Skip to content

Commit

Permalink
Set slightly strict criteria for incomplete sequence alignment (2mse)
Browse files Browse the repository at this point in the history
  • Loading branch information
@yokochi47
yokochi47 committed Mar 26, 2024
1 parent 8351aca commit 7ffbad4
Show file tree
Hide file tree
Showing 2 changed files with 13 additions and 13 deletions.
4 changes: 2 additions & 2 deletions wwpdb/utils/nmr/AlignUtil.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -950,7 +950,7 @@ def alignPolymerSequence(pA, polySeqModel, polySeqRst, conservative=True, resolv

_matched, unmapped, conflict, offset_1, offset_2 = getScoreOfSeqAlign(myAlign)

if length == unmapped + conflict or _matched <= conflict:
if length == unmapped + conflict or _matched <= conflict + 1:
inhibitList.append({chain_id, chain_id2})
continue

Expand Down Expand Up @@ -1297,7 +1297,7 @@ def alignPolymerSequenceWithConflicts(pA, polySeqModel, polySeqRst, conflictTh=1

_matched, unmapped, conflict, offset_1, offset_2 = getScoreOfSeqAlign(myAlign)

if length == unmapped + conflict or _matched <= conflict - conflictTh:
if length == unmapped + conflict or _matched <= conflict + 1 - conflictTh:
continue

if not_decided_s2_comp_id: # AMBER/GROMACS topology
Expand Down
22 changes: 11 additions & 11 deletions wwpdb/utils/nmr/NmrDpUtility.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17649,9 +17649,9 @@ def __appendPolymerSequenceAlignment(self):

alt_chain = False

if length == unmapped + conflict or _matched <= conflict or (len(polymer_sequence) > 1 and _matched < 4 and offset_1 > 0):
if length == unmapped + conflict or _matched <= conflict + 1 or (len(polymer_sequence) > 1 and _matched < 4 and offset_1 > 0):

if self.__tolerant_seq_align and _matched <= conflict and len(polymer_sequence) > 1:
if self.__tolerant_seq_align and _matched <= conflict + 1 and len(polymer_sequence) > 1:

__length = length
__matched = _matched
Expand Down Expand Up @@ -17685,7 +17685,7 @@ def __appendPolymerSequenceAlignment(self):

_matched, unmapped, conflict, offset_1, offset_2 = getScoreOfSeqAlign(myAlign)

if length == unmapped + conflict or _matched <= conflict:
if length == unmapped + conflict or _matched <= conflict + 1:
continue

if _matched - conflict < __matched - __conflict or unmapped + conflict > __unmapped + __conflict:
Expand Down Expand Up @@ -17971,9 +17971,9 @@ def __appendPolymerSequenceAlignment(self):

alt_chain = False

if length == unmapped + conflict or _matched <= conflict or (len(polymer_sequence) > 1 and _matched < 4 and offset_1 > 0):
if length == unmapped + conflict or _matched <= conflict + 1 or (len(polymer_sequence) > 1 and _matched < 4 and offset_1 > 0):

if self.__tolerant_seq_align and _matched <= conflict and len(polymer_sequence) > 1:
if self.__tolerant_seq_align and _matched <= conflict + 1 and len(polymer_sequence) > 1:

__length = length
__matched = _matched
Expand Down Expand Up @@ -18007,7 +18007,7 @@ def __appendPolymerSequenceAlignment(self):

_matched, unmapped, conflict, offset_1, offset_2 = getScoreOfSeqAlign(myAlign)

if length == unmapped + conflict or _matched <= conflict:
if length == unmapped + conflict or _matched <= conflict + 1:
continue

if _matched - conflict < __matched - __conflict or (unmapped + conflict > __unmapped + __conflict and __matched > 0):
Expand Down Expand Up @@ -18226,7 +18226,7 @@ def __appendPolymerSequenceAlignment(self):

_matched, unmapped, conflict, offset_1, offset_2 = getScoreOfSeqAlign(myAlign)

if length == unmapped + conflict or _matched <= conflict:
if length == unmapped + conflict or _matched <= conflict + 1:
break

cross = True
Expand Down Expand Up @@ -18263,7 +18263,7 @@ def __appendPolymerSequenceAlignment(self):

_matched, unmapped, conflict, offset_1, offset_2 = getScoreOfSeqAlign(myAlign)

if length == unmapped + conflict or _matched <= conflict:
if length == unmapped + conflict or _matched <= conflict + 1:
continue

_s1 = s1 if offset_1 == 0 else fillBlankCompIdWithOffset(s1, offset_1)
Expand Down Expand Up @@ -41861,7 +41861,7 @@ def __appendCoordPolymerSequenceAlignment(self):

_matched, unmapped, conflict, offset_1, offset_2 = getScoreOfSeqAlign(myAlign)

if length == unmapped + conflict or _matched <= conflict:
if length == unmapped + conflict or _matched <= conflict + 1:
continue

_s1 = s1 if offset_1 == 0 else fillBlankCompIdWithOffset(s1, offset_1)
Expand Down Expand Up @@ -41930,7 +41930,7 @@ def __appendCoordPolymerSequenceAlignment(self):

_matched, unmapped, conflict, offset_1, offset_2 = getScoreOfSeqAlign(myAlign)

if length == unmapped + conflict or _matched <= conflict:
if length == unmapped + conflict or _matched <= conflict + 1:
continue

_s1 = s1 if offset_1 == 0 else fillBlankCompIdWithOffset(s1, offset_1)
Expand Down Expand Up @@ -42066,7 +42066,7 @@ def __appendCoordPolymerSequenceAlignment(self):

_matched, unmapped, conflict, offset_1, offset_2 = getScoreOfSeqAlign(myAlign)

if length == unmapped + conflict or _matched <= conflict:
if length == unmapped + conflict or _matched <= conflict + 1:
continue

_s1 = s1 if offset_1 == 0 else fillBlankCompIdWithOffset(s1, offset_1)
Expand Down

0 comments on commit 7ffbad4

Please sign in to comment.