Coverage for PyRx.utils : 23%

#$Id: utils.py 243 2015-01-25 00:56:19Z sarkiss $ 

"""util.py currently contains which() function used to show the full path of autodock. 

""" 

import os, sys, shutil 

from about import appName 

def which (filename): 

    """Source http://mail.python.org/pipermail/python-list/2002-August/157829.html""" 

    if os.access(filename, os.X_OK): 

            return filename 

    if not os.environ.has_key('PATH') or os.environ['PATH'] == '': 

        p = os.defpath 

    else: 

        p = os.environ['PATH'] 

    pathlist = p.split (os.pathsep) 

    pathlist.append(os.path.split(sys.executable)[0]) 

    for path in pathlist: 

        f = os.path.join(path, filename) 

        if os.access(f, os.X_OK): 

            return f 

    return None 

def cpuCount(): 

    ''' 

    Returns the number of CPUs in the system 

    ''' 

    num = 1 

    if sys.platform == 'win32': 

        try: 

            num = int(os.environ['NUMBER_OF_PROCESSORS']) 

        except (ValueError, KeyError): 

            pass 

    elif sys.platform == 'darwin': 

        try: 

            num = int(os.popen('sysctl -n hw.ncpu').read()) 

        except ValueError: 

            pass 

    else: 

        try: 

            num = os.sysconf('SC_NPROCESSORS_ONLN') 

        except (ValueError, OSError, AttributeError): 

            pass 

    return num 

from misc import rcFolder 

if not os.path.isdir(rcFolder): 

    try: 

        os.mkdir(rcFolder) 

    except: #in case we can't mkdir in user.home 

        from tempfile import gettempdir 

        rcFolder = gettempdir() + os.path.sep + '.' + appName 

        if not os.path.isdir(rcFolder): 

            os.mkdir(rcFolder) 

rcFile = os.path.join(rcFolder, 'preferences.ini') 

def createPreferences(): 

    global rcFile, rcFolder 

    if not os.path.exists(rcFile): 

        try: 

            shutil.copy(os.path.join(os.path.split(__file__)[0], 'preferences.ini'), rcFile) 

        except Exception, inst: 

            print inst 

            print "Please make sure that you have a write permission for "+rcFolder 

            import tempfile 

            rcFolder =tempfile.mkdtemp() 

            rcFile = os.path.join(rcFolder, 'preferences.ini') 

            shutil.copy(os.path.join(os.path.split(__file__)[0], 'preferences.ini'), rcFile) 

        txt = open(rcFile).read() 

        txt = txt.replace("workspace = .", "workspace = "+rcFolder) 

        if cpuCount()-1 > 0: 

            txt = txt.replace("cpu_num = 1", "cpu_num = "+str(cpuCount()-1)) 

        pyrx_path = os.path.split(sys.executable)[0] 

        if sys.platform == 'win32': 

            vina = os.path.join(pyrx_path, 'vina.exe') 

            autodock = os.path.join(pyrx_path, 'autodock4.exe') 

            autogrid = os.path.join(pyrx_path, 'autogrid4.exe') 

        elif sys.platform == 'darwin': 

            #./Python.framework/Versions/2.6/lib/python2.6/site-packages 

            pyrx_home = os.path.split(os.path.split(os.path.split(os.path.split(os.path.split(os.path.split(os.path.split(os.path.split(__file__)[0])[0])[0])[0])[0])[0])[0])[0] 

            vina = os.path.join(pyrx_home, 'bin', 'vina') 

            autodock = os.path.join(pyrx_home, 'bin', 'autodock4') 

            autogrid = os.path.join(pyrx_home, 'bin', 'autogrid4') 

        elif "linux" in sys.platform: 

            vina = os.path.join(pyrx_path, 'vina') 

            autodock = os.path.join(pyrx_path, 'autodock4') 

            autogrid = os.path.join(pyrx_path, 'autogrid4') 

        txt = txt.replace("vina = vina\n", "vina = "+vina+"\n") 

        txt = txt.replace("autodock = autodock4\n", "autodock = "+autodock+"\n") 

        txt = txt.replace("autogrid = autogrid4\n", "autogrid = "+autogrid+"\n") 

        open(rcFile,'w').write(txt) 

createPreferences() 

def RemoveDirs(path): 

    """source http://docs.python.org/lib/os-file-dir.html 

    Delete everything reachable from the directory named in 'top', 

    assuming there are no symbolic links. 

    CAUTION:  This is dangerous!  For example, if top == '/', it 

    could delete all your disk files.""" 

    for root, dirs, files in os.walk(path, topdown=False): 

        for name in files: 

            try: 

                os.remove(os.path.join(root, name)) 

            except OSError: 

                pass 

        for name in dirs: 

            try: 

                os.rmdir(os.path.join(root, name)) 

            except OSError: 

                pass 

    try: 

        os.removedirs(path) # added to remove path itself 

        os.rmdir(path) 

    except OSError: 

        pass