Author: bugman
Date: Fri Aug 26 12:23:00 2011
New Revision: 14481
URL: http://svn.gna.org/viewcvs/relax?rev=14481&view=rev
Log:
Renamed the PyMOL and Molmol macro user function back ends.
Modified:
1.3/generic_fns/molmol.py
1.3/generic_fns/pymol_control.py
Modified: 1.3/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/molmol.py?rev=14481&r1=14480&r2=14481&view=diff
==============================================================================
--- 1.3/generic_fns/molmol.py (original)
+++ 1.3/generic_fns/molmol.py Fri Aug 26 12:23:00 2011
@@ -204,7 +204,7 @@
return commands
-def macro_exec(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
+def macro_apply(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
"""Execute a Molmol macro.
@keyword data_type: The data type to map to the structure.
@@ -234,69 +234,7 @@
molmol_obj.exec_cmd(command)
-def ribbon():
- """Apply the Molmol ribbon style."""
-
- # Calculate the protons.
- molmol_obj.exec_cmd("CalcAtom 'H'")
- molmol_obj.exec_cmd("CalcAtom 'HN'")
-
- # Calculate the secondary structure.
- molmol_obj.exec_cmd("CalcSecondary")
-
- # Execute the ribbon macro.
- molmol_obj.exec_cmd("XMacStand ribbon.mac")
-
-
-def tensor_pdb(file=None):
- """Display the diffusion tensor geometric structure.
-
- @keyword file: The name of the PDB file containing the tensor geometric
object.
- @type file: str
- """
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # To overlay the structure with the diffusion tensor, select all and
reorient to the PDB frame.
- molmol_obj.exec_cmd("SelectAtom ''")
- molmol_obj.exec_cmd("SelectBond ''")
- molmol_obj.exec_cmd("SelectAngle ''")
- molmol_obj.exec_cmd("SelectDist ''")
- molmol_obj.exec_cmd("SelectPrim ''")
- molmol_obj.exec_cmd("RotateInit")
- molmol_obj.exec_cmd("MoveInit")
-
- # Read in the tensor PDB file and force Molmol to recognise the CONECT
records (not that it will show the bonds)!
- molmol_obj.exec_cmd("ReadPdb " + file)
- file_parts = split(file, '.')
- molmol_obj.exec_cmd("SelectMol '@" + file_parts[0] + "'")
- molmol_obj.exec_cmd("CalcBond 1 1 1")
-
- # Apply the 'ball/stick' style to the tensor.
- molmol_obj.exec_cmd("SelectAtom '0'")
- molmol_obj.exec_cmd("SelectBond '0'")
- molmol_obj.exec_cmd("SelectAtom ':TNS'")
- molmol_obj.exec_cmd("SelectBond ':TNS'")
- molmol_obj.exec_cmd("XMacStand ball_stick.mac")
-
- # Touch up.
- molmol_obj.exec_cmd("RadiusAtom 1")
- molmol_obj.exec_cmd("SelectAtom ':TNS@C*'")
- molmol_obj.exec_cmd("RadiusAtom 1.5")
-
-
-def view():
- """Start Molmol."""
-
- # Open a Molmol pipe.
- if molmol_obj.running():
- raise RelaxError("The Molmol pipe already exists.")
- else:
- molmol_obj.open_gui()
-
-
-def write(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None, file=None, dir=None, force=False):
+def macro_write(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None, file=None, dir=None, force=False):
"""Create a Molmol macro.
@keyword data_type: The data type to map to the structure.
@@ -347,3 +285,65 @@
cdp.result_files = []
cdp.result_files.append(['grace', 'Grace', file_path])
status.observers.result_file.notify()
+
+
+def ribbon():
+ """Apply the Molmol ribbon style."""
+
+ # Calculate the protons.
+ molmol_obj.exec_cmd("CalcAtom 'H'")
+ molmol_obj.exec_cmd("CalcAtom 'HN'")
+
+ # Calculate the secondary structure.
+ molmol_obj.exec_cmd("CalcSecondary")
+
+ # Execute the ribbon macro.
+ molmol_obj.exec_cmd("XMacStand ribbon.mac")
+
+
+def tensor_pdb(file=None):
+ """Display the diffusion tensor geometric structure.
+
+ @keyword file: The name of the PDB file containing the tensor geometric
object.
+ @type file: str
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # To overlay the structure with the diffusion tensor, select all and
reorient to the PDB frame.
+ molmol_obj.exec_cmd("SelectAtom ''")
+ molmol_obj.exec_cmd("SelectBond ''")
+ molmol_obj.exec_cmd("SelectAngle ''")
+ molmol_obj.exec_cmd("SelectDist ''")
+ molmol_obj.exec_cmd("SelectPrim ''")
+ molmol_obj.exec_cmd("RotateInit")
+ molmol_obj.exec_cmd("MoveInit")
+
+ # Read in the tensor PDB file and force Molmol to recognise the CONECT
records (not that it will show the bonds)!
+ molmol_obj.exec_cmd("ReadPdb " + file)
+ file_parts = split(file, '.')
+ molmol_obj.exec_cmd("SelectMol '@" + file_parts[0] + "'")
+ molmol_obj.exec_cmd("CalcBond 1 1 1")
+
+ # Apply the 'ball/stick' style to the tensor.
+ molmol_obj.exec_cmd("SelectAtom '0'")
+ molmol_obj.exec_cmd("SelectBond '0'")
+ molmol_obj.exec_cmd("SelectAtom ':TNS'")
+ molmol_obj.exec_cmd("SelectBond ':TNS'")
+ molmol_obj.exec_cmd("XMacStand ball_stick.mac")
+
+ # Touch up.
+ molmol_obj.exec_cmd("RadiusAtom 1")
+ molmol_obj.exec_cmd("SelectAtom ':TNS@C*'")
+ molmol_obj.exec_cmd("RadiusAtom 1.5")
+
+
+def view():
+ """Start Molmol."""
+
+ # Open a Molmol pipe.
+ if molmol_obj.running():
+ raise RelaxError("The Molmol pipe already exists.")
+ else:
+ molmol_obj.open_gui()
Modified: 1.3/generic_fns/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pymol_control.py?rev=14481&r1=14480&r2=14481&view=diff
==============================================================================
--- 1.3/generic_fns/pymol_control.py (original)
+++ 1.3/generic_fns/pymol_control.py Fri Aug 26 12:23:00 2011
@@ -348,7 +348,7 @@
return commands
-def macro_exec(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
+def macro_apply(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
"""Execute a PyMOL macro.
@keyword data_type: The data type to map to the structure.
@@ -378,121 +378,7 @@
pymol_obj.exec_cmd(command)
-def tensor_pdb(file=None):
- """Display the diffusion tensor geometric structure.
-
- @keyword file: The name of the file containing the diffusion tensor
geometric object.
- @type file: str
- """
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # Read in the tensor PDB file.
- pymol_obj.exec_cmd("load " + file)
-
-
- # The tensor object.
- ####################
-
- # Select the TNS residue.
- pymol_obj.exec_cmd("select resn TNS")
-
- # Hide everything.
- pymol_obj.exec_cmd("hide ('sele')")
-
- # Show as 'sticks'.
- pymol_obj.exec_cmd("show sticks, 'sele'")
-
-
- # Centre of mass.
- #################
-
- # Select the COM residue.
- pymol_obj.exec_cmd("select resn COM")
-
- # Show the centre of mass as the dots representation.
- pymol_obj.exec_cmd("show dots, 'sele'")
-
- # Colour it blue.
- pymol_obj.exec_cmd("color blue, 'sele'")
-
-
- # The diffusion tensor axes.
- ############################
-
- # Select the AXS residue.
- pymol_obj.exec_cmd("select resn AXS")
-
- # Hide everything.
- pymol_obj.exec_cmd("hide ('sele')")
-
- # Show as 'sticks'.
- pymol_obj.exec_cmd("show sticks, 'sele'")
-
- # Colour it cyan.
- pymol_obj.exec_cmd("color cyan, 'sele'")
-
- # Select the N atoms of the AXS residue (used to display the axis
labels).
- pymol_obj.exec_cmd("select (resn AXS and elem N)")
-
- # Label the atoms.
- pymol_obj.exec_cmd("label 'sele', name")
-
-
-
- # Monte Carlo simulations.
- ##########################
-
- # Select the SIM residue.
- pymol_obj.exec_cmd("select resn SIM")
-
- # Colour it.
- pymol_obj.exec_cmd("colour cyan, 'sele'")
-
-
- # Clean up.
- ###########
-
- # Remove the selection.
- pymol_obj.exec_cmd("cmd.delete('sele')")
-
-
-def vector_dist(file=None):
- """Display the XH bond vector distribution.
-
- @keyword file: The vector distribution PDB file.
- @type file: str
- """
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # The file root.
- id = file_root(file)
-
- # Read in the vector distribution PDB file.
- pymol_obj.exec_cmd("load " + file)
-
-
- # Create a surface.
- ###################
-
- # Select the vector distribution.
- pymol_obj.exec_cmd("cmd.show('surface', " + repr(id) + ")")
-
-
-def view():
- """Start PyMOL."""
-
- # Open PyMOL.
- if pymol_obj.running():
- raise RelaxError("PyMOL is already running.")
- else:
- pymol_obj.open_gui()
-
-
-def write(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None, file=None, dir=None, force=False):
+def macro_write(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None, file=None, dir=None, force=False):
"""Create a PyMOL macro file.
@keyword data_type: The data type to map to the structure.
@@ -543,3 +429,117 @@
cdp.result_files = []
cdp.result_files.append(['pymol', 'PyMOL', file_path])
status.observers.result_file.notify()
+
+
+def tensor_pdb(file=None):
+ """Display the diffusion tensor geometric structure.
+
+ @keyword file: The name of the file containing the diffusion tensor
geometric object.
+ @type file: str
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Read in the tensor PDB file.
+ pymol_obj.exec_cmd("load " + file)
+
+
+ # The tensor object.
+ ####################
+
+ # Select the TNS residue.
+ pymol_obj.exec_cmd("select resn TNS")
+
+ # Hide everything.
+ pymol_obj.exec_cmd("hide ('sele')")
+
+ # Show as 'sticks'.
+ pymol_obj.exec_cmd("show sticks, 'sele'")
+
+
+ # Centre of mass.
+ #################
+
+ # Select the COM residue.
+ pymol_obj.exec_cmd("select resn COM")
+
+ # Show the centre of mass as the dots representation.
+ pymol_obj.exec_cmd("show dots, 'sele'")
+
+ # Colour it blue.
+ pymol_obj.exec_cmd("color blue, 'sele'")
+
+
+ # The diffusion tensor axes.
+ ############################
+
+ # Select the AXS residue.
+ pymol_obj.exec_cmd("select resn AXS")
+
+ # Hide everything.
+ pymol_obj.exec_cmd("hide ('sele')")
+
+ # Show as 'sticks'.
+ pymol_obj.exec_cmd("show sticks, 'sele'")
+
+ # Colour it cyan.
+ pymol_obj.exec_cmd("color cyan, 'sele'")
+
+ # Select the N atoms of the AXS residue (used to display the axis
labels).
+ pymol_obj.exec_cmd("select (resn AXS and elem N)")
+
+ # Label the atoms.
+ pymol_obj.exec_cmd("label 'sele', name")
+
+
+
+ # Monte Carlo simulations.
+ ##########################
+
+ # Select the SIM residue.
+ pymol_obj.exec_cmd("select resn SIM")
+
+ # Colour it.
+ pymol_obj.exec_cmd("colour cyan, 'sele'")
+
+
+ # Clean up.
+ ###########
+
+ # Remove the selection.
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+
+def vector_dist(file=None):
+ """Display the XH bond vector distribution.
+
+ @keyword file: The vector distribution PDB file.
+ @type file: str
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # The file root.
+ id = file_root(file)
+
+ # Read in the vector distribution PDB file.
+ pymol_obj.exec_cmd("load " + file)
+
+
+ # Create a surface.
+ ###################
+
+ # Select the vector distribution.
+ pymol_obj.exec_cmd("cmd.show('surface', " + repr(id) + ")")
+
+
+def view():
+ """Start PyMOL."""
+
+ # Open PyMOL.
+ if pymol_obj.running():
+ raise RelaxError("PyMOL is already running.")
+ else:
+ pymol_obj.open_gui()
r14481 - in /1.3/generic_fns: molmol.py pymol_control.py