Jarrett Johnson
07d7a790f0
Forward decls/Move headers to source
2021-08-20 11:24:10 -04:00
Guillaume Bouvier
6bdd7f5d2f
Fixing SYBYL atom types for Sulphoxide sulphur (S.o) and Sulphone sulphur (S.o2) in layer2/Mol2Typing.cpp
...
The SYBYL atom typing for Sulphoxide sulphur (S.o) and Sulphone sulphur (S.o2) doesn't match the SYBYL typing (https://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html )
2021-04-28 07:02:32 -04:00
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
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
Jarrett Johnson
37f95ef227
ObjectMolecule proper C++ inheritance
2019-03-29 13:04:12 +01:00
Thomas Holder
b3472cbace
ignore_case_chain, cartoon_gap_cutoff, ...
...
* restore ignore_case=on default
* new setting: ignore_case_chain (default off)
* new setting: cartoon_gap_cutoff
* increase PYMOL_MAX_THREADS
* amber topology loading: bond order 1 for all bonds
* improve MOL2 file handling
* new grid_mode=3: grid per object-state
2016-02-08 15:59:56 +00:00
Thomas Holder
2787af79fc
byring, distance mode=4, cartoon dash, ...
...
* distance mode=4: distance between centroids
* byring: new selection operator
* "Distances to Rings" mode in measurement wizard
* basic atom typing for MOL2 export
* cartoon dash: new dashed loop-like cartoon type
* object-level settings for measurements
* iterate: use Python exceptions
* iterate_state: ignore atomic=0 (fixes crash)
* format 'xyzstr': enable .gz and URL loading
* fix crash with object sele length >= 1024
* re-add -Wno-write-strings
* fix pmg_tk.skins.normal.encode()
* fix askopenfilename CANCEL case with multiple=0
2016-01-11 16:56:37 +00:00
