From d877cabc139390b1afb8c4009ccece054cb553b4 Mon Sep 17 00:00:00 2001 From: yokochi47 Date: Thu, 20 Feb 2025 20:31:52 +0900 Subject: [PATCH] DAOTHER-8905, 9785, BMRB internal annotation: Enable to remove empty spectral peak lists in NMR data remediation Phase 2 and BMRB internal annotation, except for OneDep --- wwpdb/utils/nmr/NmrDpUtility.py | 4 ++-- wwpdb/utils/nmr/ann/BMRBAnnTasks.py | 6 ++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/wwpdb/utils/nmr/NmrDpUtility.py b/wwpdb/utils/nmr/NmrDpUtility.py index b4b58688..de07d814 100644 --- a/wwpdb/utils/nmr/NmrDpUtility.py +++ b/wwpdb/utils/nmr/NmrDpUtility.py @@ -25295,7 +25295,7 @@ def __extractToNmrIf(self) -> bool: ann = BMRBAnnTasks(self.__verbose, self.__lfh, self.__sf_category_list, self.__entry_id, - self.__sail_flag, self.report, + self.__internal_mode, self.__sail_flag, self.report, ccU=self.__ccU, csStat=self.__csStat, c2S=self.__c2S) ann.perform(master_entry) @@ -59804,7 +59804,7 @@ def __performBMRBAnnTasks(self) -> bool: ann = BMRBAnnTasks(self.__verbose, self.__lfh, self.__sf_category_list, self.__entry_id, - self.__sail_flag, self.report, + self.__internal_mode, self.__sail_flag, self.report, ccU=self.__ccU, csStat=self.__csStat, c2S=self.__c2S) is_done = ann.perform(master_entry) diff --git a/wwpdb/utils/nmr/ann/BMRBAnnTasks.py b/wwpdb/utils/nmr/ann/BMRBAnnTasks.py index 62a0f3ec..3037e02b 100644 --- a/wwpdb/utils/nmr/ann/BMRBAnnTasks.py +++ b/wwpdb/utils/nmr/ann/BMRBAnnTasks.py @@ -83,7 +83,7 @@ class BMRBAnnTasks: def __init__(self, verbose: bool, log: IO, sfCategoryList: List[str], entryId: str, - sailFlag: bool, report: NmrDpReport, + internalMode: bool, sailFlag: bool, report: NmrDpReport, ccU: Optional[ChemCompUtil] = None, csStat: Optional[BMRBChemShiftStat] = None, c2S: Optional[CifToNmrStar] = None): self.__class_name__ = self.__class__.__name__ @@ -94,6 +94,8 @@ def __init__(self, verbose: bool, log: IO, self.__sfCategoryList = sfCategoryList self.__entryId = entryId + + self.__internalMode = internalMode self.__sailFlag = sailFlag self.__report = report @@ -1957,7 +1959,7 @@ def is_natural_abundance(isotopic_labeling: str): # resolve duplication of spectral peak lists - if sf_category in self.__sfCategoryList: + if sf_category in self.__sfCategoryList and self.__internalMode: tags_2d = ['Volume', 'Height', 'Position_1', 'Position_2', 'Auth_asym_ID_1'] tags_3d = ['Volume', 'Height', 'Position_1', 'Position_2', 'Position_3', 'Auth_asym_ID_1']