def write_distmatrix_old_format(n, dmat, ssestr):
"""
Write distance matrix to stdout in format for TableauComparer
(Arun)
full matrix, number of SSEs on first line and SSE sequence
(DSSP codes E,H) on second line.
n - order of distance matrix (n by n)
dmat - Numeric matrix for distance matrix
sse_str - SSE string correspdonding to the distance matrix
"""
sys.stdout.write(str(len(dmat)) + '\n')
sys.stdout.write(ssestr + '\n')
for k in range(n):
for l in range(n):
d = dmat[k,l]
if isNaN(d) or k == l:
d = -999.0
sys.stdout.write("% 7.1f " % d)
sys.stdout.write("\n")
def write_tableau_old_format(n, Omega, ssestr):
"""
Write tableau to stdout in the original
(Arun) TableauCreator format, with angles in degrees,
full matrix, number of SSEs on first line and SSE sequence
(DSSP codes E,H) on second line.
n - order of tableau matrix (n by n)
Omega - Numeric matrix for Omega matrix
sse_str - SSE string correspdonding to the Omega matrix
"""
sys.stdout.write(str(len(Omega)) + '\n')
sys.stdout.write(ssestr + '\n')
for k in range(n):
for l in range(n):
angle = degrees(Omega[k,l])
if isNaN(angle) or k == l:
angle = -999.0
sys.stdout.write("% 7.1f " % angle)
sys.stdout.write("\n")
def write_distmatrix_old_format(n, dmat, ssestr):
"""
Write distance matrix to stdout in format for TableauComparer
(Arun)
full matrix, number of SSEs on first line and SSE sequence
(DSSP codes E,H) on second line.
n - order of distance matrix (n by n)
dmat - Numeric matrix for distance matrix
sse_str - SSE string correspdonding to the distance matrix
"""
sys.stdout.write(str(len(dmat)) + '\n')
sys.stdout.write(ssestr + '\n')
for k in range(n):
for l in range(n):
d = dmat[k, l]
if isNaN(d) or k == l:
d = -999.0
sys.stdout.write("% 7.1f " % d)
sys.stdout.write("\n")
def write_tableau_old_format(n, Omega, ssestr):
"""
Write tableau to stdout in the original
(Arun) TableauCreator format, with angles in degrees,
full matrix, number of SSEs on first line and SSE sequence
(DSSP codes E,H) on second line.
n - order of tableau matrix (n by n)
Omega - Numeric matrix for Omega matrix
sse_str - SSE string correspdonding to the Omega matrix
"""
sys.stdout.write(str(len(Omega)) + '\n')
sys.stdout.write(ssestr + '\n')
for k in range(n):
for l in range(n):
angle = degrees(Omega[k, l])
if isNaN(angle) or k == l:
angle = -999.0
sys.stdout.write("% 7.1f " % angle)
sys.stdout.write("\n")
def main():
"""
main for convdb2.py - load PTTableauPacked pickle and Numeric.array
distance matrix pickle and
output as ascii
"""
use_sidlist = False
do_sort = False
try:
opts, args = getopt.getopt(sys.argv[1:], "ls")
except getopt.GetoptError:
usage(sys.argv[0])
for opt,arg in opts:
if opt == "-l": # read list of identifeirs on stdin
use_sidlist = True
elif opt == "-s": # sort db by size
do_sort = True
else:
usage(sys.argv[0])
if len(args) != 2:
usage(sys.argv[0])
dbfile = args[0]
distmatrixdbfile = args[1]
if use_sidlist:
# make dictionary of identifiers from list on stdin
sid_dict = dict([(x.strip(), None) for x in sys.stdin.readlines()])
sys.stderr.write('loading tableaux...\n')
db = pickle.load(open(dbfile))
sys.stderr.write('loading distance matrices...\n')
distmatrixdb = pickle.load(open(distmatrixdbfile))
sys.stderr.write('writing ASCII format tableaux+distmatrices...\n')
first = True
count = 0
total_count = 0
dblist = [ (pdbid,dbtablist) for (pdbid,dbtablist) in db.iteritems()
if len(dbtablist) > 0] # remove those with no tableaux
if do_sort:
sys.stderr.write("sorting database...\n")
dblist.sort(cmp=sizecmp)
for pdbid,dbtablist in dblist:
if use_sidlist and not sid_dict.has_key(pdbid):
continue
tabnum = 0
while tabnum < len(dbtablist):
tableau = dbtablist[tabnum]
n = len(tableau)
name = pdbid
if len(dbtablist) > 1:
name += str(tabnum)
try:
distmatrix = distmatrixdb[pdbid][tabnum]
except KeyError:
sys.stderr.write('ERROR: no distance matrix for id ' +
pdbid + ' - skipped\n')
tabnum += 1
continue
if len(distmatrix) != len(tableau):
sys.stderr.write('ERROR: dist matrix order ' +
str(len(distmatrix)) + ' but tableau order ' +
str(len(tableau)) + ' for id ' + pdbid +
' - skipped\n')
tabnum += 1
continue
if not first:
sys.stdout.write('\n')
else:
first = False
sys.stdout.write('%6s %4d\n' % (name, n))
for i in xrange(n):
for j in xrange(i+1):
sys.stdout.write(tableau[(i,j)] + ' ')
sys.stdout.write('\n')
for i in xrange(n):
for j in xrange(i+1):
if isNaN(distmatrix[i,j]):
dist = 0.0
else:
dist = distmatrix[i,j]
sys.stdout.write('%6.3f ' % dist)
sys.stdout.write('\n')
total_count += 1
tabnum += 1
count += 1
sys.stderr.write('wrote %d tableaux+distmatrices for %d entries\n'
% (total_count, count))
def write_tableau(n, tableau, permutation, use_numeric,
fortran_format, build_distance_matrix):
"""
Write tableau or distance matrix to stdout.
n - order of tableau or distance matrix (n by n)
tableau - PTTableau object for tableau or Numeric matrix for
Omega matrix or Numeric matrix for distance matrix
permutation - permuted list of ingeters in interval [0, n-1] to
permute the rows+cols of the tableau/matrix by
(so [0,1,2,...n-1] for no permutation.
use_numeric - boolean. If true, tableau is a Numeric Omega matrix
not a tableau.
fortran_format - boolean. If True, put in lower triangle format
for FORTRAN programs tsrchd etc.
build_distance_matrix - boolean. If True is a distance matrix not a
tableau or Omega matrix.
"""
if build_distance_matrix:
distmatrix = tableau
if fortran_format:
for k in range(n):
for l in range(k+1):
kprime = permutation[k]
lprime = permutation[l]
if isNaN(distmatrix[kprime,lprime]):
dist = 0.0
else:
dist = distmatrix[kprime,lprime]
if dist > 99.9:
sys.stderr.write('WARNING: distance %f at (%d,%d) truncated to 99.9 for fortran format\n' % (dist,kprime,lprime))
dist = 99.9
sys.stdout.write("%6.3f " % dist)
sys.stdout.write("\n")
else:
for k in range(n):
for l in range(n):
kprime = permutation[k]
lprime = permutation[l]
sys.stdout.write("% 6.2f " % distmatrix[kprime,lprime])
sys.stdout.write("\n")
elif use_numeric:
Omega = tableau
if fortran_format:
for k in range(n):
for l in range(k+1):
kprime = permutation[k]
lprime = permutation[l]
if isNaN(Omega[kprime,lprime]):
angle = 0.0
else:
angle = Omega[kprime,lprime]
sys.stdout.write("%6.3f " % angle)
sys.stdout.write("\n")
else:
for k in range(n):
for l in range(n):
kprime = permutation[k]
lprime = permutation[l]
sys.stdout.write("% 4.3f " % Omega[kprime,lprime])
sys.stdout.write("\n")
else:
if fortran_format:
for k in range(n):
for l in range(k+1):
kprime = permutation[k]
lprime = permutation[l]
sys.stdout.write(tableau[(kprime,lprime)] + " ")
sys.stdout.write("\n")
else:
# can't just sys.stdout.write(str(tableau)) if shuffled...
for k in range(n):
for l in range(n):
kprime = permutation[k]
lprime = permutation[l]
sys.stdout.write(tableau[(kprime,lprime)] + " ")
sys.stdout.write('\n')
def write_tableau(n, tableau, permutation, use_numeric, fortran_format,
build_distance_matrix):
"""
Write tableau or distance matrix to stdout.
n - order of tableau or distance matrix (n by n)
tableau - PTTableau object for tableau or Numeric matrix for
Omega matrix or Numeric matrix for distance matrix
permutation - permuted list of ingeters in interval [0, n-1] to
permute the rows+cols of the tableau/matrix by
(so [0,1,2,...n-1] for no permutation.
use_numeric - boolean. If true, tableau is a Numeric Omega matrix
not a tableau.
fortran_format - boolean. If True, put in lower triangle format
for FORTRAN programs tsrchd etc.
build_distance_matrix - boolean. If True is a distance matrix not a
tableau or Omega matrix.
"""
if build_distance_matrix:
distmatrix = tableau
if fortran_format:
for k in range(n):
for l in range(k + 1):
kprime = permutation[k]
lprime = permutation[l]
if isNaN(distmatrix[kprime, lprime]):
dist = 0.0
else:
dist = distmatrix[kprime, lprime]
if dist > 99.9:
sys.stderr.write(
'WARNING: distance %f at (%d,%d) truncated to 99.9 for fortran format\n'
% (dist, kprime, lprime))
dist = 99.9
sys.stdout.write("%6.3f " % dist)
sys.stdout.write("\n")
else:
for k in range(n):
for l in range(n):
kprime = permutation[k]
lprime = permutation[l]
sys.stdout.write("% 6.2f " % distmatrix[kprime, lprime])
sys.stdout.write("\n")
elif use_numeric:
Omega = tableau
if fortran_format:
for k in range(n):
for l in range(k + 1):
kprime = permutation[k]
lprime = permutation[l]
if isNaN(Omega[kprime, lprime]):
angle = 0.0
else:
angle = Omega[kprime, lprime]
sys.stdout.write("%6.3f " % angle)
sys.stdout.write("\n")
else:
for k in range(n):
for l in range(n):
kprime = permutation[k]
lprime = permutation[l]
sys.stdout.write("% 4.3f " % Omega[kprime, lprime])
sys.stdout.write("\n")
else:
if fortran_format:
for k in range(n):
for l in range(k + 1):
kprime = permutation[k]
lprime = permutation[l]
sys.stdout.write(tableau[(kprime, lprime)] + " ")
sys.stdout.write("\n")
else:
# can't just sys.stdout.write(str(tableau)) if shuffled...
for k in range(n):
for l in range(n):
kprime = permutation[k]
lprime = permutation[l]
sys.stdout.write(tableau[(kprime, lprime)] + " ")
sys.stdout.write('\n')
