dest="logfile", type='string', help="Gaussian/GAMESS-US output logfile") parser.add_option("--fchk", dest="fchkfile", type='string', help="Gaussian fchk file") (options, args) = parser.parse_args() #============================================================================== # Get the input variables #============================================================================== # Print the title of the program version = '1.0 Beta2' release_time = 'June 26 2015' print_title('MCPB.py', version, release_time) options.step = options.step.lower() # Default values cutoff = 2.8 addres = [] chgfix_resids = [] naamol2fs = [] ff_choice = 'ff14SB' gaff = 1 frcmodfs = [] gname = 'MOL' g0x = 'g03' ioninfo = [] sqmopt = 0 largeopt = 0
** M. B. Peters, Y. Yang, B. Wang, L. Fusti-Molnar, M. N. Weaver, K. M. Merz, JCTC, 2010, 6, 2935-2947 """ from pymsmtmol.readpdb import get_atominfo_fpdb, writepdbatm from pymsmtmol.element import Metalpdb, CoRadiiDict, resdict from pymsmtmol.mol import pdbatm from pymsmtmol.cal import calc_bond, det_geo from optparse import OptionParser from mcpb.title import print_title import os #============================================================================== # Print the title #============================================================================== print_title('PdbSearcher.py') #============================================================================== # Setting the options #============================================================================== parser = OptionParser("usage: -i/--ion ionname -l/--list input_file \n" " -e/--env environment_file \n" " -s/--sum summary_file \n" " [-c/--cut cutoff]") parser.add_option("-i", "--ion", type='string', dest="ionname", help="Element symbol of ion, e.g. Zn") parser.add_option("-l",
** M. B. Peters, Y. Yang, B. Wang, L. Fusti-Molnar, M. N. Weaver, K. M. Merz, JCTC, 2010, 6, 2935-2947 """ from pymsmtmol.readpdb import get_atominfo_fpdb, writepdbatm from pymsmtmol.element import Metalpdb, CoRadiiDict, resdict from pymsmtmol.mol import pdbatm from pymsmtmol.cal import calc_bond, det_geo from optparse import OptionParser from mcpb.title import print_title import os #============================================================================== # Print the title #============================================================================== print_title('PdbSearcher.py') #============================================================================== # Setting the options #============================================================================== parser = OptionParser("usage: -i/--ion ionname -l/--list input_file \n" " -e/--env environment_file \n" " -s/--sum summary_file \n" " [-c/--cut cutoff]") parser.add_option("-i", "--ion", type='string', dest="ionname", help="Element symbol of ion, e.g. Zn") parser.add_option("-l", "--list", type='string', dest="inputf", help="List file name, list file contains one PDB file name " "per line") parser.add_option("-e", "--env", type='string', dest='envrmtf',
help="Input file name") parser.add_option("-s", "--step", dest="step", type='string', help="Step number") parser.add_option("--logf", dest="logfile", type='string', help="Gaussian/GAMESS-US output logfile") parser.add_option("--fchk", dest="fchkfile", type='string', help="Gaussian fchk file") (options, args) = parser.parse_args() #============================================================================== # Get the input variables #============================================================================== # Print the title of the program version = '1.0 Beta2' release_time = 'June 26 2015' print_title('MCPB.py', version, release_time) options.step = options.step.lower() # Default values cutoff = 2.8 addres = [] chgfix_resids = [] naamol2fs = [] ff_choice = 'ff14SB' gaff = 1 frcmodfs = [] gname = 'MOL' g0x = 'g03' ioninfo = [] sqmopt = 0 largeopt = 0