add method chempy.brick.Brick.from_numpy


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4063 21428953-86e3-433d-9a34-2224224d0fc8
sourceforge bug 147, PYMOL_PATH
    
* set PYMOL_PATH=. if unknown and cannot be guessed
* use PYMOL_DATA in ShaderMgr
* remove some old code in pymol/__init__.py

http://sourceforge.net/p/pymol/bugs/147/


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4064 21428953-86e3-433d-9a34-2224224d0fc8
fix typo in menu: isolevel -1.5


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4065 21428953-86e3-433d-9a34-2224224d0fc8
th_assert -> ok_assert


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4066 21428953-86e3-433d-9a34-2224224d0fc8
bugfix: labels missing on some ATI cards

some ATI cards require the first shader attribute at position 0 to
be bound.  The problem was that the attr_pickcolor attribute was
automatically bound to position 0, and was not always being used, which
caused the ATI card to fail (not exactly sure why, but binding position 0
fixes the problem)

binding also did not always work in the open-source version, since ATI
assigns the attribute positions in alphabetical order, changing the
name of the optional attr_pickcolor attribute seems to fix the labels
on these cards


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4067 21428953-86e3-433d-9a34-2224224d0fc8
update splash, minor fixes, 1.7.0.4


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4068 21428953-86e3-433d-9a34-2224224d0fc8
fix broken label scaling on Linux

- label scaling became distorted on window resizing
- minor readability update in label.vs (no change)


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4069 21428953-86e3-433d-9a34-2224224d0fc8
fix distorted labels with stereo walleye/crosseye


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4070 21428953-86e3-433d-9a34-2224224d0fc8
volume API and panel improvements

- volume presets
- new commands: volume_color, volume_ramp_new
- improved volume panel/UI
- custom volume ramps/presets
- support for volumes from maps with transformation matrix (matrix_copy on map)


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4071 21428953-86e3-433d-9a34-2224224d0fc8
update ChangeLog, 1.7.1.0


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4072 21428953-86e3-433d-9a34-2224224d0fc8
fix CGO ALPHA should not make colors get ignored


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4073 21428953-86e3-433d-9a34-2224224d0fc8
fixed: atom_type, 2 memory leaks, solvent_radius crash

* never assign atom_type (noInvalidateMMStereoAndTextType)
* fix ExecutivePurgeSpec memory leak
* fix cartoon memory leak
* fixed small solvent_radius crashes surface generation
--This lin   and those below, will be ignored--

M    ChangeLog
M    setup.py
M    layer0/Version.h
M    layer0/Triangle.c
M    layer0/os_predef.h
M    layer0/Base.h
M    layer2/RepLabel.c
M    layer2/ObjectSlice.c
M    layer2/RepCartoon.c
M    layer2/ObjectMolecule.c
M    layer3/Selector.c
M    layer3/Executive.c
M    layer3/Selector.h
M    layer3/Executive.h
M    layer4/Cmd.c
M    layer5/main.c


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4074 21428953-86e3-433d-9a34-2224224d0fc8
volume improvements, ccp4 map type 0 support, etc.
 
* volume improvments:
  - grid_mode support
  - adjust volume ramp alphas by number of layers
  - support TTT matrix
  - bind mouse wheel to volume panel to adjust all alphas at once
* CCP4 map type 0 support
* fixed polymer detection for intra-residue N->C and O3'->P bonds
* raise exception when assigning arbitrary string to int setting
* fix group visibility issue in movie making



git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4075 21428953-86e3-433d-9a34-2224224d0fc8
fix label depth, etc.

* fix label depth issues with label_position
* fix label reappeared when zoomed in too far
* fix "scene auto, update" with wizard message
* fix setting surface_circumscribe
* 1.7.1.3 (beta)


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4076 21428953-86e3-433d-9a34-2224224d0fc8
add missing header


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4077 21428953-86e3-433d-9a34-2224224d0fc8
better CIF support, etc.

* refactor chempy.cif
    - support for multi-model
    - read secondary structure
    - rewritten tokenizer

* atom sorting: make segi match case sensitive

* fix/improve:
    A > compute > surface area > ...
    A > generate > selection > surface atoms

* PDB parser: factor out SS handling for readability

* open file dialog in CWD until the first file was selected, then
  remember that directory

* with -J immediatly cd to $HOME (or $HOME/Documents on Windows).
  This allowes to put a "cd ..." in pymolrc

* fix stereo shader invalidation

* 1.7.1.4 (beta)



git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4078 21428953-86e3-433d-9a34-2224224d0fc8
chempy.cif: fix copy/paste typo in read_struct_conn_


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4079 21428953-86e3-433d-9a34-2224224d0fc8
chempy.cif: don't bond metalc and hydrog


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4080 21428953-86e3-433d-9a34-2224224d0fc8
1.7.1.6 (beta)

* report clash score in mutagenesis wizard
* change defaults for settings "ribbon_as_cylinders" and
  "nonbonded_as_cylinders" to 0
* new commands (ported from PSICO): join_states, alphatoall, loadall,
  centerofmass, extra_fit, api
* pubchem and emd fetch support
* support to run pml and py script with the "load" command
* Fix text mode (text=1) with white background color


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4081 21428953-86e3-433d-9a34-2224224d0fc8
1.7.1.7 (beta)

* fix label_digits crash
* fixed get_angle3f to use doubles internally
* avoid ZeroDivisionError in Volume Panel
* support opaque_background with "draw"
* fix spheroid command for use_shaders=0


git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4082 21428953-86e3-433d-9a34-2224224d0fc8