def main(args):
print_title("create-calendar", "Creates Persian calendar note-book template",
"1.0", "2019", "*****@*****.**", "GPLv3+", True)
day_pattern = ('تاریخ: {}/{}/{} {}\nعنوان: {}\nبرنامه: ' +
'\nگزارش: \nبرآیند: \nتوضیحات: \n\n')
month_pattern = '\n\n {} {}\n\n\n'
month_names = ['فروردین', 'اردیبهشت', 'خرداد', 'تیر', 'مرداد', 'شهریور',
'مهر', 'آبان', 'آذر', 'دی', 'بهمن', 'اسفند']
day_names = ['شنبه', 'یکشنبه', 'دوشنبه',
'سهشنبه', 'چهارشنبه', 'پنجشنبه', 'جمعه']
day = 1
month = 1
days = 365
year = 1400
index = 1
day_name = 1
file_path = '{}.txt'.format(year)
with open(file_path, 'w') as f:
for i in range(index, index + days):
if day == 1:
f.write(month_pattern.format(
month_names[month - 1],
convert_num_to_persian_str(year)))
f.write(day_pattern.format(
convert_num_to_persian_str(year),
convert_num_to_persian_str(month),
convert_num_to_persian_str(day),
day_names[day_name],
convert_num_to_persian_str(i)))
day += 1
day_name += 1
if day_name > 6:
day_name = 0
if (month < 7 and day > 31) or (month > 6 and day > 30):
day = 1
month += 1
if month > 12:
month = 1
Year += 1
print('\033[1mOutput: \033[1;35m{}\033[0m'.format(file_path))
return 0
parser.add_option("-i", dest="inputfile", type='string',
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 = '2.0'
print_title('MCPB.py', version)
options.step = options.step.lower()
# Default values
addres = []
addbpairs = []
anglefc_avg = 0
bondfc_avg = 0
chgfix_resids = []
cutoff = 2.8
if ambv < 12:
raise pymsmtError('Only support AmberTools12 or higher version!')
elif ambv in [12, 13]:
ff_choice = 'ff12SB'
else:
parser.add_option("-i", dest="inputfile", type='string',
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'
print_title('MCPB.py', version)
options.step = options.step.lower()
# Default values
cutoff = 2.8
addres = []
addbpairs = []
chgfix_resids = []
naamol2fs = []
ff_choice = 'ff14SB'
gaff = 1
frcmodfs = []
gname = 'MOL'
g0x = 'g03'
ioninfo = []
sqmopt = 0
(with metal ion and ligating residues).
"""
from __future__ import print_function
from msmtmol.readpdb import get_atominfo_fpdb, writepdbatm
from msmtmol.element import METAL_PDB, CoRadiiDict, resdict
from msmtmol.mol import pdbatm
from msmtmol.cal import calc_bond, det_geo
from optparse import OptionParser
from 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',
print(" HFE=%6.1f (Kcal/mol), IOD=%5.2f (Angstrom), CN=%3.1f" %
(dG, iod, cn))
print(" Exp:HFE=%6.1f (Kcal/mol), IOD=%5.2f (Angstrom)" %
(HFE_VAL, IOD_VAL))
#----------------------------------------------------------------------------#
# Main Program #
#----------------------------------------------------------------------------#
parser = OptionParser("Usage: IPMach.py -i inputfile")
parser.add_option("-i", dest="inputf", type='string', help="Input file name")
(options, args) = parser.parse_args()
# Print the title of the program
version = '1.0-beta'
print_title('IPMach.py', version)
#---------------------------Default values------------------------------------
# About the program and steps of TI running
prog = 'sander'
cpus = 2
gpus = 0
mode = 'normal'
TIsteps = 2
rev = 1
ti_windows = 7
ti_vdw_windows = 3
ti_chg_windows = 7
# About the running type
parser = OptionParser("Usage: espgen.py -i input_file -o output_file "
"[-v software]")
parser.set_defaults(softversion='gau')
parser.add_option("-i",
dest="inputfile",
type='string',
help="Input file name")
parser.add_option("-o",
dest="outputfile",
type='string',
help="Output file name")
parser.add_option("-v",
dest="softversion",
type='string',
help="Software version [Default is gau (means Gaussian), \n"
" other option is gms (means GAMESS-US)]")
(options, args) = parser.parse_args()
# Print the title of the program
version = '1.0'
print_title('espgen.py', version)
if options.softversion == 'gau':
get_esp_from_gau(options.inputfile, options.outputfile)
elif options.softversion == 'gms':
get_esp_from_gms(options.inputfile, options.outputfile)
quit()
default=False,
help="Make averge of Urey-Bradley force constants based on "
"different ways of chosing sub Hessian matrices using "
"Seminario method.")
parser.add_option("--aavg",
dest="aavg",
action="store_true",
default=False,
help="Make averge of bond force constants based on "
"different ways of chosing sub Hessian matrices using "
"Seminario method.")
(options, args) = parser.parse_args()
# Print the title of the program
version = '2.0'
print_title('CartHess2FC.py', version)
# Not suport combinations
if options.softv == 'gms' and options.method == 'Z':
raise pymsmtErorr("Don\'t support Z-matrix method using GAMESS-US in "
"current verison!")
avg = options.bavg or options.avg13 or options.aavg
if avg is True and options.method == 'Z':
raise pymsmtError("Make average of force constants are not applicable "
"to Z-matrix method.")
# Get the molecular information from the PDB file
mol, atids, resids = get_atominfo_fpdb(options.pdbf)
help="The metal ion complex model chosen to calculate the "
"sum of unsigned average errors of bond lengths, angles, "
"and dihedrals (the units of them are angstrom, degree and "
"degree respectively while the weights of them are 1/100, "
"1/2 and 1 respectively). This sum is the criterion for the "
"optimization (with a smaller value, better the "
"parameters). The options are: 1 or 2. "
"1 means a small model (only contains the metal ion and "
"binding heavy atoms) while 2 means a big (contains the "
"metal ion and heavy atoms in the ligating residues). "
"[Default: 1]")
(options, args) = parser.parse_args()
# Print the title of the program
version = '1.1'
print_title('OptC4.py', version)
#lowercase the input variables
options.simupha = options.simupha.lower()
options.minm = options.minm.lower()
options.platf = options.platf.lower()
#Get the metal center information from prmtop and coordinate files
prmtop, mol, atids, resids = read_amber_prm(options.pfile, options.cfile)
mask = AmberMask(prmtop, options.ion_mask)
blist = get_blist(mol, atids)
all_list = get_all_list(mol, blist, atids, 8.0)
alist = all_list.anglist
dlist = all_list.dihlist
dest='cutoff',
help="Optional. The cut off value used to detect the bond "
"between metal ion and ligating atoms. The unit is "
"Angstroms. If there is no value specified, the "
"default algorithm will be used. The default algorithm "
"recognizes the bond when its distance is no less than "
"0.1 (smaller than 0.1 usually indicates a low quality "
"structure) and no bigger than the covalent radius sum "
"of the two atoms with a tolerance of 0.4.")
(options, args) = parser.parse_args()
#==============================================================================
# Print the title
#==============================================================================
version = '1.0'
print_title('PdbSearcher.py', version)
#==============================================================================
# Read in th pdb file names from input file
#==============================================================================
#pdb file name list
pdbfnl = []
#read the input file list
fp = open(options.inputf, 'r')
for line in fp:
line = line.strip('\n').strip()
pdbfnl.append(line)
fp.close()
#==============================================================================
iod, cn = get_IOD()
print("This result of this cycle:")
print(" Rmin/2=%5.3f (Angstrom), ep=%10.8f (Kcal/mol)" %(ion1.rmin, ion1.ep))
print(" HFE=%6.1f (Kcal/mol), IOD=%5.2f (Angstrom), CN=%3.1f" %(dG, iod, cn))
print(" Exp:HFE=%6.1f (Kcal/mol), IOD=%5.2f (Angstrom)" %(HFE_VAL, IOD_VAL))
#----------------------------------------------------------------------------#
# Main Program #
#----------------------------------------------------------------------------#
parser = OptionParser("usage: -i inputfile")
parser.add_option("-i", dest="inputf", type='string',
help="Input file name")
(options, args) = parser.parse_args()
print_title('IPMach.py', 1.0)
#---------------------------Default values------------------------------------
# About the program and steps of TI running
prog = 'sander'
cpus = 2
gpus = 0
mode = 'normal'
TIsteps = 2
rev = 1
ti_windows = 7
ti_vdw_windows = 3
ti_chg_windows = 7
# About the running type