Author: bugman
Date: Fri Aug 26 12:21:21 2011
New Revision: 14480
URL: http://svn.gna.org/viewcvs/relax?rev=14480&view=rev
Log:
Modified the Molmol macro related user function front end to match those of
PyMOL.
These are:
- molmol.macro_exec() is now molmol.macro_apply().
- molmol.write() is now molmol.macro_write().
- molmol.macro.run() has been added to execute macros from text files.
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=14480&r1=14479&r2=14480&view=diff
==============================================================================
--- 1.3/prompt/molmol.py (original)
+++ 1.3/prompt/molmol.py Fri Aug 26 12:21:21 2011
@@ -83,10 +83,10 @@
_build_doc(command)
- def macro_exec(self, data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
- # Function intro text.
- if self._exec_info.intro:
- text = self._exec_info.ps3 + "molmol.macro_exec("
+ def macro_apply(self, data_type=None, style="classic",
colour_start=None, colour_end=None, colour_list=None):
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "molmol.macro_apply("
text = text + "data_type=" + repr(data_type)
text = text + ", style=" + repr(style)
text = text + ", colour_start=" + repr(colour_start)
@@ -102,145 +102,75 @@
arg_check.is_str(colour_list, 'colour list', can_be_none=True)
# Execute the functional code.
- molmol.macro_exec(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list)
-
- # The function doc info.
- macro_exec._doc_title = "Execute Molmol macros."
- macro_exec._doc_title_short = "Molmol macro execution."
- macro_exec._doc_args = [
+ molmol.macro_apply(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list)
+
+ # The function doc info.
+ macro_apply._doc_title = "Execute Molmol macros."
+ macro_apply._doc_title_short = "Molmol macro execution."
+ macro_apply._doc_args = [
["data_type", "The data type to map to the structure."],
["style", "The style of the macro."],
["colour_start", "The starting colour, either an array or string, of
the linear colour gradient."],
["colour_end", "The ending colour, either an array or string, of the
linear colour gradient."],
["colour_list", "The list of colours to match the start and end
strings."]
]
- macro_exec._doc_desc = """
+ macro_apply._doc_desc = """
This allows spin specific values to be mapped to a structure through
Molmol macros. Currently only the 'classic' style, which is described below,
is available.
"""
- macro_exec._doc_examples = """
+ macro_apply._doc_examples = """
To map the order parameter values, S2, onto the structure using the
classic style, type:
- relax> molmol.macro_exec('S2')
- relax> molmol.macro_exec(data_type='S2')
- relax> molmol.macro_exec(data_type='S2', style="classic")
- """
- macro_exec._doc_additional = [
+ relax> molmol.macro_apply('S2')
+ relax> molmol.macro_apply(data_type='S2')
+ relax> molmol.macro_apply(data_type='S2', style="classic")
+ """
+ macro_apply._doc_additional = [
colour._linear_gradient_doc,
Molmol._molmol_classic_style_doc,
colour.__molmol_colours_prompt_doc__,
colour.__x11_colours_prompt_doc__
]
- _build_doc(macro_exec)
-
-
- def ribbon(self):
- # Function intro text.
- if self._exec_info.intro:
- text = self._exec_info.ps3 + "molmol.ribbon()"
- print(text)
-
- # Execute the functional code.
- molmol.ribbon()
-
- # The function doc info.
- ribbon._doc_title = "Apply the Molmol ribbon style."
- ribbon._doc_title_short = "Molmol ribbon style application."
- ribbon._doc_desc = """
- This applies the Molmol ribbon style which is equivalent to clicking
on 'ribbon' in the Molmol side menu. To do this, the following commands are
executed:
-
- CalcAtom 'H'
- CalcAtom 'HN'
- CalcSecondary
- XMacStand ribbon.mac
- """
- ribbon._doc_examples = """
- To apply the ribbon style to the PDB file loaded, type:
-
- relax> molmol.ribbon()
- """
- _build_doc(ribbon)
-
-
- def tensor_pdb(self, file=None):
- # Function intro text.
- if self._exec_info.intro:
- text = self._exec_info.ps3 + "molmol.tensor_pdb("
- text = text + "file=" + repr(file) + ")"
- print(text)
-
- # The argument checks.
- arg_check.is_str_or_inst(file, 'file name')
-
- # Execute the functional code.
- molmol.tensor_pdb(file=file)
-
- # The function doc info.
- tensor_pdb._doc_title = "Display the diffusion tensor PDB geometric
object over the loaded PDB."
- tensor_pdb._doc_title_short = "Diffusion tensor and structure display."
- tensor_pdb._doc_args = [
- ["file", "The name of the PDB file containing the tensor geometric
object."]
- ]
- tensor_pdb._doc_desc = """
- 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 structure.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 their original PDB frame
positions:
-
- SelectAtom ''
- SelectBond ''
- SelectAngle ''
- SelectDist ''
- SelectPrim ''
- RotateInit
- MoveInit
-
- Next the tensor PDB file is read in, selected, and the covalent
bonds of the PDB CONECT records calculated:
-
- ReadPdb file
- SelectMol '@file'
- CalcBond 1 1 1
-
- Then only the atoms and bonds of the geometric object are selected
and the 'ball/stick' style applied:
-
- SelectAtom '0'
- SelectBond '0'
- SelectAtom ':TNS'
- SelectBond ':TNS'
- XMacStand ball_stick.mac
-
- The appearance is finally touched up:
-
- RadiusAtom 1
- SelectAtom ':TNS@C*'
- RadiusAtom 1.5
- """
- _build_doc(tensor_pdb)
-
-
- def view(self):
- # Function intro text.
- if self._exec_info.intro:
- text = self._exec_info.ps3 + "molmol.view()"
- print(text)
-
- # Execute the functional code.
- molmol.view()
-
- # The function doc info.
- view._doc_title = "View the collection of molecules from the loaded PDB
file."
- view._doc_title_short = "Molecule viewing."
- view._doc_desc = """
- This will simply launch Molmol.
- """
- view._doc_examples = """
- relax> molmol.view()
- """
- _build_doc(view)
-
-
- def write(self, data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None, file=None, dir='molmol', force=False):
- # Function intro text.
- if self._exec_info.intro:
- text = self._exec_info.ps3 + "molmol.write("
+ _build_doc(macro_apply)
+
+
+ def macro_run(self, file=None, dir='molmol'):
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "molmol.macro_run("
+ text = text + "file=" + repr(file)
+ text = text + ", dir=" + repr(dir) + ")"
+ print(text)
+
+ # The argument checks.
+ arg_check.is_str(file, 'file name')
+ arg_check.is_str(dir, 'directory name', can_be_none=True)
+
+ # Execute the functional code.
+ molmol.macro_run(file=file, dir=dir)
+
+ # The function doc info.
+ macro_run._doc_title = "Open and execute the Molmol macro file."
+ macro_run._doc_title_short = "Molmol macro file execution."
+ macro_run._doc_args = [
+ ["file", "The name of the Molmol macro file."],
+ ["dir", "The directory name."],
+ ]
+ macro_run._doc_desc = """
+ This user function is for opening and running a Molmol macro located
within a text file.
+ """
+ macro_run._doc_examples = """
+ To execute the macro file 's2.mac' located in the directory
'molmol', type:
+
+ relax> molmol.macro_run(file='s2.mac')
+ relax> molmol.macro_run(file='s2.mac', dir='molmol')
+ """
+ _build_doc(macro_run)
+
+
+ def macro_write(self, data_type=None, style="classic",
colour_start=None, colour_end=None, colour_list=None, file=None,
dir='molmol', force=False):
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "molmol.macro_write("
text = text + "data_type=" + repr(data_type)
text = text + ", style=" + repr(style)
text = text + ", colour_start=" + repr(colour_start)
@@ -262,12 +192,12 @@
arg_check.is_bool(force, 'force flag')
# Execute the functional code.
- molmol.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)
-
- # The function doc info.
- write._doc_title = "Create Molmol macros."
- write._doc_title_short = "Molmol macro creation."
- write._doc_args = [
+ molmol.macro_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)
+
+ # The function doc info.
+ macro_write._doc_title = "Create Molmol macros."
+ macro_write._doc_title_short = "Molmol macro creation."
+ macro_write._doc_args = [
["data_type", "The data type to map to the structure."],
["style", "The style of the macro."],
["colour_start", "The starting colour, either an array or string, of
the linear colour gradient."],
@@ -277,21 +207,125 @@
["dir", "The directory name."],
["force", "A flag which, if set to True, will cause the file to be
overwritten."]
]
- write._doc_desc = """
+ macro_write._doc_desc = """
This allows residues specific values to be mapped to a structure
through the creation of a Molmol '*.mac' macro which can be executed in
Molmol by clicking on 'File, Macro, Execute User...'. Currently only the
'classic' style, which is described below, is available.
"""
- write._doc_examples = """
+ macro_write._doc_examples = """
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')
- """
- write._doc_additional = [
+ relax> molmol.macro_write('S2')
+ relax> molmol.macro_write(data_type='S2')
+ relax> molmol.macro_write(data_type='S2', style="classic",
file='s2.mac', dir='molmol')
+ """
+ macro_write._doc_additional = [
colour._linear_gradient_doc,
Molmol._molmol_classic_style_doc,
colour.__molmol_colours_prompt_doc__,
colour.__x11_colours_prompt_doc__
]
- _build_doc(write)
+ _build_doc(macro_write)
+
+
+ def ribbon(self):
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "molmol.ribbon()"
+ print(text)
+
+ # Execute the functional code.
+ molmol.ribbon()
+
+ # The function doc info.
+ ribbon._doc_title = "Apply the Molmol ribbon style."
+ ribbon._doc_title_short = "Molmol ribbon style application."
+ ribbon._doc_desc = """
+ This applies the Molmol ribbon style which is equivalent to clicking
on 'ribbon' in the Molmol side menu. To do this, the following commands are
executed:
+
+ CalcAtom 'H'
+ CalcAtom 'HN'
+ CalcSecondary
+ XMacStand ribbon.mac
+ """
+ ribbon._doc_examples = """
+ To apply the ribbon style to the PDB file loaded, type:
+
+ relax> molmol.ribbon()
+ """
+ _build_doc(ribbon)
+
+
+ def tensor_pdb(self, file=None):
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "molmol.tensor_pdb("
+ text = text + "file=" + repr(file) + ")"
+ print(text)
+
+ # The argument checks.
+ arg_check.is_str_or_inst(file, 'file name')
+
+ # Execute the functional code.
+ molmol.tensor_pdb(file=file)
+
+ # The function doc info.
+ tensor_pdb._doc_title = "Display the diffusion tensor PDB geometric
object over the loaded PDB."
+ tensor_pdb._doc_title_short = "Diffusion tensor and structure display."
+ tensor_pdb._doc_args = [
+ ["file", "The name of the PDB file containing the tensor geometric
object."]
+ ]
+ tensor_pdb._doc_desc = """
+ 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 structure.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 their original PDB frame
positions:
+
+ SelectAtom ''
+ SelectBond ''
+ SelectAngle ''
+ SelectDist ''
+ SelectPrim ''
+ RotateInit
+ MoveInit
+
+ Next the tensor PDB file is read in, selected, and the covalent
bonds of the PDB CONECT records calculated:
+
+ ReadPdb file
+ SelectMol '@file'
+ CalcBond 1 1 1
+
+ Then only the atoms and bonds of the geometric object are selected
and the 'ball/stick' style applied:
+
+ SelectAtom '0'
+ SelectBond '0'
+ SelectAtom ':TNS'
+ SelectBond ':TNS'
+ XMacStand ball_stick.mac
+
+ The appearance is finally touched up:
+
+ RadiusAtom 1
+ SelectAtom ':TNS@C*'
+ RadiusAtom 1.5
+ """
+ _build_doc(tensor_pdb)
+
+
+ def view(self):
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "molmol.view()"
+ print(text)
+
+ # Execute the functional code.
+ molmol.view()
+
+ # The function doc info.
+ view._doc_title = "View the collection of molecules from the loaded PDB
file."
+ view._doc_title_short = "Molecule viewing."
+ view._doc_desc = """
+ This will simply launch Molmol.
+ """
+ view._doc_examples = """
+ relax> molmol.view()
+ """
+ _build_doc(view)
r14480 - /1.3/prompt/molmol.py