RC3.16.3

CHANGELOG.md

@@ -1,10 +1,29 @@
-## v3.16.2 (2026.2)
+## v3.16.3 (2026.3)
+### Extended functions
+- altloc
+  - Added warning for possible microheterogeneity (from alternative residue names)
+- sequences
+  - Added analysis for possible sequence mismatches between canonincal and structure sequences.
+- output
+  - Added version tag to summary json output
+### Bug fixes
+- metals
+  - Fixed confusion from CX or PB atom names
+  - Detected metals as part of other residues  
+- Load
+  - Fixed errors when required fields where missing from cif files 
+  - Fixed use of cached copy when available when --no_network in use
+  - Fixed display of repeated ligand statistics from multiple models
+
+## v3.16.2 (2026.6)
 ### New functions
  - Added description of ligands/HETatms when available
  - Added --no_network to prevent network usage when not available
 ### Extended functions
 - water
   - Added support for selective removal of water molecules according to contacts
+- ligand, metals
+  - Added residue identification from PDB annotation (not available with --no_network)
 ### Bug fixes
 - sequences
   - Fixed missing initial fragment, structure sequence header

README.md

@@ -23,7 +23,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest package documentation](http://biobb-structure-checking.readthedocs.io/en/latest/).
 
 ### Version
-v3.16.2 June 2026
+v3.16.3 Aug 2026
 
 ### Requirements
 

TODO

@@ -10,10 +10,12 @@
         1.2.3 Select chains according to molecule type DONE
         1.2.4 Renumber chains & Residues DONE
     1.3. Detect/Select Alt Locations (altloc) DONE
+        1.3.1 Detect microheterogeity DONE (Added warning, should be fixed on Bio.PDB)
     1.4. Detect Heavy Metals /Remove (metals) DONE
+        1.4.1 Check for coordination sphere
     1.5. Detect Ligands /Remove (ligands) DONE
         1.5.1 Process All Hetatms in a integrated way
-        1.5.2 Detect modified amino acids (identidy and guess original residue)
+        1.5.2 Detect modified amino acids (identify and guess original residue)
     1.6. Detect DNA/RNA /Remove (na) DONE in chains
         1.6.1 Include NA Topology WITHDRAWN Too much adaptation needed, use BNSTopology instead
     1.7. Remove Water (remwat) DONE
@@ -22,6 +24,8 @@
     1.9. Get Sequences DONE
         1.9.1 Get sequence from PDB without canonical DONE
         1.9.2 Output FASTA file DONE
+        1.9.3 Detect sequences mismatches canonical/structure to detect microheterogeneity or alignment errors DONE
+        1.9.4 Check Internal alignment for some corner cases 1a7c 136d
 
 2. Fix Structure Errors/Modification
     2.1. Detect/Fix Amides Assignment (amide) DONE
@@ -31,7 +35,7 @@
     2.3. Detect insertion codes/Renum (inscode) DONE
         2.3.1 Rebuild chains with proper numbering DONE
     2.4. Complete side chains (fixside) DONE
-        2.4.1 Rebuild side chains (using modeller) DONE for protein
+        2.4.1 Rebuild side chains (using modeller) DONE for protein. 
     2.5. Mutate residues (mutate) DONE
         2.5.1 Add/remove/revert modified residues
         2.5.2 Mutate DNA residues DONE
@@ -45,6 +49,7 @@
         2.6.4 Add hydrogens for NA chains DONE
         2.6.5 Prepare input for AutoDock with flexible residues
         2.6.6 Add Metals to residue library
+        2.6.7 Ligand protonation/tautomery
     2.7. Complete backbone (backbone) DONE
         2.7.1 Complete main chains DONE
         2.7.2 Add ACE, NME caps DONE
@@ -53,6 +58,7 @@
         2.7.5 Accept multiple templates
         2.7.6 Fix modelled junctions
         2.7.8 Rebuild backbone in the context of the complete molecule (also for --rebuild options)
+        2.7.9 Detect cyclic peptides (report and consider no OXT needed)
 	2.7.9 Detect and fix extra backbone atoms (like extra OXT)
     2.8 FixALL module
         - Model and Chain selected on demand
@@ -75,7 +81,9 @@
     3.4. Possible Sequence Gaps (bckbone) DONE
         3.4.1 Fix only-CA structures (Modeller)
     3.5. Steric clashes (clashes) DONE
-        3.5.1. Severe Steric clashes DONE Revise new severe clashes
+        3.5.1. Severe Steric clashes. 
+            3.5.1.2 Revise covalent bonds, possible cyclic backbones
+            3.5.1.3 Remove clashes from backbone with insertion codes DONE
         3.5.2. CA Steric Clashes NO
         3.5.3. Polar Donor Clashes DONE
         3.5.4. Polar Acceptor Clashes DONE

biobb_structure_checking/check_structure.py

@@ -37,7 +37,7 @@ def main():
 
     if args.command == 'commands':
         help_str = header()
-        with open(opj(data_dir_path, cts.COMMANDS_HELP_PATH)) as help_file:
+        with open(opj(data_dir_path, cts.COMMANDS_HELP_PATH), 'r', encoding='utf-8') as help_file:
             help_str += help_file.read()
         pydoc.pager(help_str)
         sys.exit(0)

biobb_structure_checking/commands/add_hydrogen.py

@@ -109,7 +109,8 @@ def fix(strcheck, opts, fix_data=None):
             for r_at in fix_data['ion_res_list']:
                 res = r_at[0]
                 rcode = res.get_resname()
-                if ph_value <= std_ion[rcode]['pK']:
+
+                if float(ph_value) <= std_ion[rcode]['pK']:
                     ion_to_fix[res] = std_ion[rcode]['lowpH']
                 else:
                     ion_to_fix[res] = std_ion[rcode]['highpH']
@@ -132,6 +133,7 @@ def fix(strcheck, opts, fix_data=None):
                     for mut_res in mut.mutations:
                         ion_to_fix[mut_res['resobj']] = mut_res['new_id']
             else:
+                strcheck.summary['add_hydrogen']['selection'] = []
                 if add_h_mode == 'int':
                     if not strcheck.args['quiet']:
                         print('Selection: interactive')
@@ -143,13 +145,15 @@ def fix(strcheck, opts, fix_data=None):
                         r_at for r_at in fix_data['ion_res_list']
                         if r_at[0].get_resname() == 'HIS'
                     ]
-                    strcheck.summary['add_hydrogen']['selection'] = []
+                else:
+                    res_list = []
+
                 for r_at in res_list:
                     rcode = r_at[0].get_resname()
                     input_line = ParamInput(
                         "Select residue form for " + mu.residue_id(r_at[0]),
-                        strcheck.args['non_interactive']
-                    )
+                            strcheck.args['non_interactive']
+                        )
                     input_line.add_option_list('list', r_at[1].keys())
                     input_line.default = std_ion[rcode]['std']
 

biobb_structure_checking/commands/altloc.py

@@ -26,17 +26,21 @@ def check(strcheck):
         print(rid)
         strcheck.summary['altloc'][rid] = {}
         fix_data['altlocs'][res] = sorted(alt_loc_res[res][0].child_dict)
+        alts = set()
         for atm in alt_loc_res[res]:
             strcheck.summary['altloc'][rid][atm.id] = []
             alt_str = f"  {atm.id:4}"
             for alt in sorted(atm.child_dict):
+                alts.add(alt)
                 alt_str += f" {alt} ({atm.child_dict[alt].occupancy:4.2f})"
                 strcheck.summary['altloc'][rid][atm.id].append({
                     'loc_label': alt,
                     'occupancy': atm.child_dict[alt].occupancy
                 })
             print(alt_str)
-
+        if 'A' not in alts:
+            print(cts.MSGS['ALTLOC_NO_A'])
+            strcheck.summary['altloc'][rid]['no_altA'] = True
     return fix_data
 
 
@@ -60,7 +64,7 @@ def fix(strcheck, opts, fix_data=None):
         strcheck.args['non_interactive'],
         set_none='All'
     )
-    input_line.add_option_all()
+    input_line.add_option_none()
     input_line.add_option_list('occup', ['occupancy'])
     input_line.add_option_list('altids', altlocs, case='upper')
     input_line.add_option_list(
@@ -78,34 +82,35 @@ def fix(strcheck, opts, fix_data=None):
     if input_option == 'error':
         return cts.MSGS['UNKNOWN_SELECTION'], select_altloc
 
-    if input_option != 'all':
-        print(f"Selecting location {select_altloc}")
-        if input_option in ('occup', 'altids'):
-            select_altloc = select_altloc.upper()
-            to_fix = {
-                res: {
-                    'ats': value,
-                    'select' : select_altloc
-                } for res, value in fix_data['alt_loc_res'].items()
-            }
-
-        elif input_option == 'resnum':
-            to_fix = {}
-            selected_rnums = {}
-            for rsel in select_altloc.split(','):
-                rnum, alt = rsel.split(':')
-                selected_rnums[rnum] = alt
-            to_fix = {
-                res: {
-                    'ats': value,
-                    'select': selected_rnums[mu.residue_num(res)]
-                }
-                for res, value in fix_data['alt_loc_res'].items()
-                if mu.residue_num(res) in selected_rnums
-            }
-        for res in to_fix:
-            strcheck.strucm.select_altloc_residue(res, to_fix[res])
-
     strcheck.summary['altloc']['selected'] = select_altloc
-
+    if input_option == 'none':
+        print(cts.MSGS['ALTLOC_NO_SELECTION'])
+        return False
+
+    print(f"Selecting location {select_altloc}")
+    to_fix = {}
+    if input_option in ('occup', 'altids'):
+        select_altloc = select_altloc.upper()
+        to_fix = {
+            res: {
+                'ats': value,
+                'select' : select_altloc
+            } for res, value in fix_data['alt_loc_res'].items()
+        }
+    elif input_option == 'resnum':
+        to_fix = {}
+        selected_rnums = {}
+        for rsel in select_altloc.split(','):
+            rnum, alt = rsel.split(':')
+            selected_rnums[rnum] = alt
+        to_fix = {
+            res: {
+                'ats': value,
+                'select': selected_rnums[mu.residue_num(res)]
+            }
+            for res, value in fix_data['alt_loc_res'].items()
+            if mu.residue_num(res) in selected_rnums
+        }
+    for res in to_fix:
+        strcheck.strucm.select_altloc_residue(res, to_fix[res])
     return False

biobb_structure_checking/commands/backbone.py

@@ -86,7 +86,12 @@ def check(strcheck):
         print(cts.MSGS['MODIF_RESIDUES'])
         strcheck.summary['backbone']['mod_residues'] = []
         for brk in strcheck.strucm.st_data.modified_residue_list:
-            print(f" {mu.residue_id(brk):10}")
+            if strcheck.strucm.st_data.no_network:
+                print(f" {mu.residue_id(brk):10}")
+            else:
+                print(
+                    f" {mu.residue_id(brk):10} ({mu.fetch_residue_name_by_id(brk.get_resname())})"
+                )
             strcheck.summary['backbone']['mod_residues'].append(mu.residue_id(brk))
     # Provisional only missing atoms can be fixed
         fix_data['modified_residue_list'] = True

biobb_structure_checking/commands/chains.py

@@ -49,21 +49,19 @@ def check(strcheck):
 
 
 def fix(strcheck, opts, fix_data=None):
+    rename_chains = ''
+    rebuild_chains = False
+    renumber_chains = False
     if isinstance(opts, str):
         select_chains = opts
-        rename_chains = ''
     else:
         select_chains = opts['select']
         if 'rename' in opts:
             rename_chains = opts['rename']
-        else:
-            rename_chains = ''
         if 'renumber' in opts:
             renumber_chains = opts['renumber']
         if 'rebuild' in opts:
             rebuild_chains = opts['rebuild']
-        else:
-            rebuild_chains = False
 
     if strcheck.strucm.chains_data.has_chains_to_rename:
         input_line = ParamInput(

biobb_structure_checking/commands/sequences.py

@@ -21,6 +21,16 @@ def check(strcheck):
         'canonical': can_seq,
         'structure': pdb_seq
     }
+    mismatches = strcheck.strucm.sequence_data.compare_sequences(strcheck.strucm)
+    if mismatches:
+        print(f"Found {len(mismatches)} mismatch(es)")
+        for chain_id, mismatch in mismatches.items():
+            print(
+                f"Chain {chain_id}\n"
+                f"{mismatch['canonical']}\n"
+                f"{mismatch['structure']}"
+            )
+    strcheck.summary['sequence_mismatches'] = mismatches
     return fasta
 
 

biobb_structure_checking/constants.py

@@ -2,14 +2,13 @@
     Global constants for structure_checking module
 """
 import argparse
-import os
 from os.path import dirname
 from os.path import join as opj
 
 
 from biobb_structure_checking.pdbio.param_input import Dialog
 
-VERSION = '3.16.2'
+VERSION = '3.16.3'
 
 # Default locations and settings
 DATA_DIR_DEFAULT_PATH = 'dat'
@@ -23,7 +22,6 @@
 TIME_LIMIT = 3600
 
 ALT_SERVERS = {
-    'mmb': 'https://mmb.irbbarcelona.org/api/pdb',
     'bsc': 'http://mdb-login.bsc.es/api/pdb'
 }
 
@@ -412,7 +410,8 @@ def set_defaults(base_dir_path, args=None):
 
 DIALOGS.add_entry('water', 'Checks and optionally removes water molecules')
 DIALOGS.add_option('water', '--remove', 'remove', 'Remove All Water molecules')
-DIALOGS.add_option('water', '--keep_min_contacts', 'keep', 'Remove All Water molecules with less contacts')
+DIALOGS.add_option('water', '--keep_min_contacts', 'keep',
+                   'Remove All Water molecules with less contacts')
 
 DIALOGS.add_entry(
     'ligands',
@@ -652,7 +651,7 @@ def set_defaults(base_dir_path, args=None):
                   'use --limit to adjust',
     'TIME_LIMIT': 'Execution time limit ({}s) exceeded, aborting, use --time_limit to adjust',
     'CA_ONLY_STRUCTURE': 'CA-Only structure, skipping',
-    'NO_NETWORK': 'Network disabled, unable to download {}',
+    'NO_NETWORK': 'Network disabled, unable to download {}, and no cached file available',
     # command line
     'ERROR_OPEN_FILE': 'Error when opening file',
     'COMMAND_LIST_COMPLETED': 'Command list completed',
@@ -684,6 +683,8 @@ def set_defaults(base_dir_path, args=None):
     # altloc
     'ALTLOC_FOUND': 'Detected {} residues with alternative location labels',
     'NO_ALTLOC_FOUND': 'Detected no residues with alternative location labels',
+    'ALTLOC_NO_A': 'Possible microheterogeneity: No A altloc found',
+    'ALTLOC_NO_SELECTION': 'No selection made, keeping all alternative locations',
     # metals
     'METALS_FOUND': 'Found {} Metal ions',
     'NO_METALS_FOUND': 'No metal ions found',
@@ -784,7 +785,7 @@ def help(command=None):
             DATA_DIR_DEFAULT_PATH,
             COMMANDS_HELP_PATH
         )
-        with open(help_path) as help_file:
+        with open(help_path, 'r', encoding='utf-8') as help_file:
             print(help_file.read())
     else:
         DIALOGS.get_parameter(command, '', print_help=True)

biobb_structure_checking/docs/source/changelog.md

@@ -1,3 +1,20 @@
+## v3.16.3 (2026.3)
+### Extended functions
+- altloc
+  - Added warning for possible microheterogeneity (from alternative residue names)
+- sequences
+  - Added analysis for possible sequence mismatches between canonincal and structure sequences.
+- output
+  - Added version tag to summary json output
+### Bug fixes
+- metals
+  - Fixed confusion from CX or PB atom names
+  - Detected metals as part of other residues  
+- Load
+  - Fixed errors when required fields where missing from cif files 
+  - Fixed use of cached copy when available when --no_network in use
+  - Fixed display of repeated ligand statistics from multiple models
+
 ## v3.16.2 (2026.2)
 ### New functions
  - Added description of ligands/HETatms when available

biobb_structure_checking/docs/source/conf.py

@@ -79,9 +79,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "3.16.2"
+version = "3.16.3"
 # The full version, including alpha/beta/rc tags.
-release = "3.16.2"
+release = "3.16.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.