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1. Reconciled fix for 7x8m and recent fix, 2. Code refactoring, 3. Ad…
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…d version and license information
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@yokochi47
yokochi47 committed Jan 17, 2025
1 parent e125cc8 commit 7b70c19
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Showing 68 changed files with 1,682 additions and 1,138 deletions.
41 changes: 24 additions & 17 deletions wwpdb/utils/nmr/AlignUtil.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,12 @@
""" Utilities for pairwise alignment.
@author: Masashi Yokochi
"""
__docformat__ = "restructuredtext en"
__author__ = "Masashi Yokochi"
__email__ = "[email protected]"
__license__ = "Apache License 2.0"
__version__ = "1.0.0"

import copy
import json
import re
Expand Down Expand Up @@ -444,7 +450,7 @@ def getGaugeCode(seqIdList: List[int], offset: int = 0) -> str:
break
_offset += 1

if lastSeqId is None or nextSeqId is None or nextSeqId > lastSeqId + 1:
if None in (lastSeqId, nextSeqId) or nextSeqId > lastSeqId + 1:
p = idx + offset
gaugeCode = gaugeCode[0:p] + ' ' + gaugeCode[p:]
offset += 1
Expand Down Expand Up @@ -917,7 +923,7 @@ def syncCompIdOfPolySeqRst(polySeqRst: List[dict], compIdMap: dict):
""" Synchronize residue names of polymer sequence of the current MR file.
"""

if polySeqRst is None or compIdMap is None or len(polySeqRst) == 0 or len(compIdMap) == 0:
if None in (polySeqRst, compIdMap) or len(polySeqRst) == 0 or len(compIdMap) == 0:
return

for ps in polySeqRst:
Expand Down Expand Up @@ -1007,7 +1013,7 @@ def alignPolymerSequence(pA, polySeqModel: List[dict], polySeqRst: List[dict],

seqAlign, compIdMapping = [], []

if pA is None or polySeqModel is None or polySeqRst is None:
if None in (pA, polySeqModel, polySeqRst):
return seqAlign, compIdMapping

tabooList, inhibitList = [], []
Expand Down Expand Up @@ -1130,7 +1136,7 @@ def alignPolymerSequence(pA, polySeqModel: List[dict], polySeqRst: List[dict],
for p in range(len(s1[seq_id_name]) - 1):
s_p = s1[seq_id_name][p]
s_q = s1[seq_id_name][p + 1]
if s_p is None or s_q is None or s_p not in s2['seq_id'] or s_q not in s2['seq_id']:
if None in (s_p, s_q) or s_p not in s2['seq_id'] or s_q not in s2['seq_id']:
continue
if s_p + 1 != s_q:
beg = s2['seq_id'].index(s_p)
Expand Down Expand Up @@ -1160,7 +1166,7 @@ def alignPolymerSequence(pA, polySeqModel: List[dict], polySeqRst: List[dict],
for p in range(len(s1[seq_id_name]) - 1):
s_p = s1[seq_id_name][p]
s_q = s1[seq_id_name][p + 1]
if s_p is None or s_q is None or s_p not in __s2['seq_id'] or s_q not in __s2['seq_id']:
if None in (s_p, s_q) or s_p not in __s2['seq_id'] or s_q not in __s2['seq_id']:
continue
if s_p + 1 != s_q:
beg = __s2['seq_id'].index(s_p)
Expand Down Expand Up @@ -1197,7 +1203,7 @@ def alignPolymerSequence(pA, polySeqModel: List[dict], polySeqRst: List[dict],
for p in range(len(s1[seq_id_name]) - 1):
s_p = s1[seq_id_name][p]
s_q = s1[seq_id_name][p + 1]
if s_p is None or s_q is None or s_p not in s2['seq_id'] or s_q not in s2['seq_id']:
if None in (s_p, s_q) or s_p not in s2['seq_id'] or s_q not in s2['seq_id']:
continue
if s_p + 1 != s_q:
idx1 = idx2 = 0
Expand Down Expand Up @@ -1435,7 +1441,7 @@ def alignPolymerSequenceWithConflicts(pA, polySeqModel: List[dict], polySeqRst:

seqAlign, compIdMapping = [], []

if pA is None or polySeqModel is None or polySeqRst is None:
if None in (pA, polySeqModel, polySeqRst):
return seqAlign, compIdMapping

truncated = None
Expand Down Expand Up @@ -1513,7 +1519,7 @@ def alignPolymerSequenceWithConflicts(pA, polySeqModel: List[dict], polySeqRst:
for p in range(len(s1[seq_id_name]) - 1):
s_p = s1[seq_id_name][p]
s_q = s1[seq_id_name][p + 1]
if s_p is None or s_q is None or s_p not in s2['seq_id'] or s_q not in s2['seq_id']:
if None in (s_p, s_q) or s_p not in s2['seq_id'] or s_q not in s2['seq_id']:
continue
if s_p + 1 != s_q:
beg = s2['seq_id'].index(s_p)
Expand Down Expand Up @@ -1543,7 +1549,7 @@ def alignPolymerSequenceWithConflicts(pA, polySeqModel: List[dict], polySeqRst:
for p in range(len(s1[seq_id_name]) - 1):
s_p = s1[seq_id_name][p]
s_q = s1[seq_id_name][p + 1]
if s_p is None or s_q is None or s_p not in __s2['seq_id'] or s_q not in __s2['seq_id']:
if None in (s_p, s_q) or s_p not in __s2['seq_id'] or s_q not in __s2['seq_id']:
continue
if s_p + 1 != s_q:
beg = __s2['seq_id'].index(s_p)
Expand Down Expand Up @@ -1580,7 +1586,7 @@ def alignPolymerSequenceWithConflicts(pA, polySeqModel: List[dict], polySeqRst:
for p in range(len(s1[seq_id_name]) - 1):
s_p = s1[seq_id_name][p]
s_q = s1[seq_id_name][p + 1]
if s_p is None or s_q is None or s_p not in s2['seq_id'] or s_q not in s2['seq_id']:
if None in (s_p, s_q) or s_p not in s2['seq_id'] or s_q not in s2['seq_id']:
continue
if s_p + 1 != s_q:
idx1 = idx2 = 0
Expand Down Expand Up @@ -1749,7 +1755,7 @@ def assignPolymerSequence(pA, ccU, fileType: str, polySeqModel: List[dict], poly
""" Assign polymer sequences of restraints.
"""

if pA is None or polySeqModel is None or polySeqRst is None or seqAlign is None:
if None in (pA, polySeqModel, polySeqRst, seqAlign):
return None, []

warnings = []
Expand Down Expand Up @@ -2041,7 +2047,7 @@ def trimSequenceAlignment(seqAlign: List[dict], chainAssign: List[dict]):
""" Trim ineffective sequence alignments.
"""

if seqAlign is None or chainAssign is None:
if None in (seqAlign, chainAssign):
return

ineffSeqAlignIdx = list(range(len(seqAlign) - 1, -1, -1))
Expand Down Expand Up @@ -2693,7 +2699,7 @@ def splitPolySeqRstForMultimers(pA, polySeqModel: List[dict], polySeqRst: List[d
""" Split polymer sequence of the current MR file for multimers.
"""

if polySeqModel is None or polySeqRst is None or chainAssign is None:
if None in (polySeqModel, polySeqRst, chainAssign):
return None, None

target_chain_ids = {}
Expand Down Expand Up @@ -2858,7 +2864,7 @@ def splitPolySeqRstForExactNoes(pA, polySeqModel: List[dict], polySeqRst: List[d
""" Split polymer sequence of the current MR file for eNOEs-guided multiple conformers.
"""

if polySeqModel is None or polySeqRst is None or chainAssign is None:
if None in (polySeqModel, polySeqRst, chainAssign):
return None, None, None

target_chain_ids = {}
Expand Down Expand Up @@ -3088,6 +3094,7 @@ def retrieveRemappedChainId(chainIdRemap: dict, seqId: int) -> Tuple[Optional[st
def retrieveOriginalSeqIdFromMRMap(chainIdRemap: dict, chainId: str, seqId: int) -> int:
""" Retrieve the original seq_id from mapping dictionary based on sequence alignments.
"""

return next((_seqId for _seqId, remap in chainIdRemap.items()
if remap['chain_id'] == chainId and remap['seq_id'] == seqId), seqId)

Expand All @@ -3097,7 +3104,7 @@ def splitPolySeqRstForNonPoly(ccU, nonPolyModel: List[dict], polySeqRst: List[di
""" Split polymer sequence of the current MR file for non-polymer.
"""

if polySeqRst is None or nonPolyModel is None or seqAlign is None or chainAssign is None:
if None in (polySeqRst, nonPolyModel, seqAlign, chainAssign):
return None, None

comp_ids = set()
Expand Down Expand Up @@ -3180,7 +3187,7 @@ def splitPolySeqRstForNonPoly(ccU, nonPolyModel: List[dict], polySeqRst: List[di

for target, candidate in zip_longest(targets, candidates):

if target is None or candidate is None:
if None in (target, candidate):
break

test_chain_id = target['chain_id']
Expand Down Expand Up @@ -3229,7 +3236,7 @@ def splitPolySeqRstForBranched(pA, polySeqModel: List[dict], branchedModel: List
""" Split polymer sequence of the current MR file for branched polymer.
"""

if polySeqRst is None or polySeqModel is None or branchedModel is None or chainAssign is None:
if None in (polySeqRst, polySeqModel, branchedModel, chainAssign):
return None, None

target_chain_ids = {}
Expand Down
7 changes: 7 additions & 0 deletions wwpdb/utils/nmr/BMRBChemShiftStat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,12 @@
""" Wrapper class for retrieving BMRB chemical shift statistics.
@author: Masashi Yokochi
"""
__docformat__ = "restructuredtext en"
__author__ = "Masashi Yokochi"
__email__ = "[email protected]"
__license__ = "Apache License 2.0"
__version__ = "1.0.0"

import sys
import os
import csv
Expand Down Expand Up @@ -2318,6 +2324,7 @@ def __updateCompIdSet(self):
def updateStatCsvFiles(self) -> bool:
""" Update BMRB chemical shift statistics.
"""

import requests # pylint: disable=import-outside-toplevel
import datetime # pylint: disable=import-outside-toplevel
from dateutil.parser import parse as parsedate # pylint: disable=import-outside-toplevel
Expand Down
16 changes: 13 additions & 3 deletions wwpdb/utils/nmr/ChemCompUtil.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,12 @@
""" Wrapper class for retrieving chemical component dictionary.
@author: Masashi Yokochi
"""
__docformat__ = "restructuredtext en"
__author__ = "Masashi Yokochi"
__email__ = "[email protected]"
__license__ = "Apache License 2.0"
__version__ = "1.0.0"

import os
import sys
import pickle
Expand Down Expand Up @@ -153,21 +159,24 @@ def load_dict_from_pickle(file_name):
self.__cachedDict = load_dict_from_pickle(self.__cacheFile)
self.__failedCompId = []

def updateChemCompDict(self, compId: str) -> bool:
def updateChemCompDict(self, compId: str, ligand: bool = True) -> bool:
""" Update CCD information for a given comp_id.
@return: True for successfully update CCD information or False for the case a given comp_id does not exist in CCD
"""

if compId in emptyValue or not ccd_id_pattern.match(compId) or is_reserved_lig_code(compId):
if compId in emptyValue:
return False

compId = compId.upper()

if not ccd_id_pattern.match(compId) or (not ligand and is_reserved_lig_code(compId)):
return False

if compId in self.__failedCompId:
return False

if compId != self.lastCompId:
self.lastStatus = False if '_' in compId else self.__ccR.setCompId(compId)
self.lastStatus = False if '_' in compId else self.__ccR.setCompId(compId, ligand)
self.lastCompId = compId

if self.lastStatus:
Expand Down Expand Up @@ -468,6 +477,7 @@ def getAtomsBasedOnGreekLetterSystem(self, compId: str, atomId: str) -> List[str
def hasBond(self, compId: str, atomId1: str, atomId2: str) -> bool:
""" Return whether given two atoms are connected by a covalent bond.
"""

return atomId2 in self.getBondedAtoms(compId, atomId1)

def peptideLike(self, compId: Optional[str] = None) -> bool:
Expand Down
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