def tuplecmp(tup1, tup2):
"""
Comparison function for (chain, pdb_seqres_strt, pdb_seqres_end, type)
tuples used by sort in PTSecStruct.check_validity() and
PTSecStruct.__str__() functions.
"""
if tup1[0] < tup2[0]:
return -1
elif tup1[0] > tup2[0]:
return 1
else:
return pdb_res_seq_cmp(tup1[1], tup2[1])
def tuplecmp(tup1, tup2):
"""
Comparison function for (chain, pdb_seqres_strt, pdb_seqres_end, type)
tuples used by sort in PTSecStruct.check_validity() and
PTSecStruct.__str__() functions.
"""
if tup1[0] < tup2[0]:
return -1
elif tup1[0] > tup2[0]:
return 1
else:
return pdb_res_seq_cmp(tup1[1], tup2[1])
def check_validity_and_fix(self):
"""
Check for overlapping secondary structures. This happens for
example in the PDB HELIX records for 1DLC. In such a case we
recover from it in for example this case
by adding or subtracting one to start/end of ovlerlapping
HELIX records,
Parameters:
None
Return value:
True if OK, False if invalid (overlapping structures)
(Now returns True if it has fixed up overlaps itself)
Uses data members (READ/WRITE):
helix_list, strand_list
(start and end in helix and strand tuples may be modified;
lists are sorted by increasing residue sequence number)
"""
helices = [(chain, start, end, endchain, 'H', htype)
for (chain, start, endchain, end, htype) in self.helix_list]
strands = [(chain, start, end, endchain, 'E', None)
for (chain, start, endchain, end) in self.strand_list]
sselist = helices + strands
sselist.sort(cmp=tuplecmp)
is_valid = True
for i in xrange(1, len(sselist)):
sse = sselist[i]
prevsse = sselist[i - 1]
if (prevsse[0] == sse[0]
and pdb_res_seq_cmp(sse[1], prevsse[2]) <= 0):
sys.stderr.write('WARNING: PDB has overlapping SSE definitions'
' ' + str(prevsse) + ' and ' + str(sse) +
': ')
# remove overlap by shortening longer one and lengthing
# shorter one
# FIXME: this is ignoring insertion codes etc., really
# should convert to proper sequential residue sequence numbers
# to do this
(prevsse_start,
prevsse_start_icode) = get_int_icode(prevsse[1])
(prevsse_end, prevsse_end_icode) = get_int_icode(prevsse[2])
(sse_start, sse_start_icode) = get_int_icode(sse[1])
(sse_end, sse_end_icode) = get_int_icode(sse[2])
if (prevsse_end_icode or sse_start_icode):
sys.stderr.write('contains insertion codes, giving up\n')
is_valid = False
continue
prevsse_len = prevsse_end - prevsse_start + 1
sse_len = sse_end - sse_start + 1
overlap = prevsse_end - sse_start + 1
if sse_len > prevsse_len:
sse_start += overlap
else:
prevsse_end -= overlap
sselist[i] = (sse[0], str(sse_start), str(sse_end), sse[3],
sse[4], sse[5])
sselist[i - 1] = (prevsse[0], str(prevsse_start),
str(prevsse_end), prevsse[3], prevsse[4],
prevsse[5])
sys.stderr.write('changed to ' + str(sselist[i - 1]) +
' and ' + str(sselist[i]) + '\n')
i += 1
# rebuild the helix_list and strand_list with our modified tuples
self.helix_list = [(chain, start, endchain, end, htype)
for (chain, start, end, endchain, ssetype,
htype) in sselist if ssetype == 'H']
self.strand_list = [(chain, start, endchain, end)
for (chain, start, end, endchain, ssetype,
htype) in sselist if ssetype == 'E']
return is_valid
def check_validity_and_fix(self):
"""
Check for overlapping secondary structures. This happens for
example in the PDB HELIX records for 1DLC. In such a case we
recover from it in for example this case
by adding or subtracting one to start/end of ovlerlapping
HELIX records,
Parameters:
None
Return value:
True if OK, False if invalid (overlapping structures)
(Now returns True if it has fixed up overlaps itself)
Uses data members (READ/WRITE):
helix_list, strand_list
(start and end in helix and strand tuples may be modified;
lists are sorted by increasing residue sequence number)
"""
helices = [ (chain, start, end, endchain, 'H', htype)
for (chain, start, endchain, end, htype)
in self.helix_list ]
strands = [ (chain, start, end, endchain, 'E', None)
for (chain, start, endchain, end)
in self.strand_list ]
sselist = helices + strands
sselist.sort(cmp=tuplecmp)
is_valid = True
for i in xrange(1, len(sselist)):
sse = sselist[i]
prevsse = sselist[i-1]
if (prevsse[0] == sse[0] and
pdb_res_seq_cmp(sse[1], prevsse[2]) <= 0):
sys.stderr.write('WARNING: PDB has overlapping SSE definitions'
' ' + str(prevsse) + ' and ' + str(sse) + ': ')
# remove overlap by shortening longer one and lengthing
# shorter one
# FIXME: this is ignoring insertion codes etc., really
# should convert to proper sequential residue sequence numbers
# to do this
(prevsse_start,prevsse_start_icode) = get_int_icode(prevsse[1])
(prevsse_end,prevsse_end_icode) = get_int_icode(prevsse[2])
(sse_start,sse_start_icode) = get_int_icode(sse[1])
(sse_end,sse_end_icode) = get_int_icode(sse[2])
if (prevsse_end_icode or sse_start_icode):
sys.stderr.write('contains insertion codes, giving up\n')
is_valid = False
continue
prevsse_len = prevsse_end - prevsse_start + 1
sse_len = sse_end - sse_start + 1
overlap = prevsse_end - sse_start + 1
if sse_len > prevsse_len:
sse_start += overlap
else:
prevsse_end -= overlap
sselist[i] = (sse[0],str(sse_start),str(sse_end),
sse[3],sse[4],sse[5])
sselist[i-1] = (prevsse[0],str(prevsse_start),str(prevsse_end),
prevsse[3],prevsse[4],prevsse[5])
sys.stderr.write('changed to ' + str(sselist[i-1]) + ' and ' +
str(sselist[i]) + '\n')
i += 1
# rebuild the helix_list and strand_list with our modified tuples
self.helix_list = [ (chain, start, endchain, end, htype)
for (chain, start, end, endchain, ssetype, htype)
in sselist if ssetype == 'H' ]
self.strand_list = [ (chain, start, endchain, end)
for (chain, start, end, endchain, ssetype, htype)
in sselist if ssetype == 'E' ]
return is_valid
