def cleanUp():
# Delete any input/output files from a last run because if these are still hanging around from
# last time they can really screw things up
goToSandbox()
# Remove the input files
tempfiles = glob.glob("*input")
for tempfile in tempfiles:
os.remove(tempfile)
# Remove the output files
tempfiles = glob.glob("*output")
for tempfile in tempfiles:
os.remove(tempfile)
tempfiles = glob.glob("*temp")
for tempfile in tempfiles:
try:
os.remove(tempfile)
except:
pass
# Remove the sandbox PDBs
tempfiles = glob.glob("*.pdb")
for tempfile in tempfiles:
os.remove(tempfile)
# Remove the progress files
tempfiles = glob.glob("*progress")
for tempfile in tempfiles:
os.remove(tempfile)
# Remove the sandbox archives
tempfiles = glob.glob("*.ensb")
for tempfile in tempfiles:
os.remove(tempfile)
def cleanUp():
# Delete any input/output files from a last run because if these are still hanging around from
# last time they can really screw things up
goToSandbox()
# Remove the input files
tempfiles = glob.glob("*input")
for tempfile in tempfiles:
os.remove(tempfile)
# Remove the output files
tempfiles = glob.glob("*output")
for tempfile in tempfiles:
os.remove(tempfile)
tempfiles = glob.glob("*temp")
for tempfile in tempfiles:
try:
os.remove(tempfile)
except:
pass
# Remove the sandbox PDBs
tempfiles = glob.glob("*.pdb")
for tempfile in tempfiles:
os.remove(tempfile)
# Remove the progress files
tempfiles = glob.glob("*progress")
for tempfile in tempfiles:
os.remove(tempfile)
# Remove the sandbox archives
tempfiles = glob.glob("*.ensb")
for tempfile in tempfiles:
os.remove(tempfile)
def importModules(wxpython=False):
# This is a function for finding and importing modules
# Sometimes the extra Python packages get installed in weird places, most especially on OSX
# For Windows, everything is packaged into that Python install so we shouldn't have problems on Windows
# First let's find out if PYROSETTA_DATABASE is set, and figure out what it should be if not
if (not (wxpython)):
try:
# Is PYROSETTA_DATABASE defined?
# If not, then we don't know where PyRosetta is and have to look for it
s = os.environ["PYROSETTA_DATABASE"]
if (len(s) == 0):
raise Exception
except:
# Let's find it
# Did we find it already and save it?
if (platform.system() == "Windows"):
cfgfile = os.path.expanduser(
"~") + "/InteractiveROSETTA/seqwindow.cfg"
else:
cfgfile = os.path.expanduser(
"~") + "/.InteractiveROSETTA/seqwindow.cfg"
try:
f = open(cfgfile.strip(), "r")
rosettadir = "Not Found"
rosettadb = "Not Found"
for aline in f:
if ("[ROSETTAPATH]" in aline):
rosettapath = aline.split("\t")[1].strip()
if ("[ROSETTADB]" in aline):
rosettadb = aline.split("\t")[1].strip()
f.close()
if (rosettapath == "Not Found"):
# It wasn't saved there
raise Exception
else:
# Let's try this saved path
# On Windows you have to cd to where the folder is to import, because appending to the
# path does not appear to work
sys.path.append(rosettapath)
if (platform.system() == "Windows"):
olddir = os.getcwd()
os.chdir(rosettapath)
os.environ["PYROSETTA_DATABASE"] = rosettadb
if (platform.system() == "Windows"):
olddir = os.getcwd()
os.chdir(olddir)
except:
# We didn't save it or the saved location was bad
# The error may have been the Rosetta import, which means the file needs to be closed
try:
f.close()
except:
pass
# Tell the user we're busy looking for PyRosetta
import wx
busyDlg = wx.BusyInfo(
"Searching for PyRosetta installation, please be patient..."
)
# Okay, we still didn't get it, so let's traverse the filesystem looking for it...
foundIt = False
if (platform.system() == "Windows"):
roots = ["C:\\"]
elif (platform.system() == "Darwin"):
# To avoid long searches on Mac
roots = ["/Users", "/Applications", "/"]
else:
roots = ["/"]
for root in roots:
for dpath, dnames, fnames in os.walk(root):
try:
if (platform.system() == "Windows"):
# On Windows, we expect the PyRosetta folder to have either rosetta.pyd
# or rosetta.dll in the folder
try:
indx = fnames.index("rosetta.pyd") # 64bit
except:
indx = fnames.index("rosetta.dll") # 32bit
else:
# On Mac/Linux, there should be a libmini file in the folder
# On Mac, it's libmini.dylib, on Linux it's libmini.so
indx = dnames.index("rosetta")
files = glob.glob(dpath + "/rosetta/*libmini*")
if (len(files) == 0):
raise Exception
except:
continue
# If we got this far, then we found a candidate PyRosetta folder
# Is the database in this folder also?
# It is either called "database" or "rosetta_database"
foundIt = True
rosettapath = dpath
for dname in dnames:
if ("database" in dname):
rosettadb = dpath + "/" + dname
break
break
if (foundIt):
break
busyDlg = None
if (foundIt):
# Let's try to import what we found
# Remember on Windows we have to cd
sys.path.append(rosettapath)
if (platform.system() == "Windows"):
olddir = os.getcwd()
os.chdir(rosettapath)
os.environ["PYROSETTA_DATABASE"] = rosettadb
try:
# Now let's save these paths so the next time this gets started we don't have to traverse the filesystem again
data = []
f = open(cfgfile, "r")
for aline in f:
if (not ("[ROSETTAPATH]" in aline)
and not ("[ROSETTADB]") in aline):
data.append(aline.strip())
f.close()
f = open(cfgfile, "w")
for aline in data:
f.write(aline + "\n")
f.write("[ROSETTAPATH]\t" + rosettapath.strip() + "\n")
f.write("[ROSETTADB]\t" + rosettadb.strip() + "\n")
f.close()
if (platform.system() == "Windows"):
olddir = os.getcwd()
os.chdir(olddir)
except:
# Can't find it, it's probably not installed or it's in a hidden location
print "PyRosetta cannot be found on your system!"
print "Until you install PyRosetta, you may only use InteractiveROSETTA to visualize structures in PyMOL"
exit()
# Attempt to locate other packages that may not be on the PYTHONPATH
if (platform.system() == "Windows"):
# We want to import wxPython a bit earlier than the others, to display graphics for the license agreement
# On Windows, everything should already be in the Python package, so don't try to find anything
# If there are issues, the user should reinstall InteractiveROSETTA
if (wxpython):
import wx
else:
import numpy
import pymol
import psutil
#import requests
import poster
import Bio
import openbabel
else:
if (platform.system() == "Darwin"):
# These are the standard locations for some of these things, hopefully we'll get these right away
# These are the paths that are used in the bash installer
sys.path.append(
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages"
)
sys.path.append(
"/usr/local/Cellar/open-babel/HEAD/lib/python2.7/site-packages"
)
# Again, here's the option for either importing wx only, or all the modules
if (wxpython):
modules = ["wx"]
else:
modules = [
"numpy", "pymol", "psutil", "poster", "Bio", "openbabel"
]
notfound = []
# Try to import each of the modules and keep track of which ones throw an error
for module in modules:
try:
mod = __import__(module)
except:
notfound.append(module)
# For everything that is not found, let's first see if we've saved a location and try to import from there
cwd = os.getcwd()
goToSandbox()
for module in notfound:
keyword = "[" + module.upper() + "PATH]"
f = open("seqwindow.cfg", "r")
path = "N/A"
for aline in f:
if (keyword in aline):
path = aline.split("\t")[1].strip()
break
f.close()
# Add the saved location to the path
sys.path.append(path)
# Try to import again
try:
if (path == "N/A"):
raise Exception
mod = __import__(module)
except:
# This still didn't work, so now we have to search for it
print "Could not import " + module + "... Searching for it..."
root = "/usr/local"
foundIt = False
for dpath, dnames, fnames in os.walk(root):
# We're looking for a directory that is the name of the module, on some path that
# includes python
for dname in dnames:
if ((module in dname
and os.path.isfile(dpath + "/" + dname +
"/__init__.py"))
or module + ".py" in fnames):
if ("python3" in dpath):
# Sometimes there are duplicates for python3, and trying to import them ruins everything
break
sys.path.append(dpath)
print "Trying " + dpath.strip() + "..."
try:
# Try to import it again
mod = __import__(str(module))
# Now let's save these paths so the next time this gets started we don't have to traverse the filesystem again
data = []
f = open("seqwindow.cfg", "r")
for aline in f:
if (not (keyword in aline)):
data.append(aline.strip())
f.close()
f = open("seqwindow.cfg", "w")
for aline in data:
f.write(aline + "\n")
f.write(keyword + "\t" + dpath.strip() + "\n")
f.close()
print "Found " + module + " at " + dpath.strip(
) + "!"
foundIt = True
except:
pass
break
if (foundIt):
break
if (not (foundIt)):
# Explain how to install the packages that are missing
print module + " cannot be found on your system!"
if (module == "Bio"):
print "Install it by executing \"sudo easy_install biopython\" in a terminal."
elif (module == "openbabel"
and platform.system() == "Darwin"):
print "Install it by executing \"brew install mcs07/cheminformatics/open-babel --HEAD --with-python\" in a terminal."
elif (module == "openbabel"
and platform.system() == "Linux"):
print "Install it by executing either \"sudo apt-get install python-openbabel\" or \"sudo yum install openbabel python-openbabel\" in a terminal."
elif (module == "wx" and platform.system() == "Darwin"):
print "Download and install wxPython from here: http://www.wxpython.org/download.php, wxPython3.0-osx-cocoa-py2.7"
elif (module == "wx" and platform.system() == "Linux"):
print "Install it by executing either \"sudo apt-get install python-wxgtk2.8\" or \"sudo yum install wxPython\" in a terminal."
else:
print "Install it by executing \"sudo easy_install " + module + "\" in a terminal."
exit()
if (wxpython):
import wx
else:
import numpy
import pymol
import psutil
#import requests
import poster
import Bio
import openbabel
os.chdir(cwd)
def cleanUp():
# Delete any input/output files from a last run because if these are still hanging around from
# last time they can really screw things up
goToSandbox()
if (os.path.isfile("minimizeinput")):
os.remove("minimizeinput")
if (os.path.isfile("minimizeoutput")):
os.remove("minimizeoutput")
if (os.path.isfile("designinput")):
os.remove("designinput")
if (os.path.isfile("designoutput")):
os.remove("designoutput")
if (os.path.isfile("scoreinput")):
os.remove("scoreinput")
if (os.path.isfile("scoreoutput")):
os.remove("scoreoutput")
if (os.path.isfile("scaninput")):
os.remove("scaninput")
if (os.path.isfile("scanoutput")):
os.remove("scanoutput")
if (os.path.isfile("relaxinput")):
os.remove("relaxinput")
if (os.path.isfile("relaxoutput")):
os.remove("relaxoutput")
if (os.path.isfile("backrubinput")):
os.remove("backrubinput")
if (os.path.isfile("backruboutput")):
os.remove("backruboutput")
if (os.path.isfile("rotamerinput")):
os.remove("rotamerinput")
if (os.path.isfile("rotameroutput")):
os.remove("rotameroutput")
if (os.path.isfile("coarsekicinput")):
os.remove("coarsekicinput")
if (os.path.isfile("coarsekicoutput")):
os.remove("coarsekicoutput")
if (os.path.isfile("kicoutput")):
os.remove("kicoutput")
if (os.path.isfile("repackme.pdb")):
os.remove("repackme.pdb")
if (os.path.isfile("finekicinput")):
os.remove("finekicinput")
if (os.path.isfile("errreport")):
os.remove("errreport")
if (os.path.isfile("coarsedockinput")):
os.remove("coarsedockinput")
if (os.path.isfile("finedockinput")):
os.remove("finedockinput")
if (os.path.isfile("dockoutput")):
os.remove("dockoutput")
if (os.path.isfile("dock_progress")):
os.remove("dock_progress")
if (os.path.isfile("threadinput")):
os.remove("threadinput")
if (os.path.isfile("threadoutput")):
os.remove("threadoutput")
tempfiles = glob.glob("*temp")
for tempfile in tempfiles:
try:
os.remove(tempfile)
except:
pass
# Remove the sandbox PDBs
tempfiles = glob.glob("*.pdb")
for tempfile in tempfiles:
os.remove(tempfile)
# Remove the progress files
tempfiles = glob.glob("*progress")
for tempfile in tempfiles:
os.remove(tempfile)
# Remove the sandbox archives
tempfiles = glob.glob("*.ensb")
for tempfile in tempfiles:
os.remove(tempfile)
def importModules(wxpython=False):
# This is a function for finding and importing modules
# Sometimes the extra Python packages get installed in weird places, most especially on OSX
# For Windows, everything is packaged into that Python install so we shouldn't have problems on Windows
# First let's find out if PYROSETTA_DATABASE is set, and figure out what it should be if not
if (not(wxpython)):
try:
# Is PYROSETTA_DATABASE defined?
# If not, then we don't know where PyRosetta is and have to look for it
s = os.environ["PYROSETTA_DATABASE"]
if (len(s) == 0):
raise Exception
except:
# Let's find it
# Did we find it already and save it?
cfgfile = os.path.expanduser("~") + "/InteractiveROSETTA/seqwindow.cfg"
try:
f = open(cfgfile.strip(), "r")
rosettadir = "Not Found"
rosettadb = "Not Found"
for aline in f:
if ("[ROSETTAPATH]" in aline):
rosettapath = aline.split("\t")[1].strip()
if ("[ROSETTADB]" in aline):
rosettadb = aline.split("\t")[1].strip()
f.close()
if (rosettapath == "Not Found"):
# It wasn't saved there
raise Exception
else:
# Let's try this saved path
# On Windows you have to cd to where the folder is to import, because appending to the
# path does not appear to work
sys.path.append(rosettapath)
if (platform.system() == "Windows"):
olddir = os.getcwd()
os.chdir(rosettapath)
os.environ["PYROSETTA_DATABASE"] = rosettadb
if (platform.system() == "Windows"):
olddir = os.getcwd()
os.chdir(olddir)
except:
# We didn't save it or the saved location was bad
# The error may have been the Rosetta import, which means the file needs to be closed
try:
f.close()
except:
pass
# Tell the user we're busy looking for PyRosetta
import wx
busyDlg = wx.BusyInfo("Searching for PyRosetta installation, please be patient...")
# Okay, we still didn't get it, so let's traverse the filesystem looking for it...
foundIt = False
if (platform.system() == "Windows"):
roots = ["C:\\"]
elif (platform.system() == "Darwin"):
# To avoid long searches on Mac
roots = ["/Users", "/Applications", "/"]
else:
roots = ["/"]
for root in roots:
for dpath, dnames, fnames in os.walk(root):
try:
if (platform.system() == "Windows"):
# On Windows, we expect the PyRosetta folder to have either rosetta.pyd
# or rosetta.dll in the folder
try:
indx = fnames.index("rosetta.pyd") # 64bit
except:
indx = fnames.index("rosetta.dll") # 32bit
else:
# On Mac/Linux, there should be a libmini file in the folder
# On Mac, it's libmini.dylib, on Linux it's libmini.so
indx = dnames.index("rosetta")
files = glob.glob(dpath + "/rosetta/*libmini*")
if (len(files) == 0):
raise Exception
except:
continue
# If we got this far, then we found a candidate PyRosetta folder
# Is the database in this folder also?
# It is either called "database" or "rosetta_database"
foundIt = True
rosettapath = dpath
for dname in dnames:
if ("database" in dname):
rosettadb = dpath + "/" + dname
break
break
if (foundIt):
break
busyDlg = None
if (foundIt):
# Let's try to import what we found
# Remember on Windows we have to cd
sys.path.append(rosettapath)
if (platform.system() == "Windows"):
olddir = os.getcwd()
os.chdir(rosettapath)
os.environ["PYROSETTA_DATABASE"] = rosettadb
try:
# Now let's save these paths so the next time this gets started we don't have to traverse the filesystem again
data = []
f = open(cfgfile, "r")
for aline in f:
if (not("[ROSETTAPATH]" in aline) and not("[ROSETTADB]") in aline):
data.append(aline.strip())
f.close()
f = open(cfgfile, "w")
for aline in data:
f.write(aline + "\n")
f.write("[ROSETTAPATH]\t" + rosettapath.strip() + "\n")
f.write("[ROSETTADB]\t" + rosettadb.strip() + "\n")
f.close()
if (platform.system() == "Windows"):
olddir = os.getcwd()
os.chdir(olddir)
except:
# Can't find it, it's probably not installed or it's in a hidden location
print "PyRosetta cannot be found on your system!"
print "Until you install PyRosetta, you may only use InteractiveROSETTA to visualize structures in PyMOL"
exit()
# Attempt to locate other packages that may not be on the PYTHONPATH
if (platform.system() == "Windows"):
# We want to import wxPython a bit earlier than the others, to display graphics for the license agreement
# On Windows, everything should already be in the Python package, so don't try to find anything
# If there are issues, the user should reinstall InteractiveROSETTA
if (wxpython):
import wx
else:
import numpy
import pymol
import psutil
import requests
import poster
import Bio
import openbabel
else:
if (platform.system() == "Darwin"):
# These are the standard locations for some of these things, hopefully we'll get these right away
# These are the paths that are used in the bash installer
sys.path.append("/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages")
sys.path.append("/usr/local/Cellar/open-babel/HEAD/lib/python2.7/site-packages")
# Again, here's the option for either importing wx only, or all the modules
if (wxpython):
modules = ["wx"]
else:
modules = ["numpy", "pymol", "psutil", "requests", "poster", "Bio", "openbabel"]
notfound = []
# Try to import each of the modules and keep track of which ones throw an error
for module in modules:
try:
mod = __import__(module)
except:
notfound.append(module)
# For everything that is not found, let's first see if we've saved a location and try to import from there
cwd = os.getcwd()
goToSandbox()
for module in notfound:
keyword = "[" + module.upper() + "PATH]"
f = open("seqwindow.cfg", "r")
path = "N/A"
for aline in f:
if (keyword in aline):
path = aline.split("\t")[1].strip()
break
f.close()
# Add the saved location to the path
sys.path.append(path)
# Try to import again
try:
if (path == "N/A"):
raise Exception
mod = __import__(module)
except:
# This still didn't work, so now we have to search for it
print "Could not import " + module + "... Searching for it..."
root = "/usr/local"
foundIt = False
for dpath, dnames, fnames in os.walk(root):
# We're looking for a directory that is the name of the module, on some path that
# includes python
for dname in dnames:
if ((module in dname and os.path.isfile(dpath + "/" + dname + "/__init__.py")) or module + ".py" in fnames):
if ("python3" in dpath):
# Sometimes there are duplicates for python3, and trying to import them ruins everything
break
sys.path.append(dpath)
print "Trying " + dpath.strip() + "..."
try:
# Try to import it again
mod = __import__(str(module))
# Now let's save these paths so the next time this gets started we don't have to traverse the filesystem again
data = []
f = open("seqwindow.cfg", "r")
for aline in f:
if (not(keyword in aline)):
data.append(aline.strip())
f.close()
f = open("seqwindow.cfg", "w")
for aline in data:
f.write(aline + "\n")
f.write(keyword + "\t" + dpath.strip() + "\n")
f.close()
print "Found " + module + " at " + dpath.strip() + "!"
foundIt = True
except:
pass
break
if (foundIt):
break
if (not(foundIt)):
# Explain how to install the packages that are missing
print module + " cannot be found on your system!"
if (module == "Bio"):
print "Install it by executing \"sudo easy_install biopython\" in a terminal."
elif (module == "openbabel" and platform.system() == "Darwin"):
print "Install it by executing \"brew install mcs07/cheminformatics/open-babel --HEAD --with-python\" in a terminal."
elif (module == "openbabel" and platform.system() == "Linux"):
print "Install it by executing either \"sudo apt-get install python-openbabel\" or \"sudo yum install openbabel python-openbabel\" in a terminal."
elif (module == "wx" and platform.system() == "Darwin"):
print "Download and install wxPython from here: http://www.wxpython.org/download.php, wxPython3.0-osx-cocoa-py2.7"
elif (module == "wx" and platform.system() == "Linux"):
print "Install it by executing either \"sudo apt-get install python-wxgtk2.8\" or \"sudo yum install wxPython\" in a terminal."
else:
print "Install it by executing \"sudo easy_install " + module + "\" in a terminal."
exit()
if (wxpython):
import wx
else:
import numpy
import pymol
import psutil
import requests
import poster
import Bio
import openbabel
os.chdir(cwd)
