Implement atom name mapping history as requirement of standalone NMR …

…data conversion service

wwpdb/utils/nmr/NmrDpUtility.py

@@ -198,6 +198,7 @@
 # 14-Nov-2024  M. Yokochi - add support for CHARMM extended CRD (topology) file. file type: 'nm-aux-cha'
 # 19-Nov-2024  M. Yokochi - add support for pH titration data (NMR restraint remediation)
 # 22-Nov-2024  M. Yokochi - add support for CYANA NOA (NOE Assignment) file. file type: 'nm-res-noa'
+# 27-Nov-2024  M. Yokochi - implement atom name mapping history as requirement of standalone NMR data conversion service
 ##
 """ Wrapper class for NMR data processing.
     @author: Masashi Yokochi
@@ -36087,10 +36088,10 @@ def __calculateStatsOfExptlData__(self, file_list_id, file_name, file_type, cont
                         self.__calculateStatsOfDistanceRestraint(file_list_id, sf_framecode, lp_data, conflict_id_set, inconsistent, redundant, ent)
 
                     elif content_subtype == 'dihed_restraint':
-                        self.__calculateStatsOfDihedralRestraint(file_list_id, lp_data, conflict_id_set, inconsistent, redundant, ent)
+                        self.__calculateStatsOfDihedralRestraint(file_list_id, sf_framecode, lp_data, conflict_id_set, inconsistent, redundant, ent)
 
                     elif content_subtype == 'rdc_restraint':
-                        self.__calculateStatsOfRdcRestraint(file_list_id, lp_data, conflict_id_set, inconsistent, redundant, ent)
+                        self.__calculateStatsOfRdcRestraint(file_list_id, sf_framecode, lp_data, conflict_id_set, inconsistent, redundant, ent)
 
             if content_subtype.startswith('spectral_peak'):
 
@@ -37744,7 +37745,9 @@ def __calculateStatsOfDistanceRestraint(self, file_list_id, sf_framecode, lp_dat
         file_name = input_source_dic['file_name']
         file_type = input_source_dic['file_type']
 
-        index_tag = self.index_tags[file_type]['dist_restraint']
+        content_subtype = 'dist_restraint'
+
+        index_tag = self.index_tags[file_type][content_subtype]
         item_names = self.item_names_in_ds_loop[file_type]
         combination_id_name = item_names['combination_id']
         chain_id_1_name = item_names['chain_id_1']
@@ -37764,8 +37767,8 @@ def __calculateStatsOfDistanceRestraint(self, file_list_id, sf_framecode, lp_dat
         upper_limit_name = item_names['upper_limit']
         lower_linear_limit_name = item_names['lower_linear_limit']
         upper_linear_limit_name = item_names['upper_linear_limit']
-        weight_name = self.weight_tags[file_type]['dist_restraint']
-        id_tag = self.consist_id_tags[file_type]['dist_restraint']
+        weight_name = self.weight_tags[file_type][content_subtype]
+        id_tag = self.consist_id_tags[file_type][content_subtype]
 
         len_lp_data = len(lp_data)
 
@@ -38580,7 +38583,7 @@ def __calculateStatsOfDistanceRestraint(self, file_list_id, sf_framecode, lp_dat
                         ent['histogram_of_discrepancy'] = {'range_of_values': range_of_vals, 'number_of_values': transposed, 'annotations': dist_ann}
 
             if file_type == 'nmr-star' and self.__star_data_type[file_list_id] == 'Entry':
-                lp_category = self.lp_categories[file_type]['dist_restraint']
+                lp_category = self.lp_categories[file_type][content_subtype]
                 sf = self.__star_data[file_list_id].get_saveframe_by_name(sf_framecode)
                 lp = next(lp for lp in sf.loops if lp.category == lp_category)
 
@@ -39544,7 +39547,7 @@ def __getTypeOfCovalentBond(self, file_type, lp_data, row_id, target_value,
 
         return data_type
 
-    def __calculateStatsOfDihedralRestraint(self, file_list_id, lp_data, conflict_id_set, inconsistent, redundant, ent):
+    def __calculateStatsOfDihedralRestraint(self, file_list_id, sf_framecode, lp_data, conflict_id_set, inconsistent, redundant, ent):
         """ Calculate statistics of dihedral angle restraints.
         """
 
@@ -39553,8 +39556,10 @@ def __calculateStatsOfDihedralRestraint(self, file_list_id, lp_data, conflict_id
 
         file_type = input_source_dic['file_type']
 
-        index_tag = self.index_tags[file_type]['dihed_restraint']
-        item_names = self.potential_items[file_type]['dihed_restraint']
+        content_subtype = 'dihed_restraint'
+
+        index_tag = self.index_tags[file_type][content_subtype]
+        item_names = self.potential_items[file_type][content_subtype]
         target_value_name = item_names['target_value']
         lower_limit_name = item_names['lower_limit']
         upper_limit_name = item_names['upper_limit']
@@ -39580,8 +39585,8 @@ def __calculateStatsOfDihedralRestraint(self, file_list_id, lp_data, conflict_id
         atom_id_3_name = dh_item_names['atom_id_3']
         atom_id_4_name = dh_item_names['atom_id_4']
         angle_type_name = dh_item_names['angle_type']
-        weight_name = self.weight_tags[file_type]['dihed_restraint']
-        id_tag = self.consist_id_tags[file_type]['dihed_restraint']
+        weight_name = self.weight_tags[file_type][content_subtype]
+        id_tag = self.consist_id_tags[file_type][content_subtype]
 
         try:
 
@@ -40300,6 +40305,162 @@ def __calculateStatsOfDihedralRestraint(self, file_list_id, lp_data, conflict_id
                     if len(range_of_vals) > 1:
                         ent['histogram_of_discrepancy'] = {'range_of_values': range_of_vals, 'number_of_values': transposed, 'annotations': dihed_ann}
 
+            if file_type == 'nmr-star' and self.__star_data_type[file_list_id] == 'Entry':
+                lp_category = self.lp_categories[file_type][content_subtype]
+                sf = self.__star_data[file_list_id].get_saveframe_by_name(sf_framecode)
+                lp = next(lp for lp in sf.loops if lp.category == lp_category)
+
+                mapping, identity_mapping = [], []
+                dat1 = dat2 = dat3 = dat4 = None
+
+                tags1 = ['Comp_ID_1', 'Atom_ID_1', 'Auth_atom_name_1']
+                if set(tags1) & set(lp.tags) == set(tags1):
+                    dat1 = get_lp_tag(lp, tags1)
+
+                tags2 = ['Comp_ID_2', 'Atom_ID_2', 'Auth_atom_name_2']
+                if set(tags2) & set(lp.tags) == set(tags2):
+                    dat2 = get_lp_tag(lp, tags2)
+
+                tags3 = ['Comp_ID_3', 'Atom_ID_3', 'Auth_atom_name_3']
+                if set(tags3) & set(lp.tags) == set(tags3):
+                    dat3 = get_lp_tag(lp, tags3)
+
+                tags4 = ['Comp_ID_4', 'Atom_ID_4', 'Auth_atom_name_4']
+                if set(tags4) & set(lp.tags) == set(tags4):
+                    dat4 = get_lp_tag(lp, tags4)
+
+                if dat1 is not None:
+
+                    for row in dat1:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] != row[2]:
+                            continue
+                        key = (row[0], row[2])
+                        if key not in identity_mapping:
+                            identity_mapping.append(key)
+
+                if dat2 is not None:
+
+                    for row in dat2:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] != row[2]:
+                            continue
+                        key = (row[0], row[2])
+                        if key not in identity_mapping:
+                            identity_mapping.append(key)
+
+                if dat3 is not None:
+
+                    for row in dat3:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] != row[2]:
+                            continue
+                        key = (row[0], row[2])
+                        if key not in identity_mapping:
+                            identity_mapping.append(key)
+
+                if dat4 is not None:
+
+                    for row in dat4:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] != row[2]:
+                            continue
+                        key = (row[0], row[2])
+                        if key not in identity_mapping:
+                            identity_mapping.append(key)
+
+                if dat1 is not None:
+
+                    for row in dat1:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] == row[2]:
+                            continue
+                        comp_id = row[0]
+                        atom_id = row[1]
+                        atom_name = row[2]
+
+                        if not any(m['comp_id'] == comp_id for m in mapping):
+                            mapping.append({'comp_id': comp_id, 'history': []})
+
+                        history = next(m['history'] for m in mapping if m['comp_id'] == comp_id)
+
+                        if not any(h for h in history if h['atom_name'] == atom_name):
+                            history.append({'atom_name': atom_name, 'atom_id': [atom_name] if (comp_id, atom_name) in identity_mapping else []})
+
+                        h = next(h for h in history if h['atom_name'] == atom_name)
+                        if atom_id not in h['atom_id']:
+                            h['atom_id'].append(atom_id)
+
+                if dat2 is not None:
+
+                    for row in dat2:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] == row[2]:
+                            continue
+                        comp_id = row[0]
+                        atom_id = row[1]
+                        atom_name = row[2]
+
+                        if not any(m['comp_id'] == comp_id for m in mapping):
+                            mapping.append({'comp_id': comp_id, 'history': []})
+
+                        history = next(m['history'] for m in mapping if m['comp_id'] == comp_id)
+
+                        if not any(h for h in history if h['atom_name'] == atom_name):
+                            history.append({'atom_name': atom_name, 'atom_id': [atom_name] if (comp_id, atom_name) in identity_mapping else []})
+
+                        h = next(h for h in history if h['atom_name'] == atom_name)
+                        if atom_id not in h['atom_id']:
+                            h['atom_id'].append(atom_id)
+
+                if dat3 is not None:
+
+                    for row in dat3:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] == row[2]:
+                            continue
+                        comp_id = row[0]
+                        atom_id = row[1]
+                        atom_name = row[2]
+
+                        if not any(m['comp_id'] == comp_id for m in mapping):
+                            mapping.append({'comp_id': comp_id, 'history': []})
+
+                        history = next(m['history'] for m in mapping if m['comp_id'] == comp_id)
+
+                        if not any(h for h in history if h['atom_name'] == atom_name):
+                            history.append({'atom_name': atom_name, 'atom_id': [atom_name] if (comp_id, atom_name) in identity_mapping else []})
+
+                        h = next(h for h in history if h['atom_name'] == atom_name)
+                        if atom_id not in h['atom_id']:
+                            h['atom_id'].append(atom_id)
+
+                if dat4 is not None:
+
+                    for row in dat4:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] == row[2]:
+                            continue
+                        comp_id = row[0]
+                        atom_id = row[1]
+                        atom_name = row[2]
+
+                        if not any(m['comp_id'] == comp_id for m in mapping):
+                            mapping.append({'comp_id': comp_id, 'history': []})
+
+                        history = next(m['history'] for m in mapping if m['comp_id'] == comp_id)
+
+                        if not any(h for h in history if h['atom_name'] == atom_name):
+                            history.append({'atom_name': atom_name, 'atom_id': [atom_name] if (comp_id, atom_name) in identity_mapping else []})
+
+                        h = next(h for h in history if h['atom_name'] == atom_name)
+                        if atom_id not in h['atom_id']:
+                            h['atom_id'].append(atom_id)
+
+                if len(mapping) == 0:
+                    mapping = None
+
+                else:
+                    for m in mapping:
+                        for h in m['history']:
+                            h['atom_id'] = sorted(h['atom_id'])
+                        m['history'] = sorted(m['history'], key=itemgetter('atom_name'))
+                    mapping = sorted(mapping, key=lambda x: (len(x['comp_id']), x['comp_id']))
+
+                ent['atom_name_mapping'] = mapping
+
         except Exception as e:
 
             self.report.error.appendDescription('internal_error', "+NmrDpUtility.__calculateStatsOfDihedralRestraint() ++ Error  - " + str(e))
@@ -40330,7 +40491,7 @@ def __getTypeOfDihedralRestraint(self, data_type, peptide, nucleotide, carbohydr
 
         return data_type
 
-    def __calculateStatsOfRdcRestraint(self, file_list_id, lp_data, conflict_id_set, inconsistent, redundant, ent):
+    def __calculateStatsOfRdcRestraint(self, file_list_id, sf_framecode, lp_data, conflict_id_set, inconsistent, redundant, ent):
         """ Calculate statistics of RDC restraints.
         """
 
@@ -40339,8 +40500,10 @@ def __calculateStatsOfRdcRestraint(self, file_list_id, lp_data, conflict_id_set,
 
         file_type = input_source_dic['file_type']
 
-        index_tag = self.index_tags[file_type]['rdc_restraint']
-        item_names = self.potential_items[file_type]['rdc_restraint']
+        content_subtype = 'rdc_restraint'
+
+        index_tag = self.index_tags[file_type][content_subtype]
+        item_names = self.potential_items[file_type][content_subtype]
         target_value_name = item_names['target_value']
         if 'target_value_alt' in item_names and target_value_name not in lp_data[0].keys():
             target_value_name = item_names['target_value_alt']
@@ -40401,8 +40564,8 @@ def __calculateStatsOfRdcRestraint(self, file_list_id, lp_data, conflict_id_set,
             # comp_id_2_name = item_names['comp_id_2']
             atom_id_1_name = item_names['atom_id_1']
             atom_id_2_name = item_names['atom_id_2']
-            weight_name = self.weight_tags[file_type]['rdc_restraint']
-            id_tag = self.consist_id_tags[file_type]['rdc_restraint']
+            weight_name = self.weight_tags[file_type][content_subtype]
+            id_tag = self.consist_id_tags[file_type][content_subtype]
 
             count, comb_count, inco_count, redu_count, weights, potential_types =\
                 {}, {}, {}, {}, {}, {}
@@ -40863,6 +41026,94 @@ def __calculateStatsOfRdcRestraint(self, file_list_id, lp_data, conflict_id_set,
                     if len(range_of_vals) > 1:
                         ent['histogram_of_discrepancy'] = {'range_of_values': range_of_vals, 'number_of_values': transposed, 'annotations': rdc_ann}
 
+            if file_type == 'nmr-star' and self.__star_data_type[file_list_id] == 'Entry':
+                lp_category = self.lp_categories[file_type][content_subtype]
+                sf = self.__star_data[file_list_id].get_saveframe_by_name(sf_framecode)
+                lp = next(lp for lp in sf.loops if lp.category == lp_category)
+
+                mapping, identity_mapping = [], []
+                dat1 = dat2 = None
+
+                tags1 = ['Comp_ID_1', 'Atom_ID_1', 'Auth_atom_name_1']
+                if set(tags1) & set(lp.tags) == set(tags1):
+                    dat1 = get_lp_tag(lp, tags1)
+
+                tags2 = ['Comp_ID_2', 'Atom_ID_2', 'Auth_atom_name_2']
+                if set(tags2) & set(lp.tags) == set(tags2):
+                    dat2 = get_lp_tag(lp, tags2)
+
+                if dat1 is not None:
+
+                    for row in dat1:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] != row[2]:
+                            continue
+                        key = (row[0], row[2])
+                        if key not in identity_mapping:
+                            identity_mapping.append(key)
+
+                if dat2 is not None:
+
+                    for row in dat2:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] != row[2]:
+                            continue
+                        key = (row[0], row[2])
+                        if key not in identity_mapping:
+                            identity_mapping.append(key)
+
+                if dat1 is not None:
+
+                    for row in dat1:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] == row[2]:
+                            continue
+                        comp_id = row[0]
+                        atom_id = row[1]
+                        atom_name = row[2]
+
+                        if not any(m['comp_id'] == comp_id for m in mapping):
+                            mapping.append({'comp_id': comp_id, 'history': []})
+
+                        history = next(m['history'] for m in mapping if m['comp_id'] == comp_id)
+
+                        if not any(h for h in history if h['atom_name'] == atom_name):
+                            history.append({'atom_name': atom_name, 'atom_id': [atom_name] if (comp_id, atom_name) in identity_mapping else []})
+
+                        h = next(h for h in history if h['atom_name'] == atom_name)
+                        if atom_id not in h['atom_id']:
+                            h['atom_id'].append(atom_id)
+
+                if dat2 is not None:
+
+                    for row in dat2:
+                        if row[0] in emptyValue or row[1] in emptyValue or row[2] in emptyValue or row[1] == row[2]:
+                            continue
+                        comp_id = row[0]
+                        atom_id = row[1]
+                        atom_name = row[2]
+
+                        if not any(m['comp_id'] == comp_id for m in mapping):
+                            mapping.append({'comp_id': comp_id, 'history': []})
+
+                        history = next(m['history'] for m in mapping if m['comp_id'] == comp_id)
+
+                        if not any(h for h in history if h['atom_name'] == atom_name):
+                            history.append({'atom_name': atom_name, 'atom_id': [atom_name] if (comp_id, atom_name) in identity_mapping else []})
+
+                        h = next(h for h in history if h['atom_name'] == atom_name)
+                        if atom_id not in h['atom_id']:
+                            h['atom_id'].append(atom_id)
+
+                if len(mapping) == 0:
+                    mapping = None
+
+                else:
+                    for m in mapping:
+                        for h in m['history']:
+                            h['atom_id'] = sorted(h['atom_id'])
+                        m['history'] = sorted(m['history'], key=itemgetter('atom_name'))
+                    mapping = sorted(mapping, key=lambda x: (len(x['comp_id']), x['comp_id']))
+
+                ent['atom_name_mapping'] = mapping
+
         except Exception as e:
 
             self.report.error.appendDescription('internal_error', "+NmrDpUtility.__calculateStatsOfRdcRestraint() ++ Error  - " + str(e))