Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / ihmwg/python-ihm issues and pull requests

#155 - Check against real archive structures

Issue - State: open - Opened by benmwebb about 1 month ago - 1 comment
Labels: enhancement

#154 - Handle non-standard residues in struct_ref

Issue - State: closed - Opened by benmwebb about 1 month ago
Labels: bug

#153 - Allow skipping sanity checks on file output

Issue - State: closed - Opened by benmwebb about 1 month ago
Labels: enhancement

#152 - Inconsistent `python-ihm` read/write behavior

Issue - State: closed - Opened by aozalevsky about 2 months ago - 3 comments

#151 - Allow for dataset to have multiple locations

Issue - State: closed - Opened by benmwebb about 2 months ago
Labels: enhancement

#150 - pdbx_poly_seq_scheme for beaded residues is incorrectly populated

Issue - State: closed - Opened by brindakv 3 months ago - 2 comments

#149 - Duplicated struct_ref.id

Issue - State: closed - Opened by benmwebb 3 months ago - 3 comments
Labels: bug

#147 - Disallow empty sequence in ResidueFeature constructor

Issue - State: closed - Opened by benmwebb 4 months ago
Labels: bug

#146 - Preserve alt locs in atom_site table

Issue - State: closed - Opened by benmwebb 5 months ago
Labels: enhancement

#145 - `make-mmcif.py` does not support certain IHMCIF data items

Issue - State: closed - Opened by brindakv 5 months ago - 5 comments

#144 - Make sure all unused objects are preserved by read-write cycle

Issue - State: closed - Opened by benmwebb 6 months ago - 3 comments
Labels: enhancement

#143 - make_mmcif.py does not handle some of the IHMCIF tables

Issue - State: closed - Opened by brindakv 6 months ago

#142 - Add support for updates in IHMCIF required for unification with PDB

Pull Request - State: closed - Opened by benmwebb 7 months ago - 1 comment

#141 - Add case- and whitespace-preserving tokenizers

Issue - State: closed - Opened by benmwebb 7 months ago - 3 comments
Labels: enhancement

#140 - Error while parsing sequence information in entry PDBDEV_00000030

Issue - State: closed - Opened by aozalevsky 7 months ago - 3 comments

#139 - Improve reading of ihm_external_files category

Issue - State: closed - Opened by benmwebb 7 months ago
Labels: bug

#138 - Allow for float ihm_external_files.file_size_bytes

Issue - State: closed - Opened by benmwebb 7 months ago
Labels: bug

#136 - Installation doesn't copy ihm/util

Issue - State: closed - Opened by gtauriello 7 months ago

#135 - Add support for database_2 and pdbx_database_status tables

Issue - State: closed - Opened by benmwebb 8 months ago
Labels: enhancement

#134 - Add `make-mmcif.py` to the python package

Issue - State: closed - Opened by brindakv 9 months ago

#133 - Handle duplicate save frames

Issue - State: open - Opened by benmwebb 11 months ago
Labels: enhancement

#132 - Support for chemical component dictionary

Issue - State: open - Opened by brindakv 12 months ago - 3 comments

#131 - CifCheck validation fails on files with non-ASCII characters

Issue - State: closed - Opened by aozalevsky 12 months ago - 1 comment

#130 - Better handle seq_id for waters, branched entities

Issue - State: closed - Opened by benmwebb 12 months ago - 2 comments
Labels: enhancement

#129 - Read entity.type from input files

Issue - State: closed - Opened by benmwebb 12 months ago
Labels: enhancement

#128 - Warn on output, don't fail, if one or more empty Entities are present

Issue - State: closed - Opened by benmwebb 12 months ago
Labels: enhancement

#127 - Don't ever treat read-in objects as identical

Issue - State: closed - Opened by benmwebb 12 months ago
Labels: enhancement

#126 - Consider connectivity when comparing two branched entities for identity

Issue - State: closed - Opened by benmwebb 12 months ago
Labels: bug

#125 - make-mmcif.py fails on 4M44.cif

Issue - State: closed - Opened by benmwebb almost 1 year ago
Labels: bug

#124 - Handle original author-provided numbering

Issue - State: closed - Opened by benmwebb almost 1 year ago
Labels: enhancement

#123 - _entity.formula_weight calculation

Issue - State: open - Opened by brindakv about 1 year ago

#122 - define more crosslinkers

Pull Request - State: closed - Opened by grandrea over 1 year ago - 3 comments

#121 - Expose model_id

Issue - State: closed - Opened by aozalevsky over 1 year ago - 1 comment

#120 - Discrepancies in entities assignment

Issue - State: closed - Opened by aozalevsky over 1 year ago - 1 comment

#119 - Add support for cross-links whose endpoints don't match experimental data

Issue - State: open - Opened by benmwebb over 1 year ago
Labels: enhancement

#118 - Add missing crosslink attributes

Pull Request - State: closed - Opened by aozalevsky over 1 year ago - 4 comments

#117 - EM2D restraints are missing from the docs

Issue - State: closed - Opened by aozalevsky over 1 year ago

#116 - Database location names should follow controlled vocabulary

Issue - State: closed - Opened by aozalevsky over 1 year ago - 1 comment

#115 - Make output filename an optional argument in make-mmcif.py

Issue - State: closed - Opened by brindakv over 1 year ago

#114 - Dataset ordering

Issue - State: open - Opened by aozalevsky over 1 year ago - 2 comments

#113 - Add support for read from / write to JSON

Issue - State: open - Opened by benmwebb over 1 year ago
Labels: enhancement

#112 - ihm.analysis.FilterStep.feature value is not checked

Issue - State: closed - Opened by aozalevsky over 1 year ago - 3 comments
Labels: bug

#111 - Error when running test/test_reference.py

Issue - State: closed - Opened by CAHanke almost 2 years ago - 2 comments

#110 - Add support for multi-state schemes from IHM dictionary

Pull Request - State: closed - Opened by CAHanke almost 2 years ago - 3 comments

#109 - Add jPOSTrepo to location.py

Pull Request - State: closed - Opened by brindakv almost 2 years ago - 2 comments

#108 - Add support for collection tables

Issue - State: closed - Opened by benmwebb almost 2 years ago - 5 comments
Labels: enhancement

#107 - Dictionary parser incorrectly handles data items defined before categories

Issue - State: closed - Opened by benmwebb almost 2 years ago
Labels: bug

#106 - Add selenocysteine

Pull Request - State: closed - Opened by bienchen about 2 years ago - 1 comment

#105 - python-ihm fails on the ensemble without ihm_ensemble_info.model_group_id

Issue - State: closed - Opened by aozalevsky about 2 years ago - 1 comment

#104 - _ihm_external_files.file_size_bytes

Issue - State: closed - Opened by brindakv about 2 years ago

#103 - Added citation for MMseqs2, fixed documentation of QMEANDisCo citation.

Pull Request - State: closed - Opened by bienchen about 2 years ago

#102 - Add citation for QMEANDisCo.

Pull Request - State: closed - Opened by bienchen about 2 years ago

#101 - Don't require unique ihm_modeling_post_process.analysis_id

Issue - State: closed - Opened by benmwebb about 2 years ago
Labels: bug

#100 - Add elements for formula weight calculations

Pull Request - State: closed - Opened by bienchen about 2 years ago - 1 comment

#99 - Missing elements in `ihm.ChemComp._element_mass`

Issue - State: closed - Opened by bienchen about 2 years ago - 2 comments

#98 - Water molecules, _pdbx_nonpoly_scheme.auth_seq_num vs. _atom_site.auth_seq_id

Issue - State: closed - Opened by bienchen over 2 years ago - 3 comments
Labels: bug

#97 - Auto-populate `_ihm_modeling_protocol.ensemble_flag`

Issue - State: closed - Opened by brindakv over 2 years ago - 1 comment

#96 - Populate atom_type for multi-scale models

Issue - State: open - Opened by brindakv over 2 years ago - 1 comment

#95 - Format author names following PDB recommendations

Issue - State: closed - Opened by benmwebb over 2 years ago
Labels: enhancement

#94 - Disallow invalid clustering method/feature in Ensemble class

Issue - State: closed - Opened by benmwebb over 2 years ago
Labels: bug

#93 - EM map header for unreleased entries in EMDB

Issue - State: closed - Opened by brindakv over 2 years ago - 3 comments
Labels: invalid

#92 - make-mmcif.py overwrites assembly name and description

Issue - State: closed - Opened by benmwebb over 2 years ago - 2 comments
Labels: bug

#91 - make-mmcif.py sets linker type to "none"

Issue - State: closed - Opened by benmwebb over 2 years ago - 3 comments
Labels: enhancement

#90 - make-mmcif.py overwrites struct table with "Auto-generated system"

Issue - State: closed - Opened by benmwebb over 2 years ago - 3 comments

#89 - Add citation for ColabFold

Pull Request - State: closed - Opened by bienchen over 2 years ago

#88 - _check_duplicate_atom fails for oxygen atoms in water

Issue - State: closed - Opened by brindakv over 2 years ago

#87 - Allow for missing _ihm_derived_distance_restraint.restraint_type

Issue - State: closed - Opened by benmwebb over 2 years ago
Labels: bug

#86 - Handle missing ihm_starting_comparative_models.template_seq_id_begin/end

Issue - State: closed - Opened by benmwebb over 2 years ago
Labels: bug

#85 - Handle _ihm_starting_model_details before _ihm_entity_poly_segment

Issue - State: closed - Opened by benmwebb over 2 years ago
Labels: bug

#84 - Add additional sanity checks against external resources

Issue - State: open - Opened by benmwebb over 2 years ago
Labels: enhancement

#83 - Include _ihm_modeling_protocol_details.ensemble_flag in _ProtocolDumper

Issue - State: closed - Opened by brindakv over 2 years ago - 2 comments
Labels: enhancement

#82 - Adding custom records to the header

Issue - State: closed - Opened by jkosinski over 2 years ago - 2 comments

#81 - Reading files with incorrect model numbers

Issue - State: closed - Opened by brindakv over 2 years ago - 3 comments

#80 - Add support for _struct.pdbx_model_details

Pull Request - State: closed - Opened by bienchen over 2 years ago - 1 comment

#79 - Add _struct.pdbx_model_details

Pull Request - State: closed - Opened by bienchen over 2 years ago - 2 comments

#78 - Allow user to override Entity.is_polymeric()

Issue - State: closed - Opened by benmwebb over 2 years ago
Labels: bug

#77 - Remove UTF characters

Pull Request - State: closed - Opened by bienchen over 2 years ago - 2 comments

#76 - Make output from ligands_water.py example validate

Issue - State: closed - Opened by benmwebb over 2 years ago - 2 comments
Labels: bug

#75 - "_" as chain name

Issue - State: closed - Opened by bienchen over 2 years ago - 1 comment

#74 - Add ihm.citations.alphafold2 for AlphaFold 2.

Pull Request - State: closed - Opened by bienchen over 2 years ago

#73 - Explain ihm.Citation parametrs a bit clearer.

Pull Request - State: closed - Opened by bienchen over 2 years ago - 1 comment

#72 - Citation with ID `primary`

Issue - State: closed - Opened by bienchen over 2 years ago - 3 comments
Labels: enhancement

#71 - Allow ihm.dumper to exclude specific categories

Issue - State: closed - Opened by brindakv over 2 years ago - 4 comments

#70 - entity.type of single-amino acid entities

Issue - State: closed - Opened by bienchen almost 3 years ago - 2 comments
Labels: bug

#69 - entity_poly.pdbx_seq_one_letter_code_can/ entity_poly.nstd_monomer of non-standard polymer

Issue - State: closed - Opened by bienchen almost 3 years ago - 3 comments
Labels: bug

#68 - Allow "-" in datablock identifiers

Issue - State: closed - Opened by bienchen almost 3 years ago - 1 comment

#67 - Have make-mmcif.py handle PyMOL output files

Issue - State: closed - Opened by benmwebb almost 3 years ago
Labels: enhancement

#66 - Validation does not work for BinaryCIF files

Issue - State: closed - Opened by benmwebb about 3 years ago
Labels: bug

#64 - `struct_ref` alignment error

Issue - State: closed - Opened by brindakv about 3 years ago - 4 comments
Labels: bug

#63 - _ihm_modeling_protocol_details.struct_assembly_description spans multiple lines

Issue - State: closed - Opened by brindakv about 3 years ago - 2 comments
Labels: bug

#61 - Add auth_seq_id to atom dumper

Pull Request - State: closed - Opened by rvhonorato over 3 years ago - 3 comments

#60 - Missing auth_seq_id from _atom_site

Issue - State: closed - Opened by rvhonorato over 3 years ago - 2 comments

#59 - UnicodeDecodeError while reading Entry 44 using ihm.reader

Issue - State: closed - Opened by saijananiganesan over 3 years ago - 2 comments

#57 - uniprot fasta parsing is sometimes broken

Issue - State: closed - Opened by danpf over 4 years ago

#56 - Implement _ihm_residues_not_modeled

Pull Request - State: closed - Opened by danpf over 4 years ago - 2 comments