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))