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.
| editing.py (pymol-v2.1.0.tar.bz2) | : | editing.py (pymol-open-source-2.2.0) |
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| skipping to change at line 362 | | skipping to change at line 362 |
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| PYMOL API | | PYMOL API |
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| cmd.symmetry_copy(source_name, target_name, source_state, target_state, | | cmd.symmetry_copy(source_name, target_name, source_state, target_state, |
| target_undo, log, quiet) | | target_undo, log, quiet) |
| | |
| """ | | """ |
| | |
| r = DEFAULT_ERROR | | r = DEFAULT_ERROR |
| | |
|
| suspend_undo = _self.get("suspend_undo") | | |
| fin = 1 | | |
| push_undo(target_name, just_coordinates=0, finish_undo=0, _self=_self) | | |
| _self.set("suspend_undo", 1, updates=0) | | |
| | | |
| if source_name == None: | | if source_name == None: |
| source_name = '' | | source_name = '' |
| | |
| target_name = str(target_name).strip() | | target_name = str(target_name).strip() |
| source_name = str(source_name).strip() | | source_name = str(source_name).strip() |
| | |
| # ignored for now | | # ignored for now |
| source_mode = 1 | | source_mode = 1 |
| target_mode = 1 | | target_mode = 1 |
| | |
| | |
| skipping to change at line 392 | | skipping to change at line 387 |
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| int(source_mode), | | int(source_mode), |
| int(target_mode), | | int(target_mode), |
| int(source_state)-1, | | int(source_state)-1, |
| int(target_state)-1, | | int(target_state)-1, |
| int(target_undo), | | int(target_undo), |
| int(log), | | int(log), |
| int(quiet)) | | int(quiet)) |
| finally: | | finally: |
| _self.unlock(r,_self) | | _self.unlock(r,_self) |
| if _self._raising(r,_self): | | if _self._raising(r,_self): |
|
| _self.set("suspend_undo", suspend_undo, updates=0) | | |
| fin = -1 | | |
| push_undo("", just_coordinates=0, finish_undo=fin, _self=_self) | | |
| raise pymol.CmdException | | raise pymol.CmdException |
|
| | | |
| _self.set("suspend_undo", suspend_undo, updates=0) | | |
| push_undo("", just_coordinates=0, finish_undo=fin, _self=_self) | | |
| | | |
| return r | | return r |
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| def set_name(old_name, new_name,_self=cmd): | | def set_name(old_name, new_name,_self=cmd): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
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| "set_name" changes the name of an object or selection. | | "set_name" changes the name of an object or selection. |
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| USAGE | | USAGE |
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| skipping to change at line 2035 | | skipping to change at line 2023 |
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| matrix_reset, align, fit, pair_fit | | matrix_reset, align, fit, pair_fit |
| ''' | | ''' |
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| r = DEFAULT_ERROR | | r = DEFAULT_ERROR |
| if source_name == None: | | if source_name == None: |
| source_name = '' | | source_name = '' |
| target_name = str(target_name).strip() | | target_name = str(target_name).strip() |
| source_name = str(source_name).strip() | | source_name = str(source_name).strip() |
| if (target_name == '' and source_name != ''): # tentative -- create a ne
w command instead? | | if (target_name == '' and source_name != ''): # tentative -- create a ne
w command instead? |
|
| mat = cmd.get_object_matrix(source_name,source_state) | | mat = _self.get_object_matrix(source_name,source_state) |
| view = cmd.get_view() | | view = _self.get_view() |
| new_view = ( | | new_view = ( |
| mat[ 0]*view[ 0] + mat[ 4]*view[ 3] + mat[ 8]*view[ 6], | | mat[ 0]*view[ 0] + mat[ 4]*view[ 3] + mat[ 8]*view[ 6], |
| mat[ 0]*view[ 1] + mat[ 4]*view[ 4] + mat[ 8]*view[ 7], | | mat[ 0]*view[ 1] + mat[ 4]*view[ 4] + mat[ 8]*view[ 7], |
| mat[ 0]*view[ 2] + mat[ 4]*view[ 5] + mat[ 8]*view[ 8], | | mat[ 0]*view[ 2] + mat[ 4]*view[ 5] + mat[ 8]*view[ 8], |
| mat[ 1]*view[ 0] + mat[ 5]*view[ 3] + mat[ 9]*view[ 6], | | mat[ 1]*view[ 0] + mat[ 5]*view[ 3] + mat[ 9]*view[ 6], |
| mat[ 1]*view[ 1] + mat[ 5]*view[ 4] + mat[ 9]*view[ 7], | | mat[ 1]*view[ 1] + mat[ 5]*view[ 4] + mat[ 9]*view[ 7], |
| mat[ 1]*view[ 2] + mat[ 5]*view[ 5] + mat[ 9]*view[ 8], | | mat[ 1]*view[ 2] + mat[ 5]*view[ 5] + mat[ 9]*view[ 8], |
| mat[ 2]*view[ 0] + mat[ 6]*view[ 3] + mat[10]*view[ 6], | | mat[ 2]*view[ 0] + mat[ 6]*view[ 3] + mat[10]*view[ 6], |
| mat[ 2]*view[ 1] + mat[ 6]*view[ 4] + mat[10]*view[ 7], | | mat[ 2]*view[ 1] + mat[ 6]*view[ 4] + mat[10]*view[ 7], |
| mat[ 2]*view[ 2] + mat[ 6]*view[ 5] + mat[10]*view[ 8], | | mat[ 2]*view[ 2] + mat[ 6]*view[ 5] + mat[10]*view[ 8], |
| view[ 9] , view[10] , view[11], | | view[ 9] , view[10] , view[11], |
| mat[ 0]*view[12] + mat[ 1]*view[13] + mat[ 2]*view[14] - | | mat[ 0]*view[12] + mat[ 1]*view[13] + mat[ 2]*view[14] - |
| mat[ 0]* mat[ 3] - mat[ 4]* mat[ 7] - mat[ 8]* mat[11], | | mat[ 0]* mat[ 3] - mat[ 4]* mat[ 7] - mat[ 8]* mat[11], |
| mat[ 4]*view[12] + mat[ 5]*view[13] + mat[ 6]*view[14] - | | mat[ 4]*view[12] + mat[ 5]*view[13] + mat[ 6]*view[14] - |
| mat[ 1]* mat[ 3] - mat[ 5]* mat[ 7] - mat[ 9]* mat[11], | | mat[ 1]* mat[ 3] - mat[ 5]* mat[ 7] - mat[ 9]* mat[11], |
| mat[ 8]*view[12] + mat[ 9]*view[13] + mat[10]*view[14] - | | mat[ 8]*view[12] + mat[ 9]*view[13] + mat[10]*view[14] - |
| mat[ 2]* mat[ 3] - mat[ 6]* mat[ 7] - mat[10]* mat[11], | | mat[ 2]* mat[ 3] - mat[ 6]* mat[ 7] - mat[10]* mat[11], |
| view[15] , view[16] , view[17] ) | | view[15] , view[16] , view[17] ) |
|
| r = cmd.set_view(new_view) | | r = _self.set_view(new_view) |
| else: | | else: |
| try: | | try: |
| _self.lock(_self) | | _self.lock(_self) |
| r = _cmd.matrix_copy(_self._COb,str(source_name), | | r = _cmd.matrix_copy(_self._COb,str(source_name), |
| str(target_name), | | str(target_name), |
| int(source_mode), | | int(source_mode), |
| int(target_mode), | | int(target_mode), |
| int(source_state)-1, | | int(source_state)-1, |
| int(target_state)-1, | | int(target_state)-1, |
| int(target_undo), | | int(target_undo), |
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| skipping to change at line 2623 | | skipping to change at line 2611 |
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| if not prefix: | | if not prefix: |
| name = '%s_%s' % (model, chain) | | name = '%s_%s' % (model, chain) |
| else: | | else: |
| name = '%s%04d' % (prefix, count) | | name = '%s%04d' % (prefix, count) |
| _self.create(name, '(%s) and model %s and chain "%s"' % | | _self.create(name, '(%s) and model %s and chain "%s"' % |
| (selection, model, chain), zoom=0) | | (selection, model, chain), zoom=0) |
| names_list.append(name) | | names_list.append(name) |
| _self.disable(model) | | _self.disable(model) |
| | |
| if group: | | if group: |
|
| cmd.group(group, ' '.join(names_list), 'add') | | _self.group(group, ' '.join(names_list), 'add') |
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| def alphatoall(selection='polymer', properties='b', operator='byca', | | def alphatoall(selection='polymer', properties='b', operator='byca', |
| quiet=1, _self=cmd): | | quiet=1, _self=cmd): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
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| Expand any given property of the CA atoms to all atoms in the residue | | Expand any given property of the CA atoms to all atoms in the residue |
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| ARGUMENTS | | ARGUMENTS |
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| End of changes. 6 change blocks. |
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| 16 lines changed or deleted | | 4 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 