def main():
"""
main for pytableaucreate.py
Usage: pytableaucreate [-35nefuv] [-d|-b] [-t structprog] [-p domainprog]
[-a domainid]
[-s sse_num_list] [-c chainid] [-m min_sse_len]
[-o savefile] <PDBfile>
-3 specifies to include 3_10 helices in the diagram. Default is only
alpha helices.
-5 specifies to include pi helices in the diagram. Defaul is only
alpha helices.
-k use the HH and KK codes for respectively antiparallel and parallel
strands in the same sheet, rather than the O, P etc. codes.
-n output a numeric omega matrix instead of tableau.
-e output numeric tableau angles in degrees, in the original
TableauCreator .angles file format, with number of entries on
first line, SSE sequence description on second line (E/H), then
(full) matrix with angles in degrees (rather than radians).
For distance matrix, same format with distances between SSEs
in Angstroms.
-f output the matrix in 'FORTRAN style' lower triangle with
header line suitable for input to TMATN.
-d build SSE axis midpoint distance matrix rather than tableau.
-b build both the tableau and distance matrix and output together,
for use with tsrchd etc. for example. If -u is used to permute
the matrices, they are permuted the same way so they are still
consistent.
-p specify the domain decomposition method.
Valid values are 'none' (default), 'ddomain', 'cath:cdf_filename'.
-a domainid : only output specified domain
-t specifies the secondary structure assignment program to use.
Currently suppoed is 'pdb' and 'dfh,ssp' and 'stride' or 'pmml'.
Default 'pdb'.
-s sse_num_list specifies a comman-separated
list of SSE sequential ids to build the
tableau for. SSE sequential id's start at 1 and go from N to C
terminus. E.g. -s1,5,8 includes only the 1st, 5th and 8ths SSEs.
Numbers do not restart at chains (but do restart in each domain).
These nubmers are those assigned by 'ptgraph2 -b sequential' option.
TODO: this currently does not make sense when multiple domains
are being procssed, this option applies to each domain.
-c chainid : specify chain identifier; only build tableau for that chain
-m min_sse_len : minimum nubmer of residues in SSE for it to be included
-i identifier : when using fortran format (-f), specify the identifier
to use in the output rather than deriving it from the filename
-o savefile : save tableau in packed format for use in other
programs, such as tabsearchqpml.py
WARNING: savefile is overwritten if it exists
TODO: this currently does not make sense when multiple domains
are being procssed, this option only saves first domain.
-u randomly pemute the rows+cols (symmetric) of the tableau/distance matrix.
writes the permutation vector in form
permutation = i,j,..,m
e.g.
permutation = 3,1,2,4
as first line of output before identifier information and tableau
-v specifies verbose mode: debugging output is written to stderr.
"""
global verbose
try:
opts, args = getopt.getopt(sys.argv[1:], "35bdfknep:a:t:s:c:m:i:o:uv?")
except getopt.GetoptError:
usage(os.path.basename(sys.argv[0]))
valid_secstruct_programs = ["dssp", "stride", "pdb", "pmml"]
valid_domain_programs = getdomains.valid_domain_programs + [r"none"]
valid_domain_programs_re = [
re.compile(re_str) for re_str in valid_domain_programs
]
verbose = False # global (python globals are only 'global' to module though)
secstruct_program = "pdb"
include_310_helices = False
include_pi_helices = False
domain_program = "none"
sse_id_list = None
use_numeric = False
use_hk = False
savefilename = None
min_sse_len = None
fortran_format = False
build_distance_matrix = False
chainid = None
fident = None
do_shuffle = False
build_both = False # both tableau and dist matrix
use_old_format = False # size + SSE chain + degrees omega matrix
domainid = None
for opt, arg in opts:
if opt == "-3": # include 3_10 helices
include_310_helices = True
elif opt == "-5": # include pi helices
include_pi_helices = True
elif opt == "-d": # build SSE midpoint distance matrix not tableau
build_distance_matrix = True
elif opt == "-b": # build both tableau and distance matrix
build_both = True
elif opt == "-k": # use HH and KK codes
use_hk = True
elif opt == "-n": # output numeric matrix not tableau
use_numeric = True
elif opt == "-e": # use TableauCreator .angles file format
use_old_format = True
elif opt == "-f": # FORTRAN style format for TMATN
fortran_format = True
elif opt == "-p": # domain parsing program
domain_program = None
for valid_domarg_re in valid_domain_programs_re:
if valid_domarg_re.match(arg):
domain_program = arg
break
if domain_program == None:
sys.stderr.write("valid values for -p are: " +
str(valid_domain_programs) + "\n")
usage(sys.argv[0])
elif opt == "-a": # only output tableau for specified domain id
domainid = arg
elif opt == "-t":
if arg not in valid_secstruct_programs:
sys.stderr.write("valid values for -t are: " +
str(valid_secstruct_programs) + "\n")
usage(sys.argv[0])
secstruct_program = arg
elif opt == "-s":
sse_id_list_str = arg.split(',')
sse_id_list = []
sse_id_uniq_dict = {} # { id : True } just for checking all unique
for sse_id_str in sse_id_list_str:
if sse_id_str.isdigit():
if sse_id_uniq_dict.has_key(int(sse_id_str)):
sys.stderr.write("duplicate SSE sequential number " +
sse_id_str + "\n")
usage(sys.argv[0])
sse_id_uniq_dict[int(sse_id_str)] = True
sse_id_list.append(int(sse_id_str))
else:
sys.stderr.write("not a valid SSE sequential number '" +
sse_id_str + "'\n")
usage(sys.argv[0])
sse_id_list.sort() # ensure SSEs are in order
elif opt == "-c": # chain identifier
if len(arg) != 1:
sys.stderr.write("invalid chain identifier for -c option\n")
usage(sys.argv[0])
chainid = arg.upper()
elif opt == "-m": # min sse len
min_sse_len = int(arg)
elif opt == "-i": # identifier to use for fortran format
fident = arg
elif opt == "-o": # save tableau in packed format
savefilename = arg
elif opt == "-u": # randomly permute the tableau/matrix
do_shuffle = True
elif opt == "-v": # verbose
verbose = True # this module only
ptnode_set_verbose(True) # ptnode module
ptsecstruct.ptsecstruct_set_verbose(True) # ptsecstruct module
ptdomain_set_verbose(True) # ptdomain module
else:
usage(sys.argv[0])
if use_numeric and use_hk:
sys.stderr.write("-n (numeric) and -k (use HH and KK codes) are "
"mutually exlusive\n")
usage(sys.argv[0])
if build_distance_matrix and build_both:
sys.stderr.write("WARNING: both -d (build dist matrix) and -b "
"(build both) specified, ignoring -d\n")
build_distance_matrix = False
if savefilename and do_shuffle:
sys.stderr.write('WARNING: saved tableau will not be shuffled\n')
if build_distance_matrix:
if use_numeric:
use_numeric = False
sys.stderr.write(
"WARNING: -n (numeric) ignored for -d (distance matrix)\n")
if use_hk:
sys.stderr.write(
"-k (use HH and KK) invalid for -d (distance matrix)\n")
usage(sys.argv[0])
if (secstruct_program == "pmml"
and (min_sse_len == None or min_sse_len < 3)):
sys.stderr.write(
"WARNING: PMML can give SSEs of length 1 or 2 causing axis fitting to fail, setting minimum length to 3 as if -m3 were specfified\n"
)
min_sse_len = 3
if fident:
if not fortran_format:
sys.stderr.write("-i is only valid with -f\n")
usage(sys.argv[0])
elif len(fident) > 8:
sys.stderr.write("identifier must be 8 chars or less\n")
usage(sys.argv[0])
if use_old_format and (build_both or use_hk or use_numeric
or fortran_format or do_shuffle or savefilename):
sys.stderr.write("-e (use old .angles format) is not compatible "
"with -b -k or -n or -f or -u or -o\n")
usage(os.path.basename(sys.argv[0]))
if len(args) != 1:
usage(os.path.basename(sys.argv[0]))
pdb_filename = args[0]
# check for compressed files. We only support gzip (.gz)
# Note we are not using the zlib or GzipFile python modules
# since we are calling to external programs which require the
# file uncompressed themsevles anyway so we'll just run gzip
# to uncompress the file to a temporary directory.
pdb_file_basename = os.path.basename(pdb_filename)
(name, extension) = os.path.splitext(pdb_file_basename)
if extension == '.gz':
TMPDIR = os.tempnam(None, "ptgz")
os.mkdir(TMPDIR)
tmp_pdbfilename = os.path.join(TMPDIR, name)
os.system("gzip " + pdb_filename + " -d -c > " + tmp_pdbfilename)
our_pdb_filename = tmp_pdbfilename
used_tmp_file = True
else:
our_pdb_filename = pdb_filename
used_tmp_file = False
try:
if fortran_format and fident:
pdbid = fident
else:
pdbid = name.upper()
if len(pdbid) >= 6 and pdbid[:3] == "PDB":
pdbid = pdbid[3:7]
if chainid:
pdbid += '_' + chainid
# parse PDB file
pdb_parser = PDBParser()
pdb_struct = pdb_parser.get_structure(pdbid, our_pdb_filename)
# create the Tableaux and output them
(tableaux_list,
ssestr_list) = make_tableaux(our_pdb_filename, pdb_struct,
secstruct_program, domain_program,
include_310_helices, include_pi_helices,
(use_numeric or use_old_format),
sse_id_list, use_hk, min_sse_len,
build_distance_matrix, chainid, domainid)
if build_both:
(distmatrix_list, ssestr_list) = make_tableaux(
our_pdb_filename,
pdb_struct,
secstruct_program,
domain_program,
include_310_helices,
include_pi_helices,
use_numeric,
sse_id_list,
use_hk,
min_sse_len,
True, # build_distance_matrix
chainid,
domainid)
i = 1
for tableau in tableaux_list:
n = len(tableau)
permutation = range(
n) # used to permute rows/cols: null permutation
if do_shuffle:
random.shuffle(
permutation) # actually permute for shuffle mode
if verbose:
sys.stderr.write('permutation is: ' + str(permutation) +
'\n')
sys.stdout.write('permutation = ' +
','.join([str(x + 1)
for x in permutation]) + '\n')
if i > 1:
sys.stdout.write('\ndomain ' + str(i) + ':\n')
if fortran_format:
sys.stdout.write("%7.7s %4d\n" % (pdbid.upper(), n))
if use_old_format:
if build_distance_matrix:
write_distmatrix_old_format(n, tableau, ssestr_list[i - 1])
else:
write_tableau_old_format(n, tableau, ssestr_list[i - 1])
else:
write_tableau(n, tableau, permutation, use_numeric,
fortran_format, build_distance_matrix)
if build_both:
write_tableau(n, distmatrix_list[i - 1], permutation,
use_numeric, fortran_format, True)
i += 1
finally:
if used_tmp_file:
cleanup_tmpdir(TMPDIR)
if savefilename:
if verbose:
sys.stderr.write('writing tableau to ' + savefilename + '\n')
fh = open(savefilename, "w")
if len(tableaux_list) > 1:
sys.stderr.write('WARNING: only saving first tableau in list\n')
if build_distance_matrix:
pickle.dump(distmatrix, fh)
elif use_numeric:
# Numeric/numpy seems to have no 'packed' format for symmetric
# matrices, so we just have to dump the whole thing.
pickle.dump(Omega, fh)
else:
pickle.dump(PTTableauPacked(tableaux_list[0]), fh)
fh.close()
def main():
"""
main for pytableaucreate.py
Usage: pytableaucreate [-35nefuv] [-d|-b] [-t structprog] [-p domainprog]
[-a domainid]
[-s sse_num_list] [-c chainid] [-m min_sse_len]
[-o savefile] <PDBfile>
-3 specifies to include 3_10 helices in the diagram. Default is only
alpha helices.
-5 specifies to include pi helices in the diagram. Defaul is only
alpha helices.
-k use the HH and KK codes for respectively antiparallel and parallel
strands in the same sheet, rather than the O, P etc. codes.
-n output a numeric omega matrix instead of tableau.
-e output numeric tableau angles in degrees, in the original
TableauCreator .angles file format, with number of entries on
first line, SSE sequence description on second line (E/H), then
(full) matrix with angles in degrees (rather than radians).
For distance matrix, same format with distances between SSEs
in Angstroms.
-f output the matrix in 'FORTRAN style' lower triangle with
header line suitable for input to TMATN.
-d build SSE axis midpoint distance matrix rather than tableau.
-b build both the tableau and distance matrix and output together,
for use with tsrchd etc. for example. If -u is used to permute
the matrices, they are permuted the same way so they are still
consistent.
-p specify the domain decomposition method.
Valid values are 'none' (default), 'ddomain', 'cath:cdf_filename'.
-a domainid : only output specified domain
-t specifies the secondary structure assignment program to use.
Currently suppoed is 'pdb' and 'dfh,ssp' and 'stride' or 'pmml'.
Default 'pdb'.
-s sse_num_list specifies a comman-separated
list of SSE sequential ids to build the
tableau for. SSE sequential id's start at 1 and go from N to C
terminus. E.g. -s1,5,8 includes only the 1st, 5th and 8ths SSEs.
Numbers do not restart at chains (but do restart in each domain).
These nubmers are those assigned by 'ptgraph2 -b sequential' option.
TODO: this currently does not make sense when multiple domains
are being procssed, this option applies to each domain.
-c chainid : specify chain identifier; only build tableau for that chain
-m min_sse_len : minimum nubmer of residues in SSE for it to be included
-i identifier : when using fortran format (-f), specify the identifier
to use in the output rather than deriving it from the filename
-o savefile : save tableau in packed format for use in other
programs, such as tabsearchqpml.py
WARNING: savefile is overwritten if it exists
TODO: this currently does not make sense when multiple domains
are being procssed, this option only saves first domain.
-u randomly pemute the rows+cols (symmetric) of the tableau/distance matrix.
writes the permutation vector in form
permutation = i,j,..,m
e.g.
permutation = 3,1,2,4
as first line of output before identifier information and tableau
-v specifies verbose mode: debugging output is written to stderr.
"""
global verbose
try:
opts, args = getopt.getopt(sys.argv[1:], "35bdfknep:a:t:s:c:m:i:o:uv?")
except getopt.GetoptError:
usage(os.path.basename(sys.argv[0]))
valid_secstruct_programs = ["dssp", "stride", "pdb", "pmml"]
valid_domain_programs = getdomains.valid_domain_programs + [r"none"]
valid_domain_programs_re = [ re.compile(re_str) for re_str in
valid_domain_programs ]
verbose = False # global (python globals are only 'global' to module though)
secstruct_program = "pdb"
include_310_helices = False
include_pi_helices = False
domain_program = "none"
sse_id_list = None
use_numeric = False
use_hk = False
savefilename = None
min_sse_len = None
fortran_format = False
build_distance_matrix = False
chainid = None
fident = None
do_shuffle = False
build_both = False # both tableau and dist matrix
use_old_format = False # size + SSE chain + degrees omega matrix
domainid = None
for opt,arg in opts:
if opt == "-3": # include 3_10 helices
include_310_helices = True
elif opt == "-5": # include pi helices
include_pi_helices = True
elif opt == "-d": # build SSE midpoint distance matrix not tableau
build_distance_matrix = True
elif opt == "-b": # build both tableau and distance matrix
build_both = True
elif opt == "-k": # use HH and KK codes
use_hk = True
elif opt == "-n": # output numeric matrix not tableau
use_numeric = True
elif opt == "-e": # use TableauCreator .angles file format
use_old_format = True
elif opt == "-f": # FORTRAN style format for TMATN
fortran_format = True
elif opt == "-p": # domain parsing program
domain_program = None
for valid_domarg_re in valid_domain_programs_re:
if valid_domarg_re.match(arg):
domain_program = arg
break
if domain_program == None:
sys.stderr.write("valid values for -p are: " +
str(valid_domain_programs) + "\n")
usage(sys.argv[0])
elif opt == "-a": # only output tableau for specified domain id
domainid = arg
elif opt == "-t":
if arg not in valid_secstruct_programs:
sys.stderr.write("valid values for -t are: " +
str(valid_secstruct_programs) + "\n")
usage(sys.argv[0])
secstruct_program = arg
elif opt == "-s":
sse_id_list_str = arg.split(',')
sse_id_list = []
sse_id_uniq_dict = {} # { id : True } just for checking all unique
for sse_id_str in sse_id_list_str:
if sse_id_str.isdigit():
if sse_id_uniq_dict.has_key(int(sse_id_str)):
sys.stderr.write("duplicate SSE sequential number " +
sse_id_str + "\n")
usage(sys.argv[0])
sse_id_uniq_dict[int(sse_id_str)] = True
sse_id_list.append(int(sse_id_str))
else:
sys.stderr.write("not a valid SSE sequential number '" +
sse_id_str + "'\n")
usage(sys.argv[0])
sse_id_list.sort() # ensure SSEs are in order
elif opt == "-c": # chain identifier
if len(arg) != 1:
sys.stderr.write("invalid chain identifier for -c option\n")
usage(sys.argv[0])
chainid = arg.upper()
elif opt == "-m": # min sse len
min_sse_len = int(arg)
elif opt == "-i": # identifier to use for fortran format
fident = arg
elif opt == "-o": # save tableau in packed format
savefilename = arg
elif opt == "-u": # randomly permute the tableau/matrix
do_shuffle = True
elif opt == "-v": # verbose
verbose = True # this module only
ptnode_set_verbose(True) # ptnode module
ptsecstruct.ptsecstruct_set_verbose(True) # ptsecstruct module
ptdomain_set_verbose(True) # ptdomain module
else:
usage(sys.argv[0])
if use_numeric and use_hk:
sys.stderr.write("-n (numeric) and -k (use HH and KK codes) are "
"mutually exlusive\n")
usage(sys.argv[0])
if build_distance_matrix and build_both:
sys.stderr.write("WARNING: both -d (build dist matrix) and -b "
"(build both) specified, ignoring -d\n")
build_distance_matrix = False
if savefilename and do_shuffle:
sys.stderr.write('WARNING: saved tableau will not be shuffled\n')
if build_distance_matrix:
if use_numeric:
use_numeric = False
sys.stderr.write("WARNING: -n (numeric) ignored for -d (distance matrix)\n")
if use_hk:
sys.stderr.write("-k (use HH and KK) invalid for -d (distance matrix)\n");
usage(sys.argv[0])
if (secstruct_program == "pmml" and
(min_sse_len == None or min_sse_len < 3)):
sys.stderr.write("WARNING: PMML can give SSEs of length 1 or 2 causing axis fitting to fail, setting minimum length to 3 as if -m3 were specfified\n")
min_sse_len = 3
if fident:
if not fortran_format:
sys.stderr.write("-i is only valid with -f\n")
usage(sys.argv[0])
elif len(fident) > 8:
sys.stderr.write("identifier must be 8 chars or less\n")
usage(sys.argv[0])
if use_old_format and (build_both or
use_hk or use_numeric or fortran_format or
do_shuffle or savefilename):
sys.stderr.write("-e (use old .angles format) is not compatible "
"with -b -k or -n or -f or -u or -o\n")
usage(os.path.basename(sys.argv[0]))
if len(args) != 1:
usage(os.path.basename(sys.argv[0]))
pdb_filename = args[0]
# check for compressed files. We only support gzip (.gz)
# Note we are not using the zlib or GzipFile python modules
# since we are calling to external programs which require the
# file uncompressed themsevles anyway so we'll just run gzip
# to uncompress the file to a temporary directory.
pdb_file_basename = os.path.basename(pdb_filename)
(name,extension) = os.path.splitext(pdb_file_basename)
if extension == '.gz':
TMPDIR = os.tempnam(None, "ptgz")
os.mkdir(TMPDIR)
tmp_pdbfilename = os.path.join(TMPDIR, name)
os.system("gzip " + pdb_filename + " -d -c > " + tmp_pdbfilename)
our_pdb_filename = tmp_pdbfilename
used_tmp_file = True
else:
our_pdb_filename = pdb_filename
used_tmp_file = False
try:
if fortran_format and fident:
pdbid = fident
else:
pdbid = name.upper()
if len(pdbid) >= 6 and pdbid[:3] == "PDB":
pdbid = pdbid[3:7]
if chainid:
pdbid += '_' + chainid
# parse PDB file
pdb_parser = PDBParser()
pdb_struct = pdb_parser.get_structure(pdbid, our_pdb_filename)
# create the Tableaux and output them
(tableaux_list, ssestr_list) = make_tableaux(our_pdb_filename,
pdb_struct,
secstruct_program,
domain_program,
include_310_helices,
include_pi_helices,
(use_numeric or use_old_format),
sse_id_list,
use_hk,
min_sse_len,
build_distance_matrix,
chainid,
domainid)
if build_both:
(distmatrix_list, ssestr_list) = make_tableaux(our_pdb_filename,
pdb_struct,
secstruct_program,
domain_program,
include_310_helices,
include_pi_helices,
use_numeric,
sse_id_list,
use_hk,
min_sse_len,
True, # build_distance_matrix
chainid,
domainid)
i = 1
for tableau in tableaux_list:
n = len(tableau)
permutation = range(n) # used to permute rows/cols: null permutation
if do_shuffle:
random.shuffle(permutation) # actually permute for shuffle mode
if verbose:
sys.stderr.write('permutation is: ' + str(permutation)+'\n')
sys.stdout.write('permutation = ' + ','.join([str(x+1) for x in permutation]) + '\n')
if i > 1:
sys.stdout.write('\ndomain ' + str(i) + ':\n')
if fortran_format:
sys.stdout.write("%7.7s %4d\n" % (pdbid.upper(), n))
if use_old_format:
if build_distance_matrix:
write_distmatrix_old_format(n, tableau, ssestr_list[i-1])
else:
write_tableau_old_format(n, tableau, ssestr_list[i-1])
else:
write_tableau(n, tableau, permutation, use_numeric,
fortran_format, build_distance_matrix)
if build_both:
write_tableau(n, distmatrix_list[i-1],
permutation, use_numeric,
fortran_format, True)
i += 1
finally:
if used_tmp_file:
cleanup_tmpdir(TMPDIR)
if savefilename:
if verbose:
sys.stderr.write('writing tableau to ' + savefilename +'\n')
fh = open(savefilename, "w")
if len(tableaux_list) > 1:
sys.stderr.write('WARNING: only saving first tableau in list\n')
if build_distance_matrix:
pickle.dump(distmatrix, fh)
elif use_numeric:
# Numeric/numpy seems to have no 'packed' format for symmetric
# matrices, so we just have to dump the whole thing.
pickle.dump(Omega, fh)
else:
pickle.dump(PTTableauPacked(tableaux_list[0]), fh)
fh.close()
def main():
"""
main for buildtableauxdb.py
Usage: pytableaucreate [-35knv] [-d] [-m min_sse_len ]
[-t structprog] [-p domainprog]
<pdbroot> <dbname>
WARNING: dbname is overwritten if it exists
-3 specifies to include 3_10 helices in the diagram. Default is only
alpha helices.
-5 specifies to include pi helices in the diagram. Defaul is only
alpha helices.
-d build SSE distance matrices not tableaux
-k use the HH and KK codes for respectively antiparallel and parallel
strands in the same sheet, rather than the O, P etc. codes.
-m min_sse_len : specifies the minimum SSE length to include in tableaux.
-n use numeric values (Omega matrix) rather than tableau.
-p specify the domain decomposition method.
Valid values are 'none' (default), 'ddomain', 'cath:cdf_filename'.
-t specifies the secondary structure assignment program to use.
Currently suppoed is 'pdb' and 'dssp' and 'stride' and 'pmml'.
Default 'pdb'.
-v specifies verbose mode: debugging output is written to stderr.
"""
global verbose
try:
opts, args = getopt.getopt(sys.argv[1:], "35dknm:p:t:v?")
except getopt.GetoptError:
usage(os.path.basename(sys.argv[0]))
valid_secstruct_programs = ["dssp", "stride", "pdb", "pmml"]
valid_domain_programs = getdomains.valid_domain_programs + [r"none"]
valid_domain_programs_re = [re.compile(re_str) for re_str in valid_domain_programs]
verbose = False # global (python globals are only 'global' to module though)
secstruct_program = "dssp"
include_310_helices = False
include_pi_helices = False
use_hk = False
domain_program = "none"
min_sse_len = None
use_numeric = False
build_dist_matrices = False
for opt, arg in opts:
if opt == "-3": # include 3_10 helices
include_310_helices = True
elif opt == "-5": # include pi helices
include_pi_helices = True
elif opt == "-d": # build distance matrices not tableaux
build_dist_matrices = True
elif opt == "-k": # use HH and KK codes
use_hk = True
elif opt == "-m": # min sse length
min_sse_len = int(arg)
elif opt == "-n": # use numeric values (Omega matrix)
use_numeric = True
elif opt == "-p": # domain parsing program
domain_program = None
for valid_domarg_re in valid_domain_programs_re:
if valid_domarg_re.match(arg):
domain_program = arg
break
if domain_program == None:
sys.stderr.write("valid values for -p are: " + str(valid_domain_programs) + "\n")
usage(sys.argv[0])
elif opt == "-t":
if arg not in valid_secstruct_programs:
sys.stderr.write("valid values for -t are: " + str(valid_secstruct_programs) + "\n")
usage(sys.argv[0])
secstruct_program = arg
elif opt == "-v": # verbose
verbose = True # this module only
ptnode_set_verbose(True) # ptnode module
ptsecstruct.ptsecstruct_set_verbose(True) # ptsecstruct module
ptdomain_set_verbose(True) # ptdomain module
else:
usage(sys.argv[0])
if len(args) != 2:
usage(os.path.basename(sys.argv[0]))
if build_dist_matrices:
if use_numeric:
use_numeric = False
sys.stderr.write("WARNING: -n (numeric) ignored for -d (distance matrix)\n")
if use_hk:
sys.stderr.write("-k (use HH and KK) invalid for -d (distance matrix)\n")
usage(sys.argv[0])
if use_numeric and use_hk:
sys.stderr.write("-n (numeric) and -k (use HH and KK codes) are " "mutually exlusive\n")
usage(sys.argv[0])
sys.stdout.write(sys.argv[0] + ": version is: " + get_version() + "\n")
sys.stdout.write(sys.argv[0] + ": options are: " + str(sys.argv[1:]) + "\n")
input_root = args[0]
output_filename = args[1]
fh = open(output_filename, "w")
tableau_db = build_db(
input_root,
secstruct_program,
domain_program,
include_310_helices,
include_pi_helices,
min_sse_len,
use_numeric,
use_hk,
build_dist_matrices,
)
if build_dist_matrices:
sys.stdout.write("writing SSE distance matrix db to " + output_filename + "...\n")
else:
sys.stdout.write("writing tableaux db to " + output_filename + "...\n")
pickle.dump(tableau_db, fh)
fh.close()
sys.stdout.write("done.\n")
