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24 Commits

Author SHA1 Message Date
Jarrett Johnson
fbfda4a257 Replace NULL with nullptr 2024-05-20 09:07:33 -04:00
Jarrett Johnson
5e4342f950 Remove unused vars 2024-01-30 15:31:21 -05:00
Thomas Holder
b034d5c3e6 MMTF loader: Use entityList for HETATM flag (#296) 
Fixes https://github.com/schrodinger/pymol-open-source/issues/295
 2023-07-18 11:51:18 -04:00
Thomas Holder
dc2aff4133 Refactor: Doxygen comments, ObjectMoleculeUpdateNeighbors 
- Use proper doxygen syntax for all function comments
- ObjectMoleculeUpdateNeighbors allow const argument
- Remove obsolete ObjectMolecule::BondCounter
 2021-01-14 15:23:06 +01:00
Thomas Holder
68a18a3e09 CoordSet refactoring/cleanup 
- Remove unused CoordSet::appendIndices()
- Simplify ObjectMoleculeDummyNew
- Simplify ObjectMoleculeSort
- Turn atom_state_setting_id into a method
- Consolidate CoordSetAdjustAtmIdx and CoordSetPurge
- Convert IdxToAtm and AtmToIdx to std::vector
- Eliminate CoordSet::NAtIndex
- Use setNIndex() where possible
 2021-01-14 14:15:44 +01:00
Thomas Holder
f84389f14f Refactor CCrystal and CSymmetry 
- Make members private
- Add getters and setters
- Remove CrystalUpdate, SymmetryUpdate, SymmetryFree
- Remove unused CCrystal members (Norm, RecipDim, UnitCellVolume)
- Add CCrystal unit test
 2020-12-11 13:57:26 +01:00
Thomas Holder
75f06a974e CObject function pointers -> virtual methods 2019-10-29 16:24:12 +01:00
Jarrett Johnson
00473b5656 C++ inheritance for Object classes 2019-09-04 18:18:01 +02:00
Nandini Naidu
71f77b68ab Converted BondType Bond to a c vla 2019-08-30 17:12:59 +02:00
Nandini Naidu
1d8d6c861a float Coord and int IdxtoAtm changed to C++ vlas 2019-08-13 17:06:49 +02:00
Nandini Naidu
1b017594ae symmetry class changes to make deep copyable 2019-08-13 16:20:41 +02:00
Jarrett Johnson
37f95ef227 ObjectMolecule proper C++ inheritance 2019-03-29 13:04:12 +01:00
Thomas Holder
97d166a858 clang-tidy modernize-use-nullptr 
... and modernize-use-bool-literals for some "newer" files.
 2019-01-18 10:04:10 +01:00
Thomas Holder
3129be199e refactor: lexborrow_t 2018-11-15 16:27:43 +01:00
Thomas Holder
0a856e722f lexidx_t: use LexBorrow 2018-11-15 16:08:41 +01:00
Thomas Holder
1742d75d13 anaglyph batch mode, all_states measurements, ... 
* fix anaglyph stereo in batch (headless) mode
* fix possible memory corruption with boolean settings
* measurement wizard: distances between states (all_states=on)
* get_fastastr: nucleic acid, by chain
* menu: A (Action) > group
* sequence viewer menu: ss (Secondary Structure)
* MAE export of groups (s_m_subgroupid)
* macOS: -O3 -fno-strict-aliasing (bugs/205)
 2018-05-03 14:46:44 +00:00
Thomas Holder
7d2bb243e6 restore r4188 
r4188 was published on 2018-04-10 but lost after a sourceforge storage problem.
See for example https://sourceforge.net/p/forge/site-support/17420/

2.2.0a0 (unstable/experimental)

* sf.net/p/pymol/bugs/199 bash -> sh
* ignore zero-order bonds in neighbor lookup
* fix crash loading reduced 5ijo.mmtf
* volume panel: fix zoom (CTRL+R-Drag) and value input (R-Click)
* QOpenGLWidget support (not active by default)
* --gldebug -> backtrace on GL error
 2018-05-02 06:32:39 +00:00
Thomas Holder
e2df29a2ee polymer.protein polymer.nucleic multifilesave ... 
* new selection keywords: polymer.protein polymer.nucleic
* new command: multifilesave
* MMTF export (requires simplemmtf python module)
* select: present, state -1 -> current object state
* create: source_state = -1 -> current
  (was: source_state = -1/0 -> all)
* cif: support quoted '?' and '.' as values
  cif_get_array -> None instead of empty string for ? and .
* fix copy discrete object w/o coords
* fix loading pdbqr AutoDock 4 atom types
* fix get_model('none') and get_str('mol', 'none')
* h_add refactored: 5x faster, support discrete objects
 2018-02-07 15:44:17 +00:00
Thomas Holder
889cbb280f auto library mode 
* Python API: New "auto library mode". Automatically start a
  non-GUI PyMOL instance if the pymol.cmd API is used without
  running pymol.launch() first
* pdb_echo_tags for mmCIF and MMTF
* command parser: improve exception handling
* fix some PSE export memory leaks
* pymol2.cmd2: eliminate (non-weak) circular references
* movie making: reinterpolate after add_nutate/add_roll etc.
* support "module:callable" in loadfunctions/safefunctions
* yellow state indicator for discrete objects
* mpng modal draw improvements
 2017-12-05 18:37:16 +00:00
Thomas Holder
520bf2a72a 1.9.0.0 
* use PyMOL 2.0 setting defaults
* L > residues (oneletter)
* fix py3 crash in "A > copy to object"
* fix scene object visibility with hidden groups
* fix "ending" after loading movie session
 2017-10-18 17:21:19 +00:00
Thomas Holder
2fca882cf7 1.8.6.1 fixes 
* Python 3: fix builder bond order buttons (Red Hat Bug 1442127)
* fix MAE export PDB residue/atom names
* restored "scene_animation" setting (1.7.6 regression)
* restored "import cmd" prevention (1.8.6.0 regression)
 2017-04-17 18:13:26 +00:00
Thomas Holder
bd69129af1 mmtf fixes, documentation, auto-completion 2017-03-09 00:40:30 +00:00
Thomas Holder
5b92a73de7 mmtf updates 
- mmtf: "ignore" flag for hetatm
- mmtf: msgpack version check
- INSTALL: env variables documentation
- Tcl/Tk menu updates
 2017-02-27 20:48:56 +00:00
Thomas Holder
1e324badee 1.8.5.1 (beta) 
* fast MMTF load support in C++ (adds msgpack-c dependency)
* extra_fit: report RMS for method=cealign; Thanks to Hongbo Zhu
* CTRL-L ligand zoom
* preset > classified (auto_show_classified equivalent)
* preset > interface (ported from Incentive PyMOL 1.8.0)
* set_key auto-completion
* command completion for selection language
* fix connect_mode=4 for N-H1 and N-H3
* fix CGO ALPHA and dup COLOR issue
 2017-02-23 14:37:57 +00:00