def generate_pam_variants_from_mutant(mutant_idx,
total_pam_variants,
flag_chimera=True):
"""Generate all the pam variants for a given mutant
Args:
mutant_idx: int >= 0 (0 is default dCas9)
total_pam_variants: 64 or 256 -- represents all 3nt or 4nt pam variants
flag_chimera: [default: True] if flag_chimera, then use chimera to generate variants (else use 3DNA)
Returns:
path to the pam variant folder (containing 64 or 256 pdbs)
"""
assert total_pam_variants == 64 or total_pam_variants == 256 # currently support 3 or 4 nt PAM sites
mutant_template_pdb_path = mutant_template_pdb_path_by_idx(mutant_idx)
mutant_variants_pdb_dir = mutant_variants_dir_by_idx(mutant_idx)
# select a tool for generating the pam variants
if flag_chimera:
pam_variant_tool = generate_pam_variant_chimera
else:
pam_variant_tool = generate_pam_variant_3dna
pam_length = int(log(total_pam_variants, 4))
for pam_int in xrange(total_pam_variants):
pam_string = pam_string_from_int(pam_int, pam_length)
pam_variant_tool(pam_string, mutant_template_pdb_path,
mutant_variants_pdb_dir)
return mutant_variants_pdb_dir
def dock_variants(pam_variants,
path_to_scores,
path_to_pdbs='',
dock_partners="B_ACD",
foldtree=None,
pam_length=4,
pam_tool='Chimera',
complex_docking_flag=False):
"""Docks and scores a pdb for each PAM variant (created using pam_tool) using simple docking
Args:
pam_variants: list of integers (any from 0 to 63 without repeats) which map to pam strings
path_to_scores: path to the subdirectory of "results" where the variants are stored
path_to_pdbs: [default: current directory] path to location of chimera/3DNA folders of PAM variants
dock_partners: [default: "B_ACD"] string for thee set_partners(...) method for docking
foldtree: [default: None] string for the 2nd setup_foldtree(...) argument, None implies default foldtree
pam_length: [default: 4] length of the pam sequence to be investigated
pam_tool: [default: 'Chimera'] either "3DNA" or "Chimera"
complex_docking_flag: [default: False] if True, use complex dock function (NOT IMPLEMENTED)
Notes:
- creates a text file (e.g. 'results_agg_Chimera.txt') for each variant
- path to variants is typically root/results/<timestamped folder>/<variants>
- assumes current directory is the root of a folder that contains pdbs in Chimera and 3DNA directories
"""
assert pam_tool in PAM_TOOLS
for idx in pam_variants:
variant = pam_string_from_int(idx, pam_length)
print "Running for variant: %s_%s" % (variant, pam_tool)
pdb_path = os.path.join(path_to_pdbs, pam_tool,
"4UN3." + variant + ".pdb")
# track runtime while loading and passing pose to the simple docker
time_init_total = time()
loaded_pose = pose_from_pdb(pdb_path)
time_init_docking = time()
if complex_docking_flag:
dock_stats = dock_complex(loaded_pose)
else:
dock_stats = dock_simple(loaded_pose, dock_partners, foldtree)
time_final = time()
time_diff_total = time_final - time_init_total
time_diff_docking = time_final - time_init_docking
# write results to file
results_filename = variant + "_" + pam_tool + ".txt"
write_dock_stats(path_to_scores, results_filename, dock_stats,
time_diff_total, time_diff_docking)
print "Finished writing scores for variant: %s_%s" % (variant,
pam_tool)
return
def dock_variants(pam_variants, path_to_scores, path_to_pdbs='', dock_partners="B_ACD", foldtree=None,
pam_length=4, pam_tool='Chimera', complex_docking_flag=False):
"""Docks and scores a pdb for each PAM variant (created using pam_tool) using simple docking
Args:
pam_variants: list of integers (any from 0 to 63 without repeats) which map to pam strings
path_to_scores: path to the subdirectory of "results" where the variants are stored
path_to_pdbs: [default: current directory] path to location of chimera/3DNA folders of PAM variants
dock_partners: [default: "B_ACD"] string for thee set_partners(...) method for docking
foldtree: [default: None] string for the 2nd setup_foldtree(...) argument, None implies default foldtree
pam_length: [default: 4] length of the pam sequence to be investigated
pam_tool: [default: 'Chimera'] either "3DNA" or "Chimera"
complex_docking_flag: [default: False] if True, use complex dock function (NOT IMPLEMENTED)
Notes:
- creates a text file (e.g. 'results_agg_Chimera.txt') for each variant
- path to variants is typically root/results/<timestamped folder>/<variants>
- assumes current directory is the root of a folder that contains pdbs in Chimera and 3DNA directories
"""
assert pam_tool in PAM_TOOLS
for idx in pam_variants:
variant = pam_string_from_int(idx, pam_length)
print "Running for variant: %s_%s" % (variant, pam_tool)
pdb_path = os.path.join(path_to_pdbs, pam_tool, "4UN3." + variant + ".pdb")
# track runtime while loading and passing pose to the simple docker
time_init_total = time()
loaded_pose = pose_from_pdb(pdb_path)
time_init_docking = time()
if complex_docking_flag:
dock_stats = dock_complex(loaded_pose)
else:
dock_stats = dock_simple(loaded_pose, dock_partners, foldtree)
time_final = time()
time_diff_total = time_final - time_init_total
time_diff_docking = time_final - time_init_docking
# write results to file
results_filename = variant + "_" + pam_tool + ".txt"
write_dock_stats(path_to_scores, results_filename, dock_stats, time_diff_total, time_diff_docking)
print "Finished writing scores for variant: %s_%s" % (variant, pam_tool)
return
def generate_pam_variants_from_mutant(mutant_idx, total_pam_variants, flag_chimera=True):
"""Generate all the pam variants for a given mutant
Args:
mutant_idx: int >= 0 (0 is default dCas9)
total_pam_variants: 64 or 256 -- represents all 3nt or 4nt pam variants
flag_chimera: [default: True] if flag_chimera, then use chimera to generate variants (else use 3DNA)
Returns:
path to the pam variant folder (containing 64 or 256 pdbs)
"""
assert total_pam_variants == 64 or total_pam_variants == 256 # currently support 3 or 4 nt PAM sites
mutant_template_pdb_path = mutant_template_pdb_path_by_idx(mutant_idx)
mutant_variants_pdb_dir = mutant_variants_dir_by_idx(mutant_idx)
# select a tool for generating the pam variants
if flag_chimera:
pam_variant_tool = generate_pam_variant_chimera
else:
pam_variant_tool = generate_pam_variant_3dna
pam_length = int(log(total_pam_variants, 4))
for pam_int in xrange(total_pam_variants):
pam_string = pam_string_from_int(pam_int, pam_length)
pam_variant_tool(pam_string, mutant_template_pdb_path, mutant_variants_pdb_dir)
return mutant_variants_pdb_dir
if __name__ == '__main__':
# create parser and parse arguments
parser = argparse.ArgumentParser(description='Generate PDBs with new PAM sites based on input PDB with Cas9 variant')
parser.add_argument('-n', '--num_pams', metavar='N', type=str, # string type because of how this script must be run by Chimera
help='how many PAMs in total to run. 64 = all PAMs of length 3, 256 = all PAMs of length 4')
parser.add_argument('-i', '--input_pdb', metavar='F', type=str,
help='input PDB file containing Cas9 mutant of interest')
parser.add_argument('-o', '--output_dir', metavar='D', type=str,
help='path to output directory for new PDBs')
args = parser.parse_args()
assert args.num_pams is not None
assert args.input_pdb is not None
assert args.output_dir is not None
args.num_pams = int(args.num_pams) # convert string from command line to int
pam_length = int(math.log(args.num_pams, 4))
assert 64 == args.num_pams or 256 == args.num_pams
assert os.path.isfile(args.input_pdb)
try: # check existence again to handle concurrency problems
os.makedirs(args.output_dir)
except OSError as exc:
if exc.errno == errno.EEXIST and os.path.isdir(args.output_dir):
pass
else: raise
for i in xrange(args.num_pams):
generate_pam_variant_3dna(pam_string_from_int(i, pam_length), args.input_pdb, args.output_dir)
args.num_pams = int(
args.num_pams) # convert string from command line to int
pam_length = int(math.log(args.num_pams, 4))
assert 64 == args.num_pams or 256 == args.num_pams
assert os.path.isfile(args.input_pdb)
try: # check existence again to handle concurrency problems
os.makedirs(args.output_dir)
except OSError as exc:
if exc.errno == errno.EEXIST and os.path.isdir(args.output_dir):
pass
else:
raise
for i in xrange(args.num_pams):
pam = pam_string_from_int(i, pam_length)
# open up the file again each time, for now
runCommand("open " + args.input_pdb)
# loop through the PAM sequence and mutate positions
for pam_idx in xrange(pam_length):
'''This has been commented out so that all nucleotides are changed
regardless of whether the match the original pdb or not.'''
# If the nt matches the original PAM nt, don't change it
#if PAM_TEMPLATE_SEQUENCE[pam_idx] == pam[pam_idx]:
# continue
mutate_nt(pam_idx, pam[pam_idx])
# save and close all files
generate_pam_variant_chimera(pam, args.input_pdb, args.output_dir)
assert args.input_pdb is not None
assert args.output_dir is not None
args.num_pams = int(args.num_pams) # convert string from command line to int
pam_length = int(math.log(args.num_pams, 4))
assert 64 == args.num_pams or 256 == args.num_pams
assert os.path.isfile(args.input_pdb)
try: # check existence again to handle concurrency problems
os.makedirs(args.output_dir)
except OSError as exc:
if exc.errno == errno.EEXIST and os.path.isdir(args.output_dir):
pass
else: raise
for i in xrange(args.num_pams):
pam = pam_string_from_int(i, pam_length)
# open up the file again each time, for now
runCommand("open " + args.input_pdb)
# loop through the PAM sequence and mutate positions
for pam_idx in xrange(pam_length):
'''This has been commented out so that all nucleotides are changed
regardless of whether the match the original pdb or not.'''
# If the nt matches the original PAM nt, don't change it
#if PAM_TEMPLATE_SEQUENCE[pam_idx] == pam[pam_idx]:
# continue
mutate_nt(pam_idx, pam[pam_idx])
# save and close all files
generate_pam_variant_chimera(pam, args.input_pdb, args.output_dir)
metavar='F',
type=str,
help='input PDB file containing Cas9 mutant of interest')
parser.add_argument('-o',
'--output_dir',
metavar='D',
type=str,
help='path to output directory for new PDBs')
args = parser.parse_args()
assert args.num_pams is not None
assert args.input_pdb is not None
assert args.output_dir is not None
args.num_pams = int(
args.num_pams) # convert string from command line to int
pam_length = int(math.log(args.num_pams, 4))
assert 64 == args.num_pams or 256 == args.num_pams
assert os.path.isfile(args.input_pdb)
try: # check existence again to handle concurrency problems
os.makedirs(args.output_dir)
except OSError as exc:
if exc.errno == errno.EEXIST and os.path.isdir(args.output_dir):
pass
else:
raise
for i in xrange(args.num_pams):
generate_pam_variant_3dna(pam_string_from_int(i, pam_length),
args.input_pdb, args.output_dir)
