diff --git a/CHANGELOG.md b/CHANGELOG.md index 9e912515..ccfcc657 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/README.md b/README.md index 3cb11b03..b8d77cbb 100644 --- a/README.md +++ b/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 diff --git a/TODO b/TODO index bc42553a..279aed82 100644 --- a/TODO +++ b/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 Detect DNA/RNA /Remove (na) DONE in chains 1.6.1 Include NA Topology WITHDRAWN Too much adaptation needed, use BNSTopology instead 1.7.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 diff --git a/biobb_structure_checking/check_structure.py b/biobb_structure_checking/check_structure.py index 06cd0a03..004f6c45 100755 --- a/biobb_structure_checking/check_structure.py +++ b/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) diff --git a/biobb_structure_checking/commands/add_hydrogen.py b/biobb_structure_checking/commands/add_hydrogen.py index 49601de0..a41cc386 100644 --- a/biobb_structure_checking/commands/add_hydrogen.py +++ b/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'] diff --git a/biobb_structure_checking/commands/altloc.py b/biobb_structure_checking/commands/altloc.py index 996a15d0..30545325 100644 --- a/biobb_structure_checking/commands/altloc.py +++ b/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 diff --git a/biobb_structure_checking/commands/backbone.py b/biobb_structure_checking/commands/backbone.py index 61c76add..21342f3e 100644 --- a/biobb_structure_checking/commands/backbone.py +++ b/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 diff --git a/biobb_structure_checking/commands/chains.py b/biobb_structure_checking/commands/chains.py index 5bff886c..7c4ca64c 100644 --- a/biobb_structure_checking/commands/chains.py +++ b/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( diff --git a/biobb_structure_checking/commands/sequences.py b/biobb_structure_checking/commands/sequences.py index eb7ad132..c06f6d07 100644 --- a/biobb_structure_checking/commands/sequences.py +++ b/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 diff --git a/biobb_structure_checking/constants.py b/biobb_structure_checking/constants.py index ab6497cb..3eb735ff 100644 --- a/biobb_structure_checking/constants.py +++ b/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) diff --git a/biobb_structure_checking/docs/source/changelog.md b/biobb_structure_checking/docs/source/changelog.md index 075de168..88132866 100644 --- a/biobb_structure_checking/docs/source/changelog.md +++ b/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 diff --git a/biobb_structure_checking/docs/source/conf.py b/biobb_structure_checking/docs/source/conf.py index e46ad5ab..3cdc5bad 100755 --- a/biobb_structure_checking/docs/source/conf.py +++ b/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. diff --git a/biobb_structure_checking/docs/source/readme.md b/biobb_structure_checking/docs/source/readme.md index e9daffbf..6da3242a 100644 --- a/biobb_structure_checking/docs/source/readme.md +++ b/biobb_structure_checking/docs/source/readme.md @@ -10,7 +10,7 @@ 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 diff --git a/biobb_structure_checking/modelling/modelsdata.py b/biobb_structure_checking/modelling/modelsdata.py index a21dec4e..6b830473 100644 --- a/biobb_structure_checking/modelling/modelsdata.py +++ b/biobb_structure_checking/modelling/modelsdata.py @@ -14,7 +14,10 @@ def __init__(self, st): def stats(self, prefix='') -> None: """ Print stats """ if self.nmodels > 1: - return f"{prefix} Num. models: {self.nmodels} (type: {mu.MODEL_TYPE_LABELS[self.models_type['type']]}, {self.models_type['rmsd']:8.3f} A)" + return \ + f"{prefix} Num. models: {self.nmodels} " \ + f"(type: {mu.MODEL_TYPE_LABELS[self.models_type['type']]}, " \ + f"{self.models_type['rmsd']:8.3f} A)" return f"{prefix} Num. models: {self.nmodels}" def select(self, keep_model: str) -> None: @@ -54,10 +57,10 @@ def superimpose_models(self): fix_atoms = [ at for at in self.st[0].get_atoms() - if at.id == 'CA' or at.id == 'P' + if at.id in ('CA', 'P') ] if not fix_atoms: - print("No CA atoms found, skipping superimposition") + print("No CA or P atoms found, skipping superimposition") return False for mod in self.st.get_models(): if mod.id == 0: @@ -65,7 +68,7 @@ def superimpose_models(self): mov_atoms = [ at for at in self.st[mod.id].get_atoms() - if at.id == 'CA' or at.id == 'P' + if at.id in ('CA', 'P') ] spimp.set_atoms(fix_atoms, mov_atoms) spimp.apply(self.st[mod.id].get_atoms()) diff --git a/biobb_structure_checking/modelling/residue_set.py b/biobb_structure_checking/modelling/residue_set.py index 0d7d3304..c2cb2bb3 100644 --- a/biobb_structure_checking/modelling/residue_set.py +++ b/biobb_structure_checking/modelling/residue_set.py @@ -1,6 +1,4 @@ ''' Class to manage Residue Sets to chain building''' -import re -import sys import biobb_structure_checking.modelling.utils as mu @@ -48,8 +46,7 @@ def _find(self, item): i += 1 if i == self.n: return -1 - else: - return i + return i def _append_rset(self, item): self.sets.append(item) @@ -73,14 +70,15 @@ def __init__(self): self.items = set() self.type = '' self.id = '' + self.name = '' - def set_meta(self, id): + def set_meta(self, mol_id): """ Add molecule type to residue set""" if self._is_protein(): self.type = 'prot' else: self.type = 'na' - self.id = id + self.id = mol_id def _is_protein(self): chain_type = mu.guess_chain_type_list(self._get_residues())['type'] @@ -134,4 +132,4 @@ def get_sequence(self): def __str__(self): # residue_list = self._get_residues() return f"{self.id} ({mu.residue_id(self.inir)}-{mu.residue_id(self.finr)}) ({self.type}): {self.get_sequence()}" - + \ No newline at end of file diff --git a/biobb_structure_checking/modelling/sequencedata.py b/biobb_structure_checking/modelling/sequencedata.py index ab2bc098..3b222fa6 100644 --- a/biobb_structure_checking/modelling/sequencedata.py +++ b/biobb_structure_checking/modelling/sequencedata.py @@ -1,5 +1,10 @@ """ Module to manage sequence information for structures """ +import sys +import os +import gzip +# from typing import List, Dict +from urllib.request import urlretrieve, urlcleanup from biobb_structure_checking.constants import FASTA_DOWNLOAD_PREFIX import biobb_structure_checking.modelling.utils as mu from Bio.SeqFeature import SeqFeature, FeatureLocation @@ -8,11 +13,6 @@ from Bio.Seq import Seq, MutableSeq from Bio.PDB.Polypeptide import PPBuilder from Bio import SeqIO -import sys -import os -import gzip -# from typing import List, Dict -from urllib.request import urlretrieve, urlcleanup # pairwise2 to be deprecated, replaced by PairwiseAligner # But Alignment structure has changed from v1.79 @@ -341,7 +341,8 @@ def match_sequence_numbering(self, strucm): for ch_id, ch_data in self.data[mod.id].items(): # print(f"{ch_id=} {ch_data=}") # print(f"{self.has_canonical=} {mod.id=}") - if ch_id not in self.has_canonical.get(mod.id, []) or not self.has_canonical.get(mod.id, dict()).get(ch_id, []): + if ch_id not in self.has_canonical[mod.id] or\ + not self.has_canonical[mod.id].get(ch_id, []): continue frgs = ch_data['pdb']['frgs'] ch_data['pdb']['match_numbering'] = True @@ -573,7 +574,43 @@ def _assign_seq(self, rec): matches.append((mod_id, ch_id, score)) return matches + def compare_sequences(self, strucm): + """ SequenceData.compare_sequences + Compares canonical and structure sequences + + Args: + strucm (StructureManager) : Object containing the loaded structure + """ + summary = {} + for mod in strucm.st: + for ch_id in self.data[mod.id]: + mismatches = [] + can_seq_mis = '' + pdb_seq_mis = '' + if not self.has_canonical[mod.id][ch_id]: + continue + + can_seq = self.get_canonical().split("\n")[1] + pdb_seq = self.get_pdbseq().split("\n")[1] + + for i in range(len(can_seq)): + if can_seq[i] != pdb_seq[i] and pdb_seq[i] != '-': + mismatches.append(i) + can_seq_mis += can_seq[i] + pdb_seq_mis += pdb_seq[i] + continue + can_seq_mis += '-' + pdb_seq_mis += '-' + + if mismatches: + summary[f"{ch_id}/{mod.id}"] = { + 'mismatches': mismatches, + 'canonical': can_seq_mis, + 'structure': pdb_seq_mis + } + return summary + def _get_pack_str_seqs(strucm): strucm.revert_can_resnames(canonical=True) seqs = {} @@ -589,3 +626,4 @@ def _get_pack_str_seqs(strucm): ) strucm.revert_can_resnames(canonical=False) return seqs + diff --git a/biobb_structure_checking/modelling/structuredata.py b/biobb_structure_checking/modelling/structuredata.py index bc170097..ca780d44 100644 --- a/biobb_structure_checking/modelling/structuredata.py +++ b/biobb_structure_checking/modelling/structuredata.py @@ -1,4 +1,5 @@ ''' Class to manage internal Structure data''' +import sys import biobb_structure_checking.modelling.utils as mu @@ -148,8 +149,6 @@ def get_headers(self) -> None: for org, fin in map_fields.items(): if org in self.headers: self.meta[fin] = ', '.join(self.headers[org]) - else: - self.meta[fin] = 'N.A.' else: map_fields = { @@ -161,17 +160,17 @@ def get_headers(self) -> None: for org, fin in map_fields.items(): if org in self.headers: self.meta[fin] = self.headers[org] - else: - self.meta[fin] = 'N.A.' - if 'resolution' not in self.headers or\ - not self.headers['resolution']: - self.meta['resolution'] = 'N.A.' - else: - self.meta['resolution'] = self.headers['resolution'] if self.biounit: self.meta['biounit'] = self.biounit - if self.meta['entry_id'] == 'XXXX': # Recovering PDB id for Assemblies + if self.meta['entry_id'] == 'XXXX' or self.meta['entry_id'] == 'User': # Recovering PDB id for Assemblies self.meta['entry_id'] = self.st.id + # Missing fields from AF entries + if 'title' not in self.meta: + self.meta['title'] = 'N.A.' + if 'method' not in self.meta: + self.meta['method'] = 'N.A.' + + def print_headers(self) -> None: """ @@ -184,7 +183,7 @@ def print_headers(self) -> None: else: asstxt = "" print( - f" PDB id: {self.meta['entry_id']} {asstxt}\n" + f" Entry id: {self.meta['entry_id']} {asstxt}\n" f" Title: {self.meta['title']}\n" f" Experimental method: {self.meta['method']}" ) @@ -216,26 +215,31 @@ def guess_hetatm(self): else: self.hetatm[mu.ORGANIC].append(res) + def _print_het_group_stats(self, res_list): + for res in res_list: + if res.get_parent().get_parent().id > 0: + continue + res_label = '' + if not self.no_network: + res_label = mu.fetch_residue_name_by_id(res.get_resname()) + if len(self.st) > 1: + res_id = f"{mu.residue_id(res, False)}/*" + else: + res_id = mu.residue_id(res) + print(f"{res_id} ({res_label})") + def print_hetatm_stats(self): '''Print statistics on HETATM''' + if self.hetatm[mu.MODRES]: print('Modified residues found') - for res in self.hetatm[mu.MODRES]: - print(mu.residue_id(res)) + self._print_het_group_stats(self.hetatm[mu.MODRES]) if self.hetatm[mu.METAL]: print('Metal/Ion residues found') - for res in self.hetatm[mu.METAL]: - if self.no_network: - print(mu.residue_id(res)) - else: - print(f"{mu.residue_id(res)} ({mu.fetch_residue_name_by_id(res.get_resname())})") + self._print_het_group_stats(self.hetatm[mu.METAL]) if self.hetatm[mu.ORGANIC]: print('Small mol ligands found') - for res in self.hetatm[mu.ORGANIC]: - if self.no_network: - print(mu.residue_id(res)) - else: - print(f"{mu.residue_id(res)} ({mu.fetch_residue_name_by_id(res.get_resname())})") + self._print_het_group_stats(self.hetatm[mu.ORGANIC]) def _check_ca_only(self): ca_only = True diff --git a/biobb_structure_checking/modelling/utils.py b/biobb_structure_checking/modelling/utils.py index ef889c5c..9793e94d 100644 --- a/biobb_structure_checking/modelling/utils.py +++ b/biobb_structure_checking/modelling/utils.py @@ -53,7 +53,7 @@ MODELS_MAXRMS = 15.0 # Threshold value to detect NMR models (angs) MODEL_TYPE_LABELS = { ENSM: 'Ensembl/NMR', - BUNIT: 'BioUnit', + BUNIT: 'Assembly/Biological unit', UNKNOWN: 'Unknown' } @@ -294,11 +294,13 @@ def same_chain(res1, res2): return (res1.get_parent() == res2.get_parent()) and same_model(res1, res2) -def seq_consecutive(res1, res2): +def seq_consecutive(res1, res2, next_res_list): """ Checks whether residues belong to the same chain and - are consecutive in sequences, taken from residue number + are consecutive in sequences, taken from residue number or next_res_list if provided """ + if res1 in next_res_list: + return next_res_list[res1] == res2 rnum1 = res1.id[1] rnum2 = res2.id[1] return same_chain(res1, res2) and abs(rnum1 - rnum2) == 1 @@ -664,6 +666,7 @@ def check_r_list_clashes( rr_list, clash_dist, atom_lists, + next_res_list, join_models=True, severe=True, get_all_contacts=False, @@ -686,6 +689,7 @@ def check_r_list_clashes( res2, clash_dist, atom_lists, + next_res_list, join_models, severe, get_all_contacts=get_all_contacts @@ -702,9 +706,10 @@ def check_rr_clashes( res2, clash_dist, atom_lists, + next_res_list, join_models=True, severe=True, - get_all_contacts=False + get_all_contacts=False, ): """ Check all clashes between two residues """ clash_list = {} @@ -733,7 +738,7 @@ def check_rr_clashes( for cls in atom_lists: if is_at_in_list(atm, atom_lists[cls], res2.get_resname()): ats_list2[cls].add(atm.id) - if res1 != res2 and not seq_consecutive(res1, res2)\ + if res1 != res2 and not seq_consecutive(res1, res2, next_res_list)\ and (join_models or same_model(res1, res2)): for at_pair in get_all_rr_distances(res1, res2): at1, at2, dist2 = at_pair @@ -788,8 +793,12 @@ def get_metal_atoms(struc, metal_ats): # Check for CA in modified amino acids if 'N' in atm.get_parent() or 'C' in atm.get_parent(): continue - if atm.id in metal_ats: - met_list.append(atm) + if 'element' in dir(atm): + if atm.element in metal_ats: + met_list.append(atm) + else: + if atm.id in metal_ats: + met_list.append(atm) return met_list diff --git a/biobb_structure_checking/mutation_manager.py b/biobb_structure_checking/mutation_manager.py index 619b2733..b78853a5 100644 --- a/biobb_structure_checking/mutation_manager.py +++ b/biobb_structure_checking/mutation_manager.py @@ -208,6 +208,5 @@ def apply(self, mut_map, res_lib, remove_h): def __str__(self): if len(self.chain_ids) > 1: return self.id - else: - chn, mut = self.id.split(':') - return f"{chn.split('/')[0]}:{mut}" + chn, mut = self.id.split(':') + return f"{chn.split('/')[0]}:{mut}" diff --git a/biobb_structure_checking/pdbio/mmb_server.py b/biobb_structure_checking/pdbio/mmb_server.py index 6c2a04ae..c0a3bf14 100644 --- a/biobb_structure_checking/pdbio/mmb_server.py +++ b/biobb_structure_checking/pdbio/mmb_server.py @@ -67,20 +67,13 @@ def retrieve_pdb_file( code = pdb_code.lower() - if file_format not in ('pdb', 'cif', 'mmCif', 'xml'): - print(f'Error: MMB/BSC Server: File format {file_format} not supported') + if file_format not in ('pdb', 'cif', 'mmCif'): + print(f'Error: File format {file_format} not supported') sys.exit(1) if file_format == 'mmCif': file_format = 'cif' - # if not biounit: - # url = f'{ALT_SERVERS[self.pdb_server]}/{code}.{file_format}' - # else: - # file_format = 'pdb' - # url = f'{ALT_SERVERS[self.pdb_server]}/{code}_bn{biounit}.pdb' - # Where does the final PDB file get saved? - url = f'{ALT_SERVERS[self.pdb_server.lower()]}/{code}.{file_format}' print(f"Retrieving structure from {url}") if pdir is None: @@ -91,28 +84,13 @@ def retrieve_pdb_file( path = pdir if not os.access(path, os.F_OK): os.makedirs(path) - # if biounit: - # final = { - # 'pdb': '%s_%s.pdb', - # 'mmCif': '%s_%s.cif', - # 'cif': '%s_%s.cif', - # 'xml': '%s_%s.xml' - # } - # final_file = os.path.join(path, final[file_format] % (code, biounit)) - # else: - # final = { - # 'pdb': '%s.pdb', - # 'mmCif': '%s.cif', - # 'cif': '%s.cif', - # 'xml': '%s.xml' - # } - # final_file = os.path.join(path, final[file_format] % code) final = { 'pdb': '%s.pdb', 'mmCif': '%s.cif', 'cif': '%s.cif', 'xml': '%s.xml' } + final_file = os.path.join(path, final[file_format] % code) # Skip download if the file already exists @@ -124,13 +102,6 @@ def retrieve_pdb_file( # Retrieve the file if self._verbose: - # if biounit: - # print( - # f"Downloading PDB structure '{pdb_code}.{biounit}' " - # f"from {self.pdb_server} ..." - # ) - # else: - # print(f"Downloading PDB structure '{pdb_code}' from {self.pdb_server} ...") print(f"Downloading structure '{pdb_code}' from {url} ...") try: urlcleanup() @@ -159,15 +130,8 @@ def retrieve_assembly_file( pdir = '/tmp' self.flat_tree = False -# retrieve_assembly_file only available on biopython >= 1.80, added here to ensure -# if self.pdb_server.lower() not in ALT_SERVERS: -# return super().retrieve_assembly_file( -# pdb_code, assembly_num, pdir, file_format, overwrite -# ) - pdb_code = pdb_code.lower() - assembly_num = int(assembly_num) archive = { "pdb": f"{pdb_code}.pdb{assembly_num}.gz", diff --git a/biobb_structure_checking/pdbio/param_input.py b/biobb_structure_checking/pdbio/param_input.py index 423bf309..066a3083 100644 --- a/biobb_structure_checking/pdbio/param_input.py +++ b/biobb_structure_checking/pdbio/param_input.py @@ -67,7 +67,7 @@ def add_option_numeric( min_val, max_val, multiple=False, - label_text=None + label_text='' ): """ Add a numeric option to dialog """ self.options.append({ @@ -100,7 +100,8 @@ def _build_dialog(self): opt_strs.append(','.join(opt['opt_list'])) elif opt['type'] in ('int', 'float'): if opt['min'] != 0 or opt['max'] != 0: - opt_strs.append(f"{opt['label_text']} {opt['min']} - {opt['max']}") + opt_strs.append(f"{opt['label_text']} {str(opt['min'])} - {str(opt['max'])}") + elif opt['type'] == 'input': opt_strs.append('Enter text') elif opt['type'] == 'pair_list': @@ -112,7 +113,7 @@ def _build_dialog(self): opt_strs.append('?') prompt = self.prefix + ' (' + ' | '.join(opt_strs) + ') ' if self.default is not None: - prompt += '(' + self.default + ')' + prompt += '(' + str(self.default) + ')' prompt += ":" return prompt diff --git a/biobb_structure_checking/structure_checking.py b/biobb_structure_checking/structure_checking.py index 9ed0ab6c..e715c9b7 100644 --- a/biobb_structure_checking/structure_checking.py +++ b/biobb_structure_checking/structure_checking.py @@ -38,7 +38,7 @@ def __init__(self, base_dir_path, args): self.args = cts.set_defaults(base_dir_path, args) - self.summary = {} + self.summary = {"version": cts.VERSION} if self.args['debug'] or args['time_limit']: import psutil self.start_time = time.time() @@ -76,15 +76,6 @@ def __init__(self, base_dir_path, args): if self.args['time_limit'] and self._check_time_limit(): sys.exit(1) - # if self.args['atom_limit'] and \ - # self.strucm.st_data.stats['num_ats'] > self.args['atom_limit']: - # sys.exit( - # cts.MSGS['ATOM_LIMIT'].format( - # self.strucm.st_data.stats['num_ats'], - # self.args['atom_limit'] - # ) - # ) - def launch(self): """ StructureChecking.launch Method run from the command line invocation @@ -206,7 +197,7 @@ def command_list(self, opts): if os.path.isfile(op_list): command_list = [] try: - with open(op_list, "r") as list_file_h: + with open(op_list, "r", encoding='utf-8') as list_file_h: for line in list_file_h: if line == "\n" or line[0:1] == '#': continue @@ -319,7 +310,7 @@ def _run_method(self, command, opts): try: error_status = f_fix(self, opts, data_to_fix) except Exception as e: - error_status = [e.message] + error_status = [getattr(e, 'message', str(e))] if error_status: if isinstance(error_status, tuple): @@ -476,7 +467,6 @@ def check_report_clashes(self, residue_list=None, contact_types=None, use_wat=Fa contact_types = mu.ALL_CONTACT_TYPES if not residue_list: residue_list = self.strucm.st_data.all_residues - print(use_wat) return self._clash_report( contact_types, self.strucm.check_r_list_clashes(residue_list, contact_types, use_wat=use_wat) @@ -584,7 +574,8 @@ def inscodes(self, opts=None): def altloc(self, opts=None): """ StructureChecking.altloc - Detect/Select Alternative Locations. Check only with no options. Options accepted as command-line string, or python dictionary. + Detect/Select Alternative Locations. Check only with no options. + Options accepted as command-line string, or python dictionary. Args: opts (str | dict - Options dictionary): @@ -597,7 +588,8 @@ def altloc(self, opts=None): def metals(self, opts=None): """ StructureChecking.metals - Detect/Remove Metals. Check only with no options. Options accepted as command-line string, or python dictionary. + Detect/Remove Metals. Check only with no options. + Options accepted as command-line string, or python dictionary. Args: opts (str | dict - Options dictionary): @@ -610,7 +602,7 @@ def metals(self, opts=None): def water(self, opts=None): """ StructureChecking.water - Detect/Select Remove Water molecules. Check only with no options. + Detect/Select Remove Water molecules. Check only with no options. Options accepted as command-line string, or python dictionary. Args: @@ -642,7 +634,8 @@ def ligands(self, opts=None): def rem_hydrogen(self, opts=None): """ StructureChecking.add_hydrogen - Remove Hydrogen atoms from structure. Check only with no options. Options accepted as command-line string, or python dictionary. + Remove Hydrogen atoms from structure. Check only with no options. + Options accepted as command-line string, or python dictionary. Args: opts (str | dict - Options dictionary): @@ -664,7 +657,8 @@ def getss(self, opts=None): def amide(self, opts=None): """ StructureChecking.amide - Detect/Fix Amide atoms Assignment. Check only with no options. Options accepted as command-line string, or python dictionary. + Detect/Fix Amide atoms Assignment. Check only with no options. + Options accepted as command-line string, or python dictionary. Args: opts (str | dict - Options dictionary): @@ -678,7 +672,8 @@ def amide(self, opts=None): def chiral(self, opts=None): """ StructureChecking.chiral - Detect/Fix Improper side chain chirality. Check only with no options. Options accepted as command-line string, or python dictionary. + Detect/Fix Improper side chain chirality. Check only with no options. + Options accepted as command-line string, or python dictionary. Args: opts (str | dict - Options dictionary): @@ -703,7 +698,8 @@ def clashes(self): def fixside(self, opts=None): """ StructureChecking.fixside - Complete side chains (heavy atoms, protein only). Check only with no options. Options accepted as command-line string, or python dictionary. + Complete side chains (heavy atoms, protein only). Check only with no options. + Options accepted as command-line string, or python dictionary. Args: opts (str | dict - Options dictionary): diff --git a/biobb_structure_checking/structure_manager.py b/biobb_structure_checking/structure_manager.py index 88a45d1f..6504b2fc 100644 --- a/biobb_structure_checking/structure_manager.py +++ b/biobb_structure_checking/structure_manager.py @@ -48,7 +48,6 @@ ACCEPTED_FORMATS = ['mmCif', 'cif', 'pdb', 'pqr', 'pdbqt'] ACCEPTED_REMOTE_FORMATS = ['mmCif', 'cif', 'pdb', 'xml'] - class StructureManager: """ Main Class wrapping Bio.PDB structure object """ @@ -138,6 +137,24 @@ def __init__( # Calc internal data self.update_internals(cif_warn=True) + def _get_cache_path(self, pdb_id, cache_dir, file_format): + """ Get cache path for input structure """ + if '.' in pdb_id: + pdb_id, assembly = pdb_id.split('.') + cache_path = opj( + cache_dir, + pdb_id[1:3].lower(), + f"{pdb_id.lower()}-assembly{assembly}.{file_format}" + ) + else: + cache_path = opj( + cache_dir, + pdb_id[1:3].lower(), + pdb_id.lower() + f".{file_format}" + ) + cache_path = cache_path.replace('mmCif','cif') + return cache_path + def _load_structure_file( self, input_pdb_path, @@ -155,11 +172,14 @@ def _load_structure_file( """ Load structure file """ biounit = False self.pdb_id = 'User' - if no_network and (input_pdb_path.startswith(('pdb:', 'http'))): - print("Error: no network access to retrieve structure") - return None, None, None, None + if input_pdb_path.startswith('pdb:'): input_pdb_path = input_pdb_path[4:] + if no_network: + cache_path = self._get_cache_path(input_pdb_path, cache_dir, file_format) + print (f"WARNING: no network access, using cached structure {cache_path} if available") + if not os.path.exists(cache_path): + return None, None, None, None pdbl = MMBPDBList(pdb=cache_dir, server=pdb_server) if re.search(r'\.[1-9]+$', input_pdb_path): pdbid, biounit = input_pdb_path.split('.') @@ -217,6 +237,8 @@ def _load_structure_file( self.sequence_data.load_sequence_from_fasta(f"pdb:{pdbid}") elif input_pdb_path.startswith('http'): + if no_network and input_pdb_path.startswith('http'): + return None, None, None, None real_pdb_path = opj(cache_dir, os.path.basename(input_pdb_path)) if '.' in os.path.basename(input_pdb_path): @@ -269,9 +291,9 @@ def _load_structure_file( raise UnknownFileTypeError(input_pdb_path) if '.gz' in real_pdb_path: - pdb_file_handle = gzip.open(real_pdb_path, 'rt') + pdb_file_handle = gzip.open(real_pdb_path, 'rt', encoding='utf-8') else: - pdb_file_handle = open(real_pdb_path, 'r') + pdb_file_handle = open(real_pdb_path, 'r', encoding='utf-8') if atom_limit > 0: num_ats = sum(1 for _ in pdb_file_handle if _.startswith('ATOM') or _.startswith('HETATM')) @@ -486,6 +508,7 @@ def check_r_list_clashes( self.rr_dist, self.data_library.distances['CLASH_DIST'], self.data_library.get_atom_lists(contact_types), + self.st_data.next_residue, not self.models_data.has_superimp_models(), severe='severe' in contact_types, use_wat=use_wat, @@ -677,7 +700,7 @@ def get_backbone_breaks(self) -> Dict[str, List[List[Residue]]]: if res1 not in self.st_data.next_residue: bck_breaks_list.append([res1, res2]) - if mu.seq_consecutive(res1, res2): + if mu.seq_consecutive(res1, res2, self.st_data.next_residue): dist = 0. if 'N' in res1 and 'C' in res2: dist = res1['N'] - res2['C'] @@ -1776,8 +1799,6 @@ def prepare_mutations_from_na_seq(self, new_seq): # =============================================================================== - - def _guess_modeller_env(): """ Guessing Modeller version from conda installation if available """ import subprocess @@ -1790,45 +1811,54 @@ def _guess_modeller_env(): if len(info) >= 2 and info[1]: print(f"Modeller v{info[1]} detected") ver1, ver2 = info[1].split('.') - return f"KEY_MODELLER{ver1}v{ver2}", f"MODINSTALL{ver1}v{ver2}", f"{os.environ.get('CONDA_PREFIX','')}/lib/modeller-{ver1}.{ver2}" + return f"KEY_MODELLER{ver1}v{ver2}", f"MODINSTALL{ver1}v{ver2}", \ + f"{os.environ.get('CONDA_PREFIX','')}/lib/modeller-{ver1}.{ver2}" except subprocess.CalledProcessError: print("Modeller version not detected or Conda not installed, using default") - return 'KEY_MODELLER', 'MODINSTALL', 'modeller' + return 'KEY_MODELLER', 'MODINSTALL', 'modeller' # =============================================================================== - class WrongServerError(Exception): + ''' Raised when biounits are requested on a non-MMB server''' def __init__(self): self.message = 'ERROR: Biounits supported only on MMB server' class UnknownFileTypeError(Exception): + ''' Raised when an unknown file type is provided''' def __init__(self, typ): self.message = f'ERROR: unknown filetype ({typ})' class OutputPathNotProvidedError(Exception): + ''' Raised when the output PDB path is not provided''' def __init__(self): self.message = 'ERROR: output PDB path not provided' class NotAValidResidueError(Exception): + ''' Raised when a residue is not valid in the current context''' def __init__(self, res): self.message = f'Warning: {res} is not a valid residue in this context' class NotEnoughAtomsError(Exception): + ''' Raised when there are not enough atoms to build missing atoms''' def __init__(self): self.message = 'Warning: not enough backbone to build missing atoms' class ParseError(Exception): + ''' Raised when there is a parsing error in the input structure''' def __init__(self, err_id, err_txt): self.message = f'{err_id} ({err_txt}) found when parsing input structure' class UnknownFFError(Exception): + ''' Raised when an unknown force field is provided''' def __init__(self, ff): self.message = f'{ff} is not a valid ff for assigning atom types and charges' class SequencesDoNotMatch(Exception): + ''' Raised when the sequence lengths do not match''' def __init__(self): self.message = "Sequence lengths do not match" class UnknownAtomforResidueError(Exception): + ''' Raised when an atom is not valid for a given residue''' def __init__(self, res_id, atm_id): self.message = f"Non valid atom {atm_id} for residue {res_id}" diff --git a/biobb_structure_checking/test/Makefile b/biobb_structure_checking/test/Makefile index 6273dedf..273f4d07 100644 --- a/biobb_structure_checking/test/Makefile +++ b/biobb_structure_checking/test/Makefile @@ -152,6 +152,9 @@ sequences: @echo "Running sequences on 2ki5" ${COMMON};${APPBIN} -v -i pdb:2ki5 -o 2ki5_sequences_test.pdb --non_interactive sequences --output_fasta 2ki5_sequences.fasta > 2ki5_sequences_test.log + @echo "Running sequences on 3nir" + ${COMMON};${APPBIN} -v -i pdb:3nir -o 3nir_sequences_test.pdb --non_interactive sequences --output_fasta 3nir_sequences.fasta > 3nir_sequences_test.log + dnamut: @echo "Running dnamut on 1D23" ${COMMON};${APPBIN} -v -i pdb:1d23 -o 1d23_dnamut_test.pdb --non_interactive mutateside --mut DA3DG > 1d23_dnamut_test.log diff --git a/biobb_structure_checking/test/ref/104l_inscodes_renum_test.log b/biobb_structure_checking/test/ref/104l_inscodes_renum_test.log index 9d051dc9..a3940f25 100644 --- a/biobb_structure_checking/test/ref/104l_inscodes_renum_test.log +++ b/biobb_structure_checking/test/ref/104l_inscodes_renum_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/04/104l.cif' Structure pdb:104l loaded - PDB id: 104L + Entry id: 104L Title: HOW AMINO-ACID INSERTIONS ARE ALLOWED IN AN ALPHA-HELIX OF T4 LYSOZYME Experimental method: X-RAY DIFFRACTION Keywords: HYDROLASE(O-GLYCOSYL) diff --git a/biobb_structure_checking/test/ref/104l_inscodes_test.log b/biobb_structure_checking/test/ref/104l_inscodes_test.log index 3e8c6201..cc1c0fca 100644 --- a/biobb_structure_checking/test/ref/104l_inscodes_test.log +++ b/biobb_structure_checking/test/ref/104l_inscodes_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/04/104l.cif' Structure pdb:104l loaded - PDB id: 104L + Entry id: 104L Title: HOW AMINO-ACID INSERTIONS ARE ALLOWED IN AN ALPHA-HELIX OF T4 LYSOZYME Experimental method: X-RAY DIFFRACTION Keywords: HYDROLASE(O-GLYCOSYL) diff --git a/biobb_structure_checking/test/ref/1ark_all_test.json b/biobb_structure_checking/test/ref/1ark_all_test.json index 95f4c8bd..aa3872dd 100644 --- a/biobb_structure_checking/test/ref/1ark_all_test.json +++ b/biobb_structure_checking/test/ref/1ark_all_test.json @@ -378,6 +378,7 @@ }, "total_charge": null }, + "version": "3.16.3", "water": { "opts": "--remove Yes" } diff --git a/biobb_structure_checking/test/ref/1ark_all_test.log b/biobb_structure_checking/test/ref/1ark_all_test.log index 9125be8c..72271243 100644 --- a/biobb_structure_checking/test/ref/1ark_all_test.log +++ b/biobb_structure_checking/test/ref/1ark_all_test.log @@ -1,16 +1,16 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ar/1ark.cif' Structure pdb:1ark loaded - PDB id: 1ARK + Entry id: 1ARK Title: SH3 DOMAIN FROM HUMAN NEBULIN, NMR, 15 STRUCTURES Experimental method: SOLUTION NMR Keywords: TRANSFERASE - Num. models: 15 (type: BioUnit, 35.032 A) + Num. models: 15 (type: Assembly/Biological unit, 35.032 A) Num. chains: 15 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein) Num. residues: 900 Num. residues with ins. codes: 0 @@ -24,7 +24,7 @@ Step 1: models --select 1 Running models. Options: --select 1 Detected 15 Model(s) -Models do not superimpose, RMSd: 35.032 A, guessed as BioUnit +Models do not superimpose, RMSd: 35.032 A, guessed as Assembly/Biological unit Selecting model num. 1 Step 2: chains --select All @@ -113,7 +113,6 @@ No SS bonds detected Step 16: clashes Running clashes. -False No Severe Steric clashes/covalent bonds detected 4 Apolar steric clashes detected MET A9.CE GLU A58.OE2 2.695 A diff --git a/biobb_structure_checking/test/ref/1ark_chiral_bck_test.log b/biobb_structure_checking/test/ref/1ark_chiral_bck_test.log index 8cdf3c5b..dcf62eeb 100644 --- a/biobb_structure_checking/test/ref/1ark_chiral_bck_test.log +++ b/biobb_structure_checking/test/ref/1ark_chiral_bck_test.log @@ -1,14 +1,13 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Warning: sequence features may not be available, use --sequence for external fasta input Structure chiral_pdb_test/1ark_m1_chica_nh.pdb loaded - PDB id: + Entry id: Title: Experimental method: unknown - Resolution (A): N.A. Num. models: 1 Num. chains: 1 (A: Protein) diff --git a/biobb_structure_checking/test/ref/1ark_models_3-6_sup_test.log b/biobb_structure_checking/test/ref/1ark_models_3-6_sup_test.log index cfdb06f5..d2aac0ed 100644 --- a/biobb_structure_checking/test/ref/1ark_models_3-6_sup_test.log +++ b/biobb_structure_checking/test/ref/1ark_models_3-6_sup_test.log @@ -1,16 +1,16 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ar/1ark.cif' Structure pdb:1ark loaded - PDB id: 1ARK + Entry id: 1ARK Title: SH3 DOMAIN FROM HUMAN NEBULIN, NMR, 15 STRUCTURES Experimental method: SOLUTION NMR Keywords: TRANSFERASE - Num. models: 15 (type: BioUnit, 35.032 A) + Num. models: 15 (type: Assembly/Biological unit, 35.032 A) Num. chains: 15 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein) Num. residues: 900 Num. residues with ins. codes: 0 @@ -21,7 +21,7 @@ Structure pdb:1ark loaded Num. atoms: 13575 Running models. Options: --select 3-6 --superimpose --save_split Detected 15 Model(s) -Models do not superimpose, RMSd: 35.032 A, guessed as BioUnit +Models do not superimpose, RMSd: 35.032 A, guessed as Assembly/Biological unit Selecting model num. 3-6 Models superimposed: final RMSd 2.615 A Final Num. models: 4 (type: Ensembl/NMR, 2.615 A) diff --git a/biobb_structure_checking/test/ref/1ark_models_test_1.log b/biobb_structure_checking/test/ref/1ark_models_test_1.log index ca3f2921..0446f35f 100644 --- a/biobb_structure_checking/test/ref/1ark_models_test_1.log +++ b/biobb_structure_checking/test/ref/1ark_models_test_1.log @@ -1,16 +1,16 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ar/1ark.cif' Structure pdb:1ark loaded - PDB id: 1ARK + Entry id: 1ARK Title: SH3 DOMAIN FROM HUMAN NEBULIN, NMR, 15 STRUCTURES Experimental method: SOLUTION NMR Keywords: TRANSFERASE - Num. models: 15 (type: BioUnit, 35.032 A) + Num. models: 15 (type: Assembly/Biological unit, 35.032 A) Num. chains: 15 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein) Num. residues: 900 Num. residues with ins. codes: 0 @@ -21,7 +21,7 @@ Structure pdb:1ark loaded Num. atoms: 13575 Running models. Options: --select 1 Detected 15 Model(s) -Models do not superimpose, RMSd: 35.032 A, guessed as BioUnit +Models do not superimpose, RMSd: 35.032 A, guessed as Assembly/Biological unit Selecting model num. 1 Final Num. models: 1 Final Num. chains: 1 (A: Protein) diff --git a/biobb_structure_checking/test/ref/1ark_models_test_5.log b/biobb_structure_checking/test/ref/1ark_models_test_5.log index 168e5b6f..5bcc012d 100644 --- a/biobb_structure_checking/test/ref/1ark_models_test_5.log +++ b/biobb_structure_checking/test/ref/1ark_models_test_5.log @@ -1,16 +1,16 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ar/1ark.cif' Structure pdb:1ark loaded - PDB id: 1ARK + Entry id: 1ARK Title: SH3 DOMAIN FROM HUMAN NEBULIN, NMR, 15 STRUCTURES Experimental method: SOLUTION NMR Keywords: TRANSFERASE - Num. models: 15 (type: BioUnit, 35.032 A) + Num. models: 15 (type: Assembly/Biological unit, 35.032 A) Num. chains: 15 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein) Num. residues: 900 Num. residues with ins. codes: 0 @@ -21,7 +21,7 @@ Structure pdb:1ark loaded Num. atoms: 13575 Running models. Options: --select 5 Detected 15 Model(s) -Models do not superimpose, RMSd: 35.032 A, guessed as BioUnit +Models do not superimpose, RMSd: 35.032 A, guessed as Assembly/Biological unit Selecting model num. 5 Final Num. models: 1 Final Num. chains: 1 (A: Protein) diff --git a/biobb_structure_checking/test/ref/1ark_remh_test_None.log b/biobb_structure_checking/test/ref/1ark_remh_test_None.log index ffe33ce3..5bfb21c5 100644 --- a/biobb_structure_checking/test/ref/1ark_remh_test_None.log +++ b/biobb_structure_checking/test/ref/1ark_remh_test_None.log @@ -1,16 +1,16 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ar/1ark.cif' Structure pdb:1ark loaded - PDB id: 1ARK + Entry id: 1ARK Title: SH3 DOMAIN FROM HUMAN NEBULIN, NMR, 15 STRUCTURES Experimental method: SOLUTION NMR Keywords: TRANSFERASE - Num. models: 15 (type: BioUnit, 35.032 A) + Num. models: 15 (type: Assembly/Biological unit, 35.032 A) Num. chains: 15 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein) Num. residues: 900 Num. residues with ins. codes: 0 diff --git a/biobb_structure_checking/test/ref/1ark_remh_test_Yes.log b/biobb_structure_checking/test/ref/1ark_remh_test_Yes.log index 5661bf80..479bde42 100644 --- a/biobb_structure_checking/test/ref/1ark_remh_test_Yes.log +++ b/biobb_structure_checking/test/ref/1ark_remh_test_Yes.log @@ -1,16 +1,16 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ar/1ark.cif' Structure pdb:1ark loaded - PDB id: 1ARK + Entry id: 1ARK Title: SH3 DOMAIN FROM HUMAN NEBULIN, NMR, 15 STRUCTURES Experimental method: SOLUTION NMR Keywords: TRANSFERASE - Num. models: 15 (type: BioUnit, 35.032 A) + Num. models: 15 (type: Assembly/Biological unit, 35.032 A) Num. chains: 15 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein) Num. residues: 900 Num. residues with ins. codes: 0 @@ -22,7 +22,7 @@ Structure pdb:1ark loaded Running rem_hydrogen. Options: --remove Yes Detected 900 Residues containing H atoms Hydrogen atoms removed from 900 residues -Final Num. models: 15 (type: BioUnit, 35.032 A) +Final Num. models: 15 (type: Assembly/Biological unit, 35.032 A) Final Num. chains: 15 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein) Final Num. residues: 900 Final Num. residues with ins. codes: 0 diff --git a/biobb_structure_checking/test/ref/1bqo_all_test.json b/biobb_structure_checking/test/ref/1bqo_all_test.json index 9287e836..19032b58 100644 --- a/biobb_structure_checking/test/ref/1bqo_all_test.json +++ b/biobb_structure_checking/test/ref/1bqo_all_test.json @@ -552,6 +552,7 @@ }, "total_charge": null }, + "version": "3.16.3", "water": { "contacts": { "HOH A306": [ diff --git a/biobb_structure_checking/test/ref/1bqo_all_test.log b/biobb_structure_checking/test/ref/1bqo_all_test.log index b3d08fde..f7cb8f33 100644 --- a/biobb_structure_checking/test/ref/1bqo_all_test.log +++ b/biobb_structure_checking/test/ref/1bqo_all_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/bq/1bqo.cif' Structure pdb:1bqo loaded - PDB id: 1BQO + Entry id: 1BQO Title: DISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE INHIBITORS Experimental method: X-RAY DIFFRACTION Keywords: METALLOPROTEASE @@ -32,7 +32,7 @@ Metal/Ion residues found CA B304 (CALCIUM ION) CA B305 (CALCIUM ION) Small mol ligands found -N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE) +N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY) Step 1: models --select 1 @@ -94,7 +94,7 @@ Detected 7 Ligands CA B303 CALCIUM ION CA B304 CALCIUM ION CA B305 CALCIUM ION - N25 B401 1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE + N25 B401 1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY Contacts for CA A303: ASP A158.OD1, GLY A159.O, GLY A161.O, VAL A163.O, ASP A181.OD2, GLU A184.OE2 Contacts for CA A304: ASP A107.OD2, ASP A182.O, GLU A184.O, HOH A342.O Contacts for CA A305: ASP A141.O, GLY A173.O, ASN A175.O, ASP A177.OD1, HOH A314.O @@ -161,7 +161,6 @@ ASP A251 Adding new atom OXT Fixed 1 backbone atom(s) Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected No Polar contacts (acceptors) detected @@ -183,7 +182,6 @@ No SS bonds detected Step 16: clashes Running clashes. -False No Severe Steric clashes/covalent bonds detected 3 Apolar steric clashes detected THR A95.CG2 PRO A129.O 2.770 A @@ -222,7 +220,7 @@ Detected 7 Ligands CA B303 CALCIUM ION CA B304 CALCIUM ION CA B305 CALCIUM ION - N25 B401 1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE + N25 B401 1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY Contacts for CA A303: ASP A158.OD1, GLY A159.O, GLY A161.O, VAL A163.O, ASP A181.OD2, GLU A184.OE2 Contacts for CA A304: ASP A107.OD2, ASP A182.O, GLU A184.O Contacts for CA A305: ASP A141.O, GLY A173.O, ASN A175.O, ASP A177.OD1 diff --git a/biobb_structure_checking/test/ref/1bqo_metals_test_A305.log b/biobb_structure_checking/test/ref/1bqo_metals_test_A305.log index 0bf44a06..d8ebe8cd 100644 --- a/biobb_structure_checking/test/ref/1bqo_metals_test_A305.log +++ b/biobb_structure_checking/test/ref/1bqo_metals_test_A305.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/bq/1bqo.cif' Structure pdb:1bqo loaded - PDB id: 1BQO + Entry id: 1BQO Title: DISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE INHIBITORS Experimental method: X-RAY DIFFRACTION Keywords: METALLOPROTEASE @@ -32,7 +32,7 @@ Metal/Ion residues found CA B304 (CALCIUM ION) CA B305 (CALCIUM ION) Small mol ligands found -N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE) +N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY) Running metals. Options: --remove A305 Found 10 Metal ions ZN A301.ZN ZINC ION @@ -76,5 +76,5 @@ Metal/Ion residues found CA B304 (CALCIUM ION) CA B305 (CALCIUM ION) Small mol ligands found -N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE) +N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY) Structure saved on 1bqo_metals_test_A305.pdb diff --git a/biobb_structure_checking/test/ref/1bqo_metals_test_All.log b/biobb_structure_checking/test/ref/1bqo_metals_test_All.log index 8638b946..c3091b1a 100644 --- a/biobb_structure_checking/test/ref/1bqo_metals_test_All.log +++ b/biobb_structure_checking/test/ref/1bqo_metals_test_All.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/bq/1bqo.cif' Structure pdb:1bqo loaded - PDB id: 1BQO + Entry id: 1BQO Title: DISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE INHIBITORS Experimental method: X-RAY DIFFRACTION Keywords: METALLOPROTEASE @@ -32,7 +32,7 @@ Metal/Ion residues found CA B304 (CALCIUM ION) CA B305 (CALCIUM ION) Small mol ligands found -N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE) +N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY) Running metals. Options: --remove All Found 10 Metal ions ZN A301.ZN ZINC ION @@ -66,5 +66,5 @@ Final Num. ligands or modified residues: 1 Final Num. water mol.: 75 Final Num. atoms: 2831 Small mol ligands found -N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE) +N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY) Structure saved on 1bqo_metals_test_All.pdb diff --git a/biobb_structure_checking/test/ref/1bqo_metals_test_None.log b/biobb_structure_checking/test/ref/1bqo_metals_test_None.log index 92294740..14ed0b20 100644 --- a/biobb_structure_checking/test/ref/1bqo_metals_test_None.log +++ b/biobb_structure_checking/test/ref/1bqo_metals_test_None.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/bq/1bqo.cif' Structure pdb:1bqo loaded - PDB id: 1BQO + Entry id: 1BQO Title: DISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE INHIBITORS Experimental method: X-RAY DIFFRACTION Keywords: METALLOPROTEASE @@ -32,7 +32,7 @@ Metal/Ion residues found CA B304 (CALCIUM ION) CA B305 (CALCIUM ION) Small mol ligands found -N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE) +N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY) Running metals. Options: --remove None Found 10 Metal ions ZN A301.ZN ZINC ION diff --git a/biobb_structure_checking/test/ref/1bqo_metals_test_ZN.log b/biobb_structure_checking/test/ref/1bqo_metals_test_ZN.log index bf355f78..0752a193 100644 --- a/biobb_structure_checking/test/ref/1bqo_metals_test_ZN.log +++ b/biobb_structure_checking/test/ref/1bqo_metals_test_ZN.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/bq/1bqo.cif' Structure pdb:1bqo loaded - PDB id: 1BQO + Entry id: 1BQO Title: DISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE INHIBITORS Experimental method: X-RAY DIFFRACTION Keywords: METALLOPROTEASE @@ -32,7 +32,7 @@ Metal/Ion residues found CA B304 (CALCIUM ION) CA B305 (CALCIUM ION) Small mol ligands found -N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE) +N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY) Running metals. Options: --remove ZN Found 10 Metal ions ZN A301.ZN ZINC ION @@ -73,5 +73,5 @@ Metal/Ion residues found CA B304 (CALCIUM ION) CA B305 (CALCIUM ION) Small mol ligands found -N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY2 N25 DRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE) +N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY) Structure saved on 1bqo_metals_test_ZN.pdb diff --git a/biobb_structure_checking/test/ref/1d23_add_hydrogen_CMIP_test.log b/biobb_structure_checking/test/ref/1d23_add_hydrogen_CMIP_test.log index 8a1a7e9a..bde956a1 100644 --- a/biobb_structure_checking/test/ref/1d23_add_hydrogen_CMIP_test.log +++ b/biobb_structure_checking/test/ref/1d23_add_hydrogen_CMIP_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/d2/1d23.cif' Structure pdb:1d23 loaded - PDB id: 1D23 + Entry id: 1D23 Title: THE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALS Experimental method: X-RAY DIFFRACTION Keywords: DNA diff --git a/biobb_structure_checking/test/ref/1d23_dnamut_test.log b/biobb_structure_checking/test/ref/1d23_dnamut_test.log index f61a3850..0bd00dda 100644 --- a/biobb_structure_checking/test/ref/1d23_dnamut_test.log +++ b/biobb_structure_checking/test/ref/1d23_dnamut_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/d2/1d23.cif' Structure pdb:1d23 loaded - PDB id: 1D23 + Entry id: 1D23 Title: THE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALS Experimental method: X-RAY DIFFRACTION Keywords: DNA @@ -32,7 +32,6 @@ Replacing DA A3 into DG Adding new atom N2 Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected 1 Polar contacts (acceptors) detected diff --git a/biobb_structure_checking/test/ref/1d23_fixtest_All_test.log b/biobb_structure_checking/test/ref/1d23_fixtest_All_test.log index 86ffd35f..24603a46 100644 --- a/biobb_structure_checking/test/ref/1d23_fixtest_All_test.log +++ b/biobb_structure_checking/test/ref/1d23_fixtest_All_test.log @@ -1,14 +1,13 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Warning: sequence features may not be available, use --sequence for external fasta input Structure dna_test/1d23_fixtest.pdb loaded - PDB id: + Entry id: Title: Experimental method: unknown - Resolution (A): N.A. Num. models: 1 Num. chains: 2 (A: DNA, B: DNA) @@ -35,7 +34,6 @@ Fixing side chains Not enough atoms left on DC A5 to recover base orientation, skipping Fixed 2 side chain(s) Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected No Polar contacts (acceptors) detected diff --git a/biobb_structure_checking/test/ref/1d23_poliA_test.log b/biobb_structure_checking/test/ref/1d23_poliA_test.log index 0bfb1172..6214dd2e 100644 --- a/biobb_structure_checking/test/ref/1d23_poliA_test.log +++ b/biobb_structure_checking/test/ref/1d23_poliA_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/d2/1d23.cif' Structure pdb:1d23 loaded - PDB id: 1D23 + Entry id: 1D23 Title: THE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALS Experimental method: X-RAY DIFFRACTION Keywords: DNA @@ -268,7 +268,6 @@ Replacing DG B20 into DT Adding new atom O2 Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected 2 Polar contacts (acceptors) detected diff --git a/biobb_structure_checking/test/ref/1ldn1_checkall_test.log b/biobb_structure_checking/test/ref/1ldn1_checkall_test.log index 4fbdddc4..319e2a5d 100644 --- a/biobb_structure_checking/test/ref/1ldn1_checkall_test.log +++ b/biobb_structure_checking/test/ref/1ldn1_checkall_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ld/1ldn-assembly1.cif' Structure pdb:1ldn.1 loaded - PDB id: 1ldn (Assembly 1) + Entry id: 1ldn (Assembly 1) Title: STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: OXIDOREDUCTASE(CHOH(D)-NAD(A)) @@ -88,6 +88,7 @@ FBP B353 O4P B (0.50) D (0.50) O5P B (0.50) D (0.50) O6P B (0.50) D (0.50) +Possible microheterogeneity: No A altloc found Running check_only. Nothing else to do. Running rem_hydrogen. No residues with Hydrogen atoms found @@ -182,7 +183,6 @@ ASN B138 PRO B139 Dihedral: -1.398 No trans peptide bonds with unusual omega dihedrals found Running check_only. Nothing else to do. Running clashes. -False 1 Severe Steric clashes/covalent bonds detected LYS C16.NZ HIS D264.O 1.995 A 162 Apolar steric clashes detected diff --git a/biobb_structure_checking/test/ref/1rna_add_hydrogen_ADT_test.log b/biobb_structure_checking/test/ref/1rna_add_hydrogen_ADT_test.log index 1ae69991..9ea46c71 100644 --- a/biobb_structure_checking/test/ref/1rna_add_hydrogen_ADT_test.log +++ b/biobb_structure_checking/test/ref/1rna_add_hydrogen_ADT_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/rn/1rna.cif' Structure pdb:1rna loaded - PDB id: 1RNA + Entry id: 1RNA Title: CRYSTALLOGRAPHIC STRUCTURE OF AN RNA HELIX: [U(U-A)6A]2 Experimental method: X-RAY DIFFRACTION Keywords: RNA diff --git a/biobb_structure_checking/test/ref/1svc_all_test.json b/biobb_structure_checking/test/ref/1svc_all_test.json index 5efca281..d0ec4177 100644 --- a/biobb_structure_checking/test/ref/1svc_all_test.json +++ b/biobb_structure_checking/test/ref/1svc_all_test.json @@ -417,6 +417,7 @@ }, "total_charge": null }, + "version": "3.16.3", "water": { "contacts": { "HOH D406": [ diff --git a/biobb_structure_checking/test/ref/1svc_all_test.log b/biobb_structure_checking/test/ref/1svc_all_test.log index 688f1b05..19d2564f 100644 --- a/biobb_structure_checking/test/ref/1svc_all_test.log +++ b/biobb_structure_checking/test/ref/1svc_all_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/sv/1svc.cif' Structure pdb:1svc loaded - PDB id: 1SVC + Entry id: 1SVC Title: NFKB P50 HOMODIMER BOUND TO DNA Experimental method: X-RAY DIFFRACTION Keywords: TRANSCRIPTION/DNA @@ -110,7 +110,6 @@ GLU P353 Adding new atom OXT Fixed 1 backbone atom(s) Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected No Polar contacts (acceptors) detected @@ -132,7 +131,6 @@ No SS bonds detected Step 16: clashes Running clashes. -False No Severe Steric clashes/covalent bonds detected 13 Apolar steric clashes detected PRO P43.O LEU P232.CD2 2.898 A diff --git a/biobb_structure_checking/test/ref/1svc_chains_test_protein.log b/biobb_structure_checking/test/ref/1svc_chains_test_protein.log index b5d7fcd7..8ff54cdd 100644 --- a/biobb_structure_checking/test/ref/1svc_chains_test_protein.log +++ b/biobb_structure_checking/test/ref/1svc_chains_test_protein.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/sv/1svc.cif' Structure pdb:1svc loaded - PDB id: 1SVC + Entry id: 1SVC Title: NFKB P50 HOMODIMER BOUND TO DNA Experimental method: X-RAY DIFFRACTION Keywords: TRANSCRIPTION/DNA diff --git a/biobb_structure_checking/test/ref/1svc_chains_test_rebuild.log b/biobb_structure_checking/test/ref/1svc_chains_test_rebuild.log index 4266dbdf..9620a9f1 100644 --- a/biobb_structure_checking/test/ref/1svc_chains_test_rebuild.log +++ b/biobb_structure_checking/test/ref/1svc_chains_test_rebuild.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/sv/1svc.cif' Structure pdb:1svc loaded - PDB id: 1SVC + Entry id: 1SVC Title: NFKB P50 HOMODIMER BOUND TO DNA Experimental method: X-RAY DIFFRACTION Keywords: TRANSCRIPTION/DNA diff --git a/biobb_structure_checking/test/ref/1svc_checkall_test.log b/biobb_structure_checking/test/ref/1svc_checkall_test.log index f996d3e4..df016d2d 100644 --- a/biobb_structure_checking/test/ref/1svc_checkall_test.log +++ b/biobb_structure_checking/test/ref/1svc_checkall_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/sv/1svc-assembly1.cif' Structure pdb:1svc.1 loaded - PDB id: 1svc (Assembly 1) + Entry id: 1svc (Assembly 1) Title: NFKB P50 HOMODIMER BOUND TO DNA Experimental method: X-RAY DIFFRACTION Keywords: TRANSCRIPTION/DNA @@ -92,7 +92,6 @@ No cis peptide bonds found No trans peptide bonds with unusual omega dihedrals found Running check_only. Nothing else to do. Running clashes. -False No Severe Steric clashes/covalent bonds detected 26 Apolar steric clashes detected PRO P43.O LEU P232.CD2 2.898 A diff --git a/biobb_structure_checking/test/ref/1ubq_add_hydrogen_ADT_test.log b/biobb_structure_checking/test/ref/1ubq_add_hydrogen_ADT_test.log index 98c2db2e..4484729f 100644 --- a/biobb_structure_checking/test/ref/1ubq_add_hydrogen_ADT_test.log +++ b/biobb_structure_checking/test/ref/1ubq_add_hydrogen_ADT_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ub/1ubq.cif' Structure pdb:1ubq loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: CHROMOSOMAL PROTEIN diff --git a/biobb_structure_checking/test/ref/1ubq_add_hydrogen_CMIP_test.log b/biobb_structure_checking/test/ref/1ubq_add_hydrogen_CMIP_test.log index 3405e61d..11ffb33e 100644 --- a/biobb_structure_checking/test/ref/1ubq_add_hydrogen_CMIP_test.log +++ b/biobb_structure_checking/test/ref/1ubq_add_hydrogen_CMIP_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ub/1ubq.cif' Structure pdb:1ubq loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: CHROMOSOMAL PROTEIN diff --git a/biobb_structure_checking/test/ref/1ubq_add_hydrogen_PQR_test.log b/biobb_structure_checking/test/ref/1ubq_add_hydrogen_PQR_test.log index 0123914f..332fe397 100644 --- a/biobb_structure_checking/test/ref/1ubq_add_hydrogen_PQR_test.log +++ b/biobb_structure_checking/test/ref/1ubq_add_hydrogen_PQR_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ub/1ubq.cif' Structure pdb:1ubq loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: CHROMOSOMAL PROTEIN diff --git a/biobb_structure_checking/test/ref/1ubq_all_test.json b/biobb_structure_checking/test/ref/1ubq_all_test.json index c64e2821..4d75d1b1 100644 --- a/biobb_structure_checking/test/ref/1ubq_all_test.json +++ b/biobb_structure_checking/test/ref/1ubq_all_test.json @@ -176,6 +176,7 @@ }, "total_charge": null }, + "version": "3.16.3", "water": { "contacts": { "HOH A100": [ diff --git a/biobb_structure_checking/test/ref/1ubq_all_test.log b/biobb_structure_checking/test/ref/1ubq_all_test.log index d48b99b7..d9529b28 100644 --- a/biobb_structure_checking/test/ref/1ubq_all_test.log +++ b/biobb_structure_checking/test/ref/1ubq_all_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ub/1ubq.cif' Structure pdb:1ubq loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: CHROMOSOMAL PROTEIN @@ -117,7 +117,6 @@ No SS bonds detected Step 16: clashes Running clashes. -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected 1 Polar contacts (acceptors) detected diff --git a/biobb_structure_checking/test/ref/1ubq_all_test_debug.json b/biobb_structure_checking/test/ref/1ubq_all_test_debug.json index f1378219..4dd539b3 100644 --- a/biobb_structure_checking/test/ref/1ubq_all_test_debug.json +++ b/biobb_structure_checking/test/ref/1ubq_all_test_debug.json @@ -78,25 +78,25 @@ } }, "elapsed_times": { - "add_hydrogen": 0.022584915161132812, - "altloc": 0.00028824806213378906, - "amide": 0.06296539306640625, - "backbone": 0.001392364501953125, - "chains": 5.316734313964844e-05, - "chiral": 0.0011584758758544922, - "chiral_bck": 0.0025610923767089844, - "cistransbck": 0.005888462066650391, - "clashes": 0.24389123916625977, - "fixside": 0.0013196468353271484, - "getss": 0.00046706199645996094, - "inscodes": 0.0001690387725830078, - "ligands": 0.00015854835510253906, - "load": 0.07214713096618652, - "metals": 0.000667572021484375, - "models": 0.0009531974792480469, - "rem_hydrogen": 0.0007307529449462891, - "total": 0.5257079601287842, - "water": 0.10158896446228027 + "add_hydrogen": 0.03378558158874512, + "altloc": 0.0005023479461669922, + "amide": 0.13399314880371094, + "backbone": 0.0025322437286376953, + "chains": 9.775161743164062e-05, + "chiral": 0.002100229263305664, + "chiral_bck": 0.004730939865112305, + "cistransbck": 0.007921695709228516, + "clashes": 0.3379478454589844, + "fixside": 0.0021903514862060547, + "getss": 0.00074005126953125, + "inscodes": 0.00029730796813964844, + "ligands": 0.00046443939208984375, + "load": 0.13278675079345703, + "metals": 0.0010330677032470703, + "models": 0.0019042491912841797, + "rem_hydrogen": 0.0009434223175048828, + "total": 0.8658430576324463, + "water": 0.1919875144958496 }, "final_stats": { "biounit": false, @@ -154,87 +154,87 @@ "memsize": [ [ "load", - 52.7265625 + 52.60546875 ], [ "models", - 52.73046875 + 52.61328125 ], [ "chains", - 52.73046875 + 52.6171875 ], [ "inscodes", - 52.73046875 + 52.6171875 ], [ "altloc", - 52.73046875 + 52.625 ], [ "metals", - 52.73828125 + 52.62890625 ], [ "ligands", - 52.74609375 + 52.63671875 ], [ "water", - 52.76171875 + 52.640625 ], [ "rem_hydrogen", - 52.76171875 + 52.640625 ], [ "amide", - 52.765625 + 52.64453125 ], [ "chiral", - 52.76953125 + 52.64453125 ], [ "chiral_bck", - 52.76953125 + 52.6484375 ], [ "fixside", - 52.76953125 + 52.6484375 ], [ "backbone", - 52.7734375 + 52.66015625 ], [ "cistransbck", - 52.7734375 + 52.66015625 ], [ "getss", - 52.77734375 + 52.66015625 ], [ "clashes", - 52.77734375 + 52.66015625 ], [ "ligands", - 52.77734375 + 52.66015625 ], [ "chains", - 52.77734375 + 52.66015625 ], [ "fixside", - 52.77734375 + 52.66015625 ], [ "add_hydrogen", - 53.3203125 + 53.20703125 ] ], "metals": { @@ -283,6 +283,7 @@ }, "total_charge": null }, + "version": "3.16.3", "water": { "contacts": { "HOH A100": [ diff --git a/biobb_structure_checking/test/ref/1ubq_all_test_debug.log b/biobb_structure_checking/test/ref/1ubq_all_test_debug.log index 77de5e75..cc282a09 100644 --- a/biobb_structure_checking/test/ref/1ubq_all_test_debug.log +++ b/biobb_structure_checking/test/ref/1ubq_all_test_debug.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ub/1ubq.cif' Structure pdb:1ubq loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: CHROMOSOMAL PROTEIN @@ -20,45 +20,45 @@ Structure pdb:1ubq loaded Num. ligands or modified residues: 0 Num. water mol.: 58 Num. atoms: 660 -#DEBUG Memory used after structure load: 52.726562 MB +#DEBUG Memory used after structure load: 52.605469 MB Step 1: models --select 1 Running models. Options: --select 1 Detected 1 Model(s) Found Single model -#DEBUG Memory used after models: 52.730469 MB +#DEBUG Memory used after models: 52.613281 MB Step 2: chains --select All Running chains. Options: --select All Detected 1 Chain(s) A: Protein -#DEBUG Memory used after chains: 52.730469 MB +#DEBUG Memory used after chains: 52.617188 MB Step 3: inscodes Running inscodes. Found no residues with insertion codes -#DEBUG Memory used after inscodes: 52.730469 MB +#DEBUG Memory used after inscodes: 52.617188 MB Step 4: altloc --select occupancy Running altloc. Options: --select occupancy Detected no residues with alternative location labels -#DEBUG Memory used after altloc: 52.730469 MB +#DEBUG Memory used after altloc: 52.625000 MB Step 5: metals --remove ZN Running metals. Options: --remove ZN No metal ions found -#DEBUG Memory used after metals: 52.738281 MB +#DEBUG Memory used after metals: 52.628906 MB Step 6: ligands --remove SO4 Running ligands. Options: --remove SO4 No ligands found -#DEBUG Memory used after ligands: 52.746094 MB +#DEBUG Memory used after ligands: 52.636719 MB Step 7: water --remove Yes @@ -69,13 +69,13 @@ Water molecules in contact with 1 residues: HOH A78, HOH A80, HOH A81, HOH A84, Water molecules in contact with 2 residues: HOH A79, HOH A86, HOH A98, HOH A104, HOH A107, HOH A131 Water molecules in contact with 3 residues: HOH A96 Removed 58 Water molecules -#DEBUG Memory used after water: 52.761719 MB +#DEBUG Memory used after water: 52.640625 MB Step 8: rem_hydrogen --remove Yes Running rem_hydrogen. Options: --remove Yes No residues with Hydrogen atoms found -#DEBUG Memory used after rem_hydrogen: 52.761719 MB +#DEBUG Memory used after rem_hydrogen: 52.640625 MB Step 9: amide --fix All @@ -85,25 +85,25 @@ Found 1 unusual contact(s) involving amide atoms Amide residues fixed All (1) Rechecking Found no unusual contact(s) involving amide atoms -#DEBUG Memory used after amide: 52.765625 MB +#DEBUG Memory used after amide: 52.644531 MB Step 10: chiral --fix All Running chiral. Options: --fix All Found no residues with incorrect side-chain chirality -#DEBUG Memory used after chiral: 52.769531 MB +#DEBUG Memory used after chiral: 52.644531 MB Step 11: chiral_bck Running chiral_bck. Found no residues with incorrect backbone chirality -#DEBUG Memory used after chiral_bck: 52.769531 MB +#DEBUG Memory used after chiral_bck: 52.648438 MB Step 12: fixside --fix All Running fixside. Options: --fix All Found no residues with missing or unknown side chain atoms -#DEBUG Memory used after fixside: 52.769531 MB +#DEBUG Memory used after fixside: 52.648438 MB Step 13: backbone --fix_atoms All --fix_chain none --add_caps none --no_recheck @@ -115,25 +115,24 @@ Capping terminal ends True terminal residues: A1,A76 Nothing to do No caps added -#DEBUG Memory used after backbone: 52.773438 MB +#DEBUG Memory used after backbone: 52.660156 MB Step 14: cistransbck Running cistransbck. No cis peptide bonds found No trans peptide bonds with unusual omega dihedrals found -#DEBUG Memory used after cistransbck: 52.773438 MB +#DEBUG Memory used after cistransbck: 52.660156 MB Step 15: getss --mark All Running getss. Options: --mark All No SS bonds detected -#DEBUG Memory used after getss: 52.777344 MB +#DEBUG Memory used after getss: 52.660156 MB Step 16: clashes Running clashes. -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected 1 Polar contacts (acceptors) detected @@ -141,20 +140,20 @@ No Apolar steric clashes detected No Polar contacts (donors) detected No Positively charged contacts detected No Negatively charged contacts detected -#DEBUG Memory used after clashes: 52.777344 MB +#DEBUG Memory used after clashes: 52.660156 MB Step 17: ligands --remove All Running ligands. Options: --remove All No ligands found -#DEBUG Memory used after ligands: 52.777344 MB +#DEBUG Memory used after ligands: 52.660156 MB Step 18: chains --select protein Running chains. Options: --select protein Detected 1 Chain(s) A: Protein -#DEBUG Memory used after chains: 52.777344 MB +#DEBUG Memory used after chains: 52.660156 MB Step 19: add_hydrogen --add_mode auto --add_charges ADT @@ -169,12 +168,12 @@ Found 24 Residues requiring selection on adding H atoms WARNING: fixing side chains, override with --no_fix_side Running fixside. Options: --fix all Found no residues with missing or unknown side chain atoms -#DEBUG Memory used after fixside: 52.777344 MB +#DEBUG Memory used after fixside: 52.660156 MB Selection: auto Replacing HIS A68 by HIE Updating partial charges and atom types Total assigned charge: -0.00 -#DEBUG Memory used after add_hydrogen: 53.320312 MB +#DEBUG Memory used after add_hydrogen: 53.207031 MB Command list completed Final Num. models: 1 Final Num. chains: 1 (A: Protein) @@ -188,50 +187,50 @@ Final Num. atoms: 1231 Structure saved on 1ubq_all_test_debug.pdb #DEBUG TIMINGS #DEBUG ======= -#DEBUG load : 0.0721 s ( 13.72%) -#DEBUG models : 0.0010 s ( 0.18%) -#DEBUG chains : 0.0002 s ( 0.04%) -#DEBUG inscodes : 0.0002 s ( 0.03%) -#DEBUG altloc : 0.0003 s ( 0.05%) -#DEBUG metals : 0.0007 s ( 0.13%) -#DEBUG ligands : 0.0003 s ( 0.05%) -#DEBUG water : 0.1016 s ( 19.32%) -#DEBUG rem_hydrogen : 0.0007 s ( 0.14%) -#DEBUG amide : 0.0630 s ( 11.98%) -#DEBUG chiral : 0.0012 s ( 0.22%) -#DEBUG chiral_bck : 0.0026 s ( 0.49%) -#DEBUG fixside : 0.0009 s ( 0.16%) -#DEBUG backbone : 0.0014 s ( 0.26%) -#DEBUG cistransbck : 0.0059 s ( 1.12%) -#DEBUG getss : 0.0005 s ( 0.09%) -#DEBUG clashes : 0.2439 s ( 46.39%) -#DEBUG ligands : 0.0002 s ( 0.03%) +#DEBUG load : 0.1328 s ( 15.34%) +#DEBUG models : 0.0019 s ( 0.22%) +#DEBUG chains : 0.0003 s ( 0.04%) +#DEBUG inscodes : 0.0003 s ( 0.03%) +#DEBUG altloc : 0.0005 s ( 0.06%) +#DEBUG metals : 0.0010 s ( 0.12%) +#DEBUG ligands : 0.0005 s ( 0.06%) +#DEBUG water : 0.1920 s ( 22.17%) +#DEBUG rem_hydrogen : 0.0009 s ( 0.11%) +#DEBUG amide : 0.1340 s ( 15.48%) +#DEBUG chiral : 0.0021 s ( 0.24%) +#DEBUG chiral_bck : 0.0047 s ( 0.55%) +#DEBUG fixside : 0.0016 s ( 0.19%) +#DEBUG backbone : 0.0025 s ( 0.29%) +#DEBUG cistransbck : 0.0079 s ( 0.91%) +#DEBUG getss : 0.0007 s ( 0.09%) +#DEBUG clashes : 0.3379 s ( 39.03%) +#DEBUG ligands : 0.0005 s ( 0.05%) #DEBUG chains : 0.0001 s ( 0.01%) -#DEBUG fixside : 0.0013 s ( 0.25%) -#DEBUG add_hydrogen : 0.0226 s ( 4.30%) -#DEBUG TOTAL : 0.5257 s +#DEBUG fixside : 0.0022 s ( 0.25%) +#DEBUG add_hydrogen : 0.0338 s ( 3.90%) +#DEBUG TOTAL : 0.8658 s #DEBUG MEMORY USAGE EVOLUTION #DEBUG ====================== -#DEBUG load : 52.73 MB -#DEBUG models : 52.73 MB -#DEBUG chains : 52.73 MB -#DEBUG inscodes : 52.73 MB -#DEBUG altloc : 52.73 MB -#DEBUG metals : 52.74 MB -#DEBUG ligands : 52.75 MB -#DEBUG water : 52.76 MB -#DEBUG rem_hydrogen : 52.76 MB -#DEBUG amide : 52.77 MB -#DEBUG chiral : 52.77 MB -#DEBUG chiral_bck : 52.77 MB -#DEBUG fixside : 52.77 MB -#DEBUG backbone : 52.77 MB -#DEBUG cistransbck : 52.77 MB -#DEBUG getss : 52.78 MB -#DEBUG clashes : 52.78 MB -#DEBUG ligands : 52.78 MB -#DEBUG chains : 52.78 MB -#DEBUG fixside : 52.78 MB -#DEBUG add_hydrogen : 53.32 MB +#DEBUG load : 52.61 MB +#DEBUG models : 52.61 MB +#DEBUG chains : 52.62 MB +#DEBUG inscodes : 52.62 MB +#DEBUG altloc : 52.62 MB +#DEBUG metals : 52.63 MB +#DEBUG ligands : 52.64 MB +#DEBUG water : 52.64 MB +#DEBUG rem_hydrogen : 52.64 MB +#DEBUG amide : 52.64 MB +#DEBUG chiral : 52.64 MB +#DEBUG chiral_bck : 52.65 MB +#DEBUG fixside : 52.65 MB +#DEBUG backbone : 52.66 MB +#DEBUG cistransbck : 52.66 MB +#DEBUG getss : 52.66 MB +#DEBUG clashes : 52.66 MB +#DEBUG ligands : 52.66 MB +#DEBUG chains : 52.66 MB +#DEBUG fixside : 52.66 MB +#DEBUG add_hydrogen : 53.21 MB Summary data saved on 1ubq_all_test_debug.json diff --git a/biobb_structure_checking/test/ref/1ubq_amide_test_All.log b/biobb_structure_checking/test/ref/1ubq_amide_test_All.log index f80df3dc..9b5e539f 100644 --- a/biobb_structure_checking/test/ref/1ubq_amide_test_All.log +++ b/biobb_structure_checking/test/ref/1ubq_amide_test_All.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ub/1ubq.cif' Structure pdb:1ubq loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: CHROMOSOMAL PROTEIN diff --git a/biobb_structure_checking/test/ref/1ubq_amide_test_None.log b/biobb_structure_checking/test/ref/1ubq_amide_test_None.log index 21832b82..6767c6b5 100644 --- a/biobb_structure_checking/test/ref/1ubq_amide_test_None.log +++ b/biobb_structure_checking/test/ref/1ubq_amide_test_None.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ub/1ubq.cif' Structure pdb:1ubq loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: CHROMOSOMAL PROTEIN diff --git a/biobb_structure_checking/test/ref/1ubq_backbone_caps_test.log b/biobb_structure_checking/test/ref/1ubq_backbone_caps_test.log index 731eeeb7..dfa6c1da 100644 --- a/biobb_structure_checking/test/ref/1ubq_backbone_caps_test.log +++ b/biobb_structure_checking/test/ref/1ubq_backbone_caps_test.log @@ -1,14 +1,13 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Warning: sequence features may not be available, use --sequence for external fasta input Structure backbone_test/1ubq_caps.pdb loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: structure of ubiquitin refined at 1.8 angstroms resolution test estructure for backbone fix Experimental method: unknown - Resolution (A): N.A. Num. models: 1 Num. chains: 1 (A: Protein) @@ -75,7 +74,6 @@ Found 4 Backbone breaks NME A44 - ACE A46 No unexpected backbone links Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected No Polar contacts (acceptors) detected diff --git a/biobb_structure_checking/test/ref/1ubq_backbone_main_test.log b/biobb_structure_checking/test/ref/1ubq_backbone_main_test.log index ed0136e4..f2fec4bd 100644 --- a/biobb_structure_checking/test/ref/1ubq_backbone_main_test.log +++ b/biobb_structure_checking/test/ref/1ubq_backbone_main_test.log @@ -1,15 +1,14 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Getting canonical sequences from matching FASTA input A: "1ubq_A protein 76 UBIQUITIN", score: 46.0 Structure backbone_test/1ubq_caps.pdb loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: structure of ubiquitin refined at 1.8 angstroms resolution test estructure for backbone fix Experimental method: unknown - Resolution (A): N.A. Num. models: 1 Num. chains: 1 (A: Protein) @@ -58,10 +57,10 @@ Main chain fixes Birkbeck College, University of London, London, UK -Kind, OS, HostName, Kernel, Processor: 4, Linux portjlg7 6.18.33.1-microsoft-standard-WSL2 x86_64 +Kind, OS, HostName, Kernel, Processor: 4, Linux portjlg7 6.18.33.2-microsoft-standard-WSL2 x86_64 Date and time of compilation : 2025/05/28 18:48:33 MODELLER executable type : x86_64-intel8 -Job starting time (YY/MM/DD HH:MM:SS): 2026/06/19 16:33:07 +Job starting time (YY/MM/DD HH:MM:SS): 2026/09/01 14:46:52 Fixing chain/model A/0 0 atoms in HETATM/BLK residues constrained @@ -153,7 +152,6 @@ No caps added Fixing missing backbone atoms Nothing to do Checking for steric clashes -False 10 Severe Steric clashes/covalent bonds detected ILE A3.O GLU A16.O 1.747 A LYS A6.CA THR A14.N 1.717 A diff --git a/biobb_structure_checking/test/ref/1ubq_chi_chiral_test_All.log b/biobb_structure_checking/test/ref/1ubq_chi_chiral_test_All.log index 0fb60655..d24924f6 100644 --- a/biobb_structure_checking/test/ref/1ubq_chi_chiral_test_All.log +++ b/biobb_structure_checking/test/ref/1ubq_chi_chiral_test_All.log @@ -1,15 +1,14 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Warning: sequence features may not be available, use --sequence for external fasta input Structure chiral_pdb_test/1ubq_chi.pdb loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: structure of ubiquitin refined at 1.8 angstroms resolution Experimental method: x-ray diffraction Keywords: chromosomal protein - Resolution (A): 1.8 Num. models: 1 Num. chains: 1 (A: Protein) @@ -26,7 +25,6 @@ Found 2 residues with incorrect side-chain chirality THR A7 Chiral side chains fixed All (2) Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected No Polar contacts (acceptors) detected diff --git a/biobb_structure_checking/test/ref/1ubq_chi_none_test_None.log b/biobb_structure_checking/test/ref/1ubq_chi_none_test_None.log index e392e821..651f2c63 100644 --- a/biobb_structure_checking/test/ref/1ubq_chi_none_test_None.log +++ b/biobb_structure_checking/test/ref/1ubq_chi_none_test_None.log @@ -1,15 +1,14 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Warning: sequence features may not be available, use --sequence for external fasta input Structure chiral_pdb_test/1ubq_chi.pdb loaded - PDB id: 1UBQ + Entry id: 1UBQ Title: structure of ubiquitin refined at 1.8 angstroms resolution Experimental method: x-ray diffraction Keywords: chromosomal protein - Resolution (A): 1.8 Num. models: 1 Num. chains: 1 (A: Protein) diff --git a/biobb_structure_checking/test/ref/1vtk_1_all_test.json b/biobb_structure_checking/test/ref/1vtk_1_all_test.json index 70239ad3..bc0860dc 100644 --- a/biobb_structure_checking/test/ref/1vtk_1_all_test.json +++ b/biobb_structure_checking/test/ref/1vtk_1_all_test.json @@ -526,37 +526,7 @@ }, "loaded_structure": "pdb:1vtk.1", "metals": { - "contacts": { - "ADP A-2400": [ - "ARG A-2216.NH2", - "GLN A-2331.O", - "PRO A-2333.N", - "TMP A-2500.O2P", - "GLY A-259.N", - "MET A-260.N", - "GLY A-261.N", - "LYS A-262.N", - "THR A-263.N", - "THR A-264.N" - ], - "ADP A400": [ - "ARG A216.NH2", - "GLN A331.O", - "PRO A333.N", - "TMP A500.O2P", - "GLY A59.N", - "MET A60.N", - "GLY A61.N", - "LYS A62.N", - "THR A63.N", - "THR A64.N" - ] - }, - "detected": [ - "ADP A400", - "ADP A-2400" - ], - "error": "Unknown selection ZN" + "opts": "--remove ZN" }, "models": { "nmodels": 1 @@ -608,6 +578,7 @@ }, "total_charge": null }, + "version": "3.16.3", "water": { "contacts": { "HOH A-2601": [], diff --git a/biobb_structure_checking/test/ref/1vtk_1_models_complex.log b/biobb_structure_checking/test/ref/1vtk_1_models_complex.log index 96106957..afabc9ad 100644 --- a/biobb_structure_checking/test/ref/1vtk_1_models_complex.log +++ b/biobb_structure_checking/test/ref/1vtk_1_models_complex.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/vt/1vtk-assembly1.cif' Structure pdb:1vtk.1 loaded - PDB id: 1vtk (Assembly 1) + Entry id: 1vtk (Assembly 1) Title: THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND DEOXYTHYMIDINE-MONOPHOSPHATE Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/1vtk_1_svc_all_test.log b/biobb_structure_checking/test/ref/1vtk_1_svc_all_test.log index c019d6fc..e7eabd29 100644 --- a/biobb_structure_checking/test/ref/1vtk_1_svc_all_test.log +++ b/biobb_structure_checking/test/ref/1vtk_1_svc_all_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/vt/1vtk-assembly1.cif' Structure pdb:1vtk.1 loaded - PDB id: 1vtk (Assembly 1) + Entry id: 1vtk (Assembly 1) Title: THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND DEOXYTHYMIDINE-MONOPHOSPHATE Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE @@ -52,12 +52,7 @@ Detected no residues with alternative location labels Step 5: metals --remove ZN Running metals. Options: --remove ZN -Found 2 Metal ions - ADP A400.PB ADENOSINE-5'-DIPHOSPHATE - ADP A-2400.PB ADENOSINE-5'-DIPHOSPHATE -Contacts for ADP A400: ARG A216.NH2, GLN A331.O, PRO A333.N, TMP A500.O2P, GLY A59.N, MET A60.N, GLY A61.N, LYS A62.N, THR A63.N, THR A64.N -Contacts for ADP A-2400: ARG A-2216.NH2, GLN A-2331.O, PRO A-2333.N, TMP A-2500.O2P, GLY A-259.N, MET A-260.N, GLY A-261.N, LYS A-262.N, THR A-263.N, THR A-264.N -Input not valid (ZN) +No metal ions found Step 6: ligands --remove SO4 @@ -149,7 +144,6 @@ GLY A-2264 Adding new atom OXT Fixed 4 backbone atom(s) Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected 2 Polar contacts (acceptors) detected @@ -173,7 +167,6 @@ No SS bonds detected Step 16: clashes Running clashes. -False No Severe Steric clashes/covalent bonds detected 4 Apolar steric clashes detected GLY A59.O HIS A213.CD2 2.824 A diff --git a/biobb_structure_checking/test/ref/1vtk_checkall_test.log b/biobb_structure_checking/test/ref/1vtk_checkall_test.log index e3adfa8a..c7ea33da 100644 --- a/biobb_structure_checking/test/ref/1vtk_checkall_test.log +++ b/biobb_structure_checking/test/ref/1vtk_checkall_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/vt/1vtk-assembly1.cif' Structure pdb:1vtk.1 loaded - PDB id: 1vtk (Assembly 1) + Entry id: 1vtk (Assembly 1) Title: THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND DEOXYTHYMIDINE-MONOPHOSPHATE Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE @@ -61,11 +61,7 @@ Water molecules in contact with 3 residues: HOH A604, HOH A-2604 Water molecules in contact with 4 residues: HOH A611, HOH A635, HOH A-2611, HOH A-2635 Running check_only. Nothing else to do. Running metals. -Found 2 Metal ions - ADP A400.PB ADENOSINE-5'-DIPHOSPHATE - ADP A-2400.PB ADENOSINE-5'-DIPHOSPHATE -Contacts for ADP A400: ARG A216.NH2, GLN A331.O, PRO A333.N, TMP A500.O2P, GLY A59.N, MET A60.N, GLY A61.N, LYS A62.N, THR A63.N, THR A64.N -Contacts for ADP A-2400: ARG A-2216.NH2, GLN A-2331.O, PRO A-2333.N, TMP A-2500.O2P, GLY A-259.N, MET A-260.N, GLY A-261.N, LYS A-262.N, THR A-263.N, THR A-264.N +No metal ions found Running check_only. Nothing else to do. Running ligands. Detected 4 Ligands @@ -113,7 +109,6 @@ No cis peptide bonds found No trans peptide bonds with unusual omega dihedrals found Running check_only. Nothing else to do. Running clashes. -False No Severe Steric clashes/covalent bonds detected 4 Apolar steric clashes detected GLY A59.O HIS A213.CD2 2.824 A diff --git a/biobb_structure_checking/test/ref/2ki5_all_test.json b/biobb_structure_checking/test/ref/2ki5_all_test.json index 3664af78..325bea27 100644 --- a/biobb_structure_checking/test/ref/2ki5_all_test.json +++ b/biobb_structure_checking/test/ref/2ki5_all_test.json @@ -214,7 +214,7 @@ } ] }, - "selected": "OCCUPANCY" + "selected": "occupancy" }, "amide": { "n_amides": 32, @@ -785,6 +785,7 @@ }, "total_charge": null }, + "version": "3.16.3", "water": { "contacts": { "HOH A501": [], diff --git a/biobb_structure_checking/test/ref/2ki5_all_test.log b/biobb_structure_checking/test/ref/2ki5_all_test.log index 7726c858..ea7bc001 100644 --- a/biobb_structure_checking/test/ref/2ki5_all_test.log +++ b/biobb_structure_checking/test/ref/2ki5_all_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE @@ -158,7 +158,6 @@ ARG B220 Adding new atom NH2 Fixed 6 side chain(s) Checking for steric clashes -False 3 Severe Steric clashes/covalent bonds detected MET A46.CE VAL A352.CG2 1.843 A MET A46.CE THR A354.O 1.869 A @@ -226,7 +225,6 @@ ALA B375 Warning: not enough backbone to build missing atoms Fixed 0 backbone atom(s) Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected No Polar contacts (acceptors) detected @@ -248,7 +246,6 @@ No SS bonds detected Step 16: clashes Running clashes. -False 3 Severe Steric clashes/covalent bonds detected MET A46.CE VAL A352.CG2 1.843 A MET A46.CE THR A354.O 1.869 A diff --git a/biobb_structure_checking/test/ref/2ki5_altloc_test_B.log b/biobb_structure_checking/test/ref/2ki5_altloc_test_B.log index 20d8fc6e..b10c6c1d 100644 --- a/biobb_structure_checking/test/ref/2ki5_altloc_test_B.log +++ b/biobb_structure_checking/test/ref/2ki5_altloc_test_B.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_altloc_test_occ.log b/biobb_structure_checking/test/ref/2ki5_altloc_test_occ.log index bb1f2dd4..b332e6ab 100644 --- a/biobb_structure_checking/test/ref/2ki5_altloc_test_occ.log +++ b/biobb_structure_checking/test/ref/2ki5_altloc_test_occ.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_backbone_test.log b/biobb_structure_checking/test/ref/2ki5_backbone_test.log index a7db00aa..757c70f3 100644 --- a/biobb_structure_checking/test/ref/2ki5_backbone_test.log +++ b/biobb_structure_checking/test/ref/2ki5_backbone_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_chains_test_B.log b/biobb_structure_checking/test/ref/2ki5_chains_test_B.log index 08b76919..4d05bc4c 100644 --- a/biobb_structure_checking/test/ref/2ki5_chains_test_B.log +++ b/biobb_structure_checking/test/ref/2ki5_chains_test_B.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_chains_test_all.log b/biobb_structure_checking/test/ref/2ki5_chains_test_all.log index 47c2842b..4ef61c59 100644 --- a/biobb_structure_checking/test/ref/2ki5_chains_test_all.log +++ b/biobb_structure_checking/test/ref/2ki5_chains_test_all.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_chains_test_fix_chains.log b/biobb_structure_checking/test/ref/2ki5_chains_test_fix_chains.log index d6e3a112..b27f79a6 100644 --- a/biobb_structure_checking/test/ref/2ki5_chains_test_fix_chains.log +++ b/biobb_structure_checking/test/ref/2ki5_chains_test_fix_chains.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_chains_test_rebuild.log b/biobb_structure_checking/test/ref/2ki5_chains_test_rebuild.log index 950f9afa..2e7f8921 100644 --- a/biobb_structure_checking/test/ref/2ki5_chains_test_rebuild.log +++ b/biobb_structure_checking/test/ref/2ki5_chains_test_rebuild.log @@ -1,5 +1,5 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ @@ -9,7 +9,7 @@ Warning, no canonical sequence available for chain 0/0 Warning, no canonical sequence available for chain h/0 Warning, no canonical sequence available for chain w/0 Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_chains_test_renum_chain.log b/biobb_structure_checking/test/ref/2ki5_chains_test_renum_chain.log index 49caa315..74e7c89c 100644 --- a/biobb_structure_checking/test/ref/2ki5_chains_test_renum_chain.log +++ b/biobb_structure_checking/test/ref/2ki5_chains_test_renum_chain.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_checkall_test.log b/biobb_structure_checking/test/ref/2ki5_checkall_test.log index 8b581dfc..01ba2fca 100644 --- a/biobb_structure_checking/test/ref/2ki5_checkall_test.log +++ b/biobb_structure_checking/test/ref/2ki5_checkall_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5-assembly1.cif' Structure pdb:2ki5.1 loaded - PDB id: 2ki5 (Assembly 1) + Entry id: 2ki5 (Assembly 1) Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE @@ -139,7 +139,6 @@ No cis peptide bonds found No trans peptide bonds with unusual omega dihedrals found Running check_only. Nothing else to do. Running clashes. -False No Severe Steric clashes/covalent bonds detected 13 Apolar steric clashes detected GLY A61.O THR A65.CG2 2.799 A diff --git a/biobb_structure_checking/test/ref/2ki5_clashes_test.log b/biobb_structure_checking/test/ref/2ki5_clashes_test.log index 8c30015f..ebe3ae0a 100644 --- a/biobb_structure_checking/test/ref/2ki5_clashes_test.log +++ b/biobb_structure_checking/test/ref/2ki5_clashes_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE @@ -26,7 +26,6 @@ AC2 A1 (9-HYROXYETHOXYMETHYLGUANINE) SO4 B3 (SULFATE ION) AC2 B2 (9-HYROXYETHOXYMETHYLGUANINE) Running clashes. -False No Severe Steric clashes/covalent bonds detected 13 Apolar steric clashes detected GLY A61.O THR A65.CG2 2.799 A diff --git a/biobb_structure_checking/test/ref/2ki5_fixside_All_rb_test.log b/biobb_structure_checking/test/ref/2ki5_fixside_All_rb_test.log index 466b5c25..d2cafec6 100644 --- a/biobb_structure_checking/test/ref/2ki5_fixside_All_rb_test.log +++ b/biobb_structure_checking/test/ref/2ki5_fixside_All_rb_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE @@ -56,10 +56,10 @@ Fixing side chains Birkbeck College, University of London, London, UK -Kind, OS, HostName, Kernel, Processor: 4, Linux portjlg7 6.18.33.1-microsoft-standard-WSL2 x86_64 +Kind, OS, HostName, Kernel, Processor: 4, Linux portjlg7 6.18.33.2-microsoft-standard-WSL2 x86_64 Date and time of compilation : 2025/05/28 18:48:33 MODELLER executable type : x86_64-intel8 -Job starting time (YY/MM/DD HH:MM:SS): 2026/06/19 16:33:07 +Job starting time (YY/MM/DD HH:MM:SS): 2026/09/01 14:46:50 Fixing chain/model A/0 0 atoms in HETATM/BLK residues constrained @@ -136,7 +136,6 @@ Fixing LYS B219 - GLN B221 Fixed 0 side chain(s) Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected 1 Polar contacts (acceptors) detected diff --git a/biobb_structure_checking/test/ref/2ki5_fixside_All_test.log b/biobb_structure_checking/test/ref/2ki5_fixside_All_test.log index d6307047..f9143163 100644 --- a/biobb_structure_checking/test/ref/2ki5_fixside_All_test.log +++ b/biobb_structure_checking/test/ref/2ki5_fixside_All_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE @@ -60,7 +60,6 @@ ARG B220 Adding new atom NH2 Fixed 6 side chain(s) Checking for steric clashes -False 4 Severe Steric clashes/covalent bonds detected MET A46.CE VAL A352.CG2 1.843 A MET A46.CE THR A354.O 1.869 A diff --git a/biobb_structure_checking/test/ref/2ki5_fixside_None_test.log b/biobb_structure_checking/test/ref/2ki5_fixside_None_test.log index 744b924b..73a2dc78 100644 --- a/biobb_structure_checking/test/ref/2ki5_fixside_None_test.log +++ b/biobb_structure_checking/test/ref/2ki5_fixside_None_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_keepwat_test_3.log b/biobb_structure_checking/test/ref/2ki5_keepwat_test_3.log index 98f4c1a0..f36a78bd 100644 --- a/biobb_structure_checking/test/ref/2ki5_keepwat_test_3.log +++ b/biobb_structure_checking/test/ref/2ki5_keepwat_test_3.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_ligands_test_All.log b/biobb_structure_checking/test/ref/2ki5_ligands_test_All.log index 4d12278e..da890284 100644 --- a/biobb_structure_checking/test/ref/2ki5_ligands_test_All.log +++ b/biobb_structure_checking/test/ref/2ki5_ligands_test_All.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_ligands_test_None.log b/biobb_structure_checking/test/ref/2ki5_ligands_test_None.log index 1805760c..aef69112 100644 --- a/biobb_structure_checking/test/ref/2ki5_ligands_test_None.log +++ b/biobb_structure_checking/test/ref/2ki5_ligands_test_None.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_ligands_test_SO4.log b/biobb_structure_checking/test/ref/2ki5_ligands_test_SO4.log index 6721de8c..40a84e05 100644 --- a/biobb_structure_checking/test/ref/2ki5_ligands_test_SO4.log +++ b/biobb_structure_checking/test/ref/2ki5_ligands_test_SO4.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.json b/biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.json index 90efb663..ed254820 100644 --- a/biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.json +++ b/biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.json @@ -109,5 +109,6 @@ "res_ligands": 4 }, "total_charge": null - } + }, + "version": "3.16.3" } \ No newline at end of file diff --git a/biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.log b/biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.log index 57a9202f..4c26add0 100644 --- a/biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.log +++ b/biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE @@ -50,10 +50,10 @@ Mutations to perform Birkbeck College, University of London, London, UK -Kind, OS, HostName, Kernel, Processor: 4, Linux portjlg7 6.18.33.1-microsoft-standard-WSL2 x86_64 +Kind, OS, HostName, Kernel, Processor: 4, Linux portjlg7 6.18.33.2-microsoft-standard-WSL2 x86_64 Date and time of compilation : 2025/05/28 18:48:33 MODELLER executable type : x86_64-intel8 -Job starting time (YY/MM/DD HH:MM:SS): 2026/06/19 16:33:05 +Job starting time (YY/MM/DD HH:MM:SS): 2026/09/01 14:46:47 Fixing chain/model A/0 0 atoms in HETATM/BLK residues constrained @@ -94,7 +94,6 @@ Fixing THR B48 - LEU B50 Adding LEU B50 Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected 1 Apolar steric clashes detected ILE A49.CD1 ILE A143.CD1 2.815 A diff --git a/biobb_structure_checking/test/ref/2ki5_mutateside_test.json b/biobb_structure_checking/test/ref/2ki5_mutateside_test.json index 6d4324a7..77b90af4 100644 --- a/biobb_structure_checking/test/ref/2ki5_mutateside_test.json +++ b/biobb_structure_checking/test/ref/2ki5_mutateside_test.json @@ -124,5 +124,6 @@ "res_ligands": 4 }, "total_charge": null - } + }, + "version": "3.16.3" } \ No newline at end of file diff --git a/biobb_structure_checking/test/ref/2ki5_mutateside_test.log b/biobb_structure_checking/test/ref/2ki5_mutateside_test.log index 25eba84c..cf222001 100644 --- a/biobb_structure_checking/test/ref/2ki5_mutateside_test.log +++ b/biobb_structure_checking/test/ref/2ki5_mutateside_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE @@ -47,7 +47,6 @@ Replacing ARG B51 into LYS Adding new atom NZ Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected 4 Apolar steric clashes detected ILE A49.CG2 THR A350.OG1 2.815 A diff --git a/biobb_structure_checking/test/ref/2ki5_remwat_test_None.log b/biobb_structure_checking/test/ref/2ki5_remwat_test_None.log index 8b3aa415..17fe031c 100644 --- a/biobb_structure_checking/test/ref/2ki5_remwat_test_None.log +++ b/biobb_structure_checking/test/ref/2ki5_remwat_test_None.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_remwat_test_Yes.log b/biobb_structure_checking/test/ref/2ki5_remwat_test_Yes.log index 82805448..85e6f357 100644 --- a/biobb_structure_checking/test/ref/2ki5_remwat_test_Yes.log +++ b/biobb_structure_checking/test/ref/2ki5_remwat_test_Yes.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/2ki5_sequences_test.log b/biobb_structure_checking/test/ref/2ki5_sequences_test.log index 415d2b3d..a7e9cf16 100644 --- a/biobb_structure_checking/test/ref/2ki5_sequences_test.log +++ b/biobb_structure_checking/test/ref/2ki5_sequences_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/ki/2ki5.cif' Structure pdb:2ki5 loaded - PDB id: 2KI5 + Entry id: 2KI5 Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: TRANSFERASE diff --git a/biobb_structure_checking/test/ref/3nir_sequences.fasta b/biobb_structure_checking/test/ref/3nir_sequences.fasta new file mode 100644 index 00000000..75f783a8 --- /dev/null +++ b/biobb_structure_checking/test/ref/3nir_sequences.fasta @@ -0,0 +1,4 @@ +>can_sq_A canonical sequence chain A +TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN +>pdb_sq_A Frags: 1-46 +TTCCPSIVARSNFNVCRLPGTSEAICATYTGCIIIPGATCPGDYAN diff --git a/biobb_structure_checking/test/ref/3nir_sequences_test.log b/biobb_structure_checking/test/ref/3nir_sequences_test.log new file mode 100644 index 00000000..bf63a0f7 --- /dev/null +++ b/biobb_structure_checking/test/ref/3nir_sequences_test.log @@ -0,0 +1,42 @@ +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/ni/3nir.cif' +Structure pdb:3nir loaded + Entry id: 3NIR + Title: Crystal structure of small protein crambin at 0.48 A resolution + Experimental method: X-RAY DIFFRACTION + Keywords: PLANT PROTEIN + Resolution (A): 0.48 + + Num. models: 1 + Num. chains: 1 (A: Protein) + Num. residues: 148 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 46 (total 315 H atoms) + Num. HETATM residues: 102 + Num. ligands or modified residues: 4 + Num. water mol.: 98 + Num. atoms: 751 +Small mol ligands found +EOH A2001 (ETHANOL) +EOH A2002 (ETHANOL) +EOH A2003 (ETHANOL) +EOH A2004 (ETHANOL) +Running sequences. Options: --output_fasta 3nir_sequences.fasta +Canonical sequence +>can_sq_A canonical sequence chain A +TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN + +Structure sequence +>pdb_sq_A Frags: 1-46 +TTCCPSIVARSNFNVCRLPGTSEAICATYTGCIIIPGATCPGDYAN + +Found 1 mismatch(es) +Chain A/0 +---------------------P--L--------------------- +---------------------S--I--------------------- +Sequences written on 3nir_sequences.fasta +Structure not modified, not saving. Override with --force_save diff --git a/biobb_structure_checking/test/ref/4ku1_all_test.json b/biobb_structure_checking/test/ref/4ku1_all_test.json index bc3094db..e499fb4e 100644 --- a/biobb_structure_checking/test/ref/4ku1_all_test.json +++ b/biobb_structure_checking/test/ref/4ku1_all_test.json @@ -504,7 +504,7 @@ } ] }, - "selected": "OCCUPANCY" + "selected": "occupancy" }, "amide": { "n_amides": 40, @@ -933,6 +933,7 @@ }, "total_charge": null }, + "version": "3.16.3", "water": { "contacts": { "HOH A601": [ diff --git a/biobb_structure_checking/test/ref/4ku1_all_test.log b/biobb_structure_checking/test/ref/4ku1_all_test.log index 1cc10ef3..a871db5b 100644 --- a/biobb_structure_checking/test/ref/4ku1_all_test.log +++ b/biobb_structure_checking/test/ref/4ku1_all_test.log @@ -1,5 +1,5 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ @@ -7,7 +7,7 @@ Structure exists: 'tmpPDB/ku/4ku1.cif' Warning, no canonical sequence available for chain C/0 Warning, no canonical sequence available for chain D/0 Structure pdb:4ku1 loaded - PDB id: 4KU1 + Entry id: 4KU1 Title: Role of the hinge and C-gamma-2/C-gamma-3 interface in immunoglobin G1 Fc domain motions: implications for Fc engineering Experimental method: X-RAY DIFFRACTION Keywords: IMMUNE SYSTEM @@ -221,7 +221,6 @@ SER B444 Adding new atom OXT Fixed 2 backbone atom(s) Checking for steric clashes -False No Severe Steric clashes/covalent bonds detected No Apolar steric clashes detected No Polar contacts (acceptors) detected @@ -251,7 +250,6 @@ Warning, no canonical sequence available for chain D/0 Step 16: clashes Running clashes. -False 7 Severe Steric clashes/covalent bonds detected ASN A297.ND2 NAG C1.C1 1.903 A CYX A367.SG CYX A425.SG 1.995 A diff --git a/biobb_structure_checking/test/ref/4ku1_getss_mark_test.log b/biobb_structure_checking/test/ref/4ku1_getss_mark_test.log index e21afb61..b3084ec2 100644 --- a/biobb_structure_checking/test/ref/4ku1_getss_mark_test.log +++ b/biobb_structure_checking/test/ref/4ku1_getss_mark_test.log @@ -1,5 +1,5 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ @@ -7,7 +7,7 @@ Structure exists: 'tmpPDB/ku/4ku1.cif' Warning, no canonical sequence available for chain C/0 Warning, no canonical sequence available for chain D/0 Structure pdb:4ku1 loaded - PDB id: 4KU1 + Entry id: 4KU1 Title: Role of the hinge and C-gamma-2/C-gamma-3 interface in immunoglobin G1 Fc domain motions: implications for Fc engineering Experimental method: X-RAY DIFFRACTION Keywords: IMMUNE SYSTEM diff --git a/biobb_structure_checking/test/ref/4ku1_getss_test.log b/biobb_structure_checking/test/ref/4ku1_getss_test.log index e99f0249..2e26ec72 100644 --- a/biobb_structure_checking/test/ref/4ku1_getss_test.log +++ b/biobb_structure_checking/test/ref/4ku1_getss_test.log @@ -1,5 +1,5 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ @@ -7,7 +7,7 @@ Structure exists: 'tmpPDB/ku/4ku1.cif' Warning, no canonical sequence available for chain C/0 Warning, no canonical sequence available for chain D/0 Structure pdb:4ku1 loaded - PDB id: 4KU1 + Entry id: 4KU1 Title: Role of the hinge and C-gamma-2/C-gamma-3 interface in immunoglobin G1 Fc domain motions: implications for Fc engineering Experimental method: X-RAY DIFFRACTION Keywords: IMMUNE SYSTEM diff --git a/biobb_structure_checking/test/ref/4mdh_cistransbck_test.log b/biobb_structure_checking/test/ref/4mdh_cistransbck_test.log index 2eecc48e..7c364c44 100644 --- a/biobb_structure_checking/test/ref/4mdh_cistransbck_test.log +++ b/biobb_structure_checking/test/ref/4mdh_cistransbck_test.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/md/4mdh.cif' Structure pdb:4mdh loaded - PDB id: 4MDH + Entry id: 4MDH Title: REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION Experimental method: X-RAY DIFFRACTION Keywords: OXIDOREDUCTASE(NAD(A)-CHOH(D)) @@ -21,8 +21,8 @@ Structure pdb:4mdh loaded Num. water mol.: 471 Num. atoms: 5675 Modified residues found -ACE A0 -ACE B0 +ACE A0 (ACETYL GROUP) +ACE B0 (ACETYL GROUP) Small mol ligands found SO4 A334 (SULFATE ION) NAD A335 (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) diff --git a/biobb_structure_checking/test/ref/6m0j_amide_test_auto.log b/biobb_structure_checking/test/ref/6m0j_amide_test_auto.log index 28692fc8..ba82fe5c 100644 --- a/biobb_structure_checking/test/ref/6m0j_amide_test_auto.log +++ b/biobb_structure_checking/test/ref/6m0j_amide_test_auto.log @@ -1,11 +1,11 @@ ================================================================================ -= BioBB structure checking utility v3.16.2 = += BioBB structure checking utility v3.16.3 = = P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = ================================================================================ Structure exists: 'tmpPDB/m0/6m0j.cif' Structure pdb:6m0j loaded - PDB id: 6M0J + Entry id: 6M0J Title: Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 Experimental method: X-RAY DIFFRACTION Keywords: VIRAL PROTEIN/HYDROLASE diff --git a/biobb_structure_checking/test/ref/load_cache.log b/biobb_structure_checking/test/ref/load_cache.log new file mode 100644 index 00000000..1ba42610 --- /dev/null +++ b/biobb_structure_checking/test/ref/load_cache.log @@ -0,0 +1,399 @@ +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/ar/1ark.cif' +Structure pdb:1ark loaded + Entry id: 1ARK + Title: SH3 DOMAIN FROM HUMAN NEBULIN, NMR, 15 STRUCTURES + Experimental method: SOLUTION NMR + Keywords: TRANSFERASE + + Num. models: 15 (type: BioUnit, 35.032 A) + Num. chains: 15 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein) + Num. residues: 900 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 900 (total 6630 H atoms) + Num. HETATM residues: 0 + Num. ligands or modified residues: 0 + Num. water mol.: 0 + Num. atoms: 13575 +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/ki/2ki5.cif' +Structure pdb:2ki5 loaded + Entry id: 2KI5 + Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION + Experimental method: X-RAY DIFFRACTION + Keywords: TRANSFERASE + Resolution (A): 1.90 + + Num. models: 1 + Num. chains: 2 (A: Protein, B: Protein) + Num. residues: 908 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 296 + Num. ligands or modified residues: 4 + Num. water mol.: 292 + Num. atoms: 4961 +Small mol ligands found +SO4 A4 (SULFATE ION) +AC2 A1 (9-HYROXYETHOXYMETHYLGUANINE) +SO4 B3 (SULFATE ION) +AC2 B2 (9-HYROXYETHOXYMETHYLGUANINE) +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/sv/1svc.cif' +Structure pdb:1svc loaded + Entry id: 1SVC + Title: NFKB P50 HOMODIMER BOUND TO DNA + Experimental method: X-RAY DIFFRACTION + Keywords: TRANSCRIPTION/DNA + Resolution (A): 2.600 + + Num. models: 1 + Num. chains: 2 (D: DNA, P: Protein) + Num. residues: 393 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 63 + Num. ligands or modified residues: 0 + Num. water mol.: 63 + Num. atoms: 2903 +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/04/104l.cif' +Structure pdb:104l loaded + Entry id: 104L + Title: HOW AMINO-ACID INSERTIONS ARE ALLOWED IN AN ALPHA-HELIX OF T4 LYSOZYME + Experimental method: X-RAY DIFFRACTION + Keywords: HYDROLASE(O-GLYCOSYL) + Resolution (A): 2.8 + + Num. models: 1 + Num. chains: 2 (A: Protein, B: Protein) + Num. residues: 360 + Num. residues with ins. codes: 4 + Num. residues with H atoms: 0 + Num. HETATM residues: 32 + Num. ligands or modified residues: 0 + Num. water mol.: 32 + Num. atoms: 2636 +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/bq/1bqo.cif' +Structure pdb:1bqo loaded + Entry id: 1BQO + Title: DISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE INHIBITORS + Experimental method: X-RAY DIFFRACTION + Keywords: METALLOPROTEASE + Resolution (A): 2.3 + + Num. models: 1 + Num. chains: 2 (A: Protein, B: Protein) + Num. residues: 428 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 86 + Num. ligands or modified residues: 11 + Num. water mol.: 75 + Num. atoms: 2841 +Metal/Ion residues found + ZN A301 (ZINC ION) + ZN A302 (ZINC ION) + CA A303 (CALCIUM ION) + CA A304 (CALCIUM ION) + CA A305 (CALCIUM ION) + ZN B301 (ZINC ION) + ZN B302 (ZINC ION) + CA B303 (CALCIUM ION) + CA B304 (CALCIUM ION) + CA B305 (CALCIUM ION) +Small mol ligands found +N25 B401 (1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHY) +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/ku/4ku1.cif' +Warning, no canonical sequence available for chain C/0 +Warning, no canonical sequence available for chain D/0 +Structure pdb:4ku1 loaded + Entry id: 4KU1 + Title: Role of the hinge and C-gamma-2/C-gamma-3 interface in immunoglobin G1 Fc domain motions: implications for Fc engineering + Experimental method: X-RAY DIFFRACTION + Keywords: IMMUNE SYSTEM + Resolution (A): 1.90 + + Num. models: 1 + Num. chains: 4 (A: Protein, B: Protein, C: Unknown, D: Unknown) + Num. residues: 583 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 168 + Num. ligands or modified residues: 20 + Num. water mol.: 148 + Num. atoms: 3714 +Small mol ligands found +PG4 A511 (TETRAETHYLENE GLYCOL) +NAG C1 (2-acetamido-2-deoxy-beta-D-glucopyranose) +NAG C2 (2-acetamido-2-deoxy-beta-D-glucopyranose) +BMA C3 (beta-D-mannopyranose) +MAN C4 (alpha-D-mannopyranose) +NAG C5 (2-acetamido-2-deoxy-beta-D-glucopyranose) +GAL C6 (beta-D-galactopyranose) +MAN C7 (alpha-D-mannopyranose) +NAG C8 (2-acetamido-2-deoxy-beta-D-glucopyranose) +GAL C9 (beta-D-galactopyranose) +FUL C10 (beta-L-fucopyranose) +NAG D1 (2-acetamido-2-deoxy-beta-D-glucopyranose) +NAG D2 (2-acetamido-2-deoxy-beta-D-glucopyranose) +BMA D3 (beta-D-mannopyranose) +MAN D4 (alpha-D-mannopyranose) +NAG D5 (2-acetamido-2-deoxy-beta-D-glucopyranose) +GAL D6 (beta-D-galactopyranose) +MAN D7 (alpha-D-mannopyranose) +NAG D8 (2-acetamido-2-deoxy-beta-D-glucopyranose) +FUL D9 (beta-L-fucopyranose) +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/ub/1ubq.cif' +Structure pdb:1ubq loaded + Entry id: 1UBQ + Title: STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION + Experimental method: X-RAY DIFFRACTION + Keywords: CHROMOSOMAL PROTEIN + Resolution (A): 1.8 + + Num. models: 1 + Num. chains: 1 (A: Protein) + Num. residues: 134 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 58 + Num. ligands or modified residues: 0 + Num. water mol.: 58 + Num. atoms: 660 +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/md/4mdh.cif' +Structure pdb:4mdh loaded + Entry id: 4MDH + Title: REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION + Experimental method: X-RAY DIFFRACTION + Keywords: OXIDOREDUCTASE(NAD(A)-CHOH(D)) + Resolution (A): 2.5 + + Num. models: 1 + Num. chains: 2 (A: Protein, B: Protein) + Num. residues: 1143 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 477 + Num. ligands or modified residues: 6 + Num. water mol.: 471 + Num. atoms: 5675 +Modified residues found +ACE A0 (ACETYL GROUP) +ACE B0 (ACETYL GROUP) +Small mol ligands found +SO4 A334 (SULFATE ION) +NAD A335 (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) +SO4 B334 (SULFATE ION) +NAD B335 (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/d2/1d23.cif' +Structure pdb:1d23 loaded + Entry id: 1D23 + Title: THE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALS + Experimental method: X-RAY DIFFRACTION + Keywords: DNA + Resolution (A): 1.500 + + Num. models: 1 + Num. chains: 2 (A: DNA, B: DNA) + Num. residues: 176 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 156 + Num. ligands or modified residues: 2 + Num. water mol.: 154 + Num. atoms: 560 +Metal/Ion residues found + MG A22 (MAGNESIUM ION) + MG B21 (MAGNESIUM ION) +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/m0/6m0j.cif' +Structure pdb:6m0j loaded + Entry id: 6M0J + Title: Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 + Experimental method: X-RAY DIFFRACTION + Keywords: VIRAL PROTEIN/HYDROLASE + Resolution (A): 2.4500 + + Num. models: 1 + Num. chains: 2 (A: Protein, E: Protein) + Num. residues: 878 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 87 + Num. ligands or modified residues: 7 + Num. water mol.: 80 + Num. atoms: 6558 +Metal/Ion residues found + ZN A901 (ZINC ION) + CL A902 (CHLORIDE ION) +Small mol ligands found +NAG A903 (2-acetamido-2-deoxy-beta-D-glucopyranose) +NAG A904 (2-acetamido-2-deoxy-beta-D-glucopyranose) +NAG A905 (2-acetamido-2-deoxy-beta-D-glucopyranose) +NAG A906 (2-acetamido-2-deoxy-beta-D-glucopyranose) +NAG E601 (2-acetamido-2-deoxy-beta-D-glucopyranose) +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/ld/1ldn-assembly1.cif' +Structure pdb:1ldn.1 loaded + Entry id: 1ldn (Assembly 1) + Title: STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION + Experimental method: X-RAY DIFFRACTION + Keywords: OXIDOREDUCTASE(CHOH(D)-NAD(A)) + + Num. models: 1 + Num. chains: 4 (A: Protein, B: Protein, C: Protein, D: Protein) + Num. residues: 1561 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 297 + Num. ligands or modified residues: 10 + Num. water mol.: 287 + Num. atoms: 10319 +Small mol ligands found +FBP A353 (1,6-di-O-phosphono-beta-D-fructofuranose) +OXM A351 (OXAMIC ACID) +NAD A352 (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) +FBP B353 (1,6-di-O-phosphono-beta-D-fructofuranose) +OXM B351 (OXAMIC ACID) +NAD B352 (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) +OXM C351 (OXAMIC ACID) +NAD C352 (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) +OXM D351 (OXAMIC ACID) +NAD D352 (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/vt/1vtk-assembly1.cif' +Structure pdb:1vtk.1 loaded + Entry id: 1vtk (Assembly 1) + Title: THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND DEOXYTHYMIDINE-MONOPHOSPHATE + Experimental method: X-RAY DIFFRACTION + Keywords: TRANSFERASE + + Num. models: 1 + Num. chains: 2 (A: Protein, A-2: Protein) + Num. residues: 734 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 108 + Num. ligands or modified residues: 4 + Num. water mol.: 104 + Num. atoms: 4982 +Small mol ligands found +ADP A400 (ADENOSINE-5'-DIPHOSPHATE) +TMP A500 (THYMIDINE-5'-PHOSPHATE) +ADP A-2400 (ADENOSINE-5'-DIPHOSPHATE) +TMP A-2500 (THYMIDINE-5'-PHOSPHATE) +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/ki/2ki5-assembly1.cif' +Structure pdb:2ki5.1 loaded + Entry id: 2ki5 (Assembly 1) + Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION + Experimental method: X-RAY DIFFRACTION + Keywords: TRANSFERASE + + Num. models: 1 + Num. chains: 2 (A: Protein, B: Protein) + Num. residues: 908 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 296 + Num. ligands or modified residues: 4 + Num. water mol.: 292 + Num. atoms: 4961 +Small mol ligands found +SO4 A4 (SULFATE ION) +AC2 A1 (9-HYROXYETHOXYMETHYLGUANINE) +SO4 B3 (SULFATE ION) +AC2 B2 (9-HYROXYETHOXYMETHYLGUANINE) +Structure not modified, not saving. Override with --force_save +================================================================================ += BioBB structure checking utility v3.16.3 = += P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-26 = +================================================================================ + +Structure exists: 'tmpPDB/sv/1svc-assembly1.cif' +Structure pdb:1svc.1 loaded + Entry id: 1svc (Assembly 1) + Title: NFKB P50 HOMODIMER BOUND TO DNA + Experimental method: X-RAY DIFFRACTION + Keywords: TRANSCRIPTION/DNA + + Num. models: 1 + Num. chains: 4 (D: DNA, D-2: DNA, P: Protein, P-2: Protein) + Num. residues: 786 + Num. residues with ins. codes: 0 + Num. residues with H atoms: 0 + Num. HETATM residues: 126 + Num. ligands or modified residues: 0 + Num. water mol.: 126 + Num. atoms: 5806 +Structure not modified, not saving. Override with --force_save diff --git a/biobb_structure_checking/test/scripts/test.sh b/biobb_structure_checking/test/scripts/test.sh index f3fa3fc3..8086746e 100755 --- a/biobb_structure_checking/test/scripts/test.sh +++ b/biobb_structure_checking/test/scripts/test.sh @@ -126,8 +126,8 @@ do sed -i '/Structure exists/d' $DIR/file_b sed -i '/Structure saved on/d' $DIR/file_a sed -i '/Structure saved on/d' $DIR/file_b - sed -i '/Downloading PDB structure/d' $DIR/file_a - sed -i '/Downloading PDB structure/d' $DIR/file_b + sed -i '/Downloading structure/d' $DIR/file_a + sed -i '/Downloading structure/d' $DIR/file_b sed -i '/Structure .* loaded/d' $DIR/file_a sed -i '/Structure .* loaded/d' $DIR/file_b sed -i '/Summary data saved on/d' $DIR/file_a diff --git a/setup.py b/setup.py index 1a4369c5..c1b45eb2 100755 --- a/setup.py +++ b/setup.py @@ -3,12 +3,12 @@ """ import setuptools -with open("README.md", "r") as fh: +with open("README.md", "r", encoding="utf-8") as fh: long_description = fh.read() setuptools.setup( name="biobb_structure_checking", - version="3.16.2", + version="3.16.3", author="Biobb developers", author_email="gelpi@ub.edu",