def findQhullModule(modname):
"""return (platform-dependent) path to qhull module"""
if modname not in ['qconvex', 'qdelaunay', 'qhalf', 'qhull',
'qvoronoi', 'rbox']:
print 'QHULL ERROR! Illegal module name %s.'%modname
return None
try:
mod = __import__('binaries')
pth = mod.__path__[0]
except ImportError:
pth = ''
pth = os.path.join( pth, modname)
if which(pth):
#print pth
return pth
else:
#print 'QHULL ERROR! Module not found in %s'%pth
return None
def findQhullModule(modname):
"""return (platform-dependent) path to qhull module"""
if modname not in [
'qconvex', 'qdelaunay', 'qhalf', 'qhull', 'qvoronoi', 'rbox'
]:
print 'QHULL ERROR! Illegal module name %s.' % modname
return None
try:
mod = __import__('binaries')
pth = mod.__path__[0]
except ImportError:
pth = ''
pth = os.path.join(pth, modname)
if which(pth):
#print pth
return pth
else:
#print 'QHULL ERROR! Module not found in %s'%pth
return None
def getBlenderDir(self):
if self.plateform.find("linux") != -1:
dir=self.findDirectoryFrom(".blender",self.userDirectory+"/",sp=".*")
if len(dir) == 0 :
x = askdirectory(initialdir=self.userDirectory, title="where is blender script directory, ie .blender/script")
dir = x#self.softdir[2]
else :
dir = dir[0]
dir = dir.replace(" ","\ ")
self.dir[0].set(dir)
self.softdir[0] = dir
elif self.plateform == 'darwin':
dir=self.findDirectoryFrom("blender",self.progDirectory+"/")
if len(dir) == 0 :
x = askdirectory(initialdir=self.userDirectory, title="where is blender script directory, ie .blender/script")
dir = x#self.softdir[2]
self.dir[0].set(dir)
self.softdir[0] = dir
elif len(dir) == 1 :
dir = dir[0]
dir = dir.replace(" ","\ ")
self.dir[0].set(dir)
self.softdir[0] = dir
else :
self.chooseDirectory(0,dir)
elif self.plateform == 'win32':
#blender can be in Prgoram files or Application Data
#dir=self.findDirectoryFrom("Blender Foundation",self.progDirectory)
#if len(dir) == 0 :
dir=self.findDirectoryFrom("Blender Foundation",self.preferencesDir)
if len(dir) == 0 :
x = askdirectory(initialdir=self.userDirectory, title="where is the Blender Foundation directory")
dir = x
self.dir[0].set(dir)
self.softdir[0] = dir
elif len(dir) == 1 :
dir = dir[0]
# dir = dir+os.sep+"Blender"+os.sep+".blender"+os.sep
self.dir[0].set(dir)
self.softdir[0] = dir
else :
self.chooseDirectory(0,dir)
if self.automaticSearch :
t1=time.time()
self.progressbar.setLabelText('searching '+".blender")
#is blender define in path
dir=packageFilePath.which('blender')
if dir == None :
dir=self.findDirectory(".blender",self.progDirectory)
if dir is None :
dir=self.findDirectory(".blender",self.userDirectory)
if dir is None :
#dir=self.findDirectory(".blender",self.rootDirectory)
#if dir is None:
dir="not Found"
return
print "time to find", time.time()-t1
print dir
dir = dir.replace(" ","\ ")
self.dir[0].set(dir)
self.softdir[0] = dir
#$Id: msmsClient.py,v 1.3 2008/12/23 00:29:19 sargis Exp $
#
# Authors: M. Sanner and S. Dallakyan
import socket
import subprocess
import numpy
import struct
from mglutil.util.packageFilePath import getBinary, which
try:
msmsBinary = getBinary('msms','binaries')
except:
msmsBinary = None
if not msmsBinary: #msms not found in binaries
msmsBinary = which('msms')
msmsBinary = None #(un)comment this line to (not) use msmsClient instead of mslib
class MSMSClient:
def __init__(self, coords=None, radii=None, **kw):
self.coords = coords
self.radii = radii
soc = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
port = 2000
#find a free port
result = soc.connect_ex(('', port))
while not result:
port += 1
result = soc.connect_ex(('', port))
soc.close()
def __init__(self, name='Default', **kw):
"""Constructor for class APBSParams"""
from mglutil.util.packageFilePath import getBinary, findFilePath, which
if not hasattr(self,'APBS_Path'):
try:
self.APBS_Path = getBinary("apbs", 'binaries')
except ImportError:
self.APBS_Path = None
if not self.APBS_Path:
self.APBS_Path = which('apbs')
self.pdb2pqr_Path = findFilePath('pdb2pqr.py','MolKit.pdb2pqr')
self.name = name # name of the APBS Param instance
self.pdb2pqr_ForceField = 'amber'
self.calculationType = 'Electrostatic potential'
self.pbeType = 'Linearized'
self.boundaryConditions = 'Single Debye-Huckel'
self.chargeDiscretization = 'Cubic B-spline'
self.surfaceCalculation = 'Cubic B-spline'
self.sdens = 10.0
self.splineWindow = 0.3
self.molecule1Path = ''
self.molecule2Path = ''
self.complexPath = ''
self.energyOutput = 'Total'
self.forceOutput = ''
self.projectFolder = 'apbs-project'
self.chargeDistributionFile = ''
self.potentialFile = 'OpenDX'
self.solventAccessibilityFile = ''
self.splineBasedAccessibilityFile = ''
self.VDWAccessibilityFile = ''
self.ionAccessibilityFile = ''
self.laplacianOfPotentialFile = ''
self.energyDensityFile = ''
self.ionNumberFile = ''
self.ionChargeDensityFile = ''
self.xShiftedDielectricFile = ''
self.yShiftedDielectricFile = ''
self.zShiftedDielectricFile = ''
self.kappaFunctionFile = ''
#Grid parameters
self.gridPointsX = 65
self.gridPointsY = 65
self.gridPointsZ = 65
self.coarseLengthX = 40
self.coarseLengthY = 50
self.coarseLengthZ = 60
self.coarseCenterX = 0
self.coarseCenterY = 0
self.coarseCenterZ = 0
self.fineLengthX = 20
self.fineLengthY = 35
self.fineLengthZ = 30
self.fineCenterX = 0
self.fineCenterY = 0
self.fineCenterZ = 0
# Physical Parameters
self.proteinDielectric = 2.0
self.solventDielectric = 78.54
self.solventRadius = 1.4
self.systemTemperature = 298.15
self.saltConcentration = 0.01
self.ions = []
apply( self.Set, (), kw )
#$Id: msmsClient.py,v 1.3 2008/12/23 00:29:19 sargis Exp $
#
# Authors: M. Sanner and S. Dallakyan
import socket
import subprocess
import numpy
import struct
from mglutil.util.packageFilePath import getBinary, which
try:
msmsBinary = getBinary('msms', 'binaries')
except:
msmsBinary = None
if not msmsBinary: #msms not found in binaries
msmsBinary = which('msms')
msmsBinary = None #(un)comment this line to (not) use msmsClient instead of mslib
class MSMSClient:
def __init__(self, coords=None, radii=None, **kw):
self.coords = coords
self.radii = radii
soc = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
port = 2000
#find a free port
result = soc.connect_ex(('', port))
while not result:
port += 1
def __init__(self, name='Default', **kw):
"""Constructor for class APBSParams"""
from mglutil.util.packageFilePath import getBinary, findFilePath, which
if not hasattr(self,'APBS_Path'):
try:
self.APBS_Path = getBinary("apbs", 'binaries')
except ImportError:
self.APBS_Path = None
if not self.APBS_Path:
self.APBS_Path = which('apbs')
self.pdb2pqr_Path = findFilePath('pdb2pqr.py','MolKit.pdb2pqr')
self.name = name # name of the APBS Param instance
self.pdb2pqr_ForceField = 'amber'
self.calculationType = 'Electrostatic potential'
self.pbeType = 'Linearized'
self.boundaryConditions = 'Single Debye-Huckel'
self.chargeDiscretization = 'Cubic B-spline'
self.surfaceCalculation = 'Cubic B-spline'
self.sdens = 10.0
self.splineWindow = 0.3
self.molecule1Path = ''
self.molecule2Path = ''
self.complexPath = ''
self.energyOutput = 'Total'
self.forceOutput = ''
self.projectFolder = 'apbs-project'
self.chargeDistributionFile = ''
self.potentialFile = 'OpenDX'
self.solventAccessibilityFile = ''
self.splineBasedAccessibilityFile = ''
self.VDWAccessibilityFile = ''
self.ionAccessibilityFile = ''
self.laplacianOfPotentialFile = ''
self.energyDensityFile = ''
self.ionNumberFile = ''
self.ionChargeDensityFile = ''
self.xShiftedDielectricFile = ''
self.yShiftedDielectricFile = ''
self.zShiftedDielectricFile = ''
self.kappaFunctionFile = ''
#Grid parameters
self.gridPointsX = 65
self.gridPointsY = 65
self.gridPointsZ = 65
self.coarseLengthX = 40
self.coarseLengthY = 50
self.coarseLengthZ = 60
self.coarseCenterX = 0
self.coarseCenterY = 0
self.coarseCenterZ = 0
self.fineLengthX = 20
self.fineLengthY = 35
self.fineLengthZ = 30
self.fineCenterX = 0
self.fineCenterY = 0
self.fineCenterZ = 0
# Physical Parameters
self.proteinDielectric = 2.0
self.solventDielectric = 78.54
self.solventRadius = 1.4
self.systemTemperature = 298.15
self.saltConcentration = 0.01
self.ions = []
apply( self.Set, (), kw )
