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
