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BrownDyeTools.py
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BrownDyeTools.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Last modified: 2019-02-26 19:41:38
#
# pylint: disable=no-member,import-error,missing-docstring,invalid-name,multiple-statements
#
"""BrownDye Tools plugin for Pymol
For documentation see: https://github.com/rokdev/BrownDyeTools
Author : Robert Konecny <rok@ucsd.edu>
Release date: November 2016
License: GNU General Public License version 3
Copyright 2016-19 Robert Konecny, NBCR
This is free software, licensed under the GNU General Public License
version 3. You should have received a copy of the GNU General Public
License along with this program.
If not, see <http://www.gnu.org/licenses/>.
"""
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import
import sys
import os
import subprocess
if sys.version_info[0] < 3:
#import urllib2
#from urllib2 import URLError, HTTPError
#from urllib import quote
#from idlelib.TreeWidget import TreeItem, TreeNode
#from Tkinter import *
import Tkinter
#import tkSimpleDialog
import tkFileDialog
#import tkMessageBox
#import tkColorChooser
#import Queue
#import ttk
#from StringIO import StringIO
else:
#import urllib.request as urllib2
#from urllib.error import URLError, HTTPError
#from urllib.parse import quote
#from idlelib.tree import TreeItem, TreeNode
#from tkinter import *
import tkinter as Tkinter
#from tkinter import simpledialog as tkSimpleDialog
from tkinter import filedialog as tkFileDialog
#import tkinter.messagebox as tkMessageBox
#import tkinter.colorchooser as tkColorChooser
#import queue as Queue
#import tkinter.ttk as ttk
#from io import StringIO
#import string
import re
##import filecmp
import json
import shutil
import random
import time
import datetime
##import tkSimpleDialog
##import tkMessageBox
#import Tkinter
#import tkFileDialog
from threading import Thread
##from lxml import etree
from xml.etree import ElementTree as etree
##import importlib
import Pmw
DEBUG = 0
__version__ = '1.0.0'
__author__ = 'Robert Konecny <rok@ucsd.edu>'
PDB2PQR_PATH = None
APBS_PATH = None
BD_PATH = None
CONFIG_FILE = 'bd-config.json'
DEFAULT_CONTACTS_FILE = 'protein-protein-contacts-default.xml'
MOL = ['mol0', 'mol1']
APBS_EXE = 'apbs'
PDB2PQR_EXE = 'pdb2pqr'
BDTOP_EXE = 'bd_top'
NAM_SIMULATION_EXE = 'nam_simulation'
JOBPID = None
PQR_DEFAULTS = {
'pqr_ff': 'parse',
'pqr_opts': '--apbs-input --chain',
'pqr_ph': 7.0,
'pqr_assign_only': True,
'pqr_use_propka': False,
}
PSIZE_DEFAULTS = {
'cfac': 3.0,
'fadd': 50.0,
'gspace': 0.5,
}
APBS_DEFAULTS = {
'apbs_mode': 'lpbe',
'apbs_pdie': 4.0,
'apbs_sdie': 78.0,
'apbs_srfm': 'smol',
'apbs_chgm': 'spl2',
'apbs_bcfl': 'sdh',
'apbs_sdens': 10.,
'apbs_swin': 0.3,
'apbs_srad': 1.4,
'apbs_temp': 298.15,
'apbs_ion_charge': [1, -1],
'apbs_ion_conc': [0.15, 0.15],
'apbs_ion_radius': [1.0, 1.0],
}
BD_DEFAULTS = {
'contacts_f': DEFAULT_CONTACTS_FILE,
'default_contacts_f': True,
'ntraj': 100,
'nthreads': 1,
'mindx': 0.2,
'sdie': APBS_DEFAULTS['apbs_sdie'],
'pdie': [APBS_DEFAULTS['apbs_pdie'], APBS_DEFAULTS['apbs_pdie']],
'debyel': [0.0, 0.0],
'ntrajo': 1,
'ncopies': 200,
'nbincopies': 200,
'nsteps': 10000,
'westeps': 10000,
'maxnsteps': 10000,
'nsteps_per_output': 2,
'rxn_distance': 5.0,
'npairs': 3,
}
if DEBUG > 0:
PDB2PQR_PATH = '/opt/pdb2pqr-linux-bin64-2.1.0/'
APBS_PATH = '/export1/Builds/SandBox-2018-03-08T15.28.17/bin/'
BD_PATH = '/home/rok/BrownianDynamics/browndye-2016.4.14/bin/'
if "PDB2PQR_PATH" in os.environ: PDB2PQR_PATH = os.environ["PDB2PQR_PATH"]
if "APBS_PATH" in os.environ: APBS_PATH = os.environ["APBS_PATH"]
if "BD_PATH" in os.environ: BD_PATH = os.environ["BD_PATH"]
def __init__(self):
"""BrownDyeTools plugin for PyMol."""
self.menuBar.addmenuitem('Plugin', 'command',
'BrownDye Tools', label='BrownDye Tools',
command=lambda s=self: BDPlugin(s))
class DummyPymol(object):
"""Dummy pymol class when running standalone GUI."""
class Cmd:
def load(self, name, sel=''):
pass
def get_names(self, name):
return ['mol0', 'mol1', 'map0', 'map1']
def get_type(self, thing):
if thing.startswith('mol'):
return 'object:molecule'
else:
return 'object:map'
cmd = Cmd()
if 'pymol.gui' in sys.modules:
try:
import pymol
except ImportError:
print("::: Pymol import failed - Pymol features not available!")
pymol = DummyPymol()
else:
print("::: Pymol import failed - Pymol features will not available!")
pymol = DummyPymol()
class BDPlugin(object):
""" The main BrowDye plugin class."""
def __init__(self, app):
self.parent = app.root
Tkinter.Grid.rowconfigure(self.parent, 0, weight=1)
Tkinter.Grid.columnconfigure(self.parent, 0, weight=1)
self.createGUI()
def createGUI(self):
"""The main GUI class - sets up all GUI elements."""
self.dialog = Pmw.Dialog(self.parent, buttons=('Exit',),
title='BrownDyeTools Plugin for PyMOL',
command=self.exitBDPlugin)
Pmw.setbusycursorattributes(self.dialog.component('hull'))
self.projectDir = Tkinter.StringVar()
self.projectDir.set(self.getProjectDir())
self.pdb2pqr_path = Tkinter.StringVar()
self.pdb2pqr_path.set(PDB2PQR_PATH)
self.apbs_path = Tkinter.StringVar()
self.apbs_path.set(APBS_PATH)
self.bd_path = Tkinter.StringVar()
self.bd_path.set(BD_PATH)
self.config_file = Tkinter.StringVar()
self.config_file.set(CONFIG_FILE)
# parameters used by pdb2pqr
self.mol = [Tkinter.StringVar(), Tkinter.StringVar()]
self.mol[0].set(None)
self.mol[1].set(None)
self.pqr = [Tkinter.StringVar(), Tkinter.StringVar()]
self.pqr[0].set(None)
self.pqr[1].set(None)
self.mol_object = [Tkinter.StringVar(), Tkinter.StringVar()]
self.mol_object[0].set(None)
self.mol_object[1].set(None)
self.pqr_opts = Tkinter.StringVar()
self.pqr_opts.set(PQR_DEFAULTS['pqr_opts'])
self.pqr_assign_only = Tkinter.BooleanVar()
self.pqr_assign_only.set(PQR_DEFAULTS['pqr_assign_only'])
self.pqr_use_propka = Tkinter.BooleanVar()
self.pqr_use_propka.set(PQR_DEFAULTS['pqr_use_propka'])
self.pqr_ph = Tkinter.DoubleVar()
self.pqr_ph.set(PQR_DEFAULTS['pqr_ph'])
self.pqr_ff = Tkinter.StringVar()
self.pqr_ff.set(PQR_DEFAULTS['pqr_ff'])
# psize/APBS parameters and defaults
self.gspace = Tkinter.DoubleVar()
self.gspace.set(PSIZE_DEFAULTS['gspace'])
self.cfac = Tkinter.DoubleVar()
self.cfac.set(PSIZE_DEFAULTS['cfac'])
self.fadd = Tkinter.DoubleVar()
self.fadd.set(PSIZE_DEFAULTS['fadd'])
self.dime = [[Tkinter.IntVar() for _ in range(3)],
[Tkinter.IntVar() for _ in range(3)]]
self.cglen = [[Tkinter.DoubleVar() for _ in range(3)],
[Tkinter.DoubleVar() for _ in range(3)]]
self.fglen = [[Tkinter.DoubleVar() for _ in range(3)],
[Tkinter.DoubleVar() for _ in range(3)]]
self.apbs_mode = Tkinter.StringVar()
self.apbs_mode.set(APBS_DEFAULTS['apbs_mode'])
self.apbs_bcfl = Tkinter.StringVar()
self.apbs_bcfl.set(APBS_DEFAULTS['apbs_bcfl'])
self.apbs_ion_charge = [Tkinter.IntVar() for _ in range(2)]
self.apbs_ion_conc = [Tkinter.DoubleVar() for _ in range(2)]
self.apbs_ion_radius = [Tkinter.DoubleVar() for _ in range(2)]
for i in range(2):
self.apbs_ion_charge[i].set(APBS_DEFAULTS['apbs_ion_charge'][i])
self.apbs_ion_conc[i].set(APBS_DEFAULTS['apbs_ion_conc'][i])
self.apbs_ion_radius[i].set(APBS_DEFAULTS['apbs_ion_radius'][i])
self.apbs_pdie = Tkinter.DoubleVar()
self.apbs_pdie.set(APBS_DEFAULTS['apbs_pdie'])
self.apbs_sdie = Tkinter.DoubleVar()
self.apbs_sdie.set(APBS_DEFAULTS['apbs_sdie'])
self.apbs_chgm = Tkinter.StringVar()
self.apbs_chgm.set(APBS_DEFAULTS['apbs_chgm'])
self.apbs_sdens = Tkinter.DoubleVar()
self.apbs_sdens.set(APBS_DEFAULTS['apbs_sdens'])
self.apbs_swin = Tkinter.DoubleVar()
self.apbs_swin.set(APBS_DEFAULTS['apbs_swin'])
self.apbs_srfm = Tkinter.StringVar()
self.apbs_srfm.set(APBS_DEFAULTS['apbs_srfm'])
self.apbs_srad = Tkinter.DoubleVar()
self.apbs_srad.set(APBS_DEFAULTS['apbs_srad'])
self.apbs_temp = Tkinter.DoubleVar()
self.apbs_temp.set(APBS_DEFAULTS['apbs_temp'])
# reaction criteria
self.contacts_f = Tkinter.StringVar()
self.contacts_f.set(BD_DEFAULTS['contacts_f'])
self.default_contacts_f = Tkinter.BooleanVar()
self.default_contacts_f.set(BD_DEFAULTS['default_contacts_f'])
self.rxn_distance = Tkinter.DoubleVar()
self.rxn_distance.set(BD_DEFAULTS['rxn_distance'])
self.npairs = Tkinter.IntVar()
self.npairs.set(BD_DEFAULTS['npairs'])
# BD parameters and defaults
self.sdie = Tkinter.DoubleVar()
self.sdie.set(self.apbs_sdie.get())
self.pdie = [Tkinter.DoubleVar() for _ in range(2)]
self.debyel = [Tkinter.DoubleVar() for _ in range(2)]
for i in range(2):
self.pdie[i].set(self.apbs_pdie.get())
self.debyel[i].set(BD_DEFAULTS['debyel'][i])
self.ntraj = Tkinter.IntVar()
self.ntraj.set(BD_DEFAULTS['ntraj'])
self.nthreads = Tkinter.IntVar()
self.nthreads.set(BD_DEFAULTS['nthreads'])
self.mindx = Tkinter.DoubleVar()
self.mindx.set(BD_DEFAULTS['mindx'])
self.ntrajo = Tkinter.IntVar()
self.ntrajo.set(BD_DEFAULTS['ntrajo'])
self.ncopies = Tkinter.IntVar()
self.ncopies.set(BD_DEFAULTS['ncopies'])
self.nbincopies = Tkinter.IntVar()
self.nbincopies.set(BD_DEFAULTS['nbincopies'])
self.nsteps = Tkinter.IntVar()
self.nsteps.set(BD_DEFAULTS['nsteps'])
self.westeps = Tkinter.IntVar()
self.westeps.set(BD_DEFAULTS['westeps'])
self.maxnsteps = Tkinter.IntVar()
self.maxnsteps.set(BD_DEFAULTS['maxnsteps'])
self.nsteps_per_output = Tkinter.IntVar()
self.nsteps_per_output.set(BD_DEFAULTS['nsteps_per_output'])
self.run_in_background = Tkinter.BooleanVar()
self.run_in_background.set(False)
# Analysis
self.traj_f = Tkinter.StringVar()
self.traj_f.set('traj0.xml')
self.traj_index_n = Tkinter.IntVar()
self.traj_index_n.set(1)
#######################################################################
# Main code
pref = dict(padx=5, pady=5)
w = Tkinter.Label(self.dialog.interior(),
text=('\nBrownDye Tools for PyMOL\n'
'Version %s, NBCR 2016-19\n\n'
'Plugin for setting up and running '
'Brownian dynamics simulations with BrownDye.'
% __version__),
background='black', foreground='white')
w.pack(expand=1, fill='both', **pref)
# create a notebook
self.notebook = Pmw.NoteBook(self.dialog.interior())
self.notebook.pack(fill='both', expand=1, **pref)
self.status_bar = Pmw.MessageBar(self.dialog.interior(), entry_width=40,
entry_relief='sunken',
labelpos='w', label_text='Status: ')
self.status_bar.pack(fill='both', expand=1, **pref)
self.status_bar.message('state', 'Idle')
self.balloon = Pmw.Balloon(self.dialog.interior())
#####################
# Tab: Configuration
#####################
page = self.notebook.add('Configuration')
self.notebook.tab('Configuration').focus_set()
config = Tkinter.LabelFrame(page, text='Calculation configuration')
config.pack(fill='both', expand=True, **pref)
project_path_ent = Pmw.EntryField(config,
label_text='Create project directory:',
labelpos='wn',
entry_textvariable=self.projectDir)
project_path_but = Tkinter.Button(config, text='Create',
command=self.createProjectDir)
self.balloon.bind(project_path_but, 'Create a new project directory')
label = Tkinter.Label(config, text='or')
project_path_b_but = Tkinter.Button(config, text='Browse ...',
command=self.browseProjectDir)
pdb2pqr_path_ent = Pmw.EntryField(config,
label_text='Select PDB2PQR_PATH location:',
labelpos='wn',
entry_textvariable=self.pdb2pqr_path)
pdb2pqr_path_but = Tkinter.Button(config, text='Browse...',
command=self.getPDB2PQRpath)
apbs_path_ent = Pmw.EntryField(config,
label_text='Select APBS_PATH location:',
labelpos='w',
entry_textvariable=self.apbs_path)
apbs_path_but = Tkinter.Button(config, text='Browse...',
command=self.getAPBSpath)
bd_path_ent = Pmw.EntryField(config,
label_text='Select BD_PATH location:',
labelpos='wn',
entry_textvariable=self.bd_path)
bd_path_but = Tkinter.Button(config, text='Browse...',
command=self.getBDpath)
label1 = Tkinter.Label(config, text='')
config_ent = Pmw.EntryField(config,
label_text='Save or load calculation configuration: ',
labelpos='wn',
entry_textvariable=self.config_file)
config_but = Tkinter.Button(config, text='Browse...',
command=self.getConfigPath)
load_config_but = Tkinter.Button(config, text='Load configuration',
command=self.loadConfig)
self.balloon.bind(load_config_but, 'Load calculation configuration from a file')
save_config_but = Tkinter.Button(config, text='Save configuration',
command=self.saveConfig)
self.balloon.bind(save_config_but, 'Save calculation configuration to a file')
# arrange widgets using grid
project_path_ent.grid(sticky='we', row=1, column=0, **pref)
project_path_but.grid(sticky='we', row=1, column=3, **pref)
label.grid(sticky='we', row=1, column=2, **pref)
project_path_b_but.grid(sticky='we', row=1, column=1, **pref)
pdb2pqr_path_ent.grid(sticky='we', row=2, column=0, **pref)
pdb2pqr_path_but.grid(sticky='we', row=2, column=1, **pref)
apbs_path_ent.grid(sticky='we', row=3, column=0, **pref)
apbs_path_but.grid(sticky='we', row=3, column=1, **pref)
bd_path_ent.grid(sticky='we', row=4, column=0, **pref)
bd_path_but.grid(sticky='we', row=4, column=1, **pref)
label1.grid(sticky='we', row=5, column=2, **pref)
config_ent.grid(sticky='we', row=6, column=0, **pref)
config_but.grid(sticky='we', row=6, column=1, **pref)
load_config_but.grid(sticky='e', row=6, column=2, **pref)
save_config_but.grid(sticky='w', row=6, column=3, **pref)
config.columnconfigure(0, weight=8)
config.columnconfigure(1, weight=2)
#############################
# Tab: PQR files preparation
#############################
page = self.notebook.add('PQR files')
grp_pqr = Tkinter.LabelFrame(page, text='PQR files')
grp_pqr.grid(sticky='eswn', row=0, column=0, columnspan=3, **pref)
pdb0_ent = Pmw.EntryField(grp_pqr,
label_text='Molecule 0 PDB file:', labelpos='wn',
entry_textvariable=self.mol[0])
pdb0_but = Tkinter.Button(grp_pqr, text='Browse...',
command=lambda: self.getPDBMol(0))
label0 = Tkinter.Label(grp_pqr, text='or')
pymol_obj0_opt = Pmw.OptionMenu(grp_pqr, labelpos='w',
label_text='Select molecule 0: ',
menubutton_textvariable=self.mol_object[0],
menubutton_width=7,
items=(['None'] + pymol.cmd.get_names("all")))
pdb1_ent = Pmw.EntryField(grp_pqr,
label_text='Molecule 1 PDB file:', labelpos='wn',
entry_textvariable=self.mol[1])
pdb1_but = Tkinter.Button(grp_pqr, text='Browse...',
command=lambda: self.getPDBMol(1))
label1 = Tkinter.Label(grp_pqr, text='or')
pymol_obj1_opt = Pmw.OptionMenu(grp_pqr, labelpos='w',
label_text='Select molecule 1: ',
menubutton_textvariable=self.mol_object[1],
menubutton_width=7,
items=(['None'] + pymol.cmd.get_names("all")))
pqr_ff_opt = Pmw.OptionMenu(grp_pqr, labelpos='w',
label_text='Force field: ',
menubutton_textvariable=self.pqr_ff,
menubutton_width=7,
items=['parse', 'charmm', 'amber', 'swanson'])
pqr_an_but = Tkinter.Checkbutton(grp_pqr,
text=('Assign charge and radius only '
'(no structure optimization)'),
variable=self.pqr_assign_only,
onvalue=True, offvalue=False,
command=lambda: propka_but.toggle())
propka_but = Tkinter.Checkbutton(grp_pqr,
text=('Use PROPKA to assign protonation states'),
variable=self.pqr_use_propka,
onvalue=True, offvalue=False,
command=lambda: pqr_an_but.toggle())
ph_ent = Pmw.EntryField(grp_pqr, labelpos='w',
label_text='pH: ',
validate={'validator': 'real', 'min': 0.00},
entry_textvariable=self.pqr_ph,
entry_width=4)
pqr_opt_but = Tkinter.Button(page, text='Create PQR files',
command=self.pdb2pqr)
label2 = Tkinter.Label(page, text='or load your PQR files:')
pqr_0_ent = Pmw.EntryField(page,
label_text='Molecule 0 PQR file:', labelpos='wn',
entry_textvariable=self.pqr[0])
pqr_0_but = Tkinter.Button(page, text='Browse...',
command=lambda: self.getPQRMol(0))
pqr_1_ent = Pmw.EntryField(page,
label_text='Molecule 1 PQR file:', labelpos='wn',
entry_textvariable=self.pqr[1])
pqr_1_but = Tkinter.Button(page, text='Browse...',
command=lambda: self.getPQRMol(1))
pdb0_ent.grid(sticky='we', row=0, column=0, **pref)
pdb0_but.grid(sticky='we', row=0, column=1, **pref)
label0.grid(sticky='we', row=0, column=2, **pref)
pymol_obj0_opt.grid(sticky='we', row=0, column=3, **pref)
pdb1_ent.grid(sticky='we', row=1, column=0, **pref)
pdb1_but.grid(sticky='we', row=1, column=1, **pref)
label1.grid(sticky='we', row=1, column=2, **pref)
pymol_obj1_opt.grid(sticky='we', row=1, column=3, **pref)
pqr_ff_opt.grid(sticky='we', row=2, column=0, **pref)
pqr_an_but.grid(sticky='we', row=3, column=0, **pref)
propka_but.grid(sticky='we', row=3, column=1, columnspan=2, **pref)
ph_ent.grid(sticky='we', row=3, column=3, **pref)
pqr_opt_but.grid(sticky='we', row=4, column=0, **pref)
label2.grid(sticky='we', row=5, column=0, **pref)
pqr_0_ent.grid(sticky='we', row=6, column=0, **pref)
pqr_0_but.grid(sticky='we', row=6, column=1, **pref)
pqr_1_ent.grid(sticky='we', row=7, column=0, **pref)
pqr_1_but.grid(sticky='we', row=7, column=1, **pref)
page.columnconfigure(0, weight=1)
page.columnconfigure(1, weight=1)
############
# Tab: APBS
############
page = self.notebook.add('APBS')
grp_grids = Tkinter.LabelFrame(page, text='Grid size')
grp_apbs = Tkinter.LabelFrame(page, text='APBS options')
grp_grids.grid(sticky='eswn', row=0, column=0, columnspan=3, **pref)
grp_apbs.grid(sticky='eswn', row=0, column=3, columnspan=2, **pref)
#page.columnconfigure(0, weight=2)
#page.columnconfigure(1, weight=1)
gspace_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='Grid spacing (A): ',
validate={'validator': 'real', 'min': 0.00},
entry_textvariable=self.gspace,
entry_width=4)
fadd_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='Grid span beyond the molecule (in A) : ',
validate={'validator': 'real', 'min': 0.00},
entry_textvariable=self.fadd,
entry_width=4)
label0 = Tkinter.Label(grp_grids, text='Molecule 0')
dime0_0_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='dime: ',
validate={'validator': 'integer', 'min': 0},
entry_textvariable=self.dime[0][0],
entry_width=5)
dime0_1_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'integer', 'min': 0},
entry_textvariable=self.dime[0][1],
entry_width=5)
dime0_2_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'integer', 'min': 0},
entry_textvariable=self.dime[0][2],
entry_width=5)
cglen0_0_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='cglen: ',
validate={'validator': 'real', 'min': 0.00},
entry_textvariable=self.cglen[0][0],
entry_width=8)
cglen0_1_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'real', 'min': 0.00},
entry_textvariable=self.cglen[0][1],
entry_width=8)
cglen0_2_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'real', 'min': 0.00},
entry_textvariable=self.cglen[0][2],
entry_width=8)
fglen0_0_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='fglen: ',
validate={'validator': 'real', 'min': 0.00},
entry_textvariable=self.fglen[0][0],
entry_width=8)
fglen0_1_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'real', 'min': 0.00},
entry_textvariable=self.fglen[0][1],
entry_width=8)
fglen0_2_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'real', 'min': 0.00},
entry_textvariable=self.fglen[0][2],
entry_width=8)
get_size0_but = Tkinter.Button(grp_grids,
text="Set grid",
command=lambda: self.getSizemol(0))
label1 = Tkinter.Label(grp_grids, text='Molecule 1')
dime1_0_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='dime: ',
# value=self.dime1[0].get(),
validate={'validator': 'integer', 'min': 0},
entry_textvariable=self.dime[1][0],
entry_width=5)
dime1_1_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'integer', 'min': 0},
entry_textvariable=self.dime[1][1],
entry_width=5)
dime1_2_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'integer', 'min': 0},
entry_textvariable=self.dime[1][2],
entry_width=5)
cglen1_0_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='cglen: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.cglen[1][0],
entry_width=8)
cglen1_1_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.cglen[1][1],
entry_width=8)
cglen1_2_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.cglen[1][2],
entry_width=8)
fglen1_0_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='fglen: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.fglen[1][0],
entry_width=8)
fglen1_1_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.fglen[1][1],
entry_width=8)
fglen1_2_ent = Pmw.EntryField(grp_grids, labelpos='w',
label_text='',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.fglen[1][2],
entry_width=8)
get_size1_but = Tkinter.Button(grp_grids,
text="Set grid",
command=lambda: self.getSizemol(1))
gspace_ent.grid(sticky='we', row=0, column=0, **pref)
fadd_ent.grid(sticky='we', row=0, column=1, columnspan=2, **pref)
label0.grid(sticky='we', row=1, column=0, **pref)
dime0_0_ent.grid(sticky='we', row=2, column=0, **pref)
dime0_1_ent.grid(sticky='we', row=2, column=1, **pref)
dime0_2_ent.grid(sticky='we', row=2, column=2, **pref)
cglen0_0_ent.grid(sticky='we', row=3, column=0, **pref)
cglen0_1_ent.grid(sticky='we', row=3, column=1, **pref)
cglen0_2_ent.grid(sticky='we', row=3, column=2, **pref)
fglen0_0_ent.grid(sticky='we', row=4, column=0, **pref)
fglen0_1_ent.grid(sticky='we', row=4, column=1, **pref)
fglen0_2_ent.grid(sticky='we', row=4, column=2, **pref)
get_size0_but.grid(sticky='we', row=5, column=2, **pref)
label1.grid(sticky='we', row=6, column=0, **pref)
dime1_0_ent.grid(sticky='we', row=7, column=0, **pref)
dime1_1_ent.grid(sticky='we', row=7, column=1, **pref)
dime1_2_ent.grid(sticky='we', row=7, column=2, **pref)
cglen1_0_ent.grid(sticky='we', row=8, column=0, **pref)
cglen1_1_ent.grid(sticky='we', row=8, column=1, **pref)
cglen1_2_ent.grid(sticky='we', row=8, column=2, **pref)
fglen1_0_ent.grid(sticky='we', row=9, column=0, **pref)
fglen1_1_ent.grid(sticky='we', row=9, column=1, **pref)
fglen1_2_ent.grid(sticky='we', row=9, column=2, **pref)
get_size1_but.grid(sticky='we', row=10, column=2, **pref)
#grp_grids.columnconfigure(0, weight=9)
#grp_grids.columnconfigure(1, weight=1)
apbs_mode_ent = Pmw.OptionMenu(grp_apbs, labelpos='w',
label_text='APBS mode: ',
menubutton_textvariable=self.apbs_mode,
menubutton_width=10,
items=['lpbe', 'npbe'])
solvent_die_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='Solvent eps :',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_sdie,
entry_width=10)
solute_die_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='Molecule 0/1 eps: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_pdie,
entry_width=10)
ion1_charge_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='Ion(1) charge: ',
validate={'validator': 'integer', 'min': -2},
entry_textvariable=self.apbs_ion_charge[0],
entry_width=5)
ion1_conc_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='conc.: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_ion_conc[0],
entry_width=5)
ion1_rad_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='radius: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_ion_radius[0],
entry_width=5)
ion2_charge_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='Ion(2) charge: ',
validate={'validator': 'integer', 'min': -2},
entry_textvariable=self.apbs_ion_charge[1],
entry_width=5)
ion2_conc_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='conc.: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_ion_conc[1],
entry_width=5)
ion2_rad_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='radius: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_ion_radius[1],
entry_width=5)
sdens_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='Surf. sphere density: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_sdens, entry_width=5)
srad_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='Solvent radius: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_srad, entry_width=5)
swin_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='Spline window: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_swin, entry_width=5)
temp_ent = Pmw.EntryField(grp_apbs, labelpos='w',
label_text='Temperature: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.apbs_temp, entry_width=5)
bcfl_ent = Pmw.OptionMenu(grp_apbs, labelpos='w',
label_text='Boundary condition: ',
menubutton_textvariable=self.apbs_bcfl,
menubutton_width=5,
items=['sdh', 'zero', 'mdh', 'focus'])
chgm_ent = Pmw.OptionMenu(grp_apbs, labelpos='w',
label_text='Charge mapping: ',
menubutton_textvariable=self.apbs_chgm,
menubutton_width=5,
items=['spl2', 'spl0', 'spl4'])
srfm_ent = Pmw.OptionMenu(grp_apbs, labelpos='w',
label_text='Diel. surf. calc. method: ',
menubutton_textvariable=self.apbs_srfm,
menubutton_width=5,
items=['smol', 'mol', 'spl2', 'spl4'])
run_apbs_but = Tkinter.Button(page,
text="Run APBS to generate grids",
command=self.runAPBS)
solvent_die_ent.grid(sticky='we', row=0, column=0, **pref)
solute_die_ent.grid(sticky='we', row=1, column=0, **pref)
sdens_ent.grid(sticky='we', row=2, column=0, **pref)
srad_ent.grid(sticky='we', row=3, column=0, **pref)
swin_ent.grid(sticky='we', row=4, column=0, **pref)
temp_ent.grid(sticky='we', row=5, column=0, **pref)
ion1_charge_ent.grid(sticky='we', row=6, column=0, **pref)
ion1_conc_ent.grid(sticky='we', row=6, column=1, **pref)
ion1_rad_ent.grid(sticky='we', row=6, column=2, **pref)
ion2_charge_ent.grid(sticky='we', row=7, column=0, **pref)
ion2_conc_ent.grid(sticky='we', row=7, column=1, **pref)
ion2_rad_ent.grid(sticky='we', row=7, column=2, **pref)
apbs_mode_ent.grid(sticky='we', row=0, column=1, columnspan=2, **pref)
bcfl_ent.grid(sticky='we', row=1, column=1, columnspan=2, **pref)
chgm_ent.grid(sticky='we', row=2, column=1, columnspan=2, **pref)
srfm_ent.grid(sticky='we', row=3, column=1, columnspan=2, **pref)
run_apbs_but.grid(sticky='e', row=8, column=4, **pref)
page.columnconfigure(0, weight=1)
page.columnconfigure(1, weight=1)
###############################
# Tab: Reaction criteria setup
###############################
page = self.notebook.add('Reaction citeria')
grp_rxn = Tkinter.LabelFrame(page, text='Setup reaction criteria')
grp_rxn.grid(sticky='eswn', row=0, column=0, columnspan=2, **pref)
contacts_ent = Pmw.EntryField(grp_rxn,
label_text='Contacts file:', labelpos='w',
entry_textvariable=self.contacts_f, entry_width=50)
contacts_but = Tkinter.Button(grp_rxn, text='Browse...',
command=self.getContacts)
def_contacts_but = Tkinter.Checkbutton(grp_rxn,
text='or use default contacts file ',
variable=self.default_contacts_f,
onvalue=True, offvalue=False)
rxn_distance_ent = Pmw.EntryField(grp_rxn, labelpos='wn',
label_text='Reaction distance: ',
# value=self.rxn_distance.get(),
validate={'validator': 'real', 'min': 0.01},
entry_textvariable=self.rxn_distance,
entry_width=10)
npairs_ent = Pmw.EntryField(grp_rxn, labelpos='wn',
label_text='Number of reaction pairs: ',
# value=self.npairs.get(),
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.npairs, entry_width=10)
run_rxn_crit = Tkinter.Button(page, text="Create reaction files",
command=self.runRxnCrit)
contacts_ent.grid(sticky='we', row=0, column=0, **pref)
contacts_but.grid(sticky='e', row=0, column=1, **pref)
def_contacts_but.grid(sticky='e', row=0, column=2, **pref)
rxn_distance_ent.grid(sticky='we', row=1, column=0, **pref)
npairs_ent.grid(sticky='we', row=2, column=0, **pref)
run_rxn_crit.grid(sticky='e', row=3, column=0, **pref)
grp_rxn.columnconfigure(0, weight=1)
page.columnconfigure(0, weight=1)
######################
# Tab: BD input files
######################
page = self.notebook.add('BD setup')
grp_bdinput = Tkinter.LabelFrame(page, text='BrownDye input file')
grp_bdinput.grid(sticky='eswn', row=0, column=0, columnspan=2, **pref)
sdie_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Solvent eps: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.sdie, entry_width=5)
debyel_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Solvent Debye length: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.debyel[0], entry_width=5)
get_debyel_but = Tkinter.Button(grp_bdinput, text='Get Debye length',
command=self.getDebyeLength)
pdie0_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Molecule 0 eps: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.pdie[0], entry_width=5)
pdie1_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Molecule 1 eps: ',
validate={'validator': 'real', 'min': 0.0},
entry_textvariable=self.pdie[1], entry_width=5)
ntraj_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Number of trajectories: ',
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.ntraj, entry_width=5)
nthreads_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Number of threads: ',
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.nthreads, entry_width=5)
mindx_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Time step tolerance: ',
validate={'validator': 'real', 'min': 0.01},
entry_textvariable=self.mindx, entry_width=5)
ntrajo_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Number of trajectories per output: ',
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.ntrajo, entry_width=5)
ncopies_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Number of copies: ',
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.ncopies, entry_width=5)
nbincopies_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Number of bin copies: ',
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.nbincopies,
entry_width=5)
nsteps_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Number of steps: ',
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.nsteps, entry_width=5)
westeps_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Number of WE steps per output: ',
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.westeps, entry_width=5)
maxnsteps_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Max number of steps: ',
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.maxnsteps, entry_width=5)
nsteps_per_output_ent = Pmw.EntryField(grp_bdinput, labelpos='wn',
label_text='Number of steps per output: ',
validate={'validator': 'integer', 'min': 1},
entry_textvariable=self.nsteps_per_output,
entry_width=5)
prep_bd_but = Tkinter.Button(page, text="Generate BrownDye input files",
command=self.prepBD)
#self.status_bar = Pmw.MessageBar(page, entry_width=20, entry_relief='sunken',
# labelpos='w', label_text='Status:')
#self.status_bar.message('state', '')
sdie_ent.grid(sticky='we', row=1, column=0, **pref)
debyel_ent.grid(sticky='we', row=2, column=0, **pref)
get_debyel_but.grid(sticky='w', row=2, column=1, **pref)
pdie0_ent.grid(sticky='we', row=3, column=0, **pref)
pdie1_ent.grid(sticky='we', row=3, column=1, **pref)
ntraj_ent.grid(sticky='we', row=4, column=0, **pref)
nthreads_ent.grid(sticky='we', row=4, column=1, **pref)
mindx_ent.grid(sticky='we', row=5, column=0, **pref)
ntrajo_ent.grid(sticky='we', row=5, column=1, **pref)
ncopies_ent.grid(sticky='we', row=6, column=0, **pref)
nbincopies_ent.grid(sticky='we', row=6, column=1, **pref)
nsteps_ent.grid(sticky='we', row=7, column=0, **pref)
westeps_ent.grid(sticky='we', row=7, column=1, **pref)
maxnsteps_ent.grid(sticky='we', row=8, column=0, **pref)
nsteps_per_output_ent.grid(sticky='we', row=8, column=1, **pref)
prep_bd_but.grid(sticky='e', row=9, column=0, **pref)
#self.status_bar.grid(sticky='e', row=10, column=0, **pref)
grp_bdinput.columnconfigure(0, weight=1)
grp_bdinput.columnconfigure(1, weight=1)
page.columnconfigure(0, weight=1)
######################
# Tab: BD Simulation
######################
page = self.notebook.add('BD simulation')
grp_sim = Tkinter.LabelFrame(page, text='BrownDye simulation')
grp_sim.grid(sticky='eswn', row=0, column=0, columnspan=2, **pref)
bkgj_cb = Tkinter.Checkbutton(grp_sim,
text='Run job in background',
variable=self.run_in_background,
onvalue=True, offvalue=False)
run_bd_but = Tkinter.Button(grp_sim,
text="Start BrownDye simulation", command=self.runBD)
kill_bd_but = Tkinter.Button(grp_sim,
text="Stop background job", command=self.killBD)
self.msgbar1 = Pmw.MessageBar(grp_sim,
entry_width=10, entry_relief='sunken',
labelpos='w',
label_text='Trajectories: ')
self.msgbar2 = Pmw.MessageBar(grp_sim,
entry_width=10, entry_relief='sunken',
labelpos='w',
label_text='Completed / escaped / stuck events: ')
self.msgbar3 = Pmw.MessageBar(grp_sim,
entry_width=10, entry_relief='sunken',
labelpos='w',
label_text=('Calculated reaction rate '
'and probability: '))
self.logtxt_ent = Pmw.ScrolledText(grp_sim, labelpos='wn',
borderframe=5,
vscrollmode='dynamic',
hscrollmode='dynamic',
text_width=100, text_height=15,
text_wrap='none',
text_background='#000000',
text_foreground='white')
bkgj_cb.grid(sticky='w', row=0, column=0, columnspan=2, **pref)
run_bd_but.grid(sticky='we', row=1, column=0, **pref)
kill_bd_but.grid(sticky='we', row=1, column=1, **pref)
self.msgbar1.grid(sticky='we', row=2, column=0, columnspan=1, **pref)
self.msgbar2.grid(sticky='we', row=2, column=1, columnspan=1, **pref)
self.msgbar3.grid(sticky='we', row=3, column=0, columnspan=2, **pref)
self.logtxt_ent.grid(sticky='we', row=4, column=0, columnspan=2, **pref)
grp_sim.columnconfigure(0, weight=1)
grp_sim.columnconfigure(1, weight=1)
page.columnconfigure(0, weight=1)
######################
# Tab: Analysis
######################
page = self.notebook.add('Analysis')
grp_analysis = Tkinter.LabelFrame(page, text='Analysis and Visualization')
grp_analysis.grid(sticky='eswn', row=0, column=0, **pref)
load_traj_ent = Pmw.EntryField(grp_analysis,
label_text='Select trajectory file: ',
labelpos='w',
entry_textvariable=self.traj_f,
entry_width=20)
load_traj_but = Tkinter.Button(grp_analysis, text='Browse...',
command=self.loadTrajectoryFile)
analyze_but = Tkinter.Button(grp_analysis, text='Analyze',
command=self.analyzeTrajectoryFile)
self.msg_ent = Pmw.ScrolledText(grp_analysis, labelpos='wn',
borderframe=5,
vscrollmode='dynamic',
hscrollmode='dynamic',
text_width=80, text_height=10,
text_wrap='word',
text_background='#000000',
text_foreground='white')
self.index_list = [None]
self.dialog_idx = Pmw.SelectionDialog(page,
title='Trajectory index',
buttons=('OK', 'Cancel'),
defaultbutton='OK',
scrolledlist_labelpos='n',
label_text='Select trajectory',
scrolledlist_items=self.index_list,
command=self.selectTrajIndex)
self.dialog_idx.withdraw()
select_index_but = Tkinter.Button(grp_analysis, text='Select trajectory index',
command=self.dialog_idx.activate)
self.msgbar_idx = Pmw.MessageBar(grp_analysis,
entry_width=20, entry_relief='sunken',
labelpos='w',
label_text='Selected trajectory: ')
convert_but = Tkinter.Button(grp_analysis, text='Convert to xyz trajectory',
command=self.convertTrajectoryToXYZ)
load_xyztraj_but = Tkinter.Button(grp_analysis, text='Load xyz trajectory',
command=self.loadTrajectoryFileXYZ)
load_traj_ent.grid(sticky='we', row=0, column=0, **pref)
load_traj_but.grid(sticky='w', row=0, column=1, **pref)
analyze_but.grid(sticky='w', row=0, column=2, **pref)
self.msg_ent.grid(sticky='we', row=1, column=0, columnspan=3, **pref)
select_index_but.grid(sticky='we', row=2, column=0, **pref)
self.msgbar_idx.grid(sticky='we', row=2, column=1, **pref)
#traj_index_n_ent.grid(sticky='we', row=3, column=0, **pref)
convert_but.grid(sticky='we', row=4, column=0, **pref)
load_xyztraj_but.grid(sticky='we', row=5, column=0, **pref)
grp_analysis.columnconfigure(0, weight=1)
page.columnconfigure(0, weight=1)
#############
# Tab: About
#############
page = self.notebook.add('About')
grp_about = Tkinter.LabelFrame(page, text='About BrownDyeTools Plugin for PyMOL')
# grp_about.grid(sticky='n', row=0, column=0, columnspan=2, **pref)
grp_about.pack(fill='both', expand=True, **pref)
about_plugin = ("""
This plugin provides a GUI for setting up and running Brownian
dynamics simulations with BrownDye.