def main():
"""
main forgetnrpdblist.py
Usage: getnrpdblist.py
Input is CD-HIT cluster file on stdin
Output is list of PDB identifiers on stdout
Each has format:
<repr-id>: <list of ids in cluster>
where <repr-id> is the PDB (+ chain e.g. 2ssp_B) id in pdb_seqres
format that has been chosen as the representative for the
cluster and following is list of pdb_seqres identifiers in that
cluster. Only proteins are output, not DNA, RNA, etc.
(see module docstring at top of file).
"""
if len(sys.argv) > 1:
usage(sys.argv[0])
TMPDIR = os.tempnam(None, "pdbgz")
os.mkdir(TMPDIR)
try:
get_nr_pdb_list(TMPDIR)
finally:
cleanup_tmpdir(TMPDIR)
def get_tableau_from_pdbstruct(pdbid, domain,
pdb_structure, ptnode_list):
"""
Build a PTTableau object for the tableau by first creating a
simple PDB file with only the ATOM records for residues in the
domain we are processing, and also a .SSEsInfo file containing the
secnodary structure assignments we already have, then running
TableauCreator on it (using our simple PDB file and SSEsInfo) and
parsing the output.
Parameters:
pdbid - PDB identifier of the strucutre
domain - The PTDomain object for our current domain
pdb_structure - parsed Bio.PDB structure
ptnode_list - list of PTNode objects (ie iterable of PTNode)
representing the SSEs (helices,strands) the
tabelau is for.
Return value:
PTTableau object built from TableauCreator output
"""
TMPDIR = os.tempnam(None, "pttabin")
os.mkdir(TMPDIR)
try:
filename = pdbid
if domain.domainid != None:
filename += '-' + domain.domainid
filename += '.pdb'
domain_pdb_filename = os.path.join(TMPDIR, filename)
io = PDBIO()
io.set_structure(pdb_structure)
io.save(domain_pdb_filename, DomainSelect(domain))
ssesinfo_filename = os.path.join(TMPDIR, filename + ".input-SSEsInfo")
write_ssesinfo(ssesinfo_filename, ptnode_list)
tableau = read_tableau_from_tableaucreator(domain_pdb_filename,
ptnode_list,
ssesinfo_filename)
os.unlink(domain_pdb_filename)
os.unlink(ssesinfo_filename)
finally:
cleanup_tmpdir(TMPDIR)
return tableau
def get_tableau_from_pdbstruct(pdbid, domain, pdb_structure, ptnode_list):
"""
Build a PTTableau object for the tableau by first creating a
simple PDB file with only the ATOM records for residues in the
domain we are processing, and also a .SSEsInfo file containing the
secnodary structure assignments we already have, then running
TableauCreator on it (using our simple PDB file and SSEsInfo) and
parsing the output.
Parameters:
pdbid - PDB identifier of the strucutre
domain - The PTDomain object for our current domain
pdb_structure - parsed Bio.PDB structure
ptnode_list - list of PTNode objects (ie iterable of PTNode)
representing the SSEs (helices,strands) the
tabelau is for.
Return value:
PTTableau object built from TableauCreator output
"""
TMPDIR = os.tempnam(None, "pttabin")
os.mkdir(TMPDIR)
try:
filename = pdbid
if domain.domainid != None:
filename += '-' + domain.domainid
filename += '.pdb'
domain_pdb_filename = os.path.join(TMPDIR, filename)
io = PDBIO()
io.set_structure(pdb_structure)
io.save(domain_pdb_filename, DomainSelect(domain))
ssesinfo_filename = os.path.join(TMPDIR, filename + ".input-SSEsInfo")
write_ssesinfo(ssesinfo_filename, ptnode_list)
tableau = read_tableau_from_tableaucreator(domain_pdb_filename,
ptnode_list,
ssesinfo_filename)
os.unlink(domain_pdb_filename)
os.unlink(ssesinfo_filename)
finally:
cleanup_tmpdir(TMPDIR)
return tableau
def get_tableaux(pdb_filename,
secstruct_program='dssp',
domain_program='none',
include_310_helices=True,
include_pi_helices=True,
sse_id_list=None,
min_sse_len=None,
use_numeric=False,
use_hk=False,
build_dist_matrix=False):
"""
Get a tableau for a single PDB or ASTRAL pdb-style file
(compressed files e.g. pdb1qlp.ent.gz) or uncompressed
or the ASTRAL pdb-style hierarchy
(uncompressed files e.g. d1qlpa_.ent).
Parameters:
pdb_filename - filename of PDB or ASTRAL pdb-style file, as above.
secstruct_program - secondary structure definition program
('stride' or 'dssp' or 'pdb') to use.
domain_progam - domain decompositino method ('ddomain','cath', etc.)
include_310_helices - if True, include 3_10 helices in the graph
include_pi_helices - if True, include pi helices in the graph
sse_id_list - list of ints representing SSE sequential id numbers
to include in tableau. Default None.
When None, all SSEs are included.
min_sse_len - min number of residues in SSE to be ncluded.
Default None (no min length).
use_numeric - if True build Numeric.array Omega matrix not PTTableau
use_hk - If True build tableaux with HH and KK codes for strands in
same sheet. default False.
build_dist_matrix - If True, build SSE midpoint distance matrices
instead of tableaux.
Return value:
tuple (pdbid, tableaux_list, sse_string_list)
from the pdb file, only one in lists unless
domain decomposition is used and finds multidomains in input.
tableaux_list is list of tableaux or omega matrices
sse_string_list is SSE string description e.g. 'EEHHE' etc.
"""
tableaux_list = []
# 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:
pdbid = name
if len(pdbid) >= 6 and pdbid[:3].upper() == "PDB":
pdbid = pdbid[3:7].upper()
# parse PDB file
pdb_parser = PDBParser()
pdb_struct = pdb_parser.get_structure(pdbid, our_pdb_filename)
# create the Tableaux and output them
(tableaux_list, sse_string_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, build_dist_matrix)
finally:
if used_tmp_file:
cleanup_tmpdir(TMPDIR)
return (pdbid, tableaux_list, sse_string_list)
def read_tableau_from_tableaucreator(pdb_filename, ptnode_list,
ssesinfo_filename):
"""
Run Arun's TableauCreator program on the supplied pdb_filename
using SSEsInfo file.
Parameters:
pdb_filename - PDB file to run TableauCreator on
ptnode_list - list of PTNode objects (ie iterable of PTNode)
representing the SSEs (helices,strands) the
tabelau is for.
ssesinfo_filename - filename of the .SSEsInfo file that was written
to define SSEs for TableauCreator.
Return value:
PTTableau object built from TableauCreator output
NB: TableauCreator is not yet published or available (October 2007)
and I am using a private version which Arun sent me, which I modified
to add the -s option to use STRIDE rather than DSSP
and to have the -i option to parse .SSEsInfo files.
"""
# TableauCreator needs an output directory where it writes all its
# intermediate/output files, only puts progress information/errors
# to stdout/stderr.
tmpdir = os.tempnam(None, "pttab")
os.mkdir(tmpdir)
command = "TableauCreator "
command += "-i " + ssesinfo_filename + " "
command += pdb_filename + " " + tmpdir
command += " >/dev/null"
if verbose:
sys.stderr.write("running '" + command + "'...")
os.system(command)
if verbose:
sys.stderr.write("done\n")
# output files are:
# <pdbfilename>.angles
# <pdbfilename>.SSEsInfo
# <pdbfilename>.stride or <pdbfilename>.dssp
# <pdbfilename>.tableau
outfile_prefix = os.path.join(tmpdir, os.path.basename(pdb_filename))
if not os.path.isfile(os.path.join(tmpdir, "TABCREATE_OK")):
sys.stderr.write("ERROR: TableauCreator failed\n")
cleanup_tmpdir(tmpdir)
return None
# Now the tricky thing is TableauCreator indexes its matrix just with
# purely sequential numbers from 0 (as conventional)
# assuming all SSEs in one domain and in fact one chain
# (so we handle this by creating our own simple PDB file with only
# ATOM records for our current domain, and only one TER record on
# end so chains concatenated effectively).
# And also (as in comments above functions) we have the dodginess of
# doing the same thing in different ways in multiple places (DSSP/STRIDE
# parsing, PDB parsing, etc.).
# So let's check that the TableauCreator SSE info lines up with ours
# (otherwise we can't use the tableau data).
# parse the SSEsInfo file and check lines up with ptnodes,
# returns list of ptnodes corresponding to Tableau entries (may be shorter
# than our input node list; some removed as no equivalent in tableua).
nodelist = parse_tableaucreator_ssesinfo(outfile_prefix + '.SSEsInfo',
ptnode_list)
if nodelist != None:
tableau_filename = outfile_prefix + ".tableau"
tableau = parse_tableaucreator_output(tableau_filename, nodelist)
if tableau != None:
if verbose:
sys.stderr.write(str(tableau))
else:
sys.stderr.write(
'WARNING: problem parsing TableauCreator output;\n'
' tableau information will not be used\n')
else:
sys.stderr.write('WARNING: problem with TableauCreator output;\n'
' tableau information will not be used\n')
tableau = None
cleanup_tmpdir(tmpdir)
return tableau
def read_domains_from_ddomain(pdb_filename, pdb_model, chainid=None):
"""
Use the DDOMAIN program to parse the structure from a PDB file into
domains and return the corresponding list of PTDomain objects.
DDOMAIN is described in
Zhou, Xue, Zhou 2007 'DDOMAIN: Dividing structures into domains using a
normalized domain-domain interaction profile' Protein Science 16:947-955.
It is available as a 64-bit linux executable and FORTRAN-77 source code
from http://sparks.informatics.iupui.edu/Resource_files/DDOMAIN.tar.gz
Parameters:
pdb_filename - filename of PDB file to run DDOMAIN on
pdb_model - Bio.PDB model struct for this PDB entry. Note that this
is only needed in the case that a DDomain domain has
different chain identifiers for start and end and
is then used just to find last residue number in chain.
chainid - (default None). If not None, only the specified chain
is requested.
Return value:
List of PTDomain objects, one for each domain.
NOTE: if there is only one domain, we will return a list with a single
PTDomain with all data None, signifying a single domain protein
with no further information.
This is mainly because of when
there are multiple chains, in which case the single domain is reported
by DDOMAIN as having a different chain id for start and end. If there
is a single domain we really don't want to do anything special, so
it is better to just have it as a special case where no domain processing
is done.
"""
# DDOMAIN needs the PDB file in its working directory, and it reads
# the PDB code (e.g. 1QLP for PDB file 1QLP.pdb) from stdin
# (optionaly with chain suffix, which we won't use)
# Note it requires this filename format, so for format like pdb1qlp.ent
# we need to rename the file for DDOMAIN to 1QLP.pdb
# This is nasty, but otherwise have to modify DDOMAIN FORTRAN-77 source
# so that's even more hassle to have to have a custom version (like we
# did with STRIDE).
# So we'll work in /tmp directory, make a symlink (TODO: only UNIX allows
# this, maybe should actually copy file so works on other platforms)
# and run DDOMAIN there.
oldcwd = os.getcwd()
TMPDIR = os.tempnam(None, "ptdd")
os.mkdir(TMPDIR)
symlink_path = None
try:
pdb_file_basename = os.path.basename(pdb_filename)
(name,extension) = os.path.splitext(pdb_file_basename)
if extension.lower() == '.pdb': # e.g. 1QLP.pdb
pdb_identifier = name
pdb_file_directory = os.path.split(pdb_filename)[0]
symlink_path = os.path.join(TMPDIR, pdb_file_basename)
os.symlink(os.path.abspath(pdb_filename), symlink_path)
elif extension != '.ent' or name[:3].lower() != 'pdb':
sys.stderr.write('WARNING: unknown PDB filename format "'
+ pdb_file_basename + '"\n')
sys.stderr.write(' Not running DDomain\n')
domain_list = [PTDomain(None, None)] # one-domain protein, no further info
return domain_list
else: # e.g. pdb1qlp.ent, make a symlink to it in format 1QLP.pdb
pdb_identifier = name[3:7].upper()
symlink_path = os.path.join(TMPDIR, pdb_identifier + '.pdb')
os.symlink(os.path.abspath(pdb_filename), symlink_path)
os.chdir(TMPDIR)
if verbose:
sys.stderr.write("running DDomain...")
(ddomain_stdin, ddomain_stdout) = os.popen2("DDomain")
if chainid != None:
pdbchainid = pdb_identifier + chainid
else:
pdbchainid = pdb_identifier
ddomain_stdin.write(pdbchainid + '\n')
ddomain_stdin.close()
domain_list = parse_ddomain_output(ddomain_stdout, pdb_model)
ddomain_stdout.close()
if verbose:
sys.stderr.write("done\n")
finally:
if symlink_path:
os.unlink(symlink_path)
os.chdir(oldcwd)
cleanup_tmpdir(TMPDIR)
return domain_list
def get_tableaux(
pdb_filename,
secstruct_program="dssp",
domain_program="none",
include_310_helices=True,
include_pi_helices=True,
sse_id_list=None,
min_sse_len=None,
use_numeric=False,
use_hk=False,
build_dist_matrix=False,
):
"""
Get a tableau for a single PDB or ASTRAL pdb-style file
(compressed files e.g. pdb1qlp.ent.gz) or uncompressed
or the ASTRAL pdb-style hierarchy
(uncompressed files e.g. d1qlpa_.ent).
Parameters:
pdb_filename - filename of PDB or ASTRAL pdb-style file, as above.
secstruct_program - secondary structure definition program
('stride' or 'dssp' or 'pdb') to use.
domain_progam - domain decompositino method ('ddomain','cath', etc.)
include_310_helices - if True, include 3_10 helices in the graph
include_pi_helices - if True, include pi helices in the graph
sse_id_list - list of ints representing SSE sequential id numbers
to include in tableau. Default None.
When None, all SSEs are included.
min_sse_len - min number of residues in SSE to be ncluded.
Default None (no min length).
use_numeric - if True build Numeric.array Omega matrix not PTTableau
use_hk - If True build tableaux with HH and KK codes for strands in
same sheet. default False.
build_dist_matrix - If True, build SSE midpoint distance matrices
instead of tableaux.
Return value:
tuple (pdbid, tableaux_list, sse_string_list)
from the pdb file, only one in lists unless
domain decomposition is used and finds multidomains in input.
tableaux_list is list of tableaux or omega matrices
sse_string_list is SSE string description e.g. 'EEHHE' etc.
"""
tableaux_list = []
# 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:
pdbid = name
if len(pdbid) >= 6 and pdbid[:3].upper() == "PDB":
pdbid = pdbid[3:7].upper()
# parse PDB file
pdb_parser = PDBParser()
pdb_struct = pdb_parser.get_structure(pdbid, our_pdb_filename)
# create the Tableaux and output them
(tableaux_list, sse_string_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,
build_dist_matrix,
)
finally:
if used_tmp_file:
cleanup_tmpdir(TMPDIR)
return (pdbid, tableaux_list, sse_string_list)
try:
exit_status = 0
# parse PDB file - only needed for DDOMAIN when segment spans chains
pdb_parser = PDBParser()
pdb_struct = pdb_parser.get_structure(pdbid, our_pdb_filename)
test_domains = get_domains(test_domain_method, pdbid,
our_pdb_filename, pdb_struct)
ref_domains = get_domains(ref_domain_method, pdbid,
our_pdb_filename, pdb_struct)
if print_domains:
print test_domain_method
write_domains(sys.stdout, test_domains)
print ref_domain_method
write_domains(sys.stdout, ref_domains)
print domeval.domain_eval(test_domains, ref_domains)
except NotInCATH_Exception,ex_pdbid:
sys.stderr.write(str(ex_pdbid) + " not found in CATH CDF file\n")
exit_status = 1
finally:
if used_tmp_file:
cleanup_tmpdir(TMPDIR)
sys.exit(exit_status)
if __name__ == "__main__":
warnings.filterwarnings('ignore', 'tempnam', RuntimeWarning)
main()
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 read_tableau_from_tableaucreator(pdb_filename, ptnode_list,
ssesinfo_filename):
"""
Run Arun's TableauCreator program on the supplied pdb_filename
using SSEsInfo file.
Parameters:
pdb_filename - PDB file to run TableauCreator on
ptnode_list - list of PTNode objects (ie iterable of PTNode)
representing the SSEs (helices,strands) the
tabelau is for.
ssesinfo_filename - filename of the .SSEsInfo file that was written
to define SSEs for TableauCreator.
Return value:
PTTableau object built from TableauCreator output
NB: TableauCreator is not yet published or available (October 2007)
and I am using a private version which Arun sent me, which I modified
to add the -s option to use STRIDE rather than DSSP
and to have the -i option to parse .SSEsInfo files.
"""
# TableauCreator needs an output directory where it writes all its
# intermediate/output files, only puts progress information/errors
# to stdout/stderr.
tmpdir = os.tempnam(None, "pttab")
os.mkdir(tmpdir)
command = "TableauCreator "
command += "-i " + ssesinfo_filename + " "
command += pdb_filename + " " + tmpdir
command += " >/dev/null"
if verbose:
sys.stderr.write("running '" + command + "'...")
os.system(command)
if verbose:
sys.stderr.write("done\n")
# output files are:
# <pdbfilename>.angles
# <pdbfilename>.SSEsInfo
# <pdbfilename>.stride or <pdbfilename>.dssp
# <pdbfilename>.tableau
outfile_prefix = os.path.join(tmpdir, os.path.basename(pdb_filename))
if not os.path.isfile(os.path.join(tmpdir, "TABCREATE_OK")):
sys.stderr.write("ERROR: TableauCreator failed\n")
cleanup_tmpdir(tmpdir)
return None
# Now the tricky thing is TableauCreator indexes its matrix just with
# purely sequential numbers from 0 (as conventional)
# assuming all SSEs in one domain and in fact one chain
# (so we handle this by creating our own simple PDB file with only
# ATOM records for our current domain, and only one TER record on
# end so chains concatenated effectively).
# And also (as in comments above functions) we have the dodginess of
# doing the same thing in different ways in multiple places (DSSP/STRIDE
# parsing, PDB parsing, etc.).
# So let's check that the TableauCreator SSE info lines up with ours
# (otherwise we can't use the tableau data).
# parse the SSEsInfo file and check lines up with ptnodes,
# returns list of ptnodes corresponding to Tableau entries (may be shorter
# than our input node list; some removed as no equivalent in tableua).
nodelist = parse_tableaucreator_ssesinfo(outfile_prefix + '.SSEsInfo',
ptnode_list)
if nodelist != None:
tableau_filename = outfile_prefix + ".tableau"
tableau = parse_tableaucreator_output(tableau_filename, nodelist)
if tableau != None:
if verbose:
sys.stderr.write(str(tableau))
else:
sys.stderr.write('WARNING: problem parsing TableauCreator output;\n'
' tableau information will not be used\n')
else:
sys.stderr.write('WARNING: problem with TableauCreator output;\n'
' tableau information will not be used\n')
tableau = None
cleanup_tmpdir(tmpdir)
return tableau
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()
