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schwede
openstructure
Commits
ad7b23ae
Commit
ad7b23ae
authored
9 years ago
by
Gerardo Tauriello
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fixed Renumber-function which was failing for the given example code
parent
e70cc686
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modules/seq/alg/doc/seqalg.rst
+1
-0
1 addition, 0 deletions
modules/seq/alg/doc/seqalg.rst
modules/seq/alg/pymod/renumber.py
+40
-25
40 additions, 25 deletions
modules/seq/alg/pymod/renumber.py
with
41 additions
and
25 deletions
modules/seq/alg/doc/seqalg.rst
+
1
−
0
View file @
ad7b23ae
...
@@ -163,6 +163,7 @@ Algorithms for Alignments
...
@@ -163,6 +163,7 @@ Algorithms for Alignments
:param gap_ext: The gap extension penalty. Must be a negative number
:param gap_ext: The gap extension penalty. Must be a negative number
:returns: best-scoring alignment of *seq1* and *seq2*.
:returns: best-scoring alignment of *seq1* and *seq2*.
.. autofunction:: ost.seq.alg.renumber.Renumber
.. _contact-prediction:
.. _contact-prediction:
...
...
This diff is collapsed.
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modules/seq/alg/pymod/renumber.py
+
40
−
25
View file @
ad7b23ae
from
ost
import
io
,
seq
,
mol
,
conop
from
ost
import
seq
,
mol
from
ost
import
*
def
_RenumberSeq
(
seq_handle
):
def
_RenumberSeq
(
seq_handle
):
if
not
seq_handle
.
HasAttachedView
():
if
not
seq_handle
.
HasAttachedView
():
...
@@ -8,14 +6,13 @@ def _RenumberSeq(seq_handle):
...
@@ -8,14 +6,13 @@ def _RenumberSeq(seq_handle):
ev
=
seq_handle
.
attached_view
.
CreateEmptyView
()
ev
=
seq_handle
.
attached_view
.
CreateEmptyView
()
new_numbers
=
mol
.
ResNumList
()
new_numbers
=
mol
.
ResNumList
()
for
pos
in
range
(
len
(
seq_handle
)):
for
pos
in
range
(
len
(
seq_handle
)):
if
seq_handle
[
pos
]
!=
'
-
'
:
if
seq_handle
[
pos
]
!=
'
-
'
:
r
=
seq_handle
.
GetResidue
(
pos
)
r
=
seq_handle
.
GetResidue
(
pos
)
if
r
.
IsValid
():
if
r
.
IsValid
():
#print seq_handle[pos],r.number.num,pos+1
ev
.
AddResidue
(
r
,
mol
.
INCLUDE_ALL
)
ev
.
AddResidue
(
r
,
mol
.
INCLUDE_ALL
)
new_numbers
.
append
(
pos
+
1
)
new_numbers
.
append
(
pos
+
1
)
else
:
else
:
raise
RuntimeError
(
'
Error: renumbering failed at position %s
'
%
pos
)
raise
RuntimeError
(
'
Error: renumbering failed at position %s
'
%
pos
)
return
ev
,
new_numbers
return
ev
,
new_numbers
def
_RenumberAln
(
aln
,
seq_index
):
def
_RenumberAln
(
aln
,
seq_index
):
...
@@ -25,44 +22,62 @@ def _RenumberAln(aln, seq_index):
...
@@ -25,44 +22,62 @@ def _RenumberAln(aln, seq_index):
ev
=
aln
.
sequences
[
seq_index
].
attached_view
.
CreateEmptyView
()
ev
=
aln
.
sequences
[
seq_index
].
attached_view
.
CreateEmptyView
()
new_numbers
=
mol
.
ResNumList
()
new_numbers
=
mol
.
ResNumList
()
for
col
in
aln
:
for
col
in
aln
:
if
col
[
0
]
!=
'
-
'
and
col
[
seq_index
]
!=
'
-
'
:
if
col
[
0
]
!=
'
-
'
and
col
[
seq_index
]
!=
'
-
'
:
if
col
[
0
]
!=
col
[
seq_index
]:
if
col
[
0
]
!=
col
[
seq_index
]:
raise
RuntimeError
(
"
residue mismatch at position %d (%s vs %s) (renumbering failed)
"
%
(
counter
,
col
[
0
],
col
[
1
]))
raise
RuntimeError
(
"
residue mismatch at position %d (%s vs %s)
"
\
rnum
=
aln
.
GetSequence
(
seq_index
).
GetResidueIndex
(
counter
)
"
(renumbering failed)
"
%
(
counter
,
col
[
0
],
r
=
aln
.
GetSequence
(
seq_index
).
GetResidue
(
counter
)
col
[
seq_index
]))
rnum
=
aln
.
GetSequence
(
seq_index
).
GetResidueIndex
(
counter
)
r
=
aln
.
GetSequence
(
seq_index
).
GetResidue
(
counter
)
if
not
r
.
IsValid
():
if
not
r
.
IsValid
():
raise
RuntimeError
(
"
invalid residue at postion %s (renumbering failed)
"
%
(
counter
))
raise
RuntimeError
(
"
invalid residue at postion %s (renumbering failed)
"
\
%
(
counter
))
ev
.
AddResidue
(
r
,
mol
.
INCLUDE_ALL
)
ev
.
AddResidue
(
r
,
mol
.
INCLUDE_ALL
)
new_numbers
.
append
(
counter
+
1
)
new_numbers
.
append
(
counter
+
1
)
counter
+=
1
counter
+=
1
return
ev
,
new_numbers
return
ev
,
new_numbers
def
Renumber
(
seq_handle
,
sequence_number_with_attached_view
=
1
):
def
Renumber
(
seq_handle
,
sequence_number_with_attached_view
=
1
):
"""
"""
Function to renumber an entity according to an alignment between the model sequence
Function to renumber an entity according to an alignment between the model
and the full-length target sequence. The aligned model sequence or the alignment itself
sequence and the full-length target sequence. The aligned model sequence or
with an attached view needs to be provided. Upon succcess, the renumbered entity is returned.
the alignment itself with an attached view needs to be provided. Upon
succcess, the renumbered entity is returned.
If an alignment is given, the sequence must
.. code-block:: python
.. code-block:: python
from ost.seq.alg import renumber
from ost.seq.alg import renumber
from ost.bindings.clustalw import *
from ost.bindings.clustalw import *
ent
=
io.LoadPDB(
"
path_to_model
"
)
ent
=
io.LoadPDB(
"
path_to_model
"
)
s
=
io.LoadSequence(
"
path_to_full_length_fasta_seqeunce
"
)
s
=
io.LoadSequence(
"
path_to_full_length_fasta_seqeunce
"
)
pdb_seq
=
seq.SequenceFromChain(
"
model
"
, ent.chains[0])
pdb_seq
=
seq.SequenceFromChain(
"
model
"
, ent.chains[0])
aln
=
ClustalW(s,pdb_seq)
aln
=
ClustalW(s,
pdb_seq)
aln.AttachView(1,ent.chains[0].Select(
""
))
aln.AttachView(1,
ent.chains[0].Select(
""
))
e
=
Renumber(aln.
GetS
equence
(sequence_number_with_attached_view)
)
e
=
Renumber(aln.
s
equence
s[1]
)
io.SavePDB(e,
"
renum.pdb
"
)
io.SavePDB(e,
"
renum.pdb
"
)
:param seq_handle: Sequence or alignment handle with attached view.
:type seq_handle: :class:`SequenceHandle` / :class:`AlignmentHandle`
:param sequence_number_with_attached_view: Sequence number for the aln. handle
(not used if seq. handle given)
:type sequence_number_with_attached_view: :class:`int`
:raises: :exc:`RuntimeError` if unknown type of *seq_handle* or if attached
view is missing or if the given alignment sequence is inconsistent.
"""
"""
if
isinstance
(
seq_handle
,
seq
.
SequenceHandle
):
if
isinstance
(
seq_handle
,
seq
.
SequenceHandle
)
\
or
isinstance
(
seq_handle
,
seq
.
ConstSequenceHandle
):
ev
,
new_numbers
=
_RenumberSeq
(
seq_handle
)
ev
,
new_numbers
=
_RenumberSeq
(
seq_handle
)
elif
isinstance
(
seq_handle
,
seq
.
AlignmentHandle
):
elif
isinstance
(
seq_handle
,
seq
.
AlignmentHandle
):
ev
,
new_numbers
=
_RenumberAln
(
seq_handle
,
sequence_number_with_attached_view
)
ev
,
new_numbers
=
_RenumberAln
(
seq_handle
,
sequence_number_with_attached_view
)
else
:
raise
RuntimeError
(
"
Unknown input type
"
+
str
(
type
(
seq_handle
)))
ev
.
AddAllInclusiveBonds
()
ev
.
AddAllInclusiveBonds
()
new_ent
=
mol
.
CreateEntityFromView
(
ev
,
False
);
new_ent
=
mol
.
CreateEntityFromView
(
ev
,
False
);
new_ent
.
EditXCS
().
RenumberChain
(
new_ent
.
chains
[
0
],
new_numbers
)
new_ent
.
EditXCS
().
RenumberChain
(
new_ent
.
chains
[
0
],
new_numbers
)
return
new_ent
return
new_ent
# choose visible interface
__all__
=
(
'
Renumber
'
,
)
\ No newline at end of file
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