reduce parseCIF warnings

jamesmkrieger · Nov 8, 2023 · bb13bec · bb13bec
1 parent f6baf7c
commit bb13bec
Show file tree

Hide file tree

Showing 3 changed files with 25 additions and 28 deletions.
diff --git a/prody/proteins/ciffile.py b/prody/proteins/ciffile.py
@@ -508,12 +508,8 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
 
     anisou = None
     siguij = None
-    try:
-        data = parseSTARSection(lines, "_atom_site_anisotrop")
-        x = data[0] # check if data has anything in it
-    except IndexError:
-        LOGGER.warn("No anisotropic B factors found")
-    else:
+    data = parseSTARSection(lines, "_atom_site_anisotrop", report=False)
+    if len(data) > 0:
         anisou = np.zeros((acount, 6),
                           dtype=float)
 

diff --git a/prody/proteins/cifheader.py b/prody/proteins/cifheader.py
@@ -178,8 +178,8 @@ def _getBiomoltrans(lines):
     # 2 blocks are needed for this:
     # _pdbx_struct_assembly_gen: what to apply to which chains
     # _pdbx_struct_oper_list: everything else
-    data1 = parseSTARSection(lines, '_pdbx_struct_assembly_gen')
-    data2 = parseSTARSection(lines, '_pdbx_struct_oper_list')
+    data1 = parseSTARSection(lines, '_pdbx_struct_assembly_gen', report=False)
+    data2 = parseSTARSection(lines, '_pdbx_struct_oper_list', report=False)
 
     # extracting the data
     for n, item1 in enumerate(data1):
@@ -225,7 +225,7 @@ def _getRelatedEntries(lines):
 
     try:
         key = "_pdbx_database_related"
-        data = parseSTARSection(lines, key)
+        data = parseSTARSection(lines, key, report=False)
         for item in data:
             dbref = DBRef()
             dbref.accession = item[key + ".db_id"]
@@ -715,8 +715,8 @@ def _getReference(lines):
 
     # JRNL double block. Blocks 6 and 7 as copied from COMPND
     # Block 1 has most info. Block 2 has author info
-    items1 = parseSTARSection(lines, "_citation")
-    items2 = parseSTARSection(lines, "_citation_author")
+    items1 = parseSTARSection(lines, "_citation", report=False)
+    items2 = parseSTARSection(lines, "_citation_author", report=False)
 
     for row in items1:
         for k, value in row.items():
@@ -767,7 +767,7 @@ def _getPolymers(lines):
     entities = defaultdict(list)
 
     # SEQRES block
-    items1 = parseSTARSection(lines, '_entity_poly')
+    items1 = parseSTARSection(lines, '_entity_poly', report=False)
 
     for item in items1:
         chains = item['_entity_poly.pdbx_strand_id']
@@ -781,7 +781,7 @@ def _getPolymers(lines):
                 '_entity_poly.pdbx_seq_one_letter_code_can'].replace(';', '').split())
 
     # DBREF block 1
-    items2 = parseSTARSection(lines, '_struct_ref')
+    items2 = parseSTARSection(lines, '_struct_ref', report=False)
 
     for item in items2:
         entity = item["_struct_ref.id"]
@@ -798,7 +798,7 @@ def _getPolymers(lines):
             poly.dbrefs.append(dbref)
 
     # DBREF block 2
-    items3 = parseSTARSection(lines, "_struct_ref_seq")
+    items3 = parseSTARSection(lines, "_struct_ref_seq", report=False)
 
     for i, item in enumerate(items3):
         i += 1
@@ -884,7 +884,7 @@ def _getPolymers(lines):
             last = temp
 
     # MODRES block
-    data4 = parseSTARSection(lines, "_pdbx_struct_mod_residue")
+    data4 = parseSTARSection(lines, "_pdbx_struct_mod_residue", report=False)
 
     for data in data4:
         ch = data["_pdbx_struct_mod_residue.label_asym_id"]
@@ -904,7 +904,7 @@ def _getPolymers(lines):
                                 data["_pdbx_struct_mod_residue.details"]))
 
     # SEQADV block
-    data5 = parseSTARSection(lines, "_struct_ref_seq_dif")
+    data5 = parseSTARSection(lines, "_struct_ref_seq_dif", report=False)
 
     for i, data in enumerate(data5):
         ch = data["_struct_ref_seq_dif.pdbx_pdb_strand_id"]
@@ -964,8 +964,8 @@ def _getPolymers(lines):
 
     # COMPND double block. 
     # Block 6 has most info. Block 7 has synonyms
-    data6 = parseSTARSection(lines, "_entity")
-    data7 = parseSTARSection(lines, "_entity_name_com")
+    data6 = parseSTARSection(lines, "_entity", report=False)
+    data7 = parseSTARSection(lines, "_entity_name_com", report=False)
 
     dict_ = {}
     for molecule in data6:
@@ -1045,7 +1045,7 @@ def _getChemicals(lines):
     # 1st block we need is has info about location in structure
 
     # this instance only includes single sugars not branched structures
-    items = parseSTARSection(lines, "_pdbx_nonpoly_scheme")
+    items = parseSTARSection(lines, "_pdbx_nonpoly_scheme", report=False)
 
     for data in items:
         resname = data["_pdbx_nonpoly_scheme.mon_id"]
@@ -1064,7 +1064,7 @@ def _getChemicals(lines):
         chemicals[chem.resname].append(chem)
 
     # next we get the equivalent one for branched sugars part
-    items = parseSTARSection(lines, "_pdbx_branch_scheme")
+    items = parseSTARSection(lines, "_pdbx_branch_scheme", report=False)
 
     for data in items:
         resname = data["_pdbx_branch_scheme.mon_id"]
@@ -1080,7 +1080,7 @@ def _getChemicals(lines):
         chemicals[chem.resname].append(chem)
 
     # 2nd block to get has general info e.g. name and formula
-    items = parseSTARSection(lines, "_chem_comp")
+    items = parseSTARSection(lines, "_chem_comp", report=False)
 
     for data in items:
         resname = data["_chem_comp.id"]
@@ -1155,7 +1155,7 @@ def _getTitle(lines):
     title = ''
 
     try:
-        data = parseSTARSection(lines, "_struct")
+        data = parseSTARSection(lines, "_struct", report=False)
         for item in data:
             title += item['_struct.title'].upper()
     except:
@@ -1172,7 +1172,7 @@ def _getAuthors(lines):
     authors = []
 
     try:
-        data = parseSTARSection(lines, "_audit_author")
+        data = parseSTARSection(lines, "_audit_author", report=False)
         for item in data:
             author = ''.join(item['_audit_author.name'].split(', ')[::-1])
             authors.append(author.upper())
@@ -1192,7 +1192,7 @@ def _getSplit(lines):
     key = "_pdbx_database_related"
 
     try:
-        data, _ = parseSTARSection(lines, key)
+        data, _ = parseSTARSection(lines, key, report=False)
         for item in data:
             if item[key + '.content_type'] == 'split':
                 split.append(item[key + '.db_id'])
@@ -1227,7 +1227,7 @@ def _getOther(lines, key=None):
     data = []
 
     try:
-        data = parseSTARSection(lines, key)
+        data = parseSTARSection(lines, key, report=False)
     except:
         pass
 
@@ -1242,7 +1242,7 @@ def _getUnobservedSeq(lines):
     key_unobs = '_pdbx_unobs_or_zero_occ_residues'
 
     try:
-        unobs = parseSTARSection(lines, key_unobs)
+        unobs = parseSTARSection(lines, key_unobs, report=False)
         polymers = _getPolymers(lines)
     except:
         pass

diff --git a/prody/proteins/starfile.py b/prody/proteins/starfile.py
@@ -1026,7 +1026,7 @@ def parseImagesFromSTAR(particlesSTAR, **kwargs):
     return np.array(images), parsed_images_data
 
 
-def parseSTARSection(lines, key):
+def parseSTARSection(lines, key, report=True):
     """Parse a section of data from *lines* from a STAR file 
     corresponding to a *key* (part before the dot). 
     This can be a loop or data block.
@@ -1077,7 +1077,8 @@ def parseSTARSection(lines, key):
         else:
             data = [loop_dict["data"]]
     else:
-        LOGGER.warn("Could not find {0} in lines.".format(key))
+        if report:
+            LOGGER.warn("Could not find {0} in lines.".format(key))
         return []
 
     return data