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.
| filter.py (pymol-v2.1.0.tar.bz2) | : | filter.py (pymol-open-source-2.2.0) |
|---|
| | |
| skipping to change at line 122 | | skipping to change at line 122 |
|---|
| obj_name = cmd.index('first ?' + name)[0][0] | | obj_name = cmd.index('first ?' + name)[0][0] |
| self.set_object(obj_name) | | self.set_object(obj_name) |
| except: | | except: |
| pass | | pass |
| self.cmd.deselect() | | self.cmd.deselect() |
| | |
| def do_pick(self,bondFlag): | | def do_pick(self,bondFlag): |
| self.do_select('pk1') | | self.do_select('pk1') |
| self.cmd.unpick() | | self.cmd.unpick() |
| | |
|
| | def do_state(self, state): |
| | cmd.refresh_wizard() |
| | |
| | def get_event_mask(self): |
| | return Wizard.event_mask_pick + Wizard.event_mask_select + Wizard.event_ |
| | mask_state |
| | |
| def update_object_menu(self): | | def update_object_menu(self): |
| | |
| # find objects with > 1 state | | # find objects with > 1 state |
| | |
| self.avail_objects = [] | | self.avail_objects = [] |
| | |
| for a in cmd.get_names('objects'): | | for a in cmd.get_names('objects'): |
| if cmd.get_type(a)=='object:molecule': | | if cmd.get_type(a)=='object:molecule': |
| if cmd.count_states(a)>1: | | if cmd.count_states(a)>1: |
| self.avail_objects.append(a) | | self.avail_objects.append(a) |
| | |
| skipping to change at line 267 | | skipping to change at line 273 |
|---|
| def get_prompt(self): | | def get_prompt(self): |
| | |
| # returns text prompt | | # returns text prompt |
| | |
| self.prompt = None | | self.prompt = None |
| if self.object == None: | | if self.object == None: |
| self.prompt = [ 'Please select a multi-state object...' ] | | self.prompt = [ 'Please select a multi-state object...' ] |
| else: | | else: |
| self.prompt = [ '%s: %d accepted, %d rejected, %d deferred, %d remai
ning'%( | | self.prompt = [ '%s: %d accepted, %d rejected, %d deferred, %d remai
ning'%( |
| self.object,self.acce,self.reje,self.defe,self.togo) ] | | self.object,self.acce,self.reje,self.defe,self.togo) ] |
|
| state = cmd.get_state() | | state = cmd.get_object_state(self.object) |
| ident = self.get_ident(self.object,state) | | ident = self.get_ident(self.object,state) |
| sdo=self.dict[self.object] | | sdo=self.dict[self.object] |
| if ident in sdo: | | if ident in sdo: |
| self.prompt.append('%s: %s'%(ident,sdo[ident])) | | self.prompt.append('%s: %s'%(ident,sdo[ident])) |
| else: | | else: |
| self.prompt.append('%s?'%(ident)) | | self.prompt.append('%s?'%(ident)) |
| return self.prompt | | return self.prompt |
| | |
| def count(self,entry,str): | | def count(self,entry,str): |
| # keep track of how many compounds are in which category | | # keep track of how many compounds are in which category |
| | |
| skipping to change at line 293 | | skipping to change at line 299 |
|---|
| else: | | else: |
| self.togo = self.togo - 1 | | self.togo = self.togo - 1 |
| sdo[entry] = str | | sdo[entry] = str |
| self.adjust(sdo[entry],1) | | self.adjust(sdo[entry],1) |
| | |
| def accept(self): | | def accept(self): |
| # accept compound and advance | | # accept compound and advance |
| if self.object==None: | | if self.object==None: |
| print(" Filter-Error: Please choose an object first") | | print(" Filter-Error: Please choose an object first") |
| else: | | else: |
|
| state = cmd.get_state() | | state = cmd.get_object_state(self.object) |
| ident = self.get_ident(self.object,state) | | ident = self.get_ident(self.object,state) |
| print(" Filter: Accepting '%s'"%ident) | | print(" Filter: Accepting '%s'"%ident) |
| self.count(ident,accept_str) | | self.count(ident,accept_str) |
| cmd.forward() | | cmd.forward() |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def reject(self): | | def reject(self): |
| # reject compound and advance | | # reject compound and advance |
| if self.object==None: | | if self.object==None: |
| print(" Filter-Error: Please choose an object first") | | print(" Filter-Error: Please choose an object first") |
| else: | | else: |
|
| state = cmd.get_state() | | state = cmd.get_object_state(self.object) |
| ident = self.get_ident(self.object,state) | | ident = self.get_ident(self.object,state) |
| print(" Filter: Rejecting '%s'"%ident) | | print(" Filter: Rejecting '%s'"%ident) |
| self.check_object_dict() | | self.check_object_dict() |
| self.count(ident,reject_str) | | self.count(ident,reject_str) |
| cmd.forward() | | cmd.forward() |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def defer(self): | | def defer(self): |
| # defer compound and advance | | # defer compound and advance |
| if self.object==None: | | if self.object==None: |
| print(" Filter-Error: Please choose an object first") | | print(" Filter-Error: Please choose an object first") |
| else: | | else: |
|
| state = cmd.get_state() | | state = cmd.get_object_state(self.object) |
| ident = self.get_ident(self.object,state) | | ident = self.get_ident(self.object,state) |
| print(" Filter: Deferring '%s'"%ident) | | print(" Filter: Deferring '%s'"%ident) |
| self.check_object_dict() | | self.check_object_dict() |
| self.count(ident,defer_str) | | self.count(ident,defer_str) |
| cmd.forward() | | cmd.forward() |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def forward(self): | | def forward(self): |
| # go forward and update information | | # go forward and update information |
| cmd.forward() | | cmd.forward() |
| | | |
| End of changes. 5 change blocks. |
|---|
| 4 lines changed or deleted | | 11 lines changed or added |
|---|
"Fossies" - the Fresh Open Source Software Archive 