Author: semor Date: Thu Apr 3 17:47:42 2008 New Revision: 5264 URL: http://svn.gna.org/viewcvs/relax?rev=5264&view=rev Log: More removal of the run argument as part of the moving to the new design. Modified: 1.3/prompt/molmol.py Modified: 1.3/prompt/molmol.py URL: http://svn.gna.org/viewcvs/relax/1.3/prompt/molmol.py?rev=5264&r1=5263&r2=5264&view=diff ============================================================================== --- 1.3/prompt/molmol.py (original) +++ 1.3/prompt/molmol.py Thu Apr 3 17:47:42 2008 @@ -55,14 +55,12 @@ self.__relax__.generic.molmol.clear_history() - def command(self, run=None, command=None): + def command(self, command=None): """Function for executing a user supplied Molmol command. Keyword Arguments ~~~~~~~~~~~~~~~~~ - run: The name of the run. - command: The Molmol command to execute. @@ -76,37 +74,30 @@ Example ~~~~~~~ - To reinitialise the Molmol instance for the run 'aic', type: - - relax> molmol.command("aic", "InitAll yes") + To reinitialise the Molmol instance: + + relax> molmol.command("InitAll yes") """ # Function intro text. if self.__relax__.interpreter.intro: text = sys.ps3 + "molmol.command(" - text = text + "run=" + `run` - text = text + ", command=" + `command` + ")" - print text - - # The run name. - if type(run) != str: - raise RelaxStrError, ('run', run) + text = text + "command=" + `command` + ")" + print text # The command argument. if type(command) != str: raise RelaxStrError, ('command', command) # Execute the functional code. - self.__relax__.generic.molmol.command(run=run, command=command) - - - def macro_exec(self, run=None, data_type=None, style="classic", colour_start=None, colour_end=None, colour_list=None): + molmol_obj.command(command=command) + + + def macro_exec(self, data_type=None, style="classic", colour_start=None, colour_end=None, colour_list=None): """Function for executing Molmol macros. Keyword Arguments ~~~~~~~~~~~~~~~~~ - - run: The name of the run. data_type: The data type to map to the structure. @@ -148,28 +139,23 @@ Examples ~~~~~~~~ - To map the order parameter values, S2, of the run 'final' onto the structure using the + To map the order parameter values, S2, onto the structure using the classic style, type: - relax> molmol.macro_exec('final', 'S2') - relax> molmol.macro_exec('final', data_type='S2') - relax> molmol.macro_exec('final', data_type='S2', style="classic") + relax> molmol.macro_exec('S2') + relax> molmol.macro_exec(data_type='S2') + relax> molmol.macro_exec(data_type='S2', style="classic") """ # Function intro text. if self.__relax__.interpreter.intro: text = sys.ps3 + "molmol.macro_exec(" - text = text + "run=" + `run` - text = text + ", data_type=" + `data_type` + text = text + "data_type=" + `data_type` text = text + ", style=" + `style` text = text + ", colour_start=" + `colour_start` text = text + ", colour_end=" + `colour_end` text = text + ", colour_list=" + `colour_list` + ")" print text - - # The run name. - if type(run) != str: - raise RelaxStrError, ('run', run) # Data type for mapping to the structure. if type(data_type) != str: @@ -196,16 +182,11 @@ raise RelaxListNumError, ('ending colour of the linear gradient', colour_end) # Execute the functional code. - self.__relax__.generic.molmol.macro_exec(run=run, data_type=data_type, style=style, colour_start=colour_start, colour_end=colour_end, colour_list=colour_list) - - - def ribbon(self, run=None): + molmol_obj.macro_exec(data_type=data_type, style=style, colour_start=colour_start, colour_end=colour_end, colour_list=colour_list) + + + def ribbon(self): """Apply the Molmol ribbon style. - - Keyword Arguments - ~~~~~~~~~~~~~~~~~ - - run: The name of the run. Description @@ -223,44 +204,36 @@ Example ~~~~~~~ - To apply the ribbon style to the PDB file loaded for the run 'final', type: - - relax> molmol.ribbon("final") - """ - - # Function intro text. - if self.__relax__.interpreter.intro: - text = sys.ps3 + "molmol.ribbon(" - text = text + "run=" + `run` + ")" - print text - - # The run name. - if type(run) != str: - raise RelaxStrError, ('run', run) - - # Execute the functional code. - self.__relax__.generic.molmol.ribbon(run=run) - - - def tensor_pdb(self, run=None, file=None): + To apply the ribbon style to the PDB file loaded, type: + + relax> molmol.ribbon() + """ + + # Function intro text. + if self.__relax__.interpreter.intro: + text = sys.ps3 + "molmol.ribbon()" + print text + + # Execute the functional code. + molmol_obj.ribbon() + + + def tensor_pdb(self, file=None): """Function displaying the diffusion tensor PDB geometric object over the loaded PDB. Keyword Arguments ~~~~~~~~~~~~~~~~~ - run: The name of the run. - file: The name of the PDB file containing the tensor geometric object. Description ~~~~~~~~~~~ - In executing this user function, a PDB file must have previously been loaded into this run, - a geometric object or polygon representing the Brownian rotational diffusion tensor will be - overlain with the loaded PDB file and displayed within Molmol. The PDB file containing the - geometric object must be created using the complementary 'pdb.create_diff_tensor_pdb()' user - function. + In executing this user function, a PDB file must have previously been loaded , a geometric + object or polygon representing the Brownian rotational diffusion tensor will be overlain + with the loaded PDB file and displayed within Molmol. The PDB file containing the geometric + object must be created using the complementary 'pdb.create_diff_tensor_pdb()' user function. To display the diffusion tensor, the multiple commands will be executed. To overlay the structure with the diffusion tensor, everything will be selected and reoriented and moved to @@ -300,59 +273,41 @@ # Function intro text. if self.__relax__.interpreter.intro: text = sys.ps3 + "molmol.tensor_pdb(" - text = text + "run=" + `run` - text = text + ", file=" + `file` + ")" - print text - - # The run name. - if type(run) != str: - raise RelaxStrError, ('run', run) + text = text + "file=" + `file` + ")" + print text # The file name. if type(file) != str: raise RelaxStrError, ('file name', file) # Execute the functional code. - self.__relax__.generic.molmol.tensor_pdb(run=run, file=file) - - - def view(self, run=None): + molmol_obj.tensor_pdb(file=file) + + + def view(self): """Function for viewing the collection of molecules extracted from the PDB file. + + Example + ~~~~~~~ + + relax> molmol.view() + relax> molmol.view() + """ + + # Function intro text. + if self.__relax__.interpreter.intro: + text = sys.ps3 + "molmol.view()" + print text + + # Execute the functional code. + molmol_obj.view() + + + def write(self, data_type=None, style="classic", colour_start=None, colour_end=None, colour_list=None, file=None, dir='molmol', force=0): + """Function for creating Molmol macros. Keyword Arguments ~~~~~~~~~~~~~~~~~ - - run: The name of the run which the PDB belongs to. - - - Example - ~~~~~~~ - - relax> molmol.view('m1') - relax> molmol.view(run='pdb') - """ - - # Function intro text. - if self.__relax__.interpreter.intro: - text = sys.ps3 + "molmol.view(" - text = text + "run=" + `run` + ")" - print text - - # The run argument. - if type(run) != str: - raise RelaxStrError, ('run', run) - - # Execute the functional code. - self.__relax__.generic.molmol.view(run=run) - - - def write(self, run=None, data_type=None, style="classic", colour_start=None, colour_end=None, colour_list=None, file=None, dir='molmol', force=0): - """Function for creating Molmol macros. - - Keyword Arguments - ~~~~~~~~~~~~~~~~~ - - run: The name of the run. data_type: The data type to map to the structure. @@ -402,19 +357,18 @@ Examples ~~~~~~~~ - To create a Molmol macro mapping the order parameter values, S2, of the run 'final' onto the - structure using the classic style, type: - - relax> molmol.write('final', 'S2') - relax> molmol.write('final', data_type='S2') - relax> molmol.write('final', data_type='S2', style="classic", file='s2.mac', dir='molmol') + To create a Molmol macro mapping the order parameter values, S2, onto the structure using + the classic style, type: + + relax> molmol.write('S2') + relax> molmol.write(data_type='S2') + relax> molmol.write(data_type='S2', style="classic", file='s2.mac', dir='molmol') """ # Function intro text. if self.__relax__.interpreter.intro: text = sys.ps3 + "molmol.write(" - text = text + "run=" + `run` - text = text + ", data_type=" + `data_type` + text = text + "data_type=" + `data_type` text = text + ", style=" + `style` text = text + ", colour_start=" + `colour_start` text = text + ", colour_end=" + `colour_end` @@ -424,10 +378,6 @@ text = text + ", force=" + `force` + ")" print text - # The run name. - if type(run) != str: - raise RelaxStrError, ('run', run) - # Data type for mapping to the structure. if type(data_type) != str: raise RelaxStrError, ('data type', data_type) @@ -465,7 +415,7 @@ raise RelaxBinError, ('force flag', force) # Execute the functional code. - self.__relax__.generic.molmol.write(run=run, data_type=data_type, style=style, colour_start=colour_start, colour_end=colour_end, colour_list=colour_list, file=file, dir=dir, force=force) + molmol_obj.write(data_type=data_type, style=style, colour_start=colour_start, colour_end=colour_end, colour_list=colour_list, file=file, dir=dir, force=force)