-
Notifications
You must be signed in to change notification settings - Fork 10
/
changelog
229 lines (176 loc) · 6.23 KB
/
changelog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
Version 7.0.7
- Set CIFPP_DATA_DIR on target cifpp for use in projects that include
libcifpp directly
Version 7.0.6
- Fix linking to std::atomic
Version 7.0.5
- Fix case where category index was not updated for updated value
Version 7.0.4
- Do not install headers and library in case we're not the top project
Version 7.0.3
- Fix installation, write exports.hpp again
Version 7.0.2
- Fix in testing error_code results.
Version 7.0.1
- Various reconstruction fixes
- category order in output fixed
- better implementation of constructors for file, datablock and category
- small optimisation in iterator
Version 7.0.0
- Renaming many methods and parameters to be more
consistent with the mmCIF dictionaries.
(Most notably, item used to be called column or
tag sometimes).
- validation_error is now a std::system_error error
value. The exception is gone.
- Added repairSequenceInfo to repair invalid files
Version 6.1.0
- Add formula weight to entity in pdb2cif
- Change order of categories inside a datablock to match order in file
- Change default order to write out categories in a file based on
parent/child relationship
- Added validate_pdbx and recover_pdbx
- Fixed a serious bug in category_index when moving categories
Version 6.0.0
- Drop the use of CCP4's monomer library for compound information
Version 5.2.5
- Correctly import the Eigen3 library
Version 5.2.4
- Changes required to build on Windows
Version 5.2.3
- New constructors for cif::item, one taking std::optional values
and another taking only a name resulting in a value '.' (i.e. inapplicable).
- added cif::cell::get_volume
Version 5.2.2
- Remove dependency on Eigen3 for users of libcifpp
- Fix typos in documentation
- Do not build latex files in documentation
- Fixed conversion from string to integer, would fail on +2 e.g.
- sqrt is not constexpr, thus kGoldenRatio should be const, not constexpr
Version 5.2.1
- New versionstring module
- small fixes for generating documentation
- correctly setting SONAME
Version 5.2.0
- With lots of documentation
- Refactored coloured text output
- Removed the subdirectory cif++/pdb, there now is a single
header file pdb.hpp for I/O of legacy PDB files.
Version 5.1.3
- Dropped pkgconfig support
Version 5.1.2
- New version string code
- Added check for Eigen3 in cifppConfig.cmake
Version 5.1.1
- Added missing include <compare> in symmetry.hpp
- Added empty() to matrix
- Fix for parsing legacy PDB files with a last line that does
not end with a new line character.
Version 5.1
- New parser, optimised for speed
- Fix in unique ID generator
Version 5.0.10
- Fix in progress_bar, was using too much CPU
- Optimised mmCIF parser
Version 5.0.9
- Fix in dihedral angle calculations
- Added create_water to model
- Writing twin domain info in PDB files and more PDB fixes
- remove_atom improved (remove struct_conn records)
- Added a specialisation for category::find1<std::optional>
- fix memory leak in category
Version 5.0.8
- implemented find_first, find_min, find_max and count in category
- find1 now throws an exception if condition does not not exactly match one row
- Change in writing out PDB files, now looking up the original auth_seq_num
via the pdbx_xxx_scheme categories based on the atom_site.auth_seq_num ->
pdbx_xxx_scheme.pdb_seq_num relationship.
- fix memory leak in category
Version 5.0.7.1
- Use the implementation from zeep for std::experimental::is_detected
Version 5.0.7
- Reintroduce exports file. For DLL's
Version 5.0.6
- Fix file::contains, using iequals
- Fix is_cis
Version 5.0.5
- Fix code to work on 32 bit machines
Version 5.0.4
- Revert removal of CIFPP_SHARE_DIR export
Version 5.0.3
- Fix installation of libcifpp into the correct locations
Version 5.0.2
- Fix export of CISPEP records in PDB format
- Better support for exporting package_source
Version 5.0.1
- Fix loading dictionaries
- Support for cifv1.0 files
Version 5.0.0
- Total rewrite of cif part
- Removed DSSP code, moved into dssp project itself
Version 4.2.1
- Improved REMARK 3 parser (for TLS in large molecules)
Version 4.2.0
- Yet another rewrite of resource loading
Version 4.1.1
- Fall back to zero charge for scattering factors if the atom
was not found in the table.
- Improve code to locate resources, failing less.
Version 4.1.0
- Some interface changes for mmcif::Atom
Version 4.0.1
- Added a bunch of const methods to Datablock and Category.
- Changed PDB writing interface to accept Datablock instead of File.
Version 4.0.0
- getResidue in mmcif::Structure now requires both a
sequence ID and an auth sequence ID. As a result the code was cleaned
up considerably.
Version 3.0.5
- mmcif::Structure redesign. It is now a wrapper around a cif::Datablock.
Version 3.0.4
- Fix in mmCIF parser, now correctly handles the unquoted
string ??
Version 3.0.3
- Better configuration checks, for atomic e.g.
- Fixed a problem introduced in refactoring mmcif::Atom
- Version string creation
Version 3.0.2
- refactored mmcif::Atom for performance reasons
Version 3.0.1
- Fixed processing of proline restraints file from CCP4, proline
is a peptide, really.
- Added code to facilitate DSSP
Version 3.0.0
- Replaced many strings in the API with string_view for
performance reasons.
- Upgraded mmcif::Structure
- various other small fixes
Version 2.0.5
- Backporting updated CMakeLists.txt file
Version 2.0.4
- Reverted a too strict test when reading cif files.
Version 2.0.3
- Fixed reading mmCIF files where model numbers are used and
model number 1 is missing.
Version 2.0.2
- Added configuration flag to disable downloading CCD data during build
Note that there are now two flags for CCD data:
DOWNLOAD_CCD to enable downloading during build
INSTALL_UPDATE_SCRIPT to install an update mechanism for this file
- Updated unit tests to work even if no CCD data is available
Version 2.0.1
- Fixed the generator for the symmetry operator table
Version 2.0.0
- New API interface for accessing query results
- Removed bzip2 support
- improved makefiles
Version 1.1.1
- Now with full support for MS Windows
Version 1.1.0
- Changed from GNU configure to CMake.
- Loading compound information from CCD file
Version 1.0.1
- Changed the way resources are looked up, local dir first,
then /var/cache and finally compiled in resources (with mrc).
Version 1.0.0
- First public release