options.py

# Very simple option class
class Option:
    def __init__(self,func=str,num=1,default=None,description=""):
        self.func        = func
        self.num         = num
        self.value       = default
        self.description = description
    def __nonzero__(self): 
        return self.value != None
    def __str__(self):
        return self.value and str(self.value) or ""
    def setvalue(self,v):
        if len(v) == 1:
            self.value = self.func(v[0])
        else:
            self.value = [ self.func(i) for i in v ]


tm       = []
lipL     = []
lipU     = []
sol      = []
usrmols  = []
usrheads = []
usrtails = []
usrlinks = []



# Description
desc = ""


# Option list
options = [
#   option           type number default description
# HII edit - lipid definition (last options are for additional lipid specification)
    """
Input/output related options
""",
    ("-f",      Option(tm.append,   1,        None, "Input GRO or PDB file 1: Protein")),
    ("-o",      Option(str,         1,        None, "Output GRO file: Membrane with Protein")),
    ("-p",      Option(str,         1,        None, "Optional rudimentary topology file")),
    """
Periodic boundary conditions 
If -d is given, set up PBC according to -pbc such that no periodic
images are closer than the value given.  This will make the numbers
provided for lipids be interpreted as relative numbers. If -d is
omitted, those numbers are interpreted as absolute numbers, and the
PBC are set to fit the given number of lipids in.
""",
    ("-pbc",    Option(str,         1, "hexagonal", "PBC type: hexagonal, rectangular, square, cubic, optimal or keep")),
    ("-d",      Option(float,       1,           0, "Distance between periodic images (nm)")),
    ("-dz",     Option(float,       1,           0, "Z distance between periodic images (nm)")),
    ("-n",      Option(str,         1,        None, "Index file --- TO BE IMPLEMENTED")),
    """
Membrane/lipid related options.  
The options -l and -u can be given multiple times. Option -u can be
used to set the lipid type and abundance for the upper leaflet. Option
-l sets the type and abundance for the lower leaflet if option -u is
also given, or for both leaflets if option -u is not given. The
meaning of the number depends on whether option -d is used to set up
PBC
""",
    ("-l",      Option(lipL.append, 1,   None, "Lipid type and relative abundance (NAME[:#])")),
    ("-u",      Option(lipU.append, 1,   None, "Lipid type and relative abundance (NAME[:#])")),
    ("-a",      Option(float,       1,        0.60, "Area per lipid (nm*nm)")),
    ("-asym",   Option(int,         1,        None, "Membrane asymmetry (number of lipids)")),
    ("-hole",   Option(float,       1,        None, "Make a hole in the membrane with specified radius")),
    ("-rand",   Option(float,       1,         0.1, "Random kick size (maximum atom displacement)")),
    ("-bd",     Option(float,       1,         0.3, "Bead distance unit for scaling z-coordinates (nm)")),
    """
Protein related options.
""",
    ("-center", Option(bool,        0,        None, "Center the protein on z")),
    ("-orient", Option(bool,        0,        None, "Orient protein in membrane")),
    ("-rotate", Option(str,         0,        None, "Rotate protein (random|princ|angle(float))")),
    ("-od",     Option(float,       1,         1.0, "Grid spacing for determining orientation")),
    ("-op",     Option(float,       1,         4.0, "Hydrophobic ratio power for determining orientation")),
    ("-fudge",  Option(float,       1,         0.1, "Fudge factor for allowing lipid-protein overlap")),
    ("-ring",   Option(bool,        0,        None, "Put lipids inside the protein")),
    ("-dm",     Option(float,       1,        None, "Shift protein with respect to membrane")),
    """
Solvent related options.
""",
    ("-sol",    Option(solv.append, 1,        None, "Solvent type and relative abundance (NAME[:#])")),
    ("-sold",   Option(float,       1,         0.5, "Solvent diameter")),
    ("-solr",   Option(float,       1,         0.1, "Solvent random kick")),
    ("-excl",   Option(float,       1,         1.5, "Exclusion range (nm) for solvent addition relative to membrane center")),
    """
Salt related options.
""",
    ("-salt",   Option(str,         1,        None, "Salt concentration")),
    ("-charge", Option(str,         1,      "auto", "Charge of system. Set to auto to infer from residue names")),
    """
Define additional lipid types (same format as in lipid-martini-itp-v01.py)
""",
    ("-alname",  Option(usrmols.append,         1,        None, "Additional lipid name, x4 letter")),
    ("-alhead",  Option(usrheads.append,        1,        None, "Additional lipid head specification string")),
    ("-allink",  Option(usrlinks.append,        1,        None, "Additional lipid linker specification string")),
    ("-altail",  Option(usrtails.append,        1,        None, "Additional lipid tail specification string")),
    ]

    
args = sys.argv[1:]

if '-h' in args or '--help' in args:
    print "\n",__file__
    print desc or "\nSomeone ought to write a description for this script...\n"
    for thing in options:
        print type(thing) != str and "%10s  %s"%(thing[0],thing[1].description) or thing
    print
    sys.exit()


# Convert the option list to a dictionary, discarding all comments
options = dict([i for i in options if not type(i) == str])


# Process the command line
while args:
    ar = args.pop(0)
    options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])