User:Mglerner
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My name is Michael Lerner. I'm currently an IRTA postdoctoral fellow at NIH in the NHLBI's Laboratory of Computational Biology. Before that, I was a member of Heather Carlson's lab at the University of Michigan.
I wrote the PyMOL/APBS plugin.
-- Michael G. Lerner, PhD
m dot g dot lerner (_at-) gmail dot com
Check out a new pre-release version of the PyMOL-APBS plugin!
New Features
I've been working with Jason Vertrees on a new version of the PyMOL-APBS plugin and it's now ready for pre-release. There are three big advantages of the new version:
- It's been tested modern OS X, Windows and Linux systems and fixes several long-standing bugs.
- It allows you to call through to PDB2PQR directly.
- It has two visualization panels to aid in showing multiple potential surfaces at once.
I've also upped the default maximum allowed memory since typical users have bigger and faster computers these days.
A slightly longer list of changes is included below.
How to get it
There are two ways to get the new plugin
- If you have subversion installed,
svn co https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/pymolapbsplugin
- Copy the text directly from http://pymolwiki.org/index.php/User:Mglerner and put it in a file called apbsplugin.py
Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install
Note that the plugin will be installed as "APBS Tools2" so that you can continue to use your old version.
Longer feature list
- The ability to call through directly to PDB2PQR
- More modern apbs input files
- Two visualization panels. It's often quite useful to look at two different electrostatic potentials at once. It's also quite useful to look at electrostatic potentials mapped onto two different surfaces at once. Multiple visualization panels makes this a snap: just set up one surface on panel 1 and another surface on panel 2.
- Fixes several bugs that caused crashes on both OS X and Linux systems
- Increased maximum allowed memory
- Switch from os.system to subprocess for running external programs
- Deals with paths on Windows properly
- Gives better diagnostic information so that PyMOL/APBS developers can find bugs more easily
- Lots of internal code cleanup
Plugin code
#!/usr/bin/env python
# TODO:
# - provide diff for pdb2pqr freemol
# - use remove_alt to count alternate atom locations and warn the user
#
# - Note to users that they should remove freemol's pymol.exe on OS X.
### (all) and resn glu and resi 154+157
### flag ignore, atom-selection, clear
# APBS TOOLS Copyright Notice
# ============================
#
# The APBS TOOLS source code is copyrighted, but you can freely use and
# copy it as long as you don't change or remove any of the copyright
# notices.
#
# ----------------------------------------------------------------------
# APBS TOOLS is Copyright (C) 2009 by Michael G. Lerner
#
# All Rights Reserved
#
# Permission to use, copy, modify, distribute, and distribute modified
# versions of this software and its documentation for any purpose and
# without fee is hereby granted, provided that the above copyright
# notice appear in all copies and that both the copyright notice and
# this permission notice appear in supporting documentation, and that
# the name of Michael G. Lerner not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
#
# MICHAEL G. LERNER DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS
# SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
# FITNESS. IN NO EVENT SHALL MICHAEL G. LERNER BE LIABLE FOR ANY
# SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER
# RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF
# CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN
# CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
# ----------------------------------------------------------------------
"""
A NOTE TO USERS:
You can change the default locations for the APBS and PDB2PQR binaries
as well as the default temporary file directory below. If you set them
in this file, they will be preserved each time you load up the
plugin. Scroll down to the section entitled "Global config variables"
(no quotes) below.
A NOTE TO OTHER DEVELOPERS:
I understand that I'm giving this code away for Free, and that there's
not a ton of great sample PyMOL plugin code out there, so you're
certainly encouraged to use this as a template. However, please
acknowledge me in some way if you do (somewhere in the comments if you
only use a little bit of code or something more if you use a lot).
Thanks.
-Michael
Features under consideration:
- Use 'acc' to calculate solvent-accessible surface areas. We'll use
the PyMOL 'standard' method and store this data as B-factors.
- Show the field lines. Relevant code from menu.py:
def map_gradient(self_cmd, sele):
return [[ 2, 'Gradient:', '' ],
[ 1, 'default' , 'cmd.gradient("'+sele+'_grad","'+sele+'");cmd.ramp_new("'+sele+
'_grad_ramp","'+sele+'");cmd.color("'+sele+'_grad_ramp","'+sele+'_grad");' ]
]
Known hacks:
1. (code in execute() )There's a bug in the version of APBS shipped
with Ubuntu 9.10 (version 1.1.0) that causes the name to become
foo-PE0.dx instead of foo.dx. This would normally only occur in
mg-para calcs or MPI versions of apbs. It's clearly bug-possible,
but we will check for foo-PE0 if we can't find foo.dx.
2. We look for dylib errors in the APBS executable that's shipped with
freemol on OS X. Code in get_default()'s verify().
"""
from __future__ import division
from __future__ import generators
global DEBUG
DEBUG = 1
APBS_DEFAULT=True
import os,math,re
import string
import Tkinter
from Tkinter import *
import Pmw
import distutils.spawn # used for find_executable
import traceback
import pymol
#
# Global config variables
#
# To change the default locations, change these to something like
# APBS_BINARY_LOCATION = '/opt/bin/apbs'
#
APBS_BINARY_LOCATION = None
APBS_PSIZE_LOCATION = None
APBS_PDB2PQR_LOCATION = None
TEMPORARY_FILE_DIR = None
apbs_plea = ("IMPORTANT REQUEST: If you have not already done so, please register\n"
"your use of the open-source Adaptive Poisson-Boltzmann Solver (APBS) at\n"
"-> http://agave.wustl.edu/apbs/download\n"
"Such proof of usage is vital in securing funding for APBS development!\n")
pdb2pqr_plea = ("IMPORTANT REQUEST: If you have not already done so, please register\n"
"your use of the open-source PDB2PQR at\n"
"-> http://www.poissonboltzmann.org/pdb2pqr/d\n"
"Such proof of usage is vital in securing funding for PDB2PQR development!\n")
global apbs_message, pdb2pqr_message
apbs_message = """You must have APBS installed on your system."""
pdb2pqr_message = """PDB2PQR can be used to generate .PQR files."""
def get_default_location(name):
"""
Given the name of an APBS-related binary, look in
* pymol path,
* freemol path,
* user defined places,
* the system path,
* Known other paths (/usr/local/bin and /opt/local/bin)
for the parameter, name.
Some programs are verified with additional tests. In particular,
some versions of PyMOL ship with a broken apbs.exe, so we verify
that it can be run.
PARAMS
name, (string) the basename of the file we're looking for
EXAMPLE
get_default_location("apbs.exe")
RETURNS
(string) path/to/file on success or "" on failure
NOTES
For any program name <foo>.exe we will also search for
<foo>. We'll search for the .exe version first. We do not
automatically check for .exe versions of programs when .exe is
not specified.
"""
def verify(name,f):
if name in 'apbs.exe apbs'.split():
# You'd think we could just check the return code, but
# APBS doesn't return zero on success. Instead, it returns
# things like 3328. It seems to return 5 or -5 in this
# particular failure case, but I'm not sure we can depend
# on that always.
(retcode,prog_out) = run(f,'--version')
if 'dyld: Library not loaded' in prog_out:
print "Skipping",f,"because it appears to be broken (dyld)"
return False
return True
searchDirs = []
if "FREEMOL" in os.environ:
searchDirs.append(os.environ["FREEMOL"])
if "PYMOL_PATH" in os.environ:
searchDirs.append(os.path.join(os.environ["PYMOL_PATH"], "ext", "bin"))
searchDirs.append(os.path.join(os.environ["PYMOL_PATH"], "freemol", "bin"))
searchDirs.append(os.path.join(os.environ["PYMOL_PATH"], "freemol", "share", "apbs"))
searchDirs.append(os.path.join(os.environ["PYMOL_PATH"], "freemol", "share", "pdb2pqr"))
for x in (APBS_BINARY_LOCATION, APBS_PSIZE_LOCATION, APBS_PDB2PQR_LOCATION):
if x != None and x != "":
searchDirs.append(x)
if name=="temp":
searchDirs = []
if TEMPORARY_FILE_DIR != None and TEMPORARY_FILE_DIR != "":
searchDirs.append(TEMPORARY_FILE_DIR)
searchDirs.append("/tmp")
searchDirs.append(".")
searchDirs.extend(string.split(os.environ["PATH"], ":"))
searchDirs.append(os.path.join("/usr", "local", "bin"))
searchDirs.append(os.path.join("/opt", "local", "bin"))
print "Search dirs",searchDirs
if DEBUG:
print "get_default_location will search the following: ", searchDirs
for d in searchDirs:
if name=="temp":
f = d # just search for the directory
else:
f = os.path.join( d, name ) # make path/name.py
print "trying",f
if os.path.exists(f) and verify(name,f):
return f
elif name.endswith('.exe'):
f = os.path.join( d, name[:-4] ) # make path/name.py
if os.path.exists(f) and verify(name,f):
return f
print "Could not find default location for file: %s" % name
return ""
def __init__(self):
"""
Init PyMOL, by adding APBSTools to the GUI under Plugins
Creates the APBS widget/notebook. Once the event is received,
we create a new instance of APBSTools2 which is a Pmw, which upon
creation shows itself.
"""
self.menuBar.addmenuitem('Plugin', 'command',
'Launch APBS Tools2',
label='APBS Tools2...',
command = lambda s=self: APBSTools2(s))
def run(prog,args):
'''
wrapper to handle spaces on windows.
prog is the full path to the program.
args is a string that we will split up for you.
or a tuple. or a list. your call.
return value is (retval,prog_out)
e.g.
(retval,prog_out) = run("/bin/ls","-al /tmp/myusername")
'''
import subprocess,tempfile
if type(args) == type(''):
args = tuple(args.split())
elif type(args) in (type([]),type(())):
args = tuple(args)
args = (prog,) + args
try:
output_file = tempfile.TemporaryFile(mode="w+") # <-- shouldn't this point to the temp dir
except IOError:
print "Error opening output_file when trying to run the APBS command."
print "Running",args
retcode = subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
output_file.seek(0)
#prog_out = output_file.read()
prog_out = ''.join(output_file.readlines())
output_file.close() #windows doesn't do this automatically
if DEBUG:
print "Results were:"
print "Return value:",retcode
print "Output:"
print prog_out
return (retcode,prog_out)
class util:
"""
A quick collection of utility functions.
"""
#@staticmethod
def getMolecules():
"""returns all molecules that PyMOL knows about"""
return [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:molecule']
getMolecules = staticmethod(getMolecules)
#@staticmethod
def getMaps():
"""returns all maps that PyMOL knows about"""
return [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:map']
getMaps = staticmethod(getMaps)
#def hasAlt(sel):
# """returns true if non-standard locations (rotamers) are present for this selection"""
# return cmd.count_atoms(sel + " and not alt ''")!=0
#hasAlt = staticmethod(hasAlt)
util = util()
##############################################################################
##############################################################################
### ###
### ApbsInterface ###
### ###
##############################################################################
##############################################################################
def getApbsInputFile(pqr_filename,
grid_points,
cglen,
fglen,
cent,
apbs_mode,
bcfl,
ion_plus_one_conc,ion_plus_one_rad,
ion_minus_one_conc,ion_minus_one_rad,
ion_plus_two_conc,ion_plus_two_rad,
ion_minus_two_conc,ion_minus_two_rad,
interior_dielectric, solvent_dielectric,
chgm,
srfm,
solvent_radius,
system_temp,
sdens,
dx_filename,
):
print "Getting APBS input"
#print "system_temp",system_temp,type(system_temp)
#print "sdens",sdens,type(sdens)
#
# How shall we set up the grid? We'll use cglen, fglen, cgcent, fgcent
# and dime.
# This allows people to automate things (e.g. "Alanine scanning")
#
#
# New template using mg-auto
# See http://agave.wustl.edu/apbs/doc/api/html/#mg-auto
#
apbs_template = """#
# Note that most of the comments here were taken from sample
# input files that came with APBS. You can find APBS at
# http://agave.wustl.edu/apbs/
# Note that APBS is GPL'd code.
#
read
mol pqr %s # read molecule 1
end
elec
mg-auto
dime %d %d %d # number of find grid points
# calculated by psize.py
cglen %f %f %f # coarse mesh lengths (A)
fglen %f %f %f # fine mesh lengths (A)
# calculated by psize.py
cgcent %f %f %f # (could also give (x,y,z) form psize.py) #known center
fgcent %f %f %f # (could also give (x,y,z) form psize.py) #known center
%s # solve the full nonlinear PBE with npbe
#lpbe # solve the linear PBE with lpbe
bcfl %s # Boundary condition flag
# 0 => Zero
# 1 => Single DH sphere
# 2 => Multiple DH spheres
# 4 => Focusing
#
#ion 1 0.000 2.0 # Counterion declaration:
ion charge 1 conc %f radius %f # Counterion declaration:
ion charge -1 conc %f radius %f # ion <charge> <conc (M)> <radius>
ion charge 2 conc %f radius %f # ion <charge> <conc (M)> <radius>
ion charge -2 conc %f radius %f # ion <charge> <conc (M)> <radius>
pdie %f # Solute dielectric
sdie %f # Solvent dielectric
chgm %s # Charge disc method
# 0 is linear splines
# 1 is cubic b-splines
mol 1 # which molecule to use
srfm smol # Surface calculation method
# 0 => Mol surface for epsilon;
# inflated VdW for kappa; no
# smoothing
# 1 => As 0 with harmoinc average
# smoothing
# 2 => Cubic spline
srad %f # Solvent radius (1.4 for water)
swin 0.3 # Surface cubic spline window .. default 0.3
temp %f # System temperature (298.15 default)
sdens %f # Specify the number of grid points per square-angstrom to use in Vacc object. Ignored when srad is 0.0 (see srad) or srfm is spl2 (see srfm). There is a direct correlation between the value used for the Vacc sphere density, the accuracy of the Vacc object, and the APBS calculation time. APBS default value is 10.0.
#gamma 0.105 # Surface tension parameter for apolar forces (in kJ/mol/A^2)
# only used for force calculations, so we don't care, but
# it *used to be* always required, and 0.105 is the default
calcenergy no # Energy I/O to stdout
# 0 => don't write out energy
# 1 => write out total energy
# 2 => write out total energy and all
# components
calcforce no # Atomic forces I/O (to stdout)
# 0 => don't write out forces
# 1 => write out net forces on molecule
# 2 => write out atom-level forces
write pot dx %s # What to write .. this says write the potential in dx
# format to a file.
end
quit
"""
return apbs_template % (pqr_filename,
grid_points[0], grid_points[1], grid_points[2],
cglen[0],cglen[1],cglen[2],
fglen[0],fglen[1],fglen[2],
cent[0],cent[1],cent[2],
cent[0],cent[1],cent[2],
apbs_mode,
bcfl,
ion_plus_one_conc,ion_plus_one_rad,
ion_minus_one_conc,ion_minus_one_rad,
ion_plus_two_conc,ion_plus_two_rad,
ion_minus_two_conc,ion_minus_two_rad,
interior_dielectric, solvent_dielectric,
chgm,
solvent_radius,
system_temp,
sdens,
dx_filename,
)
##############################################################################
##############################################################################
### ###
### PluginCode ###
### ###
##############################################################################
##############################################################################
class APBSTools2:
# The current goal is to factor all of the APBS-specific code into
# an ApbsInterface class. The functions defined here before
# __init__, as well as the functions defined on the various
# Panels/Panes, will call through to self.ApbsInterface.
def setPqrFile(self,name):
print " APBS Tools: set pqr file to",name
self.pqr_to_use.setvalue(name)
self.radiobuttons.setvalue('Use another PQR')
def getPqrFilename(self):
if self.radiobuttons.getvalue() != 'Use another PQR':
return self.pymol_generated_pqr_filename.getvalue()
else:
return self.pqr_to_use.getvalue()
def setPsizeLocation(self,value):
self.psize.setvalue(value)
def setBinaryLocation(self,value):
self.binary.setvalue(value)
def setPdb2pqrLocation(self,value):
self.pdb2pqr.setvalue(value)
def setPymolGeneratedPqrFilename(self,value):
self.pymol_generated_pqr_filename.setvalue(value)
def setPymolGeneratedPdbFilename(self,value):
self.pymol_generated_pdb_filename.setvalue(value)
def setPymolGeneratedDxFilename(self,value):
self.pymol_generated_dx_filename.setvalue(value)
def setPymolGeneratedInFilename(self,value):
self.pymol_generated_in_filename.setvalue(value)
def getPymolGeneratedPqrFilename(self):
return self.pymol_generated_pqr_filename.getvalue()
def getPymolGeneratedPdbFilename(self):
return self.pymol_generated_pdb_filename.getvalue()
def getPymolGeneratedDxFilename(self):
return self.pymol_generated_dx_filename.getvalue()
def getPymolGeneratedInFilename(self):
return self.pymol_generated_in_filename.getvalue()
defaults = {
"interior_dielectric" : 2.0,
"solvent_dielectric" : 78.0,
"solvent_radius" : 1.4,
"system_temp" : 310.0,
"apbs_mode" : 'Linearized Poisson-Boltzmann Equation',
"ion_plus_one_conc" : 0.15,
"ion_plus_one_rad" : 2.0,
"ion_plus_two_conc" : 0.0,
"ion_plus_two_rad" : 2.0,
"ion_minus_one_conc" : 0.15,
"ion_minus_one_rad" : 1.8,
"ion_minus_two_conc" : 0.0,
"ion_minus_two_rad" : 2.0,
#"max_mem_allowed" : 400,
"max_mem_allowed" : 1500,
"potential_at_sas" : 0,
"surface_solvent" : 1,
"show_surface_for_scanning" : 1,
#"grid_buffer" : 0,
#"grid_buffer" : 20,
"bcfl" : 'Single DH sphere', # Boundary condition flag for APBS
"sdens": 10.0, # Specify the number of grid points per
# square-angstrom to use in Vacc
# object. Ignored when srad is 0.0 (see srad)
# or srfm is spl2 (see srfm). There is a direct
# correlation between the value used for the
# Vacc sphere density, the accuracy of the Vacc
# object, and the APBS calculation time. APBS
# default value is 10.0.
"chgm" : 'Cubic B-splines', # Charge disc method for APBS
}
def __init__(self,app):
self.parent = app.root
# Create the dialog.
self.dialog = Pmw.Dialog(self.parent,
buttons = ('Register APBS Use', 'Register PDB2PQR Use', 'Set grid', 'Run APBS', 'Exit APBS tools'),
title = 'PyMOL APBS Tools',
command = self.execute)
self.dialog.withdraw()
Pmw.setbusycursorattributes(self.dialog.component('hull'))
w = Tkinter.Label(self.dialog.interior(),
text = 'PyMOL APBS Tools\nMichael G. Lerner, Heather A. Carlson, 2009 - http://pymolwiki.org/index.php/APBS\n(incorporates modifications by Warren L. DeLano)',
background = 'black',
foreground = 'white',
#pady = 20,
)
w.pack(expand = 1, fill = 'both', padx = 4, pady = 4)
self.notebook = Pmw.NoteBook(self.dialog.interior())
self.notebook.pack(fill='both',expand=1,padx=10,pady=10)
# Set up the Main page
page = self.notebook.add('Main')
group = Pmw.Group(page,tag_text='Main options')
group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
self.selection = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Selection to use: ',
value='(polymer)',
)
self.map = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='What to call the resulting map: ',
value='apbs_map',
)
self.radiobuttons = Pmw.RadioSelect(group.interior(),
buttontype = 'radiobutton',
orient = 'vertical',
labelpos = 'w',
)
for text in ('Use PyMOL generated PQR and existing Hydrogens and termini',
'Use PyMOL generated PQR and PyMOL generated Hydrogens and termini',
'Use another PQR',
'Use PDB2PQR',):
self.radiobuttons.add(text)
self.radiobuttons.setvalue('Use PyMOL generated PQR and PyMOL generated Hydrogens and termini')
self.pdb2pqr_options = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='pdb2pqr command line options: ',
value='--ff=AMBER',
)
self.pqr_to_use = Pmw.EntryField(group.interior(),
labelpos='w',
label_pyclass = FileDialogButtonClassFactory.get(self.setPqrFile,'*.pqr'),
label_text='\tChoose Externally Generated PQR:',
)
for entry in (self.selection,self.map,self.radiobuttons,self.pdb2pqr_options,self.pqr_to_use):
#for entry in (self.selection,self.map,self.radiobuttons,):
entry.pack(fill='x',padx=4,pady=1) # vertical
# Set up the main "Calculation" page
page = self.notebook.add('Configuration')
group = Pmw.Group(page,tag_text='Dielectric Constants')
group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
group.grid(column=0, row=0)
self.interior_dielectric = Pmw.EntryField(group.interior(),labelpos='w',
label_text = 'Protein Dielectric:',
value = str(APBSTools2.defaults['interior_dielectric']),
validate = {'validator' : 'real',
'min':0,}
)
self.solvent_dielectric = Pmw.EntryField(group.interior(),labelpos='w',
label_text = 'Solvent Dielectric:',
value = str(APBSTools2.defaults['solvent_dielectric']),
validate = {'validator' : 'real',
'min':0,}
)
entries = (self.interior_dielectric,self.solvent_dielectric)
for entry in entries:
#entry.pack(side='left',fill='both',expand=1,padx=4) # side-by-side
entry.pack(fill='x',expand=1,padx=4,pady=1) # vertical
group = Pmw.Group(page,tag_text='Other')
group.pack(fill='both',expand=1, padx=4, pady=5)
group.grid(column=1, row=1,columnspan=4)
self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w',
label_text = 'Maximum Memory Allowed (MB):',
value = str(APBSTools2.defaults['max_mem_allowed']),
validate = {'validator' : 'real',
'min':1,}
)
self.apbs_mode = Pmw.OptionMenu(group.interior(),
labelpos = 'w',
label_text = 'APBS Mode',
items = ('Nonlinear Poisson-Boltzmann Equation','Linearized Poisson-Boltzmann Equation',),
initialitem = APBSTools2.defaults['apbs_mode'],
)
self.apbs_mode.pack(fill='x',expand=1,padx=4)
#self.apbs_mode.grid(column=0,row=0,columnspan=3)
self.solvent_radius = Pmw.EntryField(group.interior(),
labelpos = 'w',
label_text = 'Solvent Radius:',
validate = {'validator':'real','min':0},
value = str(APBSTools2.defaults['solvent_radius']),
)
self.system_temp = Pmw.EntryField(group.interior(),
labelpos = 'w',
label_text = 'System Temperature:',
validate = {'validator':'real','min':0},
value = str(APBSTools2.defaults['system_temp']),
)
self.sdens = Pmw.EntryField(group.interior(),
labelpos = 'w',
label_text = 'Vacc sphere density (grid points/A^2)',
validate = {'validator':'real','min':0},
value = str(APBSTools2.defaults['sdens']),
)
self.bcfl = Pmw.OptionMenu(group.interior(),
labelpos = 'w',
label_text = 'Boundary Condition',
items = ('Zero','Single DH sphere','Multiple DH spheres',), #'Focusing',),
initialitem = APBSTools2.defaults['bcfl'],
)
self.chgm = Pmw.OptionMenu(group.interior(),
labelpos = 'w',
label_text = 'Charge disc method',
items = ('Linear','Cubic B-splines','Quintic B-splines',),
initialitem = APBSTools2.defaults['chgm'],
)
self.srfm = Pmw.OptionMenu(group.interior(),
labelpos = 'w',
label_text = 'Surface Calculation Method',
items = ('Mol surf for epsilon; inflated VdW for kappa, no smoothing','Same, but with harmonic average smoothing','Cubic spline','Similar to cubic spline, but with 7th order polynomial'),
initialitem = 'Same, but with harmonic average smoothing',
)
#for entry in (self.apbs_mode,self.system_temp,self.solvent_radius,):
for entry in (self.max_mem_allowed,self.solvent_radius,self.system_temp,self.sdens,self.apbs_mode,self.bcfl,self.chgm,self.srfm):
entry.pack(fill='x',expand=1,padx=4,pady=1) # vertical
group = Pmw.Group(page,tag_text='Ions')
group.pack(fill='both',expand=1, padx=4, pady=5)
group.grid(column=0, row=1, )
self.ion_plus_one_conc = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Ion Concentration (M) (+1):',
validate={'validator':'real','min':0},
value = str(APBSTools2.defaults['ion_plus_one_conc']),
)
self.ion_plus_one_rad = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Ion Radius (+1):',
validate={'validator':'real','min':0},
value = str(APBSTools2.defaults['ion_plus_one_rad']),
)
self.ion_minus_one_conc = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Ion Concentration (M) (-1):',
validate={'validator':'real','min':0},
value = str(APBSTools2.defaults['ion_minus_one_conc']),
)
self.ion_minus_one_rad = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Ion Radius (-1):',
validate={'validator':'real','min':0},
value = str(APBSTools2.defaults['ion_minus_one_rad']),
)
self.ion_plus_two_conc = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Ion Concentration (M) (+2):',
validate={'validator':'real','min':0},
value = str(APBSTools2.defaults['ion_plus_two_conc']),
)
self.ion_plus_two_rad = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Ion Radius (+2):',
validate={'validator':'real','min':0},
value = str(APBSTools2.defaults['ion_plus_two_rad']),
)
self.ion_minus_two_conc = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Ion Concentration (M) (-2):',
validate={'validator':'real','min':0},
value = str(APBSTools2.defaults['ion_minus_two_conc']),
)
self.ion_minus_two_rad = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Ion Radius (-2):',
validate={'validator':'real','min':0},
value = str(APBSTools2.defaults['ion_minus_two_rad']),
)
entries = (self.ion_plus_one_conc,self.ion_plus_one_rad,
self.ion_minus_one_conc,self.ion_minus_one_rad,
self.ion_plus_two_conc,self.ion_plus_two_rad,
self.ion_minus_two_conc,self.ion_minus_two_rad,
)
for entry in entries:
entry.pack(fill='x',expand=1,padx=4)
group = Pmw.Group(page,tag_text = 'Coarse Mesh Length')
group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
group.grid(column = 1, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_coarse_%s'%coord,Pmw.EntryField(group.interior(),
labelpos='w',
label_text=coord,
validate={'validator':'real','min':0},
value = -1,
entry_width=15,
)
)
getattr(self,'grid_coarse_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1)
group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
group.grid(column = 2, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_fine_%s'%coord,Pmw.EntryField(group.interior(),
labelpos='w',
label_text=coord,
validate={'validator':'real','min':0},
value = -1,
entry_width=15,
)
)
getattr(self,'grid_fine_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1)
group = Pmw.Group(page,tag_text = 'Grid Center')
group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
group.grid(column = 3, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_center_%s'%coord,Pmw.EntryField(group.interior(),
labelpos='w',
label_text=coord,
validate={'validator':'real'},
value = 0,
entry_width=10,
)
)
getattr(self,'grid_center_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1)
group = Pmw.Group(page,tag_text = 'Grid Points')
group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
group.grid(column = 4, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_points_%s'%coord,Pmw.EntryField(group.interior(),
labelpos='w',
label_text=coord,
validate={'validator':'integer','min':0},
value = -1,
entry_width=8,
)
)
getattr(self,'grid_points_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1)
page.grid_rowconfigure(2,weight=1)
page.grid_columnconfigure(5,weight=1)
page = self.notebook.add('Program Locations')
group = Pmw.Group(page,tag_text='Locations')
group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
def quickFileValidation(s):
if s == '': return Pmw.PARTIAL
elif os.path.isfile(s): return Pmw.OK
elif os.path.exists(s): return Pmw.PARTIAL
else: return Pmw.PARTIAL
def quickFileDirValidation(s):
'''
assumes s ends in filename
'''
if os.path.exists(s) and not os.path.isfile(s):
return Pmw.PARTIAL
if os.path.isdir(os.path.split(s)[0]):
return Pmw.OK
return Pmw.PARTIAL
self.binary = Pmw.EntryField(group.interior(),
labelpos='w',
label_pyclass = FileDialogButtonClassFactory.get(self.setBinaryLocation),
validate = {'validator':quickFileValidation,},
value = get_default_location('apbs.exe'),
label_text = 'APBS binary location:',
)
self.binary.pack(fill = 'x', padx = 20, pady = 10)
self.psize = Pmw.EntryField(group.interior(),
labelpos='w',
label_pyclass = FileDialogButtonClassFactory.get(self.setPsizeLocation),
validate = {'validator':quickFileValidation,},
#value = '/usr/local/apbs-0.3.1/tools/manip/psize.py',
value = get_default_location('psize.py'),
label_text = 'APBS psize.py location:',
)
self.psize.pack(fill = 'x', padx = 20, pady = 10)
self.pdb2pqr = Pmw.EntryField(group.interior(),
labelpos='w',
label_pyclass = FileDialogButtonClassFactory.get(self.setPdb2pqrLocation),
validate = {'validator':quickFileValidation,},
value = get_default_location('pdb2pqr.py'),
label_text = 'pdb2pqr location:',
)
self.pdb2pqr.pack(fill = 'x', padx = 20, pady = 10)
label = Tkinter.Label(group.interior(),
pady = 10,
justify=LEFT,
text = """
The PyMOL APBS tools can calculate proper grid dimensions and spacing (we attempt to make
the fine mesh spacing 0.5A or finer, but we will make it coarser if forced to by the
Maximum Grid Points setting in the configuration pane). If you wish to use APBS's psize.py
to set up the grid, make sure that the path is set correctly above.
PyMOL can generate PQR files using standard protein residues and AMBER charges. If you
wish to use PDB2PQR instead, make sure that it is installed and that the path is set
correctly above.
If PyMOL does not automatically find apbs, psize.py, or pdb2pqr, you may set the environment
variables APBS_BINARY, APBS_PSIZE and APBS_PDB2PQR to point to them respectively.
""",
)
label.pack()
page = self.notebook.add('Temp File Locations')
group = Pmw.Group(page,tag_text='Locations')
group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
labelpos = 'w',
label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
validate = {'validator':quickFileDirValidation,},
label_text = 'Temporary PQR file: ',
value = os.path.join(get_default_location('temp'),'pymol-generated.pqr'),
)
self.pymol_generated_pqr_filename.pack(fill = 'x', padx = 20, pady = 10)
self.pymol_generated_pdb_filename = Pmw.EntryField(group.interior(),
labelpos = 'w',
label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPdbFilename),
validate = {'validator':quickFileDirValidation,},
label_text = 'Temporary PDB file: ',
value = os.path.join(get_default_location('temp'),'pymol-generated.pdb'),
)
self.pymol_generated_pdb_filename.pack(fill = 'x', padx = 20, pady = 10)
self.pymol_generated_dx_filename = Pmw.EntryField(group.interior(),
labelpos = 'w',
label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedDxFilename),
validate = {'validator':quickFileDirValidation,},
label_text = 'Temporary DX file: ',
value = os.path.join(get_default_location('temp'),'pymol-generated.dx'),
)
self.pymol_generated_dx_filename.pack(fill = 'x', padx = 20, pady = 10)
self.pymol_generated_in_filename = Pmw.EntryField(group.interior(),
labelpos='w',
label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedInFilename),
validate = {'validator':quickFileDirValidation,},
value = os.path.join(get_default_location('temp'),'pymol-generated.in'),
label_text = 'APBS input file:')
self.pymol_generated_in_filename.pack(fill = 'x', padx = 20, pady = 10)
label = Tkinter.Label(group.interior(),
pady = 10,
justify=LEFT,
text = """You can automatically set the default location of temporary files
by setting the environment variable TEMP.
""",
)
label.pack()
# Create the visualization pages
page = self.notebook.add('Visualization (1)')
group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
self.visualization_group_1 = group
group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
page = self.notebook.add('Visualization (2)')
group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
self.visualization_group_2 = group
group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
# Create a couple of other empty pages
page = self.notebook.add('About')
group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
Documentation may be found at
http://pymolwiki.org/index.php/APBS
and
http://apbs.wustl.edu/MediaWiki/index.php/APBS_electrostatics_in_PyMOL
It requires APBS version >= 0.5.0.
In the simplest case,
1) Load a structure into PyMOL.
2) Start this plugin.
3) Make sure that the path to the APBS binary is correct on the "Program Locations" tab.
4) Click the "Set grid" button to set up the grid.
5) Click the "Run APBS" button.
Many thanks to
- Warren DeLano and Jason Vertrees for everything involving PyMOL
- Nathan Baker, Todd Dolinsky and David Gohara for everything involving APBS
- William G. Scott for help with several APBS+PyMOL issues and documentation
Created by Michael Lerner (http://pymolwiki.org/index.php/User:Mglerner) mglerner@gmail.com
Carlson Group, University of Michigan (http://www.umich.edu/~carlsonh/)
Please contact the author and cite this plugin if you use it in a publication.
Citation for this plugin:
MG Lerner and HA Carlson. APBS plugin for PyMOL, 2006,
University of Michigan, Ann Arbor.
Citation for PyMOL may be found here:
http://pymol.sourceforge.net/faq.html#CITE
Citation for APBS:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
Citation for PDB2PQR:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
PDB2PQR: an automated pipeline for the setup, execution,
and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 (2004).
"""
#
# Add this as text in a scrollable pane.
# Code based on Caver plugin
# http://loschmidt.chemi.muni.cz/caver/index.php
#
interior_frame=Frame(group.interior())
bar=Scrollbar(interior_frame,)
text_holder=Text(interior_frame,yscrollcommand=bar.set,background="#ddddff",font="Times 14")
bar.config(command=text_holder.yview)
text_holder.insert(END,text)
text_holder.pack(side=LEFT,expand="yes",fill="both")
bar.pack(side=LEFT,expand="yes",fill="y")
interior_frame.pack(expand="yes",fill="both")
self.notebook.setnaturalsize()
self.showAppModal()
def showAppModal(self):
#self.dialog.activate() #geometry = 'centerscreenfirst',globalMode = 'nograb')
self.dialog.show()
def execute(self, result, refocus=True):
if result == 'Register APBS Use':
import webbrowser
webbrowser.open("http://agave.wustl.edu/apbs/download")
elif result == 'Register PDB2PQR Use':
import webbrowser
webbrowser.open("http://www.poissonboltzmann.org/pdb2pqr/d/downloads")
elif result == 'Run APBS':
good = self.generateApbsInputFile()
if not good:
if DEBUG:
print "ERROR: Something went wrong trying to generate the APBS input file."
return False
if self.radiobuttons.getvalue() == 'Use another PQR':
pass
elif self.radiobuttons.getvalue() == 'Use PDB2PQR':
if DEBUG: print "GENERATING PQR FILE via PDB2PQR"
good = self.generatePdb2pqrPqrFile()
if not good:
if DEBUG:
print "Could not generate PDB2PQR file. generatePdb2pqrPqrFile failed."
return False
if DEBUG: print "GENERATED"
else: # it's one of the pymol-generated options
if DEBUG: print "GENERATING PQR FILE via PyMOL"
good = self.generatePymolPqrFile()
if not good:
if DEBUG:
print "Could not generate the PyMOL-basd PQR file. generatePyMOLPqrFile failed."
return False
if DEBUG: print "GENERATED"
if os.path.exists(self.pymol_generated_dx_filename.getvalue()):
try:
os.unlink(self.pymol_generated_dx_filename.getvalue())
except:
traceback.print_exc()
pass
#command = "%s %s" % (self.binary.getvalue(),self.pymol_generated_in_filename.getvalue())
#os.system(command)
#
# NOTE: if there are spaces in the directory name that contains pymol_generated_in_filename,
# our run command will want to split it up into several arguments if we pass it as a
# string. So, we pass it as a tuple.
#
(retval,progout) = run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),))
if refocus:
#
# There's a bug in the version of APBS shipped with
# Ubuntu 9.10 (version 1.1.0) that causes the name to
# become foo-PE0.dx instead of foo.dx. This would
# normally only occur in mg-para calcs or MPI versions
# of apbs. It's clearly bug-possible, but we will
# check for foo-PE0 if we can't find foo.dx.
#
fname = self.pymol_generated_dx_filename.getvalue()
if not os.path.isfile(fname):
print "Could not find",fname,"so searching for",
fname = '-PE0'.join(os.path.splitext(fname))
print fname
pymol.cmd.load(fname)
self.visualization_group_1.refresh()
self.visualization_group_2.refresh()
self.notebook.tab('Visualization (1)').focus_set()
self.notebook.selectpage('Visualization (1)')
elif result == 'Set grid':
self.runPsize()
else:
#
# Doing it this way takes care of clicking on the x in the top of the
# window, which as result set to None.
#
global APBS_BINARY_LOCATION, APBS_PSIZE_LOCATION
APBS_BINARY_LOCATION = self.binary.getvalue()
APBS_PSIZE_LOCATION = self.psize.getvalue()
self.quit()
def quit(self):
self.dialog.destroy() # stops CPU hogging, perhaps fixes Ubuntu bug MGL
def runPsize(self):
class NoPsize(Exception):
pass
class NoPDB(Exception):
pass
try:
if not self.psize.valid():
raise NoPsize
pqr_filename = self.pymol_generated_pqr_filename.getvalue()
try:
f = file(pqr_filename,'w')
f.close()
except:
raise NoPDB
#
# Do some magic to load the psize module
#
import imp
f,fname,description = imp.find_module('psize',[os.path.split(self.psize.getvalue())[0]])
psize = imp.load_module('psize',f,fname,description)
# WLD
sel = "((%s) or (neighbor (%s) and hydro))"%(
self.selection.getvalue(), self.selection.getvalue())
if pymol.cmd.count_atoms( self.selection.getvalue() + " and not alt ''")!=0:
print "WARNING: You have alternate locations for some of your atoms!"
pymol.cmd.save(pqr_filename,sel)
f.close()
size = psize.Psize()
size.setConstant('gmemceil',int(self.max_mem_allowed.getvalue()))
size.runPsize(pqr_filename)
coarsedim = size.getCoarseGridDims() # cglen
finedim = size.getFineGridDims() # fglen
# could use procgrid for multiprocessors
finegridpoints = size.getFineGridPoints() # dime
center = size.getCenter() # cgcent and fgcent
print "APBS's psize.py was used to calculated grid dimensions"
except (NoPsize,ImportError):
print "This plugin was used to calculated grid dimensions"
#
# First, we need to get the dimensions of the molecule
#
# WLD
sel = "((%s) or (neighbor (%s) and hydro))"%(
self.selection.getvalue(), self.selection.getvalue())
model = pymol.cmd.get_model(sel)
mins = [None,None,None]
maxs = [None,None,None]
for a in model.atom:
for i in (0,1,2):
if mins[i] is None or a.coord[i] < mins[i]:
mins[i] = a.coord[i]
if maxs[i] is None or a.coord[i] > maxs[i]:
maxs[i] = a.coord[i]
if None in mins or None in maxs:
error_dialog = Pmw.MessageDialog(self.parent,
title = 'Error',
message_text = "No atoms were in your selection",
)
junk = error_dialog.activate()
return False
box_length = [maxs[i] - mins[i] for i in range(3)]
center = [(maxs[i] + mins[i])/2.0 for i in range(3)]
#
# psize expands the molecular dimensions by CFAC (which defaults
# to 1.7) for the coarse grid
#
CFAC = 1.7
coarsedim = [length*CFAC for length in box_length]
#
# psize also does something strange .. it adds a buffer FADD to
# the box lengths to get the fine lengths. you'd think it'd also
# have FFAC or CADD, but we'll mimic it here. it also has the
# requirement that the fine grid lengths must be <= the corase
# grid lengths. FADD defaults to 20.
#
FADD = 20
finedim = [min(coarsedim[i],box_length[i] + FADD) for i in range(3)]
#
# And now the hard part .. setting up the grid points.
# From the APBS manual at http://agave.wustl.edu/apbs/doc/html/user-guide/x594.html#dime
# we have the formula
# n = c*2^(l+1) + 1
# where l is the number of levels in the MG hierarchy. The typical
# number of levels is 4.
#
nlev = 4
mult_fac = 2**(nlev + 1) # this will typically be 2^5==32
# and c must be a non-zero integer
# If we didn't have to be c*mult_fac + 1, this is what our grid points
# would look like (we use the ceiling to be on the safe side .. it never
# hurts to do too much.
SPACE = 0.5 # default desired spacing = 0.5A
#desired_points = [int(math.ceil(flen / SPACE)) for flen in finedim] # as integers
desired_points = [flen / SPACE for flen in finedim] # as floats .. use int(math.ceil(..)) later
# Now we set up our cs, taking into account mult_fac
# (we use the ceiling to be on the safe side .. it never hurts to do
# too much.)
cs = [int(math.ceil(dp/mult_fac)) for dp in desired_points]
finegridpoints = [mult_fac * c + 1 for c in cs]
print "cs",cs
print "finedim",finedim
print "nlev",nlev
print "mult_fac",mult_fac
print "finegridpoints",finegridpoints
except NoPDB:
error_dialog = Pmw.MessageDialog(self.parent,
title = 'Error',
message_text = "Please set a temporary PDB file location",
)
junk = error_dialog.activate()
return False
if (finegridpoints[0]>0) and (finegridpoints[1]>0) and (finegridpoints[2]>0):
max_mem_allowed = float(self.max_mem_allowed.getvalue())
def memofgrid(finegridpoints):
return 200. * float(finegridpoints[0] * finegridpoints[1] * finegridpoints[2]) / 1024. / 1024
def gridofmem(mem):
return mem * 1024. * 1024. / 200.
max_grid_points = gridofmem(max_mem_allowed)
print "Estimated memory usage",memofgrid(finegridpoints),'MB out of maximum allowed',max_mem_allowed
if memofgrid(finegridpoints) > max_mem_allowed:
print "Maximum memory usage exceeded. Old grid dimensions were",finegridpoints
product = float(finegridpoints[0] * finegridpoints[1] * finegridpoints[2])
factor = pow(max_grid_points/product,0.333333333)
finegridpoints[0] = (int(factor*finegridpoints[0]/2))*2+1
finegridpoints[1] = (int(factor*finegridpoints[1]/2))*2+1
finegridpoints[2] = (int(factor*finegridpoints[2]/2))*2+1
print "Fine grid points rounded down from",finegridpoints
#
# Now we have to make sure that this still fits the equation n = c*2^(l+1) + 1. Here, we'll
# just assume nlev == 4, which means that we need to be (some constant times 32) + 1.
#
# This can be annoying if, e.g., you're trying to set [99, 123, 99] .. it'll get rounded to [99, 127, 99].
# First, I'll try to round to the nearest 32*c+1. If that doesn't work, I'll just round down.
#
new_gp = [0,0,0]
for i in 0,1,2:
dm = divmod(finegridpoints[i] - 1,32)
if dm[1]>16:
new_gp[i] = (dm[0]+1)*32+1
else:
new_gp[i] = (dm[0])*32+1
new_prod = new_gp[0]*new_gp[1]*new_gp[2]
#print "tried new_prod",new_prod,"max_grid_points",max_grid_points,"small enough?",new_prod <= max_grid_points
if new_prod <= max_grid_points:
#print "able to round to closest"
for i in 0,1,2: finegridpoints[i] = new_gp[i]
else:
# darn .. have to round down.
# Note that this can still fail a little bit .. it can only get you back down to the next multiple <= what was in
# finegridpoints. So, if finegridpoints was exactly on a multiple, like (99,129,99), you'll get rounded down to
# (99,127,99), which is still just a bit over the default max of 1200000. I think that's ok. It's the rounding error
# from int(factor*finegridpoints ..) above, but it'll never be a huge error. If we needed to, we could easily fix this.
#
#print "rounding down more"
for i in 0,1,2:
#print finegridpoints[i],divmod(finegridpoints[i] - 1,32),
finegridpoints[i] = divmod(finegridpoints[i] - 1,32)[0]*32 + 1
print "New grid dimensions are",finegridpoints
print " APBS Tools: coarse grid: (%5.3f,%5.3f,%5.3f)"%tuple(coarsedim)
self.grid_coarse_x.setvalue(coarsedim[0])
self.grid_coarse_y.setvalue(coarsedim[1])
self.grid_coarse_z.setvalue(coarsedim[2])
print " APBS Tools: fine grid: (%5.3f,%5.3f,%5.3f)"%tuple(finedim)
self.grid_fine_x.setvalue(finedim[0])
self.grid_fine_y.setvalue(finedim[1])
self.grid_fine_z.setvalue(finedim[2])
print " APBS Tools: center: (%5.3f,%5.3f,%5.3f)"%tuple(center)
self.grid_center_x.setvalue(center[0])
self.grid_center_y.setvalue(center[1])
self.grid_center_z.setvalue(center[2])
print " APBS Tools: fine grid points (%d,%d,%d)"%tuple(finegridpoints)
self.grid_points_x.setvalue(finegridpoints[0])
self.grid_points_y.setvalue(finegridpoints[1])
self.grid_points_z.setvalue(finegridpoints[2])
def fixColumns(self,sel):
"""
Make sure that everything fits into the correct columns.
This means doing some rounding. It also means getting rid of
chain, occupancy and b-factor information.
"""
#pymol.cmd.alter_state(1,'all','(x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0, int(z*1000)/1000.0)')
#pymol.cmd.alter_state(1,'all','(x,y,z)=float("%.2f"%x),float("%.2f"%y),float("%.2f"%z)')
pymol.cmd.alter_state(1,'all','(x,y,z)=float("%.3f"%x),float("%.3f"%y),float("%.3f"%z)')
pymol.cmd.alter(sel,'chain=""')
pymol.cmd.alter(sel,'b=0')
pymol.cmd.alter(sel,'q=0')
def cleanupGeneratedPdbOrPqrFile(self,filename):
"""
More cleanup on PQR files.
pdb2pqr will happily write out a file where the coordinate
columns overlap if you have -100.something as one of the
coordinates, like
90.350 97.230-100.010
and so will PyMOL. We can't just assume that it's 0-1
because pdb2pqr will debump things and write them out with
3 digits post-decimal. Bleh.
"""
f = file(filename,'r')
txt = f.read()
f.close()
f = file(filename,'w')
# APBS accepts whitespace-delimited columns
# it doesn't care about non-coord lines, so there's not need to be careful about
# where we replace dashes.
txt = txt.replace('-',' -')
f.write(txt)
f.close()
def getUnassignedAtomsFromPqr(self,fname):
"""
Here is a comment from Todd Dolinsky via email:
There's a couple of different errors which can be printed out via REMARK 5 lines; a good sample is:
REMARK 1 PQR file generated by PDB2PQR (Version 1.2.0)
REMARK 1
REMARK 1 Forcefield Used: charmm
REMARK 1
REMARK 1 pKas calculated by propka and assigned using pH 7.00
REMARK 1
REMARK 5 WARNING: Propka determined the following residues to be
REMARK 5 in a protonation state not supported by the
REMARK 5 charmm forcefield!
REMARK 5 All were reset to their standard pH 7.0 state.
REMARK 5
REMARK 5 CYS 61 2 (negative)
REMARK 5 CYS 79 2 (negative)
REMARK 5
REMARK 5 WARNING: Unable to debump ALA 1 19
REMARK 5 WARNING: Unable to debump MET 1 151
REMARK 5 WARNING: Unable to debump PRO 1 258
REMARK 5 WARNING: Unable to debump GLY 2 8
REMARK 5 WARNING: Unable to debump THR 3 118
REMARK 5
REMARK 5 WARNING: PDB2PQR was unable to assign charges
REMARK 5 to the following atoms (omitted below):
REMARK 5 6657 O1 in TRS 900
REMARK 5 6658 C2 in TRS 900
REMARK 5 6659 C3 in TRS 900
REMARK 5 6660 C4 in TRS 900
REMARK 5 6661 O5 in TRS 900
REMARK 5 6662 C6 in TRS 900
REMARK 5 6663 O7 in TRS 900
REMARK 5 6664 N8 in TRS 900
REMARK 5
REMARK 6 Total charge on this protein: -1.0000 e
REMARK 6
If all you care about is the atom number, you can probably regexp match on the 'in' field, something like
>>> re.compile('REMARK 5 *(\d)* \w* in').findall(text) # Text contains PQR output string
['6657', '6658', '6659', '6660', '6661', '6662', '6663', '6664']
Or you can grab any other useful information - I'd say that using a regular expression like this would be the best option to ensure you don't get false positives.
"""
f = file(fname)
unassigned = re.compile('REMARK 5 *(\d+) \w* in').findall(f.read()) # Text contains PQR output string
f.close()
return '+'.join(unassigned)
def generateApbsInputFile(self):
if self.checkInput(silent=False):
#
# set up our variables
#
pqr_filename = self.getPqrFilename()
grid_points = [int(getattr(self,'grid_points_%s'%i).getvalue()) for i in 'x y z'.split()]
cglen = [float(getattr(self,'grid_coarse_%s'%i).getvalue()) for i in 'x y z'.split()]
fglen = [float(getattr(self,'grid_fine_%s'%i).getvalue()) for i in 'x y z'.split()]
cent = [float(getattr(self,'grid_center_%s'%i).getvalue()) for i in 'x y z'.split()]
apbs_mode = self.apbs_mode.getvalue()
if apbs_mode == 'Nonlinear Poisson-Boltzmann Equation':
apbs_mode = 'npbe'
else:
apbs_mode = 'lpbe'
bcflmap = {'Zero': 'zero',
'Single DH sphere': 'sdh',
'Multiple DH spheres': 'mdh',
#'Focusing': 'focus',
}
bcfl = bcflmap[self.bcfl.getvalue()]
chgmmap = {'Linear':'spl0',
'Cubic B-splines':'spl2',
'Quintic B-splines':'spl4',
}
chgm = chgmmap[self.chgm.getvalue()]
srfmmap = {'Mol surf for epsilon; inflated VdW for kappa, no smoothing':'mol',
'Same, but with harmonic average smoothing':'smol',
'Cubic spline':'spl2',
'Similar to cubic spline, but with 7th order polynomial':'spl4',}
srfm = srfmmap[self.srfm.getvalue()]
dx_filename = self.pymol_generated_dx_filename.getvalue()
if dx_filename.endswith('.dx'):
dx_filename = dx_filename[:-3]
apbs_input_text = getApbsInputFile(pqr_filename,
grid_points,
cglen,
fglen,
cent,
apbs_mode,
bcfl,
float(self.ion_plus_one_conc.getvalue()), float(self.ion_plus_one_rad.getvalue()),
float(self.ion_minus_one_conc.getvalue()), float(self.ion_minus_one_rad.getvalue()),
float(self.ion_plus_two_conc.getvalue()), float(self.ion_plus_two_rad.getvalue()),
float(self.ion_minus_two_conc.getvalue()), float(self.ion_minus_two_rad.getvalue()),
float(self.interior_dielectric.getvalue()), float(self.solvent_dielectric.getvalue()),
chgm,
srfm,
float(self.solvent_radius.getvalue()),
float(self.system_temp.getvalue()),
float(self.sdens.getvalue()),
dx_filename,
)
if DEBUG:
print "GOT THE APBS INPUT FILE"
#
# write out the input text
#
try:
f = file(self.pymol_generated_in_filename.getvalue(),'w')
f.write(apbs_input_text)
f.close()
except IOError:
print "ERROR: Got the input file from APBS, but failed when trying to write to %s" % self.pymol_generated_in_filename.getvalue()
return True
else:
self.checkInput()
return False
def checkInput(self,silent=False):
"""If silent is True, we'll just return a True/False value
"""
if not silent:
def show_error(message):
error_dialog = Pmw.MessageDialog(self.parent,
title = 'Error',
message_text = message,
)
junk = error_dialog.activate()
else:
def show_error(message):
pass
#
# First, check to make sure we have valid locations for apbs and psize
#
if not self.binary.valid():
show_error('Please set the APBS binary location')
return False
#
# If the path to psize is not correct, that's fine .. we'll
# do the calculations ourself.
#
#if not self.psize.valid():
# show_error("Please set APBS's psize location")
# return False
#
# Now check the temporary filenames
#
if self.radiobuttons.getvalue() != 'Use another PQR':
if not self.pymol_generated_pqr_filename.getvalue():
show_error('Please choose a name for the PyMOL\ngenerated PQR file')
return False
elif not self.pqr_to_use.valid():
show_error('Please select a valid pqr file or tell\nPyMOL to generate one')
return False
if not self.pymol_generated_pdb_filename.getvalue():
show_error('Please choose a name for the PyMOL\ngenerated PDB file')
return False
if not self.pymol_generated_dx_filename.getvalue():
show_error('Please choose a name for the PyMOL\ngenerated DX file')
return False
if not self.pymol_generated_in_filename.getvalue():
show_error('Please choose a name for the PyMOL\ngenerated APBS input file')
return False
if not self.map.getvalue():
show_error('Please choose a name for the generated map.')
return False
#
# Now, the ions
#
for sign in 'plus minus'.split():
for value in 'one two'.split():
for parm in 'conc rad'.split():
if not getattr(self,'ion_%s_%s_%s'%(sign,value,parm)).valid():
show_error('Please correct Ion concentrations and radii')
return False
#
# Now the grid
#
for grid_type in 'coarse fine points center'.split():
for coord in 'x y z'.split():
if not getattr(self,'grid_%s_%s'%(grid_type,coord)).valid():
show_error('Please correct grid dimensions\nby clicking on the "Set grid" button')
return False
#
# Now other easy things
#
for (message, thing) in (('solvent dielectric',self.solvent_dielectric),
('protein dielectric',self.interior_dielectric),
('solvent radius',self.solvent_radius),
('system temperature',self.system_temp),
('sdens',self.sdens),
):
if not thing.valid():
show_error('Please correct %s'%message)
return False
return True
def generatePdb2pqrPqrFile(self,silent=False):
"""use pdb2pqr to generate a pqr file
"""
if not silent:
def show_error(message):
error_dialog = Pmw.MessageDialog(self.parent,
title = 'Error',
message_text = message,
)
junk = error_dialog.activate()
else:
def show_error(message):
pass
#
# First, generate a PDB file
#
pdb_filename = self.pymol_generated_pdb_filename.getvalue()
try:
f = file(pdb_filename,'w')
f.close()
except:
show_error('Please set a temporary PDB file location that you have permission to edit')
return False
# copied from WLD code
sel = "((%s) or (neighbor (%s) and hydro))"%(
self.selection.getvalue(), self.selection.getvalue())
self.fixColumns(sel)
pymol.cmd.save(pdb_filename,sel)
self.cleanupGeneratedPdbOrPqrFile(pdb_filename)
#
# Now, generate a PQR file
#
## command_line = '%s %s %s %s'%(self.pdb2pqr.getvalue(),
## self.pdb2pqr_options.getvalue(),
## pdb_filename,
## self.pymol_generated_pqr_filename.getvalue(),
## )
## print "RAN",command_line
## result = os.system(command_line)
#
# We have to be a little cute about args, because pdb2pqr_options could have several options in it.
args = '%s %s %s' %(self.pdb2pqr_options.getvalue(),
pdb_filename,
self.pymol_generated_pqr_filename.getvalue(),
)
(retval,progout) = run(self.pdb2pqr.getvalue(),args)
if retval != 0:
show_error('Could not run pdb2pqr: %s %s\n\n%s'%(self.pdb2pqr.getvalue(),
args,
progout)
)
return False
self.cleanupGeneratedPdbOrPqrFile(self.pymol_generated_pqr_filename.getvalue())
unassigned_atoms = self.getUnassignedAtomsFromPqr(self.pymol_generated_pqr_filename.getvalue())
if unassigned_atoms:
pymol.cmd.select('unassigned','ID %s'%unassigned_atoms)
message_text = "Unable to assign parameters for the %s atoms in selection 'unassigned'.\nPlease either remove these unassigned atoms and re-start the calculation\nor fix their parameters in the generated PQR file and run the calculation\nusing the modified PQR file (select 'Use another PQR' in 'Main')."%len(unassigned_atoms.split('+'))
print "Unassigned atom IDs",unassigned_atoms
show_error(message_text)
return False
return True
def generatePymolPqrFile(self):
"""generate a pqr file from pymol
This will also call through to champ to set the Hydrogens and charges
if it needs to. If it does that, it may change the value self.selection
to take the new Hydrogens into account.
To make it worse, APBS seems to freak out when there are chain ids. So,
this gets rid of the chain ids.
"""
# CHAMP will break in many cases if retain_order is set. So,
# we unset it here and reset it later. Note that it's fine to
# reset it before things are written out.
ret_order = pymol.cmd.get('retain_order')
pymol.cmd.set('retain_order',0)
# WLD
sel = "((%s) or (neighbor (%s) and hydro))"%(
self.selection.getvalue(), self.selection.getvalue())
pqr_filename = self.getPqrFilename()
try:
f = file(pqr_filename,'w')
f.close()
except:
error_dialog = Pmw.MessageDialog(self.parent,
title = 'Error',
message_text = "Could not write PQR file.\nPlease check that temporary PQR filename is valid.",
)
junk = error_dialog.activate()
return False
# PyMOL + champ == pqr
from chempy.champ import assign
if self.radiobuttons.getvalue() == 'Use PyMOL generated PQR and PyMOL generated Hydrogens and termini':
pymol.cmd.remove('hydro and %s'%sel)
assign.missing_c_termini(sel)
assign.formal_charges(sel)
pymol.cmd.h_add(sel)
# WLD (code now unnecessary)
# new_hydros = '(hydro and neighbor %s)'%sel
# sel = '%s or %s' % (sel,new_hydros)
assign.amber99(sel)
pymol.cmd.set('retain_order',ret_order)
# WLD (code now unnecessary)
# if not self.selection.getvalue() in '(all) all'.split():
# self.selection.setvalue(sel)
#
# Get rid of chain information
#
# WLD -- PyMOL now does this automatically with PQR files
# pymol.cmd.alter(sel,'chain = ""')
self.fixColumns(sel)
pymol.cmd.save(pqr_filename,sel)
self.cleanupGeneratedPdbOrPqrFile(pqr_filename)
missed_count = pymol.cmd.count_atoms("("+sel+") and flag 23")
if missed_count > 0:
pymol.cmd.select("unassigned","("+sel+") and flag 23")
error_dialog = Pmw.MessageDialog(self.parent,
title = 'Error',
message_text = "Unable to assign parameters for the %s atoms in selection 'unassigned'.\nPlease either remove these unassigned atoms and re-start the calculation\nor fix their parameters in the generated PQR file and run the calculation\nusing the modified PQR file (select 'Use another PQR' in 'Main')."%missed_count,
)
junk = error_dialog.activate()
return False
return True
############################################################
############################################################
############################################################
## ##
## PmwExtensions ##
## ##
############################################################
############################################################
############################################################
"""
This contains all of the visualization groups that we'll use for our
PMW interface.
"""
#
# Generically useful PMW extensions
import os,fnmatch,time
import Tkinter,Pmw
#Pmw.setversion("0.8.5")
#
# The classes PmwFileDialog and PmwExistingFileDialog and the _errorpop function
# are taken from the Pmw contrib directory. The attribution given in that file
# is:
################################################################################
# Filename dialogs using Pmw
#
# (C) Rob W.W. Hooft, Nonius BV, 1998
#
# Modifications:
#
# J. Willem M. Nissink, Cambridge Crystallographic Data Centre, 8/2002
# Added optional information pane at top of dialog; if option
# 'info' is specified, the text given will be shown (in blue).
# Modified example to show both file and directory-type dialog
#
# No Guarantees. Distribute Freely.
# Please send bug-fixes/patches/features to <r.hooft@euromail.com>
#
################################################################################
def _errorpop(master,text):
d=Pmw.MessageDialog(master,
title="Error",
message_text=text,
buttons=("OK",))
d.component('message').pack(ipadx=15,ipady=15)
d.activate()
d.destroy()
class PmwFileDialog(Pmw.Dialog):
"""File Dialog using Pmw"""
def __init__(self, parent = None, **kw):
# Define the megawidget options.
optiondefs = (
('filter', '*', self.newfilter),
('directory', os.getcwd(), self.newdir),
('filename', '', self.newfilename),
('historylen',10, None),
('command', None, None),
('info', None, None),
)
self.defineoptions(kw, optiondefs)
# Initialise base class (after defining options).
Pmw.Dialog.__init__(self, parent)
self.withdraw()
# Create the components.
interior = self.interior()
if self['info'] is not None:
rowoffset=1
dn = self.infotxt()
dn.grid(row=0,column=0,columnspan=2,padx=3,pady=3)
else:
rowoffset=0
dn = self.mkdn()
dn.grid(row=0+rowoffset,column=0,columnspan=2,padx=3,pady=3)
del dn
# Create the directory list component.
dnb = self.mkdnb()
dnb.grid(row=1+rowoffset,column=0,sticky='news',padx=3,pady=3)
del dnb
# Create the filename list component.
fnb = self.mkfnb()
fnb.grid(row=1+rowoffset,column=1,sticky='news',padx=3,pady=3)
del fnb
# Create the filter entry
ft = self.mkft()
ft.grid(row=2+rowoffset,column=0,columnspan=2,padx=3,pady=3)
del ft
# Create the filename entry
fn = self.mkfn()
fn.grid(row=3+rowoffset,column=0,columnspan=2,padx=3,pady=3)
fn.bind('<Return>',self.okbutton)
del fn
# Buttonbox already exists
bb=self.component('buttonbox')
bb.add('OK',command=self.okbutton)
bb.add('Cancel',command=self.cancelbutton)
del bb
Pmw.alignlabels([self.component('filename'),
self.component('filter'),
self.component('dirname')])
def infotxt(self):
""" Make information block component at the top """
return self.createcomponent(
'infobox',
(), None,
Tkinter.Label, (self.interior(),),
width=51,
relief='groove',
foreground='darkblue',
justify='left',
text=self['info']
)
def mkdn(self):
"""Make directory name component"""
return self.createcomponent(
'dirname',
(), None,
Pmw.ComboBox, (self.interior(),),
entryfield_value=self['directory'],
entryfield_entry_width=40,
entryfield_validate=self.dirvalidate,
selectioncommand=self.setdir,
labelpos='w',
label_text='Directory:')
def mkdnb(self):
"""Make directory name box"""
return self.createcomponent(
'dirnamebox',
(), None,
Pmw.ScrolledListBox, (self.interior(),),
label_text='directories',
labelpos='n',
hscrollmode='none',
dblclickcommand=self.selectdir)
def mkft(self):
"""Make filter"""
return self.createcomponent(
'filter',
(), None,
Pmw.ComboBox, (self.interior(),),
entryfield_value=self['filter'],
entryfield_entry_width=40,
selectioncommand=self.setfilter,
labelpos='w',
label_text='Filter:')
def mkfnb(self):
"""Make filename list box"""
return self.createcomponent(
'filenamebox',
(), None,
Pmw.ScrolledListBox, (self.interior(),),
label_text='files',
labelpos='n',
hscrollmode='none',
selectioncommand=self.singleselectfile,
dblclickcommand=self.selectfile)
def mkfn(self):
"""Make file name entry"""
return self.createcomponent(
'filename',
(), None,
Pmw.ComboBox, (self.interior(),),
entryfield_value=self['filename'],
entryfield_entry_width=40,
entryfield_validate=self.filevalidate,
selectioncommand=self.setfilename,
labelpos='w',
label_text='Filename:')
def dirvalidate(self,string):
if os.path.isdir(string):
return Pmw.OK
else:
return Pmw.PARTIAL
def filevalidate(self,string):
if string=='':
return Pmw.PARTIAL
elif os.path.isfile(string):
return Pmw.OK
elif os.path.exists(string):
return Pmw.PARTIAL
else:
return Pmw.OK
def okbutton(self):
"""OK action: user thinks he has input valid data and wants to
proceed. This is also called by <Return> in the filename entry"""
fn=self.component('filename').get()
self.setfilename(fn)
if self.validate(fn):
self.canceled=0
self.deactivate()
def cancelbutton(self):
"""Cancel the operation"""
self.canceled=1
self.deactivate()
def tidy(self,w,v):
"""Insert text v into the entry and at the top of the list of
the combobox w, remove duplicates"""
if not v:
return
entry=w.component('entry')
entry.delete(0,'end')
entry.insert(0,v)
list=w.component('scrolledlist')
list.insert(0,v)
index=1
while index<list.index('end'):
k=list.get(index)
if k==v or index>self['historylen']:
list.delete(index)
else:
index=index+1
w.checkentry()
def setfilename(self,value):
if not value:
return
value=os.path.join(self['directory'],value)
dir,fil=os.path.split(value)
self.configure(directory=dir,filename=value)
c=self['command']
if callable(c):
c()
def newfilename(self):
"""Make sure a newly set filename makes it into the combobox list"""
self.tidy(self.component('filename'),self['filename'])
def setfilter(self,value):
self.configure(filter=value)
def newfilter(self):
"""Make sure a newly set filter makes it into the combobox list"""
self.tidy(self.component('filter'),self['filter'])
self.fillit()
def setdir(self,value):
self.configure(directory=value)
def newdir(self):
"""Make sure a newly set dirname makes it into the combobox list"""
self.tidy(self.component('dirname'),self['directory'])
self.fillit()
def singleselectfile(self):
"""Single click in file listbox. Move file to "filename" combobox"""
cs=self.component('filenamebox').curselection()
if cs!=():
value=self.component('filenamebox').get(cs)
self.setfilename(value)
def selectfile(self):
"""Take the selected file from the filename, normalize it, and OK"""
self.singleselectfile()
value=self.component('filename').get()
self.setfilename(value)
if value:
self.okbutton()
def selectdir(self):
"""Take selected directory from the dirnamebox into the dirname"""
cs=self.component('dirnamebox').curselection()
if cs!=():
value=self.component('dirnamebox').get(cs)
dir=self['directory']
if not dir:
dir=os.getcwd()
if value:
if value=='..':
dir=os.path.split(dir)[0]
else:
dir=os.path.join(dir,value)
self.configure(directory=dir)
self.fillit()
def askfilename(self,directory=None,filter=None):
"""The actual client function. Activates the dialog, and
returns only after a valid filename has been entered
(return value is that filename) or when canceled (return
value is None)"""
if directory!=None:
self.configure(directory=directory)
if filter!=None:
self.configure(filter=filter)
self.fillit()
self.canceled=1 # Needed for when user kills dialog window
self.activate()
if self.canceled:
return None
else:
return self.component('filename').get()
lastdir=""
lastfilter=None
lasttime=0
def fillit(self):
"""Get the directory list and show it in the two listboxes"""
# Do not run unnecesarily
if self.lastdir==self['directory'] and self.lastfilter==self['filter'] and self.lasttime>os.stat(self.lastdir)[8]:
return
self.lastdir=self['directory']
self.lastfilter=self['filter']
self.lasttime=time.time()
dir=self['directory']
if not dir:
dir=os.getcwd()
dirs=['..']
files=[]
try:
fl=os.listdir(dir)
fl.sort()
except os.error,arg:
if arg[0] in (2,20):
return
raise
for f in fl:
if os.path.isdir(os.path.join(dir,f)):
dirs.append(f)
else:
filter=self['filter']
if not filter:
filter='*'
if fnmatch.fnmatch(f,filter):
files.append(f)
self.component('filenamebox').setlist(files)
self.component('dirnamebox').setlist(dirs)
def validate(self,filename):
"""Validation function. Should return 1 if the filename is valid,
0 if invalid. May pop up dialogs to tell user why. Especially
suited to subclasses: i.e. only return 1 if the file does/doesn't
exist"""
return 1
class PmwExistingFileDialog(PmwFileDialog):
def filevalidate(self,string):
if os.path.isfile(string):
return Pmw.OK
else:
return Pmw.PARTIAL
def validate(self,filename):
if os.path.isfile(filename):
return 1
elif os.path.exists(filename):
_errorpop(self.interior(),"This is not a plain file")
return 0
else:
_errorpop(self.interior(),"Please select an existing file")
return 0
class FileDialogButtonClassFactory:
def get(fn,filter='*'):
"""This returns a FileDialogButton class that will
call the specified function with the resulting file.
"""
class FileDialogButton(Tkinter.Button):
# This is just an ordinary button with special colors.
def __init__(self, master=None, cnf={}, **kw):
'''when we get a file, we call fn(filename)'''
self.fn = fn
self.__toggle = 0
apply(Tkinter.Button.__init__, (self, master, cnf), kw)
self.configure(command=self.set)
def set(self):
fd = PmwFileDialog(self.master,filter=filter)
fd.title('Please choose a file')
n=fd.askfilename()
if n is not None:
self.fn(n)
return FileDialogButton
get = staticmethod(get)
############################################################
############################################################
############################################################
## ##
## PmwGroups ##
## ##
############################################################
############################################################
############################################################
class VisualizationGroup(Pmw.Group):
def __init__(self,*args,**kwargs):
my_options = 'visgroup_num'.split()
for option in my_options:
# use these options as attributes of this class
# and remove them from the kwargs dict before
# passing on to Pmw.Group.__init__().
setattr(self,option,kwargs.pop(option))
kwargs['tag_text'] = kwargs['tag_text'] + ' (%s)'%self.visgroup_num
Pmw.Group.__init__(self,*args,**kwargs)
self.refresh()
self.show_ms = False
self.show_pi = False
self.show_ni = False
def refresh(self):
things_to_kill = 'error_label update_buttonbox mm_group ms_group pi_group ni_group'.split()
for thing in things_to_kill:
try:
getattr(self,thing).destroy()
#print "destroyed",thing
except AttributeError:
#print "couldn't destroy",thing
# note: this attributeerror will also hit if getattr(self,thing) misses.
# another note: both halves of the if/else make an update_buttonbox.
# if you rename the one in the top half to something else, you'll cause nasty Pmw errors.
pass
if [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:map'] and [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:molecule']:
self.mm_group = Pmw.Group(self.interior(),tag_text = 'Maps and Molecules')
self.map = Pmw.OptionMenu(self.mm_group.interior(),
labelpos = 'w',
label_text = 'Map',
items = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:map'],
)
self.map.pack(padx=4,side=LEFT)
self.molecule = Pmw.OptionMenu(self.mm_group.interior(),
labelpos = 'w',
label_text = 'Molecule',
items = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:molecule'],
)
self.molecule.pack(padx=4,side=LEFT)
self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0)
self.update_buttonbox.pack(side=LEFT)
self.update_buttonbox.add('Update',command=self.refresh)
self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
self.ms_buttonbox.pack()
self.ms_buttonbox.add('Show',command=self.showMolSurface)
self.ms_buttonbox.add('Hide',command=self.hideMolSurface)
self.ms_buttonbox.add('Update',command=self.updateMolSurface)
self.ms_buttonbox.alignbuttons()
self.surface_solvent = IntVar()
self.surface_solvent.set(APBSTools2.defaults['surface_solvent'])
self.sol_checkbutton = Checkbutton(self.ms_group.interior(),
text = "Solvent accessible surface",
variable = self.surface_solvent)
self.sol_checkbutton.pack()
self.potential_at_sas = IntVar()
self.potential_at_sas.set(APBSTools2.defaults['potential_at_sas'])
self.pot_checkbutton = Checkbutton(self.ms_group.interior(),
text = "Color by potential on sol. acc. surf.",
variable = self.potential_at_sas)
self.pot_checkbutton.pack()
self.mol_surf_low = Pmw.Counter(self.ms_group.interior(),
labelpos = 'w',
label_text = 'Low',
orient = 'vertical',
entry_width = 4,
entryfield_value = -1,
datatype = 'real',
entryfield_validate = {'validator' : 'real'},
)
self.mol_surf_middle = Pmw.Counter(self.ms_group.interior(),
labelpos = 'w',
label_text = 'Middle',
orient = 'vertical',
entry_width = 4,
entryfield_value = 0,
datatype = 'real',
entryfield_validate = {'validator' : 'real'}
)
self.mol_surf_high = Pmw.Counter(self.ms_group.interior(),
labelpos = 'w',
label_text = 'High',
orient = 'vertical',
entry_width = 4,
entryfield_value = 1,
datatype = 'real',
entryfield_validate = {'validator' : 'real'}
)
bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
Pmw.alignlabels(bars)
for bar in bars: bar.pack(side=LEFT)
self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
self.pi_buttonbox.pack()
self.pi_buttonbox.add('Show',command=self.showPosSurface)
self.pi_buttonbox.add('Hide',command=self.hidePosSurface)
self.pi_buttonbox.add('Update',command=self.updatePosSurface)
self.pi_buttonbox.alignbuttons()
self.pos_surf_val = Pmw.Counter(self.pi_group.interior(),
labelpos = 'w',
label_text = 'Contour (kT/e)',
orient = 'vertical',
entry_width = 4,
entryfield_value = 1,
datatype = 'real',
entryfield_validate = {'validator' : 'real', 'min':0}
)
self.pos_surf_val.pack(side=LEFT)
self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')
self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)
self.ni_buttonbox.pack()
self.ni_buttonbox.add('Show',command=self.showNegSurface)
self.ni_buttonbox.add('Hide',command=self.hideNegSurface)
self.ni_buttonbox.add('Update',command=self.updateNegSurface)
self.ni_buttonbox.alignbuttons()
self.neg_surf_val = Pmw.Counter(self.ni_group.interior(),
labelpos = 'w',
label_text = 'Contour (kT/e)',
orient = 'vertical',
entry_width = 4,
entryfield_value = -1,
datatype = 'real',
entryfield_validate = {'validator' : 'real', 'max':0}
)
self.neg_surf_val.pack(side=LEFT)
self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
else:
self.error_label = Tkinter.Label(self.interior(),
pady = 10,
justify=LEFT,
text = '''You must have at least a molecule and a map loaded.
If you have a molecule and a map loaded, please click "Update"''',
)
self.error_label.pack()
self.update_buttonbox = Pmw.ButtonBox(self.interior(), padx=0)
self.update_buttonbox.pack()
self.update_buttonbox.add('Update',command=self.refresh)
def showMolSurface(self):
self.updateMolSurface()
def hideMolSurface(self):
pymol.cmd.hide('surface',self.molecule.getvalue())
def getRampName(self):
#return 'e_lvl'
idx = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:molecule'].index(self.molecule.getvalue())
return '_'.join(('e_lvl',str(idx),str(self.visgroup_num)))
def getIsoPosName(self):
idx = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:map'].index(self.map.getvalue())
return '_'.join(('iso_pos',str(idx),str(self.visgroup_num)))
def getIsoNegName(self):
idx = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:map'].index(self.map.getvalue())
return '_'.join(('iso_neg',str(idx),str(self.visgroup_num)))
def updateMolSurface(self):
molecule_name = self.molecule.getvalue()
ramp_name = self.getRampName()
map_name = self.map.getvalue()
low = float(self.mol_surf_low.getvalue())
mid = float(self.mol_surf_middle.getvalue())
high = float(self.mol_surf_high.getvalue())
range = [low,mid,high]
print " APBS Tools: range is",range
pymol.cmd.delete(ramp_name)
pymol.cmd.ramp_new(ramp_name,map_name,range)
pymol.cmd.set('surface_color',ramp_name,molecule_name)
if self.surface_solvent.get()==1:
pymol.cmd.set('surface_solvent',1,molecule_name)
pymol.cmd.set('surface_ramp_above_mode',0,molecule_name)
else:
pymol.cmd.set('surface_solvent',0,molecule_name)
pymol.cmd.set('surface_ramp_above_mode',self.potential_at_sas.get(),molecule_name)
pymol.cmd.show('surface',molecule_name)
pymol.cmd.refresh()
pymol.cmd.recolor(molecule_name)
def showPosSurface(self):
self.updatePosSurface()
def hidePosSurface(self):
pymol.cmd.hide('everything',self.getIsoPosName())
def updatePosSurface(self):
pymol.cmd.delete(self.getIsoPosName())
pymol.cmd.isosurface(self.getIsoPosName(),self.map.getvalue(),float(self.pos_surf_val.getvalue()))
pymol.cmd.color('blue',self.getIsoPosName())
pymol.cmd.show('everything',self.getIsoPosName())
def showNegSurface(self):
self.updateNegSurface()
def hideNegSurface(self):
pymol.cmd.hide('everything',self.getIsoNegName())
def updateNegSurface(self):
pymol.cmd.delete(self.getIsoNegName())
pymol.cmd.isosurface(self.getIsoNegName(),self.map.getvalue(),float(self.neg_surf_val.getvalue()))
pymol.cmd.color('red',self.getIsoNegName())
pymol.cmd.show('everything',self.getIsoNegName())
APBS Plugin FAQ
There is an issue with the freemol version of APBS shipped with PyMOL 1.2r2 for OS X.
Leopard and Snow Leopard (10.5 and 10.6)
There are three fairly easy ways to resolve it
1. Download and install the most recent (post Dec. 1 2009) version of APBS from [1]. Then copy the apbs binary into the freemol directory (mv it to /Applications/PyMOLX11Hybrid.app/pymol/freemol/bin/apbs.exe, overwriting the version that comes installed with PyMOL).
2. Download File:Libgfortran.3.dylib.bz2, unzip it ("bunzip2 libgfortran.3.dylib.gz2") and move it to /usr/local/lib ("mv libgfortran.3.dylib /usr/local/lib" ... on some machines, you may need "sudo mv libgfortran.3.dylib /usr/local/lib").
bunzip2 libgfortran.3.dylib.gz2
mv libgfortran.3.dylib /usr/local/lib
3. Use macports to install gcc 4.4.2 and link the appropriate library ("ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib" ... on some machines, you may need "sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib").
ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
If you're curious, the problem is that APBS is dynamically linked, but Apple does not provide FORTRAN libraries.
The version of libgfortran above is covered by the GNU General Public License (GPL). A copy of the GPL may be found at [2], and the source may be obtained from MacPorts ([3]).
Tiger (10.4)
You'll need to install APBS yourself via MacPorts or via fink. Fink instructions may be found on the APBS page. Installation via MacPorts requires first installing MacPorts from [4] and then typing
sudo port install apbs
from the command line. This process could easily take several hours on an older machine, as MacPorts will recompile gcc, gfortran, and several other packages along the way.
My open-source toolchain
- PyMOL (visualization, system setup, etc)
- Python (all scripting/automation tasks)
- numpy (efficient numerical library)
- scipy (including traits for simple GUIs)
- matplotlib (2D plotting)
- GROMACS (simulations)
I also make significant use of CHARMM and Amber.
My ~/.pymolrc runs this .py script
#!/usr/bin/env python
from pymol import cmd,stored
cmd.set('pdb_retain_ids',1)
cmd.set('retain_order',1)
import os
def gro(fnm,name=None):
os.system("/usr/local/bin/editconf -f %s -o /tmp/tmp.pdb" % fnm)
print "Just did","/usr/local/bin/editconf -f %s -o /tmp/tmp.pdb" % fnm
if name is None:
name = fnm[:-4]
cmd.load("/tmp/tmp.pdb",name)
cmd.extend("gro",gro)
def splitseq(seq,size):
""" Split up seq in pieces of size """
return [seq[i:i+size] for i in range(0, len(seq), size)]
def getIDsInSel(sel, sorted=True, reversed=False):
"""
PARAMETERS
sel,
The selection, object or group to iterate over
sorted (boolean),
Should the list be sorted?
reversed (boolean)
Should the list be reversed before returned? (Combined
with the above, you can return a decreasing-sorted list
of names
RETURNS
list[] of strings, representing the object IDs desired.
CREDITS
This is a very slightly modified version of getNamesInSel
from http://pymolwiki.org/index.php/GetNamesInSel
"""
stored.tempNames = set()
cmd.iterate(sel, "stored.tempNames.add(ID)")
rList = list(stored.tempNames)
# if you want the list reversed or sorted,
# uncomment the following lines
if sorted:
rList.sort()
if reversed:
rList.reverse()
return rList
cmd.extend("getIDsInSel", getIDsInSel)
def togrp(selname,fname):
'''Make a GROMACS index group from a selection'''
f = file(fname,'w')
f.write('[ %s ]\n'%selname)
# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
#7267 7268 7269 7270 7271 7272 7273 7274 7275 7276 7277 7278 7279 7280 7281
idxs = getIDsInSel(selname)
for g in splitseq(idxs,15):
line = ' '.join(['%4s'%i for i in g])
line = line + '\n'
f.write(line)
f.write('\n')
f.close()
cmd.extend('togrp',togrp)
def rayy(width=-1,height=-1,units='in',dpi=-1,**kwargs):
"""
Slightly better version of the ray command.
You can specify width and height in the units of your choice, e.g.
rayy 3,2,units=in,dpi=300
rayy 3in,2in
rayy 1in, 2 cm, dpi=600
Extra keyword arguments get passed on to the normal ray command.
Units can be 'in' or 'cm'.
For backwards compatibility, the conversion to dpi (or dots per
centimeter) is only performed when dpi is specified.
"""
if type(dpi) in [type('')]: dpi = int(dpi)
in_per_cm = 0.393700787
def todots(x,units,dpi):
if type(x) in [type('')]:
x = x.lower()
if 'in' in x: units = 'in'
elif 'cm' in x: units = 'cm'
x = float(x.replace(units,'').strip())
if (dpi == -1):
return x
if units == 'cm': x = x * in_per_cm
elif units == 'in': pass
else: raise ValueError('Unknown units (%s)'%units)
print '%s%s at %sdpi'%(x,units,dpi)
return int(x * dpi)
# How do we get current width/height of viewport? MainSceneGetSize perhaps
# But it doesn't matter, as PyMOL will autoscale internally for us when given -1.
try:
width,height = todots(width,units,dpi),todots(height,units,dpi)
except ValueError:
print "Unknown units"
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
cmd.extend('rayy',rayy)
To Do
- Update the PyMOL/APBS plugin page
mglerner Tue Nov 17 14:46:42 EST 2009