inputs
project name, the name of the project. a directory will be created in current dir
structure(s) only proteins!
index file (needed to center the protein)
index group (to center on)
mutations (optional)
protonation states (optional)
'''
#assuming we are in project dir
parser =ArgumentParser()
parser.add_argument("protein",help="A pdb file of your protein structure")
parser.add_argument("indexGroup",help="The index group to center the protein to the center of the simulation box",type=int)
parser.add_argument("-index",help="A gromacs ndx file")
parser.add_argument("-m --mutations",help="mutations that we want to perform")
parser.add_argument("--ph",help="the ph value to start this system with",choices=glicTools.phChoices)
args = parser.parse_args()
print args
protonationStates=None
if args.ph:
protonationStates = glicTools.getProtonationSelections(args.protein,args.ph)
runMembed(args,protonationString=protonationStates)
from lib.membrane import pdb2gmxOptions, injectLinesIntoTop
from lib.pdb_util import findAllAminoAcidLines
from lib.util import MDToolsDirectories
parser = ArgumentParser()
parser.add_argument("proteins",
help="protein files, accepts wildcard selections only")
#defult ph 7
parser.add_argument("--ph",help="the ph value to start this system with",choices=glicTools.phChoices)
args = parser.parse_args()
protonationString=None
if args.ph:
protonationString = glicTools.getProtonationSelections(args.proteins,args.ph)
#copy in itp files
membrane.copyItpFiles()
path = os.path.abspath(args.proteins)
os.chdir("confs")
files = glob.glob(path)
files = sorted_nicely(set(files))
