is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| menu.py (pymol-v1.8.6.0.tar.bz2) | : | menu.py (pymol-v2.1.0.tar.bz2) |
|---|
| | |
| skipping to change at line 62 | | skipping to change at line 62 |
|---|
| ] | | ] |
| | |
| def camera_store_with_scene(self_cmd,frame): | | def camera_store_with_scene(self_cmd,frame): |
| list = self_cmd.get_scene_list()[0:40] # keep this practical | | list = self_cmd.get_scene_list()[0:40] # keep this practical |
| result = [[ 2, 'Scene:', '']] | | result = [[ 2, 'Scene:', '']] |
| for a in list: | | for a in list: |
| result.append([1,a,'cmd.mview("store",scene="'+a+'",first=%s)'%frame]) | | result.append([1,a,'cmd.mview("store",scene="'+a+'",first=%s)'%frame]) |
| return result | | return result |
| | |
| def store_with_state(self_cmd,obj='',frame=0): | | def store_with_state(self_cmd,obj='',frame=0): |
|
| n_state = self_cmd.count_states() | | n_state = self_cmd.count_states('%' + obj if obj else '') |
| result = [[ 2, 'State:', ''], | | result = [[ 2, 'State:', ''], |
| [ 1, 'current','cmd.mview("store",object="'+obj+'",state=-1,first=
%s)'%(frame)], | | [ 1, 'current','cmd.mview("store",object="'+obj+'",state=-1,first=
%s)'%(frame)], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, '1', 'cmd.mview("store",object="'+obj+'",state=1,first=%s)'%(
frame) ], | | [ 1, '1', 'cmd.mview("store",object="'+obj+'",state=1,first=%s)'%(
frame) ], |
| ] | | ] |
| if (n_state>1): | | if (n_state>1): |
| result.extend([ | | result.extend([ |
| [ 1, str(n_state),'cmd.mview("store",object="'+obj+'",state=%d,fir
st=%s)'%(n_state,frame)], | | [ 1, str(n_state),'cmd.mview("store",object="'+obj+'",state=%d,fir
st=%s)'%(n_state,frame)], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
|
| [ 1, str(1+n_state/4), 'cmd.mview("store",object="'+obj+'",state=% | | ]) |
| d,first=%s)'%(1+n_state/4,frame) ], | | n_show = min(8, n_state) |
| [ 1, str(1+n_state/3), 'cmd.mview("store",object="'+obj+'",state=% | | result.extend([ |
| d,first=%s)'%(1+n_state/3,frame) ], | | [ 1, str(state), 'cmd.mview("store",object="'+obj+'",state=%d,firs |
| [ 1, str(n_state/2), 'cmd.mview("store",object="'+obj+'",state=%d, | | t=%s)'%(state,frame) ] |
| first=%s)'%(n_state/2,frame) ], | | for state in [(n_state * i) // n_show for i in range(2, n_show)] |
| [ 1, str(1+n_state/2), 'cmd.mview("store",object="'+obj+'",state=% | | |
| d,first=%s)'%(1+n_state/2,frame) ], | | |
| [ 1, str((2*n_state)/3), 'cmd.mview("store",object="'+obj+'",state | | |
| =%d,first=%s)'%((2*n_state)/3,frame) ], | | |
| [ 1, str((3*n_state)/4), 'cmd.mview("store",object="'+obj+'",state | | |
| =%d,first=%s)'%((3*n_state)/4,frame) ], | | |
| ]) | | ]) |
| | |
| return result | | return result |
| | |
| def mouse_config(self_cmd): | | def mouse_config(self_cmd): |
| result = [[ 1, '3-Button Motions', | | result = [[ 1, '3-Button Motions', |
| 'cmd.config_mouse("three_button_motions")' ], | | 'cmd.config_mouse("three_button_motions")' ], |
| [ 1, '3-Button Editing', | | [ 1, '3-Button Editing', |
| 'cmd.config_mouse("three_button_editing")' ], | | 'cmd.config_mouse("three_button_editing")' ], |
| [ 1, '3-Button Viewing', | | [ 1, '3-Button Viewing', |
| | |
| skipping to change at line 147 | | skipping to change at line 146 |
|---|
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'smooth key frames' , smooth(self_cmd,',object="'+obj+'"') ], | | [ 1, 'smooth key frames' , smooth(self_cmd,',object="'+obj+'"') ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'interpolate' , 'cmd.mview("interpolate",object="'+obj+'")'
], | | [ 1, 'interpolate' , 'cmd.mview("interpolate",object="'+obj+'")'
], |
| [ 1, 'reinterpolate' , 'cmd.mview("reinterpolate",object="'+obj+
'")' ], | | [ 1, 'reinterpolate' , 'cmd.mview("reinterpolate",object="'+obj+
'")' ], |
| [ 1, 'uninterpolate' , 'cmd.mview("uninterpolate",object="'+obj+
'")' ], | | [ 1, 'uninterpolate' , 'cmd.mview("uninterpolate",object="'+obj+
'")' ], |
| ] | | ] |
| | |
| def rep_action(self_cmd, sele, action) : | | def rep_action(self_cmd, sele, action) : |
| return [ | | return [ |
|
| [ 1, 'lines' , 'cmd.'+action+'("lines" ,"'+sele+'")' ], | | [ 1, 'wire' , 'cmd.'+action+'("wire" ,"'+sele+'")' ], |
| [ 1, 'sticks' , 'cmd.'+action+'("sticks" ,"'+sele+'")' ], | | [ 1, ' lines' , 'cmd.'+action+'("lines" ,"'+sele+'")' ], |
| | [ 1, ' nonbonded', 'cmd.'+action+'("nonbonded" ,"'+sele+'")' ], |
| | [ 0, '' , '' ], |
| | [ 1, 'licorice' , 'cmd.'+action+'("licorice" ,"'+sele+'")' ], |
| | [ 1, ' sticks' , 'cmd.'+action+'("sticks" ,"'+sele+'")' ], |
| | [ 1, ' nb_spheres','cmd.'+action+'("nb_spheres","'+sele+'")' ], |
| | [ 0, '' , '' ], |
| [ 1, 'ribbon' , 'cmd.'+action+'("ribbon" ,"'+sele+'")' ], | | [ 1, 'ribbon' , 'cmd.'+action+'("ribbon" ,"'+sele+'")' ], |
| [ 1, 'cartoon' , 'cmd.'+action+'("cartoon" ,"'+sele+'")' ], | | [ 1, 'cartoon' , 'cmd.'+action+'("cartoon" ,"'+sele+'")' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'label' , 'cmd.'+action+'("labels" ,"'+sele+'")' ], | | [ 1, 'label' , 'cmd.'+action+'("labels" ,"'+sele+'")' ], |
| [ 1, 'cell' , 'cmd.'+action+'("cell" ,"'+sele+'")' ], | | [ 1, 'cell' , 'cmd.'+action+'("cell" ,"'+sele+'")' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
|
| [ 1, 'nonbonded' , 'cmd.'+action+'("nonbonded" ,"'+sele+'")' ], | | |
| [ 1, 'dots' , 'cmd.'+action+'("dots" ,"'+sele+'")' ], | | [ 1, 'dots' , 'cmd.'+action+'("dots" ,"'+sele+'")' ], |
| [ 1, 'spheres' , 'cmd.'+action+'("spheres" ,"'+sele+'")' ], | | [ 1, 'spheres' , 'cmd.'+action+'("spheres" ,"'+sele+'")' ], |
|
| [ 1, 'nb_spheres' , 'cmd.'+action+'("nb_spheres","'+sele+'")' ], | | |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'mesh' , 'cmd.'+action+'("mesh" ,"'+sele+'")' ], | | [ 1, 'mesh' , 'cmd.'+action+'("mesh" ,"'+sele+'")' ], |
| [ 1, 'surface' , 'cmd.'+action+'("surface" ,"'+sele+'")' ], | | [ 1, 'surface' , 'cmd.'+action+'("surface" ,"'+sele+'")' ], |
| ] | | ] |
| | |
| def mol_as(self_cmd, sele): | | def mol_as(self_cmd, sele): |
| return ( | | return ( |
| [[ 2, 'As:' , '']] | | [[ 2, 'As:' , '']] |
| +rep_action(self_cmd, sele,'show_as') | | +rep_action(self_cmd, sele,'show_as') |
| ) | | ) |
| | |
| skipping to change at line 836 | | skipping to change at line 839 |
|---|
| return [[ 2, 'Selections:', '' ], | | return [[ 2, 'Selections:', '' ], |
| [ 1, 'all', 'cmd.select("'+sele+'_all","'+sele+'")'], | | [ 1, 'all', 'cmd.select("'+sele+'_all","'+sele+'")'], |
| [ 1, 'polymer', 'cmd.select("'+sele+'_polymer","('+sele+') and pol
ymer")'], | | [ 1, 'polymer', 'cmd.select("'+sele+'_polymer","('+sele+') and pol
ymer")'], |
| [ 1, 'organic', 'cmd.select("'+sele+'_organic","('+sele+') and org
anic")'], | | [ 1, 'organic', 'cmd.select("'+sele+'_organic","('+sele+') and org
anic")'], |
| [ 1, 'solvent', 'cmd.select("'+sele+'_solvent","('+sele+') and sol
vent")'], | | [ 1, 'solvent', 'cmd.select("'+sele+'_solvent","('+sele+') and sol
vent")'], |
| [ 1, 'polar hydrogens', 'cmd.select("'+sele+'_polar_h","('+sele+')
and (e. H and bound_to e. S+O+N)")'], | | [ 1, 'polar hydrogens', 'cmd.select("'+sele+'_polar_h","('+sele+')
and (e. H and bound_to e. S+O+N)")'], |
| [ 1, 'non-polar hydrogens', 'cmd.select("'+sele+'_npolar_h","('+se
le+') and (e. H and (not bound_to e. S+O+N))")'], | | [ 1, 'non-polar hydrogens', 'cmd.select("'+sele+'_npolar_h","('+se
le+') and (e. H and (not bound_to e. S+O+N))")'], |
| [ 1, 'donors', 'cmd.select("'+sele+'_donors","('+sele+') and hbd")
'], | | [ 1, 'donors', 'cmd.select("'+sele+'_donors","('+sele+') and hbd")
'], |
| [ 1, 'acceptors', 'cmd.select("'+sele+'_acceptors","('+sele+') and
hba")'], | | [ 1, 'acceptors', 'cmd.select("'+sele+'_acceptors","('+sele+') and
hba")'], |
| [ 1, 'surface atoms', 'util.find_surface_atoms(sele="'+sele+'", _s
elf=cmd)' ], | | [ 1, 'surface atoms', 'util.find_surface_atoms(sele="'+sele+'", _s
elf=cmd)' ], |
|
| | [ 1, 'C-alphas', 'cmd.select("'+sele+'_calpha","bycalpha ('+sele+'
)")'], |
| ] | | ] |
| | |
| def mol_generate(self_cmd, sele): | | def mol_generate(self_cmd, sele): |
| return [[ 2, 'Generate:' ,'' ], | | return [[ 2, 'Generate:' ,'' ], |
| [ 1, 'selection', selection(self_cmd, sele) ], | | [ 1, 'selection', selection(self_cmd, sele) ], |
| [ 1, 'symmetry mates', symmetry(self_cmd, sele) ], | | [ 1, 'symmetry mates', symmetry(self_cmd, sele) ], |
| [ 1, 'vacuum electrostatics', vacuum(self_cmd, sele) ], | | [ 1, 'vacuum electrostatics', vacuum(self_cmd, sele) ], |
| # [ 1, 'assign', mol_assign(self_cmd, sele) ], | | # [ 1, 'assign', mol_assign(self_cmd, sele) ], |
| ] | | ] |
| | |
| | |
| skipping to change at line 1094 | | skipping to change at line 1098 |
|---|
| return [[ 2, 'Modify:', ''], | | return [[ 2, 'Modify:', ''], |
| [ 1, 'around' , around(self_cmd, sele) ], | | [ 1, 'around' , around(self_cmd, sele) ], |
| [ 1, 'expand' , expand(self_cmd, sele) ], | | [ 1, 'expand' , expand(self_cmd, sele) ], |
| [ 1, 'extend' , extend(self_cmd, sele) ], | | [ 1, 'extend' , extend(self_cmd, sele) ], |
| [ 1, 'invert' , invert(self_cmd, sele) ], | | [ 1, 'invert' , invert(self_cmd, sele) ], |
| [ 1, 'complete' , complete(self_cmd, sele) ], | | [ 1, 'complete' , complete(self_cmd, sele) ], |
| [ 1, 'restrict' , restrict(self_cmd, sele) ], | | [ 1, 'restrict' , restrict(self_cmd, sele) ], |
| [ 1, 'include' , include(self_cmd, sele) ], | | [ 1, 'include' , include(self_cmd, sele) ], |
| [ 1, 'exclude' , exclude(self_cmd, sele) ]] | | [ 1, 'exclude' , exclude(self_cmd, sele) ]] |
| | |
|
| | def copy_to(self_cmd, sele): |
| | onames = self_cmd.get_object_list('enabled')[:25] # keep this practical |
| | selected = self_cmd.get_object_list(sele) |
| | return [[ 2, 'Copy To:', '' ], |
| | [ 1, 'new', 'cmd.create(None,"' + sele + '",zoom=0)' ], |
| | [ 0, '', '' ], |
| | ] + [ |
| | [ 1, oname, 'cmd.copy_to("' + oname + '","' + sele + '",zoom=0 |
| | ,quiet=0)' ] |
| | for oname in onames |
| | if oname not in selected |
| | ] |
| | |
| def sele_action(self_cmd, sele): | | def sele_action(self_cmd, sele): |
| return [[ 2, 'Action:' ,'' ], | | return [[ 2, 'Action:' ,'' ], |
| [ 1, del_col + 'delete selection', 'cmd.delete("'+sele+'")'
], | | [ 1, del_col + 'delete selection', 'cmd.delete("'+sele+'")'
], |
| [ 1, 'rename selection', 'cmd.wizard("renaming","'+sele+'")'
], | | [ 1, 'rename selection', 'cmd.wizard("renaming","'+sele+'")'
], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)'
], | | [ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)'
], |
| [ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)'
], | | [ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)'
], |
| [ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)'
], | | [ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)'
], |
| [ 1, 'origin' ,'cmd.origin("'+sele+'")' ], | | [ 1, 'origin' ,'cmd.origin("'+sele+'")' ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| | |
| skipping to change at line 1116 | | skipping to change at line 1132 |
|---|
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'modify', modify_sele(self_cmd, sele) ], | | [ 1, 'modify', modify_sele(self_cmd, sele) ], |
| [ 1, 'preset' ,presets(self_cmd, sele) ], | | [ 1, 'preset' ,presets(self_cmd, sele) ], |
| [ 1, 'find', find(self_cmd, sele) ], | | [ 1, 'find', find(self_cmd, sele) ], |
| [ 1, 'align', sele_align(self_cmd, sele) ], | | [ 1, 'align', sele_align(self_cmd, sele) ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, rem_col + 'remove atoms' ,'cmd.remove("'+sele+'");cmd.delet
e("'+sele+'")' ], | | [ 1, rem_col + 'remove atoms' ,'cmd.remove("'+sele+'");cmd.delet
e("'+sele+'")' ], |
| [ 1, 'hydrogens' , hydrogens(self_cmd, sele) ], | | [ 1, 'hydrogens' , hydrogens(self_cmd, sele) ], |
| [ 0, '' ,''
], | | [ 0, '' ,''
], |
| [ 1, 'duplicate' ,'cmd.select(None,"'+sele+'")' ], #
broken... | | [ 1, 'duplicate' ,'cmd.select(None,"'+sele+'")' ], #
broken... |
|
| [ 1, 'copy to object' ,'cmd.create(None,"'+sele+'",zoom=0)' ], | | [ 1, 'copy to object' , lambda: copy_to(self_cmd, sele) ], |
| [ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ], | | [ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'masking' , masking(self_cmd, sele) ], | | [ 1, 'masking' , masking(self_cmd, sele) ], |
| [ 1, 'movement' , movement(self_cmd, sele) ], | | [ 1, 'movement' , movement(self_cmd, sele) ], |
| [ 1, 'compute' , compute(self_cmd, sele) ], | | [ 1, 'compute' , compute(self_cmd, sele) ], |
| ] | | ] |
| | |
| def sele_action2(self_cmd, sele): | | def sele_action2(self_cmd, sele): |
| return [[ 2, 'Action:' ,'' ], | | return [[ 2, 'Action:' ,'' ], |
| [ 1, del_col + 'delete selection', 'cmd.delete("'+sele+'")'
], | | [ 1, del_col + 'delete selection', 'cmd.delete("'+sele+'")'
], |
| | |
| skipping to change at line 1141 | | skipping to change at line 1157 |
|---|
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, rem_col + 'remove atoms' ,'cmd.remove("'+sele+'");cmd.delet
e("'+sele+'")' ], | | [ 1, rem_col + 'remove atoms' ,'cmd.remove("'+sele+'");cmd.delet
e("'+sele+'")' ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'around' , around(self_cmd, sele) ], | | [ 1, 'around' , around(self_cmd, sele) ], |
| [ 1, 'expand' , expand(self_cmd, sele) ], | | [ 1, 'expand' , expand(self_cmd, sele) ], |
| [ 1, 'extend' , extend(self_cmd, sele) ], | | [ 1, 'extend' , extend(self_cmd, sele) ], |
| [ 1, 'invert' , invert(self_cmd, sele) ], | | [ 1, 'invert' , invert(self_cmd, sele) ], |
| [ 1, 'complete' , complete(self_cmd, sele) ], | | [ 1, 'complete' , complete(self_cmd, sele) ], |
| [ 0, '' ,''
], | | [ 0, '' ,''
], |
| [ 1, 'duplicate selection' ,'cmd.select(None,"'+sele+'")'
], | | [ 1, 'duplicate selection' ,'cmd.select(None,"'+sele+'")'
], |
|
| [ 1, 'copy to object' ,'cmd.create(None,"'+sele+'",zoom=0)' ]
, | | [ 1, 'copy to object' , lambda: copy_to(self_cmd, sele) ], |
| [ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ], | | [ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'masking' , masking(self_cmd, sele) ], | | [ 1, 'masking' , masking(self_cmd, sele) ], |
| [ 1, 'movement' , movement(self_cmd, sele) ], | | [ 1, 'movement' , movement(self_cmd, sele) ], |
| [ 1, 'compute' , compute(self_cmd, sele) ], | | [ 1, 'compute' , compute(self_cmd, sele) ], |
| ] | | ] |
| | |
| def group_action(self_cmd, sele): | | def group_action(self_cmd, sele): |
| return [[ 2, 'Action:' , '' ], | | return [[ 2, 'Action:' , '' ], |
| [ 1, 'zoom' , 'cmd.zoom("'+sele+'",animate=-1)' ], | | [ 1, 'zoom' , 'cmd.zoom("'+sele+'",animate=-1)' ], |
| | |
| skipping to change at line 1200 | | skipping to change at line 1216 |
|---|
| [ 1, 'clean' , 'cmd.clean("'+sele+'")' ], | | [ 1, 'clean' , 'cmd.clean("'+sele+'")' ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'preset' , presets(self_cmd, sele) ], | | [ 1, 'preset' , presets(self_cmd, sele) ], |
| [ 1, 'find', find(self_cmd, sele) ], | | [ 1, 'find', find(self_cmd, sele) ], |
| [ 1, 'align', mol_align(self_cmd, sele) ], | | [ 1, 'align', mol_align(self_cmd, sele) ], |
| [ 1, 'generate' , mol_generate(self_cmd, sele) ], | | [ 1, 'generate' , mol_generate(self_cmd, sele) ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'assign sec. struc.' ,'cmd.dss("'+sele+'")' ], | | [ 1, 'assign sec. struc.' ,'cmd.dss("'+sele+'")' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'rename object', 'cmd.wizard("renaming","'+sele+'")' ]
, | | [ 1, 'rename object', 'cmd.wizard("renaming","'+sele+'")' ]
, |
|
| [ 1, 'duplicate object' ,'cmd.create(None,"'+sele+'")' ], | | [ 1, 'copy to object' , lambda: copy_to(self_cmd, sele) ], |
| [ 1, del_col + 'delete object', 'cmd.delete("'+sele+'")' ], | | [ 1, del_col + 'delete object', 'cmd.delete("'+sele+'")' ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'hydrogens' , hydrogens(self_cmd, sele) ], | | [ 1, 'hydrogens' , hydrogens(self_cmd, sele) ], |
| [ 1, rem_col + 'remove waters', 'cmd.remove("(solvent and ('+sele+')
)")' ], | | [ 1, rem_col + 'remove waters', 'cmd.remove("(solvent and ('+sele+')
)")' ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'state' , state(self_cmd, sele) ], | | [ 1, 'state' , state(self_cmd, sele) ], |
| [ 1, 'masking' , masking(self_cmd, sele) ], | | [ 1, 'masking' , masking(self_cmd, sele) ], |
| [ 1, 'sequence' , sequence(self_cmd, sele) ], | | [ 1, 'sequence' , sequence(self_cmd, sele) ], |
| [ 1, 'movement' , movement(self_cmd, sele) ], | | [ 1, 'movement' , movement(self_cmd, sele) ], |
| [ 1, 'compute' , compute(self_cmd, sele) ], | | [ 1, 'compute' , compute(self_cmd, sele) ], |
| | |
| skipping to change at line 1475 | | skipping to change at line 1491 |
|---|
| [ 1, 'ID' , 'cmd.label("'+sele+'","ID")' ], | | [ 1, 'ID' , 'cmd.label("'+sele+'","ID")' ], |
| [ 1, 'index' , 'cmd.label("'+sele+'","index")' ], | | [ 1, 'index' , 'cmd.label("'+sele+'","index")' ], |
| ] | | ] |
| | |
| def mol_labels(self_cmd, sele): | | def mol_labels(self_cmd, sele): |
| with menucontext(self_cmd, sele) as mc: | | with menucontext(self_cmd, sele) as mc: |
| return [[ 2, 'Label:' , '' ], | | return [[ 2, 'Label:' , '' ], |
| [ 1, 'clear' , 'cmd.label("'+sele+'","\'\'")' ], | | [ 1, 'clear' , 'cmd.label("'+sele+'","\'\'")' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'residues' , """cmd.label('''(name """+self_cmd.get("la
bel_anchor")+"""+C1*+C1' and (byres("""+sele+""")))''','''"%s-%s"%(resn,resi)'''
)""" ], | | [ 1, 'residues' , """cmd.label('''(name """+self_cmd.get("la
bel_anchor")+"""+C1*+C1' and (byres("""+sele+""")))''','''"%s-%s"%(resn,resi)'''
)""" ], |
|
| | [ 1, 'residues (oneletter)', "cmd.label('''byca(" + sele + ")''',
'oneletter+resi')"], |
| [ 1, 'chains' , 'util.label_chains("'+sele+'",_self=cmd)'
], | | [ 1, 'chains' , 'util.label_chains("'+sele+'",_self=cmd)'
], |
| [ 1, 'segments' , 'util.label_segments("'+sele+'",_self=cm
d)' ], | | [ 1, 'segments' , 'util.label_segments("'+sele+'",_self=cm
d)' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'atom name' , 'cmd.label("'+sele+'","name")' ], | | [ 1, 'atom name' , 'cmd.label("'+sele+'","name")' ], |
| [ 1, 'element symbol' , 'cmd.label("'+sele+'","elem")' ], | | [ 1, 'element symbol' , 'cmd.label("'+sele+'","elem")' ], |
| [ 1, 'residue name' , 'cmd.label("'+sele+'","resn")' ], | | [ 1, 'residue name' , 'cmd.label("'+sele+'","resn")' ], |
|
| | [ 1, 'one letter code', 'cmd.label("'+sele+'","oneletter")' ], |
| [ 1, 'residue identifier' , 'cmd.label("'+sele+'","resi")'
], | | [ 1, 'residue identifier' , 'cmd.label("'+sele+'","resi")'
], |
| [ 1, 'chain identifier' , 'cmd.label("'+sele+'","chain")'
], | | [ 1, 'chain identifier' , 'cmd.label("'+sele+'","chain")'
], |
| [ 1, 'segment identifier' , 'cmd.label("'+sele+'","segi")'
], | | [ 1, 'segment identifier' , 'cmd.label("'+sele+'","segi")'
], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'b-factor' , 'cmd.label("'+sele+'","\'%1.2f\'%b")' ], | | [ 1, 'b-factor' , 'cmd.label("'+sele+'","\'%1.2f\'%b")' ], |
| [ 1, 'occupancy' , 'cmd.label("'+sele+'","\'%1.2f\'%q")' ], | | [ 1, 'occupancy' , 'cmd.label("'+sele+'","\'%1.2f\'%q")' ], |
| [ 1, 'vdw radius' , 'cmd.label("'+sele+'","\'%1.2f\'%vdw")'
], | | [ 1, 'vdw radius' , 'cmd.label("'+sele+'","\'%1.2f\'%vdw")'
], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'other properties' , label_props(self_cmd, sele) ], | | [ 1, 'other properties' , label_props(self_cmd, sele) ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| | |
| skipping to change at line 1562 | | skipping to change at line 1580 |
|---|
| [ 2, 'Scene', '' ], | | [ 2, 'Scene', '' ], |
| [ 1, 'next' , 'cmd.scene()' ], | | [ 1, 'next' , 'cmd.scene()' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'append' , 'cmd.scene("new","append",quiet=0)' ], | | [ 1, 'append' , 'cmd.scene("new","append",quiet=0)' ], |
| [ 1, 'update' , 'cmd.scene("auto","update",quiet=0)' ], | | [ 1, 'update' , 'cmd.scene("auto","update",quiet=0)' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'recall' , recall_list ], | | [ 1, 'recall' , recall_list ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'buttons', scene_buttons(self_cmd)] ] | | [ 1, 'buttons', scene_buttons(self_cmd)] ] |
| | |
|
| def main_pseudoatom_sub(self_cmd,pos): | | def main_pseudoatom_sub(self_cmd,pos, screenpos): |
| return [ | | return [ |
| [ 2, 'Pseudoatom' ,'' ], | | [ 2, 'Pseudoatom' ,'' ], |
| [ 1, 'label' ,'cmd.wizard("pseudoatom","label",pos=[%1.7f,%1.7f,%1.7f])'
%pos ], | | [ 1, 'label' ,'cmd.wizard("pseudoatom","label",pos=[%1.7f,%1.7f,%1.7f])'
%pos ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'single ', 'cmd.pseudoatom(pos=[%1.7f,%1.7f,%1.7f])'%pos ], | | [ 1, 'single ', 'cmd.pseudoatom(pos=[%1.7f,%1.7f,%1.7f])'%pos ], |
| ] | | ] |
| | |
|
| def main_pseudoatom(self_cmd,pos): | | def main_pseudoatom(self_cmd,pos, screenpos): |
| return [ | | return [ |
| [ 2, 'New' , '' ], | | [ 2, 'New' , '' ], |
|
| [ 1, 'pseudoatom' , main_pseudoatom_sub(self_cmd,pos) ], | | [ 1, 'pseudoatom' , main_pseudoatom_sub(self_cmd,pos, screenpos) ], |
| ] | | ] |
| | |
| def movie_panel(self_cmd): | | def movie_panel(self_cmd): |
| return [[ 2, 'Panel', '' ], | | return [[ 2, 'Panel', '' ], |
| [ 1, 'on', 'cmd.set("movie_panel")'], | | [ 1, 'on', 'cmd.set("movie_panel")'], |
| [ 1, 'off', 'cmd.set("movie_panel", 0)']] | | [ 1, 'off', 'cmd.set("movie_panel", 0)']] |
| | |
| def movie_main(self_cmd): | | def movie_main(self_cmd): |
| return [ | | return [ |
| [ 2, 'Movie', ''], | | [ 2, 'Movie', ''], |
| [ 1, 'play', 'cmd.mplay()'], | | [ 1, 'play', 'cmd.mplay()'], |
| [ 1, 'stop', 'cmd.mstop()'], | | [ 1, 'stop', 'cmd.mstop()'], |
| [ 0, '', '' ], | | [ 0, '', '' ], |
| [ 1, 'rewind', 'cmd.rewind()'], | | [ 1, 'rewind', 'cmd.rewind()'], |
| [ 0, '', '' ], | | [ 0, '', '' ], |
| [ 1, 'panel', movie_panel(self_cmd) ] | | [ 1, 'panel', movie_panel(self_cmd) ] |
| ] | | ] |
| | |
|
| def main_menu(self_cmd,pos): | | def main_menu(self_cmd,pos, screenpos): |
| return [ | | return [ |
| [ 2, 'Main Pop-Up' , '' ], | | [ 2, 'Main Pop-Up' , '' ], |
|
| [ 1, 'new' , main_pseudoatom(self_cmd,pos) ], | | [ 1, 'new' , main_pseudoatom(self_cmd,pos, screenpos) ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'zoom (vis)' ,'cmd.zoom("visible",animate=-1)'
], | | [ 1, 'zoom (vis)' ,'cmd.zoom("visible",animate=-1)'
], |
| [ 1, 'orient (vis)' ,'cmd.orient("visible",animate=-1)'
], | | [ 1, 'orient (vis)' ,'cmd.orient("visible",animate=-1)'
], |
| [ 1, 'center (vis)' ,'cmd.center("visible",animate=-1)'
], | | [ 1, 'center (vis)' ,'cmd.center("visible",animate=-1)'
], |
| [ 1, 'reset' ,'cmd.reset()' ], | | [ 1, 'reset' ,'cmd.reset()' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'movie' , movie_main(self_cmd) ], | | [ 1, 'movie' , movie_main(self_cmd) ], |
| [ 1, 'scene' , scene_main(self_cmd) ], | | [ 1, 'scene' , scene_main(self_cmd) ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'enable', enable_disable(self_cmd, 1) ], | | [ 1, 'enable', enable_disable(self_cmd, 1) ], |
| | |
| skipping to change at line 1618 | | skipping to change at line 1636 |
|---|
| [ 1, '(all)' , all_option(self_cmd,"all") ], | | [ 1, '(all)' , all_option(self_cmd,"all") ], |
| [ 1, '(visible)' , all_option(self_cmd,"visible") ], | | [ 1, '(visible)' , all_option(self_cmd,"visible") ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'ray' ,'cmd.ray()' ], | | [ 1, 'ray' ,'cmd.ray()' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, del_col + 'delete all', 'cmd.delete("all")' ], | | [ 1, del_col + 'delete all', 'cmd.delete("all")' ], |
| [ 1, del_col + 'reinitialize', 'cmd.reinitialize()' ], | | [ 1, del_col + 'reinitialize', 'cmd.reinitialize()' ], |
| [ 1, del_col + 'quit', 'cmd.quit()' ], | | [ 1, del_col + 'quit', 'cmd.quit()' ], |
| ] | | ] |
| | |
|
| def pick_sele_sub(self_cmd, sele): | | |
| result = [ | | |
| [ 2, 'Actions' , '' ], | | |
| [ 1, 'rename', 'cmd.wizard("renaming","'+sele+'")' ], | | |
| [ 1, 'clear' , 'cmd.select("'+sele+'","none")' ], | | |
| [ 1, del_col + 'delete selection', 'cmd.delete("'+sele+'")' ], | | |
| [ 1, 'copy to object','cmd.create(None,"'+sele+'",zoom=0)' ], | | |
| [ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ], | | |
| [ 1, rem_col + 'remove atoms', 'cmd.remove("'+sele+'")' ], | | |
| ] | | |
| return result | | |
| | | |
| def pick_sele(self_cmd, sele, title): | | def pick_sele(self_cmd, sele, title): |
| result = [ | | result = [ |
| [ 2, title, '' ], | | [ 2, title, '' ], |
| [ 1, 'disable' , 'cmd.disable("'+sele+'")' ], | | [ 1, 'disable' , 'cmd.disable("'+sele+'")' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'actions', sele_action2(self_cmd, sele) ], | | [ 1, 'actions', sele_action2(self_cmd, sele) ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'color' , mol_color(self_cmd, sele) ], | | [ 1, 'color' , mol_color(self_cmd, sele) ], |
| [ 1, 'show' , mol_show(self_cmd, sele) ], | | [ 1, 'show' , mol_show(self_cmd, sele) ], |
| [ 1, 'hide' , mol_hide(self_cmd, sele) ], | | [ 1, 'hide' , mol_hide(self_cmd, sele) ], |
| | |
| skipping to change at line 1657 | | skipping to change at line 1663 |
|---|
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, 'drag' ,'cmd.drag("'+sele+'")' ], | | [ 1, 'drag' ,'cmd.drag("'+sele+'")' ], |
| [ 1, 'clean' ,'cmd.clean("'+sele+'")' ], | | [ 1, 'clean' ,'cmd.clean("'+sele+'")' ], |
| [ 0, '' ,'' ], | | [ 0, '' ,'' ], |
| [ 1, rem_col + 'remove', 'cmd.remove("'+sele+'")' ], | | [ 1, rem_col + 'remove', 'cmd.remove("'+sele+'")' ], |
| ] | | ] |
| return result | | return result |
| | |
| def pick_option(self_cmd, sele, title, object=0): | | def pick_option(self_cmd, sele, title, object=0): |
| if object: | | if object: |
|
| save_sele = sele | | sele = self_cmd.identify(sele, 1)[0][0] |
| sele = "(byobj ("+sele+"))" | | |
| else: | | |
| save_sele = sele | | |
| result = [ | | result = [ |
| [ 2, title, '' ], | | [ 2, title, '' ], |
| [ 1, 'color' , lambda: mol_color(self_cmd, sele) ], | | [ 1, 'color' , lambda: mol_color(self_cmd, sele) ], |
| [ 1, 'show' , mol_show(self_cmd, sele) ], | | [ 1, 'show' , mol_show(self_cmd, sele) ], |
| [ 1, 'hide' , mol_hide(self_cmd, sele) ], | | [ 1, 'hide' , mol_hide(self_cmd, sele) ], |
| [ 1, 'preset' , presets(self_cmd, sele) ], | | [ 1, 'preset' , presets(self_cmd, sele) ], |
| [ 1, 'label' , mol_labels(self_cmd, sele) ], | | [ 1, 'label' , mol_labels(self_cmd, sele) ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)' ], | | [ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)' ], |
| [ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)'
], | | [ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)'
], |
| [ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)'
], | | [ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)'
], |
| [ 1, 'origin' ,'cmd.origin("'+sele+'")' ], | | [ 1, 'origin' ,'cmd.origin("'+sele+'")' ], |
| [ 1, 'select' ,'cmd.select("'+sele+'",enable=1,merge=2)'
], | | [ 1, 'select' ,'cmd.select("'+sele+'",enable=1,merge=2)'
], |
| [ 0, '' ,'' ]] | | [ 0, '' ,'' ]] |
| | |
| if object: | | if object: |
| result.append([ 1, 'drag' , [[ 1, 'coordinates', 'cmd.drag
("'+sele+'")'], | | result.append([ 1, 'drag' , [[ 1, 'coordinates', 'cmd.drag
("'+sele+'")'], |
|
| [ 1, 'matrix', 'cmd.drag("'+save_sele+'",mo
de=1)']]]) | | [ 1, 'matrix', 'cmd.drag("'+sele+'",mode=1)
']]]) |
| else: | | else: |
| result.append([ 1, 'drag' , 'cmd.drag("'+sele+'")']) | | result.append([ 1, 'drag' , 'cmd.drag("'+sele+'")']) |
| | |
| result.extend([ | | result.extend([ |
| [ 1, 'clean' ,'cmd.clean("'+sele+'")' ], | | [ 1, 'clean' ,'cmd.clean("'+sele+'")' ], |
| [ 1, 'masking' , masking(self_cmd, sele) ], | | [ 1, 'masking' , masking(self_cmd, sele) ], |
| [ 1, 'movement' , movement(self_cmd, sele) ], | | [ 1, 'movement' , movement(self_cmd, sele) ], |
| ]) | | ]) |
| | |
| if object: | | if object: |
| result.extend([ | | result.extend([ |
| [ 1, del_col + 'delete', 'cmd.delete("'+sele+'")' ], | | [ 1, del_col + 'delete', 'cmd.delete("'+sele+'")' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'disable' ,'cmd.disable("'+sele+'")' ], | | [ 1, 'disable' ,'cmd.disable("'+sele+'")' ], |
| ]) | | ]) |
| else: | | else: |
| result.extend([ | | result.extend([ |
| [ 1, rem_col + 'remove atoms', 'cmd.remove("'+sele+'")' ], | | [ 1, rem_col + 'remove atoms', 'cmd.remove("'+sele+'")' ], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
|
| [ 1, 'copy to object','cmd.create(None,"'+sele+'",zoom=0)'
], | | [ 1, 'copy to object' , lambda: copy_to(self_cmd, sele) ], |
| [ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ], | | [ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ], |
| ]) | | ]) |
| return result | | return result |
| | |
|
| def pick_option_rev(self_cmd, sele, title, object=0): | | |
| result = pick_option(self_cmd, sele, title, object)[1:] | | |
| result.reverse() | | |
| return result | | |
| | | |
| def pick_menu(self_cmd, title, sele2): | | def pick_menu(self_cmd, title, sele2): |
| with menucontext(self_cmd, sele2): | | with menucontext(self_cmd, sele2): |
| return [[ 2, title , '' ], | | return [[ 2, title , '' ], |
| [ 1, 'drag object matrix' ,'cmd.drag("(byobj ('+sele2+'))",mode
=1)' ], | | [ 1, 'drag object matrix' ,'cmd.drag("(byobj ('+sele2+'))",mode
=1)' ], |
| [ 1, 'drag object coords' ,'cmd.drag("(byobj ('+sele2+'))")'
], | | [ 1, 'drag object coords' ,'cmd.drag("(byobj ('+sele2+'))")'
], |
| [ 0, '' , '' ], | | [ 0, '' , '' ], |
| [ 1, 'atom' , pick_option(self_cmd, sele2, "Atom") ], | | [ 1, 'atom' , pick_option(self_cmd, sele2, "Atom") ], |
| [ 1, 'residue' , pick_option(self_cmd, "(byres ("+sele2+"))", "Resid
ue") ], | | [ 1, 'residue' , pick_option(self_cmd, "(byres ("+sele2+"))", "Resid
ue") ], |
| [ 1, 'chain' , pick_option(self_cmd, "(bychain ("+sele2+"))", "Cha
in") ], | | [ 1, 'chain' , pick_option(self_cmd, "(bychain ("+sele2+"))", "Cha
in") ], |
| [ 1, 'segment' , pick_option(self_cmd, "(byseg ("+sele2+"))", "Segme
nt") ], | | [ 1, 'segment' , pick_option(self_cmd, "(byseg ("+sele2+"))", "Segme
nt") ], |
| | | |
| End of changes. 22 change blocks. |
|---|
| 48 lines changed or deleted | | 42 lines changed or added |
|---|
"Fossies" - the Fresh Open Source Software Archive 