Add NMRView peak reader and parserlistener

wwpdb/utils/nmr/NEFTranslator/NEFTranslator.py

@@ -120,7 +120,7 @@
 
 from packaging import version
 from operator import itemgetter
-from typing import List
+from typing import List, Optional, Union
 
 from wwpdb.utils.align.alignlib import PairwiseAlign  # pylint: disable=no-name-in-module
 
@@ -474,7 +474,7 @@
                         }
 
 
-def get_first_sf_tag(sf=None, tag=None) -> str:
+def get_first_sf_tag(sf: Optional[pynmrstar.Saveframe] = None, tag: Optional[str] = None) -> str:
     """ Return the first value of a given saveframe tag.
         @return: The first tag value, empty string otherwise.
     """
@@ -490,7 +490,7 @@ def get_first_sf_tag(sf=None, tag=None) -> str:
     return array[0] if array[0] is not None else ''
 
 
-def get_idx_msg(idx_tag_ids: List[int], tags: List[str], row) -> str:
+def get_idx_msg(idx_tag_ids: List[int], tags: List[str], row: dict) -> str:
     """ Return description about current index.
         @author: Masashi Yokochi
         @return: description
@@ -512,7 +512,7 @@ def get_idx_msg(idx_tag_ids: List[int], tags: List[str], row) -> str:
         return ''
 
 
-def is_empty_loop(star_data, lp_category: str) -> bool:
+def is_empty_loop(star_data: Union[pynmrstar.Entry, pynmrstar.Saveframe, pynmrstar.Loop], lp_category: str) -> bool:
     """ Return whether one of specified loops is empty loop.
         @return: True for empty loop exists, False otherwise
     """
@@ -530,7 +530,7 @@ def is_empty_loop(star_data, lp_category: str) -> bool:
     return len(star_data) == 0
 
 
-def count_non_empty_loops(star_data, lp_category: str) -> int:
+def count_non_empty_loops(star_data: Union[pynmrstar.Entry, pynmrstar.Saveframe, pynmrstar.Loop], lp_category: str) -> int:
     """ Return the number of non-empty loops.
         @return: the number of non-empty loops.
     """
@@ -548,7 +548,7 @@ def count_non_empty_loops(star_data, lp_category: str) -> int:
     return 0 if len(star_data) == 0 else 1
 
 
-def get_sf_tag_values_with_empty_loop(star_data, lp_category: str, sf_category: str) -> List[str]:
+def get_sf_tag_values_with_empty_loop(star_data: Union[pynmrstar.Entry, pynmrstar.Saveframe, pynmrstar.Loop], lp_category: str, sf_category: str) -> List[str]:
     """ Return list of saveframe tag values with empty loop.
         @return: list of saveframe tag values
     """

wwpdb/utils/nmr/NmrDpReport.py

@@ -98,15 +98,15 @@
 import re
 
 from operator import itemgetter
-from typing import Optional
+from typing import Any, Optional
 
 try:
     from wwpdb.utils.nmr.AlignUtil import emptyValue, monDict3, unknownResidue, getPrettyJson
 except ImportError:
     from nmr.AlignUtil import emptyValue, monDict3, unknownResidue, getPrettyJson
 
 
-def get_value_safe(d=None, key=None) -> Optional[str]:
+def get_value_safe(d: Optional[dict] = None, key: Any = None) -> Optional[str]:
     """ Return value of a given dictionary for a key.
         @return: value for a key, None otherwise
     """

wwpdb/utils/nmr/NmrDpUtility.py

@@ -223,7 +223,7 @@
 from munkres import Munkres
 from operator import itemgetter
 from striprtf.striprtf import rtf_to_text
-from typing import List, Tuple, Optional
+from typing import Any, List, Tuple, Optional
 
 from mmcif.io.IoAdapterPy import IoAdapterPy
 from wwpdb.utils.align.alignlib import PairwiseAlign  # pylint: disable=no-name-in-module
@@ -569,7 +569,7 @@
                           'nm-res-syb', 'nm-res-ros', 'nm-res-xpl')
 
 
-def detect_bom(fPath: str, default='utf-8') -> str:
+def detect_bom(fPath: str, default: str = 'utf-8') -> str:
     """ Detect BOM of input file.
     """
 
@@ -586,7 +586,7 @@ def detect_bom(fPath: str, default='utf-8') -> str:
     return default
 
 
-def convert_codec(inPath: str, outPath: str, in_codec='utf-8', out_codec='utf-8'):
+def convert_codec(inPath: str, outPath: str, in_codec: str = 'utf-8', out_codec: str = 'utf-8'):
     """ Convert codec of input file.
     """
 
@@ -701,7 +701,7 @@ def get_type_of_star_file(fPath: str) -> str:
                 pass
 
 
-def has_key_value(d=None, key=None) -> bool:
+def has_key_value(d: Optional[dict] = None, key: Any = None) -> bool:
     """ Return whether a given dictionary has effective value for a key.
         @return: True if d[key] has effective value, False otherwise
     """
@@ -715,7 +715,7 @@ def has_key_value(d=None, key=None) -> bool:
     return False
 
 
-def get_first_sf_tag(sf=None, tag=None) -> str:
+def get_first_sf_tag(sf: Optional[pynmrstar.Saveframe] = None, tag: Optional[str] = None) -> str:
     """ Return the first value of a given saveframe tag.
         @return: The first tag value, empty string otherwise.
     """
@@ -731,7 +731,7 @@ def get_first_sf_tag(sf=None, tag=None) -> str:
     return array[0] if array[0] is not None else ''
 
 
-def set_sf_tag(sf, tag: str, value):
+def set_sf_tag(sf: pynmrstar.Saveframe, tag: str, value):
     """ Set saveframe tag.
     """
 
@@ -1062,7 +1062,7 @@ def concat_nmr_restraint_names(content_subtype: Optional[str]) -> str:
     return ', '.join(f)
 
 
-def is_peak_list(line: str, has_header=True) -> bool:
+def is_peak_list(line: str, has_header: bool = True) -> bool:
     """ Return whether a given input is derived from peak list in any native format.
     """
 
@@ -1082,7 +1082,7 @@ def is_peak_list(line: str, has_header=True) -> bool:
     return False
 
 
-def get_peak_list_format(line: str, has_header=True) -> Optional[str]:
+def get_peak_list_format(line: str, has_header: bool = True) -> Optional[str]:
     """ Return peak list format for a given input.
     """
 
@@ -1137,7 +1137,7 @@ def get_number_of_dimensions_of_peak_list(file_format: str, line: str) -> Option
     return None
 
 
-def is_like_planality_boundary(row, lower_limit_name: str, upper_limit_name: str) -> bool:
+def is_like_planality_boundary(row: dict, lower_limit_name: str, upper_limit_name: str) -> bool:
     """ Return whether boundary conditions like planality restraint.
     """
 
@@ -1165,7 +1165,7 @@ def is_like_planality_boundary(row, lower_limit_name: str, upper_limit_name: str
         return False
 
 
-def get_atom_name_mapping(lp, list_of_tags: List[List[str]]) -> Optional[List[dict]]:
+def get_atom_name_mapping(lp: pynmrstar.Loop, list_of_tags: List[List[str]]) -> Optional[List[dict]]:
     """ Return atom name mapping history for each comp_id.
         Each tags should be array of 'comp_id', 'atom_id', and 'atom_name'.
     """
@@ -29956,7 +29956,7 @@ def __retrieveCoordAssemblyChecker(self):
         self.__caC = coordAssemblyChecker(self.__verbose, self.__lfh,
                                           self.__representative_model_id,
                                           self.__representative_alt_id,
-                                          self.__cR, None, nmrPolySeq)
+                                          self.__cR, self.__ccU, None, nmrPolySeq)
 
         if self.__caC is not None and self.__asmChkCachePath is not None:
             write_as_pickle(self.__caC, self.__asmChkCachePath)

wwpdb/utils/nmr/NmrVrptUtility.py

@@ -96,7 +96,7 @@ def compress_as_gzip_file(inPath: str, outPath: str):
             ofh.write(line)
 
 
-def load_from_pickle(file_name: str, default=None) -> Any:
+def load_from_pickle(file_name: str, default: Any = None) -> Any:
     """ Load object from pickle file.
     """
 
@@ -1177,7 +1177,7 @@ def __retrieveCoordAssemblyChecker(self):
             self.__caC = coordAssemblyChecker(self.__verbose, self.__lfh,
                                               self.__representative_model_id,
                                               self.__representative_alt_id,
-                                              self.__cR, None, None)
+                                              self.__cR, self.__ccU, None, None)
 
             if self.__caC is not None and cache_path:
                 write_as_pickle(self.__caC, cache_path)
@@ -1186,7 +1186,7 @@ def __retrieveCoordAssemblyChecker(self):
             self.__caC = coordAssemblyChecker(self.__verbose, self.__lfh,
                                               self.__representative_model_id,
                                               self.__representative_alt_id,
-                                              self.__cR, None, None, False)
+                                              self.__cR, self.__ccU, None, None, False)
 
         return True
 

wwpdb/utils/nmr/mr/AmberMRParserListener.py

@@ -530,9 +530,12 @@ def __init__(self, verbose=True, log=sys.stdout,
         self.__cR = cR
         self.__hasCoord = cR is not None
 
+        # CCD accessing utility
+        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
+
         if self.__hasCoord:
             ret = coordAssemblyChecker(verbose, log, representativeModelId, representativeAltId,
-                                       cR, caC)
+                                       cR, self.__ccU, caC)
             self.__modelNumName = ret['model_num_name']
             self.__authAsymId = ret['auth_asym_id']
             self.__authSeqId = ret['auth_seq_id']
@@ -574,9 +577,6 @@ def __init__(self, verbose=True, log=sys.stdout,
                         self.__concatHetero = False
                         break
 
-        # CCD accessing utility
-        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
-
         # BMRB chemical shift statistics
         self.__csStat = BMRBChemShiftStat(verbose, log, self.__ccU) if csStat is None else csStat
 

wwpdb/utils/nmr/mr/AmberMRReader.py

@@ -65,16 +65,16 @@ def __init__(self, verbose=True, log=sys.stdout,
         self.__representativeAltId = representativeAltId
         self.__mrAtomNameMapping = mrAtomNameMapping
 
+        # CCD accessing utility
+        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
+
         if cR is not None and caC is None:
             caC = coordAssemblyChecker(verbose, log, representativeModelId, representativeAltId,
-                                       cR, None, None, fullCheck=False)
+                                       cR, self.__ccU, None, None, fullCheck=False)
 
         self.__cR = cR
         self.__caC = caC
 
-        # CCD accessing utility
-        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
-
         # BMRB chemical shift statistics
         self.__csStat = BMRBChemShiftStat(verbose, log, self.__ccU) if csStat is None else csStat
 

wwpdb/utils/nmr/mr/AmberPTParserListener.py

@@ -160,9 +160,12 @@ def __init__(self, verbose=True, log=sys.stdout,
 
         self.__hasCoord = cR is not None
 
+        # CCD accessing utility
+        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
+
         if self.__hasCoord:
             ret = coordAssemblyChecker(verbose, log, representativeModelId, representativeAltId,
-                                       cR, caC, None, fullCheck=True)
+                                       cR, self.__ccU, caC, None, fullCheck=True)
             self.__polySeqModel = ret['polymer_sequence']
             self.__nonPolyModel = ret['non_polymer']
             self.__branchedModel = ret['branched']
@@ -175,9 +178,6 @@ def __init__(self, verbose=True, log=sys.stdout,
         self.__hasBranchedModel = self.__branchedModel is not None and len(self.__branchedModel) > 0
         self.__noWaterMol = not self.__hasNonPolyModel or not any(np['comp_id'][0] == 'HOH' for np in self.__nonPolyModel)
 
-        # CCD accessing utility
-        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
-
         # BMRB chemical shift statistics
         self.__csStat = BMRBChemShiftStat(verbose, log, self.__ccU) if csStat is None else csStat
 

wwpdb/utils/nmr/mr/AmberPTReader.py

@@ -59,16 +59,16 @@ def __init__(self, verbose=True, log=sys.stdout,
         self.__representativeAltId = representativeAltId
         self.__mrAtomNameMapping = mrAtomNameMapping
 
+        # CCD accessing utility
+        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
+
         if cR is not None and caC is None:
             caC = coordAssemblyChecker(verbose, log, representativeModelId, representativeAltId,
-                                       cR, None, None, fullCheck=False)
+                                       cR, self.__ccU, None, None, fullCheck=False)
 
         self.__cR = cR
         self.__caC = caC
 
-        # CCD accessing utility
-        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
-
         # BMRB chemical shift statistics
         self.__csStat = BMRBChemShiftStat(verbose, log, self.__ccU) if csStat is None else csStat
 

wwpdb/utils/nmr/mr/AriaMRParserListener.py

@@ -315,9 +315,12 @@ def __init__(self, verbose=True, log=sys.stdout,
         self.__cR = cR
         self.__hasCoord = cR is not None
 
+        # CCD accessing utility
+        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
+
         if self.__hasCoord:
             ret = coordAssemblyChecker(verbose, log, representativeModelId, representativeAltId,
-                                       cR, caC)
+                                       cR, self.__ccU, caC)
             self.__modelNumName = ret['model_num_name']
             self.__authAsymId = ret['auth_asym_id']
             self.__authSeqId = ret['auth_seq_id']
@@ -352,9 +355,6 @@ def __init__(self, verbose=True, log=sys.stdout,
             else:
                 self.__nonPolySeq = self.__branched
 
-        # CCD accessing utility
-        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
-
         # BMRB chemical shift statistics
         self.__csStat = BMRBChemShiftStat(verbose, log, self.__ccU) if csStat is None else csStat
 

wwpdb/utils/nmr/mr/AriaMRReader.py

@@ -61,16 +61,16 @@ def __init__(self, verbose=True, log=sys.stdout,
         self.__representativeAltId = representativeAltId
         self.__mrAtomNameMapping = mrAtomNameMapping
 
+        # CCD accessing utility
+        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
+
         if cR is not None and caC is None:
             caC = coordAssemblyChecker(verbose, log, representativeModelId, representativeAltId,
-                                       cR, None, None, fullCheck=False)
+                                       cR, self.__ccU, None, None, fullCheck=False)
 
         self.__cR = cR
         self.__caC = caC
 
-        # CCD accessing utility
-        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
-
         # BMRB chemical shift statistics
         self.__csStat = BMRBChemShiftStat(verbose, log, self.__ccU) if csStat is None else csStat
 

wwpdb/utils/nmr/mr/BiosymMRParserListener.py

@@ -326,9 +326,12 @@ def __init__(self, verbose=True, log=sys.stdout,
         self.__cR = cR
         self.__hasCoord = cR is not None
 
+        # CCD accessing utility
+        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
+
         if self.__hasCoord:
             ret = coordAssemblyChecker(verbose, log, representativeModelId, representativeAltId,
-                                       cR, caC)
+                                       cR, self.__ccU, caC)
             self.__modelNumName = ret['model_num_name']
             self.__authAsymId = ret['auth_asym_id']
             self.__authSeqId = ret['auth_seq_id']
@@ -363,9 +366,6 @@ def __init__(self, verbose=True, log=sys.stdout,
             else:
                 self.__nonPolySeq = self.__branched
 
-        # CCD accessing utility
-        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
-
         # BMRB chemical shift statistics
         self.__csStat = BMRBChemShiftStat(verbose, log, self.__ccU) if csStat is None else csStat
 

wwpdb/utils/nmr/mr/BiosymMRReader.py

@@ -61,16 +61,16 @@ def __init__(self, verbose=True, log=sys.stdout,
         self.__representativeAltId = representativeAltId
         self.__mrAtomNameMapping = mrAtomNameMapping
 
+        # CCD accessing utility
+        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
+
         if cR is not None and caC is None:
             caC = coordAssemblyChecker(verbose, log, representativeModelId, representativeAltId,
-                                       cR, None, None, fullCheck=False)
+                                       cR, self.__ccU, None, None, fullCheck=False)
 
         self.__cR = cR
         self.__caC = caC
 
-        # CCD accessing utility
-        self.__ccU = ChemCompUtil(verbose, log) if ccU is None else ccU
-
         # BMRB chemical shift statistics
         self.__csStat = BMRBChemShiftStat(verbose, log, self.__ccU) if csStat is None else csStat