reversals
global REV_FILENAME_BASE; set REV_FILENAME_BASE "REV_COMPLETED.txt"
global FWD_FILENAME_BASE; set FWD_FILENAME_BASE "FWD_COMPLETED.txt"
global RESTART_FREQ; set RESTART_FREQ $restart_freq
global RUN_FREQ; set RUN_FREQ $run_freq
set ENS_EQUIL_FIRST_FRAME $begin
set ENS_EQUIL_STRIDE $stride
set LAUNCHES_PER_CONFIG $launches_per_config
set FRAME_CHUNK_SIZE $frame_chunk_size
set UMBRELLA_GLOB_DIR "../ens_equil/" ;# the umbrella sampling directory
set UMBRELLA_GLOB_NAME "ens_equil_0_?.dcd" ;# the umbrella sampling trajs
set nr [numReplicas]
set replica_id [myReplica] ;# get the ID of this replica'''
hedron = positions_orient.get_hedron(settings['quat_hedron'])
settings['care_about_self'] = 'False'
settings['phase'] = 'reverse'
settings['abort_on_crossing'] = 'True'
#settings['fhpd_file'] = '../reverse/fhpd.txt'
settings['max_num_steps'] = stage_settings['max_num_steps']
settings['milestone_string'] = make_milestone_list(
settings['raw_milestone_list'], hedron)
namd_settings['tclforces_vars'] = tclforces(settings).get_output()
num_frames = settings['ensemble_equil_settings']['namd_settings'][
'numsteps']
dcd_write_freq = int(
settings['ensemble_equil_settings']['namd_settings']['dcdfreq'])
begin = stage_settings['extract_first'] # new parameter
end = int(num_frames) / dcd_write_freq + 1
stride = stage_settings['extract_stride'] # new parameter
launches_per_config = stage_settings['launches_per_config']
frame_chunk_size = stage_settings['frame_chunk_size']
restart_freq = stage_settings['restart_freq'] # New parameter
run_freq = stage_settings['run_freq'] # new parameter
num_reversals = int((end - begin) / stride)
namd_settings['inpfilename'] = inpname
namd_settings['outfilename'] = outname + ".$replica_id"
namd_settings[
'coordinates'] = "../holo_wet.pdb" # this gets overwritten...
namd_settings[
'ambercoor'] = '' # this has to be disabled when coordinates are presented
namd_settings['velocities'] = ''
if bool(stage_settings['extract_xst']):
namd_settings[
'extendedsystem'] = "../ens_equil/ens_equil_0_1.restart.xsc"
namd_settings['bincoordinates'] = ""
namd_settings['binvelocities'] = ""
namd_settings['temperature'] = temperature
namd_settings['replicaUniformPatchGrids'] = 'on'
namd_settings['numsteps'] = ''
namd_settings['restartfreq'] = '$RESTART_FREQ'
#namd_settings['id'] = i
prelim_settings = {
'temperature': temperature,
'num_reversals': num_reversals,
'restart_freq': restart_freq,
'run_freq': run_freq,
'begin': begin,
'stride': stride,
'launches_per_config': launches_per_config,
'frame_chunk_size': frame_chunk_size
}
prelim_string = Adv_template(
prelim_string_template,
prelim_settings).get_output() # fill in the missing values
namd_settings['prelim_string'] = prelim_string
post_string_settings = {}
namd_settings['post_string'] = File_template(
fwd_rev_template_location, post_string_settings).get_output()
inp, namd_params = namd_inputs.make_input(holo,
ff,
stage,
temperature,
write_freq,
fixed=fixed,
ensemble=ensemble,
get_cell=get_cell,
constraints=const,
settings=namd_settings) #...
input_name = os.path.join(path, 'fwd_rev1.namd')
inp.save(input_name)
param_filename = (os.path.join(path, 'namd_parameters.pkl'))
param_file = open(param_filename, 'wb')
pickle.dump(namd_params, param_file)
param_file.close()
#make_fhpd_script(path, 'forward_template.namd', settings['fhpd_file'], number_of_neighbors=number_of_neighbors)
return os.path.join(stage, namd_settings['outfilename'])
counter = 1
for temperature in temperatures:
namd_settings['inpfilename'] = inpname
namd_settings['outfilename'] = outname + str(counter)
inp, namd_params = namd_inputs.make_input(
holo,
ff,
stage,
temperature,
write_freq,
receptor_type=settings['receptor_type'],
ensemble=ensemble,
fixed=fixed,
get_cell=get_cell,
constraints=const,
settings=namd_settings) #...
input_name = os.path.join(path, '%s%d.namd' % (stage, counter))
inp.save(input_name)
counter += 1
inpname = namd_settings['outfilename']
return os.path.join(stage, namd_settings['outfilename'])
def main(settings):
rec_struct = settings['rec_struct']
lig_struct = settings['lig_struct']
lig_center = pdb.center_of_mass(lig_struct)
browndye_bin = settings['browndye_bin_dir']
empty_pqrxml = os.path.abspath(settings['empty_pqrxml_path'])
#b surface for FHPD preparation
pqrs = [copy.deepcopy(rec_struct), copy.deepcopy(lig_struct)]
pqrs[1].struct_id = 'bd_ligand'
b_surface_path = settings['b_surface_path']
if not os.path.exists(b_surface_path): os.mkdir(b_surface_path)
b_surface_criteria = []
b_surface_criteria.append({
'centerx': settings['bd_centerx'],
'centery': settings['bd_centery'],
'centerz': settings['bd_centerz'],
'ligx': lig_center[0],
'ligy': lig_center[1],
'ligz': lig_center[2],
'radius': settings['b_surf_distance'],
'index': settings['bd_index']
}) # add every site to the criteria list
print("bsurface_criteria:", b_surface_criteria)
b_surface_pqrxmls = _write_browndye_input(
pqrs,
settings,
b_surface_criteria,
work_dir=b_surface_path,
browndye_bin=browndye_bin,
start_at_site='false',
) # write input for this part
#generate BD milestone files
pqrs = [copy.deepcopy(rec_struct), copy.deepcopy(lig_struct)]
pqrs[1].struct_id = 'bd_ligand'
bd_file_path = settings['bd_milestone_path']
if not os.path.exists(bd_file_path): os.mkdir(bd_file_path)
criteria = []
criteria.append({
'centerx': settings['bd_centerx'],
'centery': settings['bd_centery'],
'centerz': settings['bd_centerz'],
'ligx': lig_center[0],
'ligy': lig_center[1],
'ligz': lig_center[2],
'radius': settings['bd_lower_bound'],
'index': settings['bd_lower_bound_index']
}) # add every site to the criteria list
# make BD preparation scripts extract_bd_frames.py and bd_fhpd.pyp
#print "settings['starting_surfaces'][i]:", settings['starting_surfaces'][i]
# Write the script to extract all frames from the successful b_surface bd trajectories
extract_bd_frames_dict = {
'TRAJDIR': "../b_surface",
'WORKDIR': "./trajs",
'PQRXML0': os.path.basename(b_surface_pqrxmls[0]),
'PQRXML1': os.path.basename(b_surface_pqrxmls[1]),
'EMPTY': empty_pqrxml,
'SITENAME': 'milestone_%s' % (settings['bd_index']),
'NUMBER_OF_TRAJS': settings['threads']
}
extract_bd_frames = Adv_template(extract_bd_frames_template,
extract_bd_frames_dict)
extract_file = open(os.path.join(bd_file_path, "extract_bd_frames.py"),
'w')
extract_file.write(extract_bd_frames.get_output()
) # write an xml file for the input to bd
extract_file.close()
# construct the FHPD distribution prep scripts
make_fhpd_dict = {
'INPUT_TEMPLATE_FILENAME': 'input.xml',
'RECEPTOR_PQRXML': os.path.basename(b_surface_pqrxmls[0]),
'RXNS': 'rxns.xml',
'NTRAJ': settings['fhpd_numtraj'],
'ARGS': "glob.glob(os.path.join('./trajs','lig*.pqr'))"
} # NOTE: should change NTRAJ to be consistent with the number of reaction events in the b_surface phase
make_fhpd = Adv_template(make_fhpd_template, make_fhpd_dict)
make_fhpd_file = open(os.path.join(bd_file_path, "make_fhpd.py"), 'w')
make_fhpd_file.write(
make_fhpd.get_output()) # write an xml file for the input to bd
make_fhpd_file.close()
# Consolidate all result files from the FHPD simulations into one large results.xml file
fhpd_consolidate_dict = {
'FHPD_DIR': "fhpd",
'LIG_DIR_GLOB': "lig*/",
'RESULTS_NAME': 'results.xml'
}
fhpd_consolidate = Adv_template(fhpd_consolidate_template,
fhpd_consolidate_dict)
fhpd_consolidate_file = open(
os.path.join(bd_file_path, "fhpd_consolidate.py"), 'w')
fhpd_consolidate_file.write(
fhpd_consolidate.get_output()) # write an xml file for the input to bd
fhpd_consolidate_file.close()
#counter += 1
bd_pqrxmls = _write_browndye_input(pqrs,
settings,
criteria,
work_dir=bd_file_path,
browndye_bin=browndye_bin,
fhpd_mode=True)
return
def main(settings):
'''
main function for bd.py
takes a list of pqr filenames, reaction coordinate pairs/distances
'''
if verbose: print '\n', '#'*40, "\n Now creating BD files using bd.py\n", '#'*40
rec_struct = settings['rec_struct']
#milestones = settings['milestones']
milestone_pos_rot_list = settings['milestone_pos_rot_list'] # NOTE: may want to clean up code referring to this variable
if settings['starting_conditions'] == 'configs':
lig_configs = settings['lig_configs']
elif settings['starting_conditions'] == 'spheres':
# then generate the anchors from random positions/orientations in a sphere
# NOTE: there is a random orientation function in positions_orient.py
pass
else:
raise Exception, "option not allowed: %s" % settings['starting_conditions']
bd_file_paths = settings['bd_file_paths']
browndye_bin = settings['browndye_bin_dir']
empty_pqrxml = os.path.abspath(settings['empty_pqrxml_path'])
bd_configs = []
# fill the b_surface folder
lig_config = lig_configs[0] # get the first config of the ligand
lig_center = pdb.center_of_mass(lig_config)
pqrs = [copy.deepcopy(rec_struct), copy.deepcopy(lig_config)]
#print "PQR1 ID", pqrs[1].struct_id
pqrs[1].struct_id='bd_ligand'
#print "PQR1 ID", pqrs[1].struct_id
b_surface_path = settings['b_surface_path']
if not os.path.exists(b_surface_path): os.mkdir(b_surface_path)
b_surface_criteria = []
for site in settings['b_surface_ending_surfaces']:
b_surface_criteria.append({'centerx':site['x'], 'centery':site['y'], 'centerz':site['z'], 'ligx':lig_center[0], 'ligy':lig_center[1], 'ligz':lig_center[2], 'radius':site['radius'], 'index':site['index'], 'siteid':site['siteid']}) # add every site to the criteria list
print "bsurface_criteria:", b_surface_criteria
b_surface_pqrxmls = write_browndye_input(pqrs, settings, b_surface_criteria, work_dir=b_surface_path, browndye_bin=browndye_bin, start_at_site='false', fhpd_mode = False) # write input for this part
for bd_file_path in bd_file_paths:
if not bd_file_path:
pass
#bd_configs.append(None)
#continue # then don't do BD for this portion
#print "bd_file_path:", bd_file_path
anchor_folder_name = bd_file_path.split('/')[-2] # reading the file tree to get the index of every existing folder
#print "anchor_folder_name:", anchor_folder_name
folder_index = anchor_folder_name.split('_')[1] # getting the index out of the folder name
bd_configs.append(int(folder_index))
counter = 0 # the index of the loop itself
print "bd_file_paths:", bd_file_paths
print "bd_configs:", bd_configs
for i in bd_configs: #len(milestones) should equal len(lig_configs); the index of the milestone/lig_config
#lig_config = lig_configs[i]
bd_file_path = bd_file_paths[counter]
print "bd_file_path:", bd_file_path
pqrs = [copy.deepcopy(rec_struct), copy.deepcopy(lig_config)]
pqrs[1].struct_id='bd_ligand'
#lig_center = pdb.center_of_mass(lig_config)
bd_needed = True
m=0
for m in range(len(milestone_pos_rot_list)): # m will represent the proper milestone index
if milestone_pos_rot_list[m][0].index == i:
break
criteria = [] #[[(31.121, 37.153, 35.253), (38.742, 51.710, 68.137), 9.0],] # a list of all reaction criteria
for site in settings['starting_surfaces']:
#site_center = [site['x'], site['y'],site['z']]
#radius = site['radius'] # NOTE: at this time, only spherical reaction criteria are allowed in BrownDye
if milestone_pos_rot_list[m][0].siteid == site['siteid']: # then its the same site, we need to go one shell in
proper_radius = site['inner_radius'] # the radius in the same site
proper_index = site['inner_index']
else: # this is a different site, choose the same radius as starting
proper_radius = site['outer_radius']
proper_index = site['outer_index']
criteria.append({'centerx':site['x'], 'centery':site['y'], 'centerz':site['z'], 'ligx':lig_center[0], 'ligy':lig_center[1], 'ligz':lig_center[2], 'radius':proper_radius, 'index':proper_index, 'siteid':site['siteid']}) # add every site to the criteria list
#print "pqrs:", pqrs, 'criteria:', criteria
site_pqrxmls = write_browndye_input(pqrs, settings, criteria, work_dir=bd_file_path, browndye_bin=browndye_bin,fhpd_mode=True)
# make BD preparation scripts extract_bd_frames.py and bd_fhpd.pyp
#print "settings['starting_surfaces'][i]:", settings['starting_surfaces'][i]
# Write the script to extract all frames from the successful b_surface bd trajectories
extract_bd_frames_dict = {'TRAJDIR':"../../b_surface", 'WORKDIR':"./trajs", 'PQRXML0':os.path.basename(b_surface_pqrxmls[0]), 'PQRXML1':os.path.basename(b_surface_pqrxmls[1]), 'EMPTY':empty_pqrxml, 'SITENAME':'%s_%s' % (milestone_pos_rot_list[m][0].siteid,milestone_pos_rot_list[m][0].index), 'NUMBER_OF_TRAJS':settings['threads']}
extract_bd_frames = Adv_template(extract_bd_frames_template,extract_bd_frames_dict)
extract_file = open(os.path.join(bd_file_path,"extract_bd_frames.py"), 'w')
extract_file.write(extract_bd_frames.get_output()) # write an xml file for the input to bd
extract_file.close()
# construct the FHPD distribution prep scripts
make_fhpd_dict = {'INPUT_TEMPLATE_FILENAME':'input.xml', 'RECEPTOR_PQRXML':os.path.basename(b_surface_pqrxmls[0]), 'RXNS':'rxns.xml', 'NTRAJ':settings['fhpd_numtraj'], 'ARGS':"glob.glob(os.path.join('./trajs','lig*.pqr'))"} # NOTE: should change NTRAJ to be consistent with the number of reaction events in the b_surface phase
make_fhpd = Adv_template(make_fhpd_template,make_fhpd_dict)
make_fhpd_file = open(os.path.join(bd_file_path,"make_fhpd.py"), 'w')
make_fhpd_file.write(make_fhpd.get_output()) # write an xml file for the input to bd
make_fhpd_file.close()
# Consolidate all result files from the FHPD simulations into one large results.xml file
fhpd_consolidate_dict = {'FHPD_DIR':"fhpd", 'LIG_DIR_GLOB':"lig*/", 'RESULTS_NAME':'results.xml'}
fhpd_consolidate = Adv_template(fhpd_consolidate_template,fhpd_consolidate_dict)
fhpd_consolidate_file = open(os.path.join(bd_file_path,"fhpd_consolidate.py"), 'w')
fhpd_consolidate_file.write(fhpd_consolidate.get_output()) # write an xml file for the input to bd
fhpd_consolidate_file.close()
counter += 1
def prep(
settings,
milestones,
stage,
inpname,
outname='',
):
#print("creating %s files" % stage)
i = settings['index']
path = settings['md_file_paths'][i][stage]
ff = settings['ff'] # forcefield
anchor_list = settings['anchor_list']
temperature = settings['master_temperature']
if not outname: outname = stage # provide the default outname
get_cell = False
if stage == 'equil':
stage_settings = settings['equil_settings']
#_prep_colvars(settings, milestones)
if not stage_settings['namd_settings'][
'extendedsystem']: # if they didn't define a starting XSC file
get_cell = settings[
'cell_shape'] # create the periodic boundary conditions
stage_settings = settings['equil_settings']
if stage == 'prod':
stage_settings = settings['prod_settings']
ensemble = stage_settings['ensemble']
namd_settings = stage_settings[
'namd_settings'] # extra settings to send to the NAMD input file
namd_settings['master_temperature'] = temperature
#settings['whoami'] = str(pos_milestone.index)
#settings['siteid'] = str(pos_milestone.siteid)
#settings['grid_edge_rad'] = '0.0' # temporary value until this can be more effectively predicted; will speed up TCL script evaluation
if ff == 'amber':
namd_settings['parmfile'] = _make_relative_path(
settings['prmtop'], path
) # Find the relative location of the prmtop/inpcrd to be used in the mins
namd_settings['ambercoor'] = _make_relative_path(
settings['inpcrd'], path)
#namd_settings['bincoordinates']= _make_relative_path(settings['bincoor'],path)
#namd_settings['extendedsystem']= _make_relative_path(settings['xsc'],path)
elif ff == 'charmm':
namd_settings['amber'] = 'no'
namd_settings['coordinates'] = '../holo_wet.pdb'
namd_settings['structure'] = '../building/holo_wet.psf'
namd_settings['paratypecharmm'] = 'on'
counter = 1
for parameter in settings['charmm_settings']['parameters']:
if counter == 1: # we need to make sure the namd input file can get more than one parameter file
i = ""
else:
i = str(counter)
namd_settings['parameters%s' % i] = parameter
counter += 1
namd_settings['watermodel'] = settings['watermodel']
if stage == 'equil':
print("creating equilibration files")
holo = settings['system_pdb_filename']
namd_settings['inpfilename'] = inpname
namd_settings['outfilename'] = outname + "_1"
namd_settings['bincoordinates'] = _make_relative_path(
settings['bincoor'], path)
namd_settings['extendedsystem'] = _make_relative_path(
settings['xsc'], path)
#print(settings['equil_settings']['namd_settings']['write_freq'])
write_freq = settings['equil_settings']['namd_settings']['write_freq']
ensemble = settings['equil_settings']['ensemble']
colvars, colvars_params = namd_inputs._make_colvars_input(
milestones, stage, i)
colvars_name = os.path.join(path, 'colvars.script')
colvars.save(colvars_name)
#print(namd_settings)
inp, namd_params = namd_inputs._make_input(
holo,
stage,
ff,
write_freq,
ensemble=ensemble,
get_cell=get_cell,
settings=namd_settings) #...
input_name = os.path.join(path, '%s_1.namd' % (stage))
inp.save(input_name)
param_filename = (os.path.join(path, 'namd_parameters.pkl'))
param_file = open(param_filename, 'wb')
pickle.dump(namd_params, param_file)
param_file.close()
return os.path.join(stage,
namd_settings['outfilename']) # return ens_equil
if stage == 'prod':
print("creating production files")
holo = settings['system_pdb_filename']
namd_settings['inpfilename'] = inpname
namd_settings['outfilename'] = outname + "_1"
#print(settings['equil_settings']['namd_settings']['write_freq'])
write_freq = settings['prod_settings']['namd_settings']['write_freq']
ensemble = settings['prod_settings']['ensemble']
colvars, colvars_params = namd_inputs._make_colvars_input(
milestones, stage, i)
colvars_name = os.path.join(path, 'colvars.script')
colvars.save(colvars_name)
post_string_settings = {
'prod_steps': namd_settings['numsteps'],
'eval_stride': namd_settings['eval_stride'],
}
anchor_milestone_params = _gen_anchor_milestone_params(milestones, i)
##TODO fix for multiple milestones
post_string_settings.update(anchor_milestone_params[0])
post_string_template = '''set crossing 0
set whoami none
set incubation_time 0
set max_steps $prod_steps
set EVAL_STRIDE $eval_stride
set CURR_ANCHOR $curr_anchor
set LOWER_ANCHOR $lower_anchor
set LOWER_MILESTONE $lower_milestone_index
set LOWER_BOUND $lower_bound
set UPPER_ANCHOR $upper_anchor
set UPPER_MILESTONE $upper_milestone_index
set UPPER_BOUND $upper_bound
for {set stepnum 0} {$stepnum < $max_steps} {incr stepnum $eval_stride} {
run $EVAL_STRIDE
set cv_val [cv colvar milestone1 value]
if {$cv_val <= $LOWER_BOUND} {
if {$rev_last} {
print "trajectory stuck"
}
puts "SEEKR: Cell Collision: current: $CURR_ANCHOR, new: $LOWER_ANCHOR, stepnum: $stepnum"
if {$whoami != $LOWER_MILESTONE} {
puts "SEEKR: Milestone Transition: anchor: $CURR_ANCHOR, source: $whoami, destination: $LOWER_MILESTONE, stepnum: $stepnum, incubation time: $incubation_time"
set incubation_time 0
}
revert
rescalevels -1
checkpoint
set rev_last True
set whoami $LOWER_MILESTONE
} elseif {$cv_val >= $UPPER_BOUND} {
if {$rev_last} {
print "trajectory stuck"
}
puts "SEEKR: Cell Collision: current: $CURR_ANCHOR, new: $UPPER_ANCHOR, stepnum: $stepnum"
if {$whoami != $UPPER_MILESTONE} {
puts "SEEKR: Milestone Transition: anchor: $CURR_ANCHOR, source: $whoami, destination: $UPPER_MILESTONE, stepnum: $stepnum, incubation time: $incubation_time"
set incubation_time 0
}
revert
rescalevels -1
checkpoint
set rev_last True
set whoami $UPPER_MILESTONE
} else {
checkpoint
set rev_last False
}
incr incubation_time $EVAL_STRIDE
}
'''
post_string = Adv_template(
post_string_template,
post_string_settings).get_output() # fill in the missing values
namd_settings['post_string'] = post_string
inp, namd_params = namd_inputs._make_input(
holo,
stage,
ff,
write_freq,
ensemble=ensemble,
get_cell=get_cell,
settings=namd_settings) #...
input_name = os.path.join(path, '%s_1.namd' % (stage))
inp.save(input_name)
param_filename = (os.path.join(path, 'namd_parameters.pkl'))
param_file = open(param_filename, 'wb')
pickle.dump(namd_params, param_file)
param_file.close()
return os.path.join(stage, namd_settings['outfilename'])
def build_bd(seekrcalc):
'''
build all structures and necessary files for BD calculations
takes a list of pqr filenames, reaction coordinate pairs/distances
'''
if verbose: print '\n', '#'*40, "\n Now creating BD files using bd.py\n", '#'*40
parser = pdb.Big_PDBParser()
rec_struct = parser.get_structure('bd_receptor_dry_pqr', seekrcalc.browndye.rec_dry_pqr_filename, pqr=True)
#milestone_pos_rot_list = settings['milestone_pos_rot_list'] # NOTE: may want to clean up code referring to this variable
''' # TODO: marked for removal because feature probably not needed
if settings['starting_conditions'] == 'configs':
lig_configs = settings['lig_configs']
elif settings['starting_conditions'] == 'spheres':
# then generate the anchors from random positions/orientations in a sphere
# NOTE: there is a random orientation function in positions_orient.py
pass
else:
raise Exception, "option not allowed: %s" % settings['starting_conditions']
'''
#bd_file_paths = settings['bd_file_paths']
#browndye_bin = settings['browndye_bin_dir']
#if not os.path.exists(empty_pqrxml)
bd_configs = []
# fill the b_surface folder
lig_config = seekrcalc.browndye.starting_lig_config # get the first config of the ligand
lig_center = pdb.center_of_mass(lig_config)
pqrs = [copy.deepcopy(rec_struct), copy.deepcopy(lig_config)]
pqrs[1].struct_id='bd_ligand'
#for site in settings['b_surface_ending_surfaces']:
b_surface_criteria = []
starting_surfaces = []
for milestone in seekrcalc.milestones:
if milestone.end:
b_surface_criteria.append({'centerx':milestone.center_vec[0], 'centery':milestone.center_vec[1], 'centerz':milestone.center_vec[2], 'ligx':lig_center[0], 'ligy':lig_center[1], 'ligz':lig_center[2], 'radius':milestone.radius, 'index':milestone.index, 'siteid':milestone.siteid}) # add every site to the criteria list
if milestone.bd:
starting_surfaces.append({'site':milestone.siteid, 'radius':milestone.radius, 'index':milestone.index})
print "bsurface_criteria:", b_surface_criteria
b_surface_pqrxmls = write_browndye_input(pqrs, seekrcalc, b_surface_criteria, work_dir=seekrcalc.browndye.b_surface_path, browndye_bin=seekrcalc.browndye.browndye_bin, start_at_site='false', fhpd_mode = False) # write input for this part
'''
for bd_file_path in bd_file_paths:
if not bd_file_path:
pass
#bd_configs.append(None)
#continue # then don't do BD for this portion
#print "bd_file_path:", bd_file_path
anchor_folder_name = bd_file_path.split('/')[-2] # reading the file tree to get the index of every existing folder
#print "anchor_folder_name:", anchor_folder_name
folder_index = anchor_folder_name.split('_')[1] # getting the index out of the folder name
bd_configs.append(int(folder_index))
'''
counter = 0 # the index of the loop itself
for milestone in seekrcalc.milestones:
if milestone.bd:
lig_config = milestone.config
bd_file_path = os.path.join(seekrcalc.project.rootdir, milestone.directory, 'bd')
print "bd_file_path:", bd_file_path
pqrs = [copy.deepcopy(rec_struct), copy.deepcopy(lig_config)]
pqrs[1].struct_id='bd_ligand'
bd_needed = True
'''
m=0
for m in range(len(milestone_pos_rot_list)): # m will represent the proper milestone index
if milestone_pos_rot_list[m][0].index == i:
break
'''
criteria = []
for surface in starting_surfaces:
if surface['site'] == milestone.siteid:
proper_radius = milestone.bd_adjacent.radius
proper_index = milestone.bd_adjacent.index
else:
proper_radius = surface['radius']
proper_index = surface['index']
criteria.append({'centerx':milestone.center_vec[0], 'centery':milestone.center_vec[1], 'centerz':milestone.center_vec[2], 'ligx':lig_center[0], 'ligy':lig_center[1], 'ligz':lig_center[2], 'radius':proper_radius, 'index':proper_index, 'siteid':milestone.siteid})
'''
criteria = [] #[[(31.121, 37.153, 35.253), (38.742, 51.710, 68.137), 9.0],] # a list of all reaction criteria
for site in settings['starting_surfaces']:
#site_center = [site['x'], site['y'],site['z']]
#radius = site['radius'] # NOTE: at this time, only spherical reaction criteria are allowed in BrownDye
if milestone_pos_rot_list[m][0].siteid == site['siteid']: # then its the same site, we need to go one shell in
proper_radius = site['inner_radius'] # the radius in the same site
proper_index = site['inner_index']
else: # this is a different site, choose the same radius as starting
proper_radius = site['outer_radius']
proper_index = site['outer_index']
criteria.append({'centerx':site['x'], 'centery':site['y'], 'centerz':site['z'], 'ligx':lig_center[0], 'ligy':lig_center[1], 'ligz':lig_center[2], 'radius':proper_radius, 'index':proper_index, 'siteid':site['siteid']}) # add every site to the criteria list
'''
#print "pqrs:", pqrs, 'criteria:', criteria
site_pqrxmls = write_browndye_input(pqrs, seekrcalc, criteria, work_dir=bd_file_path, browndye_bin=seekrcalc.browndye.browndye_bin,fhpd_mode=True)
# make BD preparation scripts extract_bd_frames.py and bd_fhpd.pyp
# Write the script to extract all frames from the successful b_surface bd trajectories
extract_bd_frames_dict = {'TRAJDIR':"../../b_surface", 'WORKDIR':"./trajs", 'PQRXML0':os.path.basename(b_surface_pqrxmls[0]), 'PQRXML1':os.path.basename(b_surface_pqrxmls[1]), 'EMPTY':empty_pqrxml, 'SITENAME':'%s_%s' % (milestone.siteid, milestone.index), 'NUMBER_OF_TRAJS':seekrcalc.browndye.num_threads}
extract_bd_frames = Adv_template(extract_bd_frames_template, extract_bd_frames_dict)
extract_file = open(os.path.join(bd_file_path,"extract_bd_frames.py"), 'w')
extract_file.write(extract_bd_frames.get_output()) # write an xml file for the input to bd
extract_file.close()
# construct the FHPD distribution prep scripts
make_fhpd_dict = {'INPUT_TEMPLATE_FILENAME':'input.xml', 'RECEPTOR_PQRXML':os.path.basename(b_surface_pqrxmls[0]), 'RXNS':'rxns.xml', 'NTRAJ':seekrcalc.browndye.fhpd_numtraj, 'ARGS':"glob.glob(os.path.join('./trajs','lig*.pqr'))"} # NOTE: should change NTRAJ to be consistent with the number of reaction events in the b_surface phase
make_fhpd = Adv_template(make_fhpd_template,make_fhpd_dict)
make_fhpd_file = open(os.path.join(bd_file_path,"make_fhpd.py"), 'w')
make_fhpd_file.write(make_fhpd.get_output()) # write an xml file for the input to bd
make_fhpd_file.close()
# Consolidate all result files from the FHPD simulations into one large results.xml file
fhpd_consolidate_dict = {'FHPD_DIR':"fhpd", 'LIG_DIR_GLOB':"lig*/", 'RESULTS_NAME':'results.xml'}
fhpd_consolidate = Adv_template(fhpd_consolidate_template,fhpd_consolidate_dict)
fhpd_consolidate_file = open(os.path.join(bd_file_path,"fhpd_consolidate.py"), 'w')
fhpd_consolidate_file.write(fhpd_consolidate.get_output()) # write an xml file for the input to bd
fhpd_consolidate_file.close()
make_empty_pqrxml(os.path.join(bd_file_path, 'empty.pqrxml'))
counter += 1