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
示例#2
0
文件: MCPB.py 项目: aslyons/pymsmt
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:
示例#3
0
文件: MCPB.py 项目: pengfeili1/pymsmt
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
示例#4
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',
示例#5
0
    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
示例#6
0
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()
示例#7
0
                  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)
示例#8
0
                  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
示例#9
0
                  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()

#==============================================================================
示例#10
0
    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