def add_complex_index(self, refseq, index, pregaps=0):
if isinstance(self._idx[refseq], list):
raise AttributeError('A complex index cannot be modified')
if not isinstance(index, list):
raise AttributeError(
'A complex index is a list of IndexedNum or integers')
if len(index) < len(re.sub('-', '', self._seq[refseq].sequence)):
raise AttributeError(
'The given index is not long enought to cover que assigned sequence'
)
init_value = self._idx[refseq]
part_to_add = index[init_value - 1 - pregaps:]
self._idx[refseq] = []
count = 0
for x in range(len(self._seq[refseq])):
if self._seq[refseq][x] != '-':
self._idx[refseq].append(IndexedNum(part_to_add[count]))
count += 1
for x in range(len(self._segment[refseq])):
if self._segment[refseq][x] != '-':
self._segment[refseq][x] = self._sequence_position_id(
refseq, self._segment[refseq][x] - init_value + 1)
self._has_complex_index = True
def _alignment_position_from_sequence_position(self, refseq, pos):
if not isinstance(self._idx[refseq], list):
return super(IndexedSeqAli,
self)._alignment_position_from_sequence_position(
refseq, pos)
pos = IndexedNum(pos)
if not self._seq[refseq].is_gapped:
try:
return self._idx[refseq].index(pos) + 1
except ValueError, e:
raise IndexError(e.message)
def process_DBREF_line(line):
'''
The line format is such as:
COLUMNS DATA TYPE FIELD DEFINITION
----------------------------------------------------------------
1 - 6 Record name "DBREF "
8 - 11 IDcode idCode ID code of this entry.
13 Character chainID Chain identifier.
15 - 18 Integer seqBegin Initial sequence number
of the PDB sequence segment.
19 AChar insertBegin Initial insertion code
of the PDB sequence segment.
21 - 24 Integer seqEnd Ending sequence number
of the PDB sequence segment.
25 AChar insertEnd Ending insertion code
of the PDB sequence segment.
27 - 32 LString database Sequence database name.
34 - 41 LString dbAccession Sequence database accession code.
43 - 54 LString dbIdCode Sequence database
identification code.
56 - 60 Integer dbseqBegin Initial sequence number of the
database seqment.
61 AChar idbnsBeg Insertion code of initial residue
of the segment, if PDB is the
reference.
63 - 67 Integer dbseqEnd Ending sequence number of the
database segment.
68 AChar dbinsEnd Insertion code of the ending
residue of the segment, if PDB is
the reference.
For example:
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
DBREF 1ABC B 1B 36 PDB 1ABC 1ABC 1B 36
DBREF 3AKY 3 220 SWS P07170 KAD1_YEAST 5 222
DBREF 1HAN 2 288 GB 397884 X66122 1 287
DBREF 3HSV A 1 92 SWS P22121 HSF_KLULA 193 284
DBREF 3HSV B 1 92 SWS P22121 HSF_KLULA 193 284
DBREF 1ARL 1 307 SWS P00730 CBPA_BOVIN 111 417
DBREF 249D A 1 12 NDB BDL070 BDL070 1 12
DBREF 249D B 13 24 NDB BDL070 BDL070 13 24
DBREF 249D C 26 36 NDB BDL070 BDL070 26 36
DBREF 249D D 37 48 NDB BDL070 BDL070 37 48
Detailed info @ http://www.wwpdb.org/documentation/format23/sect3.html
'''
data = []
data.append(line[7:11].strip())
data.append(fix_chain(line[12:13].strip()))
data.append(IndexedNum(line[14:19].strip()))
data.append(IndexedNum(line[20:25].strip()))
data.append(line[25:29].strip())
data.append(line[30:41].strip())
return data
def end(self):
return IndexedNum(self.line[32:39].strip())
def init(self):
return IndexedNum(self.line[20:27].strip())
def end(self):
return IndexedNum(self.line[33:38].strip())
def init(self):
return IndexedNum(self.line[22:28].strip())