How to use the parmed.amber.AmberParameterSet function in ParmEd

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github alanwilter / acpype / amber17-6_linux / dat / leap / parm / validate_torsions.py View on Github external
"""
This script will validate the torsions specified in a particular database and
will highlight any specific torsions that need additional terms to explicitly
override generic torsions
"""
import os
import parmed as pmd
import sys

if len(sys.argv) < 2:
    sys.exit('%s  [ [ ...]]' %
             os.path.split(sys.argv[0])[1])

params = pmd.amber.AmberParameterSet(sys.argv[1:])

# First separate the generic terms and the specific terms. Store the generics as
# *just* the middle terms, and do both permutations
generics = dict()
generic_type_ids = set()
specifics = dict()
specific_type_ids = set()

for key, dihtype in params.dihedral_types.items():
    if key[0] == 'X' and key[3] == 'X':
        if id(dihtype) in generic_type_ids:
            continue
        generics[(key[1], key[2])] = generics[(key[2], key[1])] = dihtype
        generic_type_ids.add(id(dihtype))
    else:
        if id(dihtype) in specific_type_ids:
github alanwilter / acpype / amber19-0_linux / bin / amb2chm_par.py View on Github external
#    del ATOM_TYPE_DICT2

if options.fopt not in [1, 2]:
    raise ValueError('-f should be followed by 1 or 2!')
if options.newtype not in [0, 1]:
    raise ValueError('--nat should be followed by 0 or 1!')

# Setting the option to re-arrange the improper torsion order
imp_rearg = 1

# Generate an empty CHARMM parameter set
params = pmd.charmm.CharmmParameterSet()

# Update the parameter files
if options.fopt == 1:
    params1 = pmd.amber.AmberParameterSet(options.inputf)
    params = params_update(params, params1, options.newtype, imp_rearg)
elif options.fopt == 2:
    frc_files = []
    with open(options.inputf, 'r') as f:
        for rline in f:
            line = rline.strip('\n')
            line = line.strip()
            frc_files.append(line)
        for i in frc_files:
            params1 = pmd.amber.AmberParameterSet(i)
            params = params_update(params, params1, options.newtype, imp_rearg)

# Write the output parameter file
params.write(par=options.outputf)

quit()
github alanwilter / acpype / amber19-0_linux / bin / amb2chm_par.py View on Github external
# Generate an empty CHARMM parameter set
params = pmd.charmm.CharmmParameterSet()

# Update the parameter files
if options.fopt == 1:
    params1 = pmd.amber.AmberParameterSet(options.inputf)
    params = params_update(params, params1, options.newtype, imp_rearg)
elif options.fopt == 2:
    frc_files = []
    with open(options.inputf, 'r') as f:
        for rline in f:
            line = rline.strip('\n')
            line = line.strip()
            frc_files.append(line)
        for i in frc_files:
            params1 = pmd.amber.AmberParameterSet(i)
            params = params_update(params, params1, options.newtype, imp_rearg)

# Write the output parameter file
params.write(par=options.outputf)

quit()