Thomas Holder
10af8bd0b9
Refactor ObjectMolecule::Neighbor access
...
- Make ObjectMolecule::Neighbor private
- Use AtomNeighbors or ObjectMolecule::getNeighborArray
- Eliminate ObjectMoleculeUpdateNeighbors
2021-04-28 04:34:33 -04:00
Thomas Holder
5308f66381
Refactor: ITERNEIGHBORATOMS -> AtomNeighbors
2021-01-14 15:31:38 +01:00
Thomas Holder
68a18a3e09
CoordSet refactoring/cleanup
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- 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
b1d9cee8aa
Fix PYMOL-3582 Crash in CoordSetPurge
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- Remove obsolete CoordSet::LabPos
- Fix AppendAtomVertex (HydrogenAdder): It was not resizing
has_atom_state_settings, atom_state_setting_id, and RefPos
2021-01-14 14:07:22 +01:00
Thomas Holder
385df0b0c4
doxygen-ize some documentation
2020-04-09 15:39:51 +02:00
Thomas Holder
5ecf711f3f
h_add: fix crash with I->Bond == NULL
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Example: pseudoatom; h_add
2020-02-20 12:08:18 +01:00
Thomas Holder
75f06a974e
CObject function pointers -> virtual methods
2019-10-29 16:24:12 +01:00
Jarrett Johnson
37f95ef227
ObjectMolecule proper C++ inheritance
2019-03-29 13:04:12 +01:00
Thomas Holder
97d166a858
clang-tidy modernize-use-nullptr
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... and modernize-use-bool-literals for some "newer" files.
2019-01-18 10:04:10 +01:00
Thomas Holder
e2df29a2ee
polymer.protein polymer.nucleic multifilesave ...
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* 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
