16 Commits

Author SHA1 Message Date
Jarrett Johnson
b52b6f2174 Port code changes from incentive (06/2023) 2025-01-04 12:09:32 -05:00
Jarrett Johnson
83f11bc317 More Replace NULL with nullptr 2024-06-02 20:44:43 -04:00
Jarrett Johnson
fbfda4a257 Replace NULL with nullptr 2024-05-20 09:07:33 -04:00
Jarrett Johnson
eea082966b Remove orthoCGO defines; fix warnings 2022-03-08 15:31:11 -05:00
Jarrett Johnson
bacc3256d5 TTT Rework 2022-02-22 15:34:44 -05:00
Jarrett Johnson
65835f9991 Remove OOMac 2021-07-07 12:03:25 -04:00
Thomas Holder
bdce35f844 cleanup: os_gl_*.h headers 2020-03-13 09:33:11 +01:00
Thomas Holder
4f50d7568a eliminate pymol::vla non-const legacy VLA cast
Avoid assignment of pymol::vla<T> return values to T*.

Refactoring to facilitate this:
- const-correctness (const T* cast still works)
- .data()
- T* -> pymol::vla<T> function arguments
2019-09-23 15:56:55 +02:00
Thomas Holder
da1d4dfe14 PYMOL-3288 Show movie panel for states 2019-08-30 11:49:36 +02:00
Thomas Holder
1edb8363f4 UtilGetSecondsEpoch
- document UtilGetSeconds
- make ViewElemInterpolate timing interpolation more robust (would fail
  with large "timing" values)
2019-02-21 18:41:02 +01:00
Thomas Holder
b59ce09d8a refactor: pymol::malloc<T>
- use typed/namespaced malloc wrapper
- remove Alloc et al.
- remove mmalloc et al.
- remove CINTERFACE define
2019-02-21 17:41:58 +01:00
Thomas Holder
4bbe42513c stick_round_nub, UTF-8, display_scale_factor, ...
* stick_round_nub for COLLADA export
* UTF-8 in feedback
* display_scale_factor (ported from Incentive PyMOL)
* dx map import: support "type float" and skewed delta
2018-02-28 13:16:16 +00:00
Thomas Holder
5acb6c4637 py37, align alt, flag 6+7
* Python 3.7 support (https://sf.net/p/pymol/bugs/197/)
* enable align with alt-codes
  - allow matching of non-alt-code to alt-code atoms in alignments
  - swap sorting priority of 'name' and 'alt' identifiers
  - sort empty 'alt' before non-empty 'alt'
* flags 6 and 7 for protein and nucleic acid
* mmCIF: read _atom_site.pdbx_formal_charge
* improve coordinate loading from mmcif chem_comp files
  - ignore columns with all ? (missing) values
  - select columns with "chem_comp_cartn_use" setting
* fix h_add: skip missing coordinates
2017-12-21 12:50:47 +00:00
Thomas Holder
5cbfe6b0d4 fix invalid memory access during PyMOL_Stop
- https://sourceforge.net/p/pymol/bugs/162/
  - Free ShaderMgr after Scene
  - check (G != NULL) in MainOnExit
- https://sourceforge.net/p/pymol/bugs/161/
  apply clang logical-op-parentheses suggestion
- more `const char *` arguments refactoring
2015-03-16 18:58:36 +00:00
Thomas Holder
9bb5c2d971 1.7.5.0 (unstable/experimental)
* mmCIF _atom_sites.fract_transf support (SCALEn equivalent)
* Complete port of scenes to C++
* warn user if setting a setting on the wrong level
* cmd.extendaa: shortcut for cmd.extend with argument auto-completion
* reduced memory footprint of AtomInfoType
* expose "reps" to iterate/alter
* expose "protons" to iterate/alter
* adaptive cartoon quality and sampling, depending on number of atoms
* fix ring center color with cartoon_ring_color=default
* make SelectorGetTmp strictly molecular, fixes for example "dss" with group names
* fix "copy" can cause crash
* fix "custom" selection operator
* consider spec_count in shaders
* don't invalidate shaders for lighting settings
* don't disable shaders for all Intel chips
* don't touch sphere_mode when disabling shaders
* map_new buffer == -1 -> gaussian_resolution
* fix all_states picking
* remove cylinder_shader_ff_workaround and cylinders_shader_filter_faces
* remove unused gl_ambient setting
* fix Tcl/Tk menu settings logging
* fix: grid mode scales down label size incorrectly
* fix: no animate argument for cmd.origin
* fix side_chain_helper for hetatm polymer atoms
* fix .mmd export
* refactor many function to take "const" pointer arguments
2015-03-12 17:44:19 +00:00
Thomas Holder
f42840260b c++ for all PyMOL c files
- renaming files c -> cpp
- c++ specific syntax (::)
2014-09-08 13:42:11 +00:00