Maarten L. Hekkelman
6eda9aaf36
better center_and_radius for residue
2025-11-18 16:44:53 +01:00
Maarten L. Hekkelman
f94e9aece9
create_non_poly, another
2025-11-05 11:03:56 +01:00
Maarten L. Hekkelman
10a6b5649b
Using fast float instead of home baked version
2025-10-01 16:14:07 +02:00
Maarten L. Hekkelman
95b007d38f
Merge branch 'trunk' into develop
2025-09-24 11:38:01 +02:00
Maarten L. Hekkelman
bd1fb5c5cd
Added model::create_link
2025-09-16 13:29:51 +02:00
Maarten L. Hekkelman
da500025c3
swap atoms should swap type_symbol as well
2025-09-10 17:16:22 +02:00
Maarten L. Hekkelman
0fa3d6aa94
Removing warning using MSVC
2025-09-02 12:54:07 +02:00
Maarten L. Hekkelman
e56b568c42
use cif::format... sigh
2025-08-27 15:46:41 +02:00
Maarten L. Hekkelman
8b0f92aa9a
Merge remote-tracking branch 'github/using-fmt' into develop
2025-08-27 07:43:22 +02:00
Maarten L. Hekkelman
8944906fd2
fix warning, pcre2
2025-08-26 12:41:08 +02:00
Maarten L. Hekkelman
cb02969604
Using std::format
2025-08-25 16:31:00 +02:00
Maarten L. Hekkelman
82eae05868
changed b-factor options for structure loading
2025-06-11 14:17:50 +02:00
Maarten L. Hekkelman
e8fb53c49b
Alternate implementation of structure_open_options
2025-06-11 13:35:58 +02:00
Maarten L. Hekkelman
604c97afe1
Merge branch 'develop' into clebreto-feature/enrich_structure_options
2025-06-11 11:43:01 +02:00
Maarten L. Hekkelman
a7a4a16f79
remove debug code
2025-06-11 09:45:45 +02:00
Maarten L. Hekkelman
6717059934
Revert renaming compound_id to mon_id in residue
2025-06-11 09:41:49 +02:00
Maarten L. Hekkelman
81cd305c80
rename mm::polymer fields and methods to better match mmcif_pdbx naming.
...
fix building mm::structure using pdb_seq_num instead of auth_seq_num
2025-06-11 09:30:54 +02:00
Maarten L. Hekkelman
874a5cb2f2
missing code added
2025-06-02 15:09:49 +02:00
Maarten L. Hekkelman
af319866c7
added get_atom_by_atom_id
2025-05-06 14:11:05 +02:00
Maarten L. Hekkelman
2f3514689d
Default value for b_iso_or_equiv, better sorting of atoms
2025-04-09 15:12:11 +02:00
Maarten L. Hekkelman
5b32ca15f7
Fix cleanup_empty_categories
2025-04-09 13:06:45 +02:00
LE BRETON Come
f86f34e5e1
WIP Enrich StructureOpenOptions
2025-03-07 15:54:30 +01:00
Maarten L. Hekkelman
5e7b52b7de
loading dictionaries
2025-02-17 12:57:08 +01:00
Maarten L. Hekkelman
ae0e9fbe77
fix cif::item constructor
...
fix ordering atoms
2024-04-29 12:06:50 +02:00
Maarten L. Hekkelman
f12e529c0b
default alt id for new atoms
2024-04-24 13:21:32 +02:00
Maarten L. Hekkelman
01b90a2ba5
set occupancy of newly added atom
2024-04-23 15:42:55 +02:00
Maarten L. Hekkelman
cd1e952812
residue::create_new_atom
2024-04-23 13:50:25 +02:00
Maarten L. Hekkelman
996f1e4277
check existence of alternate for specific atoms
2024-04-17 16:49:37 +02:00
Maarten L. Hekkelman
65718c64cc
fix updating index for change in value in category
2024-04-17 12:54:58 +02:00
Maarten L. Hekkelman
588e075325
Fix query generation when using constant numeric values
...
replace size_t with std::size_t to silence warnings
2024-04-03 14:01:51 +02:00
Maarten L. Hekkelman
a4680f7d38
error_code should be checked differently?
2024-03-09 13:54:53 +01:00
Maarten L. Hekkelman
93375a5087
Develop ( #54 )
...
* - renamed exists to contains
- fix compare for ints where item is empty
* - checking and optionally dropping ndb_poly_seq_scheme
- fix in iterator_proxy
* formatting data in reconstruction
* Version bump
* Attempt to get code compiling on macOS
* attempt 2 to build on macOS
* Added remove column
* Added rename_column
Added item_alias
Rename columns in reconstruct
* macOS...
* Fixed serious bug in emplace of both datablock and file.
* renaming field and column to item
* replace tag with item or item_name
* Fix validate pdbx
* version bump
* atom_site_anisotrop check
* - changed compound::is_known_peptide/is_know_base
- Add audit_conform only if file is really valid
- Added reconstruction code for PDBx
* pdb2cif work
* gcc diagnostics and clipper
* Fixing pdb2cif, and sequence checking
* work around bug in old gcc
* fix reconstruct sequence
* formatting
* some small optimisations
* Fix url in compound message
* Fix operator= for item_handle
* Fix operator= for item_handle
* new update_value in category
* test builds faster now
* Use Catch2 version 3 if installed
* catch22
2024-02-17 16:03:14 +01:00
Maarten L. Hekkelman
abd97cc1c9
Merge
2024-01-02 10:52:09 +01:00
Maarten L. Hekkelman
b83ef112a9
Fix in structure::change_residue
2023-11-13 10:50:27 +01:00
Maarten L. Hekkelman
b737dd7df4
Even more documentation
2023-09-13 14:59:57 +02:00
Maarten L. Hekkelman
0b5d28338e
replacing std::endl where appropriate
...
more docs
2023-09-12 09:06:45 +02:00
Maarten L. Hekkelman
26a5410b38
documenting model
2023-09-06 10:59:48 +02:00
Maarten L. Hekkelman
1c02a451e1
improved has_atom_id
...
added couple of comparison operators to sym_op class
2023-05-16 13:55:07 +02:00
Maarten L. Hekkelman
448855a2d3
catch error in create entity for branch
2023-05-09 11:46:37 +02:00
Maarten L. Hekkelman
2281f59401
Remove struct_conn records as well in remove_branch
2023-05-02 13:44:36 +02:00
Maarten L. Hekkelman
4acca8a3e3
Merge branch 'trunk' into develop
2023-04-07 09:31:11 +02:00
Maarten L. Hekkelman
16a185c6c0
More include changes
2023-04-07 09:16:38 +02:00
Maarten L. Hekkelman
b6143f3652
optimise load atom data
2023-03-30 20:49:03 +02:00
Maarten L. Hekkelman
cfa46ec954
Added model::has_atom_id
2023-03-23 14:32:21 +01:00
Maarten L. Hekkelman
9addc8f873
fix remove_atom
...
add create_water
2023-03-21 19:49:11 +01:00
Maarten L. Hekkelman
343465cef0
Added test for create_non_poly with initializers
2023-03-08 16:00:40 +01:00
Maarten L. Hekkelman
fb2ad7b75d
Fix in REMARK3 parser for more strict mmcif_pdbx dictionary
2023-02-10 16:24:53 +01:00
Maarten L. Hekkelman
4613084e1b
find_first, find_min, find_max, count added
...
PDB writing changed for auth_seq_num
version bump
2023-02-01 13:46:08 +01:00
Maarten L. Hekkelman
4de981a3c0
better handling of missing residues in pdb2cif
2023-01-31 20:32:57 +01:00
Maarten L. Hekkelman
15db026e27
Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop
2023-01-31 19:10:44 +01:00
