"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pmg_tk/startup/apbs_tools.py" between
pymol-v1.8.6.0.tar.bz2 and pymol-v2.1.0.tar.bz2

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

apbs_tools.py  (pymol-v1.8.6.0.tar.bz2)	:	apbs_tools.py  (pymol-v2.1.0.tar.bz2)
skipping to change at line 148		skipping to change at line 148
INCLUDEWEBAPBS = False		INCLUDEWEBAPBS = False
DEBUG = 0		DEBUG = 0
APBS_DEFAULT=True		APBS_DEFAULT=True
import tempfile		import tempfile
import os,math,re		import os,math,re
import string		import string
		import sys
try:		if sys.version_info[0] < 3:
import Tkinter		import Tkinter
from Tkinter import *		from Tkinter import *
except ImportError:		else:
import tkinter as Tkinter		import tkinter as Tkinter
from tkinter import *		from tkinter import *
import Pmw		import Pmw
import distutils.spawn # used for find_executable		import distutils.spawn # used for find_executable
import traceback		import traceback
import pymol		import pymol
#		#
# Global config variables		# Global config variables
skipping to change at line 175		skipping to change at line 176
# APBS_BINARY_LOCATION = '/opt/bin/'		# APBS_BINARY_LOCATION = '/opt/bin/'
#		#
APBS_BINARY_LOCATION = None # corresponding environment variable: APBS_BINARY_DI R		APBS_BINARY_LOCATION = None # corresponding environment variable: APBS_BINARY_DI R
APBS_WEB_LOCATION = None # corresponding environment variable: APBS_WEB_DIR		APBS_WEB_LOCATION = None # corresponding environment variable: APBS_WEB_DIR
APBS_PSIZE_LOCATION = None # corresponding environment variable: APBS_PSIZE_DIR		APBS_PSIZE_LOCATION = None # corresponding environment variable: APBS_PSIZE_DIR
APBS_PDB2PQR_LOCATION = None # corresponding environment variable: APBS_PDB2PQR_ DIR		APBS_PDB2PQR_LOCATION = None # corresponding environment variable: APBS_PDB2PQR_ DIR
TEMPORARY_FILE_DIR = tempfile.gettempdir() # corresponding environment variable: TEMP		TEMPORARY_FILE_DIR = tempfile.gettempdir() # corresponding environment variable: TEMP
apbs_plea = ("IMPORTANT REQUEST: If you have not already done so, please registe r\n"		apbs_plea = ("IMPORTANT REQUEST: If you have not already done so, please registe r\n"
"your use of the open-source Adaptive Poisson-Boltzmann Solver (APB S) at\n"		"your use of the open-source Adaptive Poisson-Boltzmann Solver (APB S) at\n"
"-> http://www.poissonboltzmann.org/apbs/downloads\n"		"-> http://www.poissonboltzmann.org/\n"
"Such proof of usage is vital in securing funding for APBS developm ent!\n")		"Such proof of usage is vital in securing funding for APBS developm ent!\n")
pdb2pqr_plea = ("IMPORTANT REQUEST: If you have not already done so, please regi ster\n"		pdb2pqr_plea = ("IMPORTANT REQUEST: If you have not already done so, please regi ster\n"
"your use of the open-source PDB2PQR at\n"		"your use of the open-source PDB2PQR at\n"
"-> http://www.poissonboltzmann.org/pdb2pqr/d\n"		"-> http://www.poissonboltzmann.org/\n"
"Such proof of usage is vital in securing funding for PDB2PQR devel opment!\n")		"Such proof of usage is vital in securing funding for PDB2PQR devel opment!\n")
global apbs_message, pdb2pqr_message		global apbs_message, pdb2pqr_message
apbs_message = """You must have APBS installed on your system."""		apbs_message = """You must have APBS installed on your system."""
pdb2pqr_message = """PDB2PQR can be used to generate .PQR files."""		pdb2pqr_message = """PDB2PQR can be used to generate .PQR files."""
def get_default_location(name):		def get_default_location(name):
"""		"""
Given the name of an APBS-related binary, look in		Given the name of an APBS-related binary, look in
* pymol path,		* pymol path,
* freemol path,		* freemol path,
skipping to change at line 1098		skipping to change at line 1099
good = self._generatePymolPqrFile()		good = self._generatePymolPqrFile()
if not good:		if not good:
if DEBUG:		if DEBUG:
print("Could not generate the PyMOL-basd PQR file. generate PyMOLPqrFile failed.")		print("Could not generate the PyMOL-basd PQR file. generate PyMOLPqrFile failed.")
return False		return False
if DEBUG: print("GENERATED")		if DEBUG: print("GENERATED")
return True		return True
def execute(self, result, refocus=True):		def execute(self, result, refocus=True):
if result == 'Register APBS Use':		if result == 'Register APBS Use':
import webbrowser		import webbrowser
webbrowser.open("http://www.poissonboltzmann.org/docs/apbs-registrat ion/")		webbrowser.open("http://www.poissonboltzmann.org/")
elif result == 'Register PDB2PQR Use':		elif result == 'Register PDB2PQR Use':
import webbrowser		import webbrowser
webbrowser.open("http://www.poissonboltzmann.org/docs/apbs-registrat ion/")		webbrowser.open("http://www.poissonboltzmann.org/")
elif result == 'Run APBS':		elif result == 'Run APBS':
good = self.generateApbsInputFile()		good = self.generateApbsInputFile()
if not good:		if not good:
if DEBUG:		if DEBUG:
print("ERROR: Something went wrong trying to generate the AP BS input file.")		print("ERROR: Something went wrong trying to generate the AP BS input file.")
return False		return False
# START		# START
good = self.generatePqrFile()		good = self.generatePqrFile()
if not good:		if not good:
return False		return False
End of changes. 7 change blocks.
6 lines changed or deleted		7 lines changed or added

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