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 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 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 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