Python load_all_magresの例

コード例 #1

  Only show couplings where the coupling in the opposite direction exists in another calculation.
"""

import os
import sys

from magres.format import BadVersion
from magres.atoms import MagresAtoms
from magres.utils import load_all_magres

cwd = "."

if len(sys.argv)>1:
    cwd = str(sys.argv[1])

magres_atoms = load_all_magres(cwd)

find_s = str(sys.argv[2])

if len(sys.argv) >= 4:
  find_i = int(sys.argv[3])
else:
  find_i = None

tensors = ['efg', 'efg_local', 'efg_nonlocal']

lines = []

def get_numeric(s):
  return "".join([c for c in s if ord("0") <= ord(c) <= ord("9")])

コード例 #2

ファイル: extract-ms.py プロジェクト: davedavemckay/magres-format

if atoms_filter_str:
  atoms_filter = parse_atom_list(atoms_filter_str)
else:
  atoms_filter = lambda x: True

tensors = ['ms']

lines = []

print "# Number\tAtom\tIso\tAniso\tAsym\tPath"

if os.path.isfile(a.source_dir):
  magres_atoms = [MagresAtoms.load_magres(a.source_dir)]
else:
  magres_atoms = load_all_magres(a.source_dir)

isos = {}

for iso_ in a.iso:
  num = re.findall('([0-9]+)', iso_)[0]
  sym = re.findall('([A-Za-z]+)', iso_)[0]

  isos[sym] = int(num)

for i, atoms in enumerate(magres_atoms):
  num = get_numeric(atoms.magres_file.path)

  for s, iso in isos.items():
    for atom in atoms.species(s):
      atom.isotope = iso

コード例 #3

ファイル: extract-jc.py プロジェクト: ccp9-community/magres-format

  Only show couplings where the coupling in the opposite direction exists in another calculation.
"""

import os
import sys

from magres.format import BadVersion
from magres.atoms import MagresAtoms
from magres.utils import load_all_magres

cwd = "."

if len(sys.argv)>1:
    cwd = str(sys.argv[1])

magres_atoms = load_all_magres(cwd)

find_s1 = str(sys.argv[2])
find_i1 = int(sys.argv[3])

if len(sys.argv) >= 5:
  find_s2 = str(sys.argv[4])
else:
  find_s2 = None

if len(sys.argv) >= 6:
  find_i2 = int(sys.argv[5])
else:
  find_i2 = None

all_Js = {}

コード例 #4

tensors = [
    'efg',
]  # 'efg_local', 'efg_nonlocal']

lines = []

if a.numbers:
    print("# Number\tAtom\tCq\tEta\tPath")
else:
    print("# Atom\tCq\tEta\tPath")

if os.path.isfile(a.source):
    magres_atoms = [MagresAtoms.load_magres(a.source)]
else:
    magres_atoms = load_all_magres(a.source)

for i, atoms in enumerate(magres_atoms):
    num = get_numeric(atoms.magres_file.path)

    if num:
        idx = num
    else:
        idx = [i]

    for atom in atoms:
        if atoms_filter(atom) and \
                hasattr(atom, 'efg'):

            lines.append(
                (idx, atoms.magres_file.path, str(atom),

コード例 #5

ファイル: nqr.py プロジェクト: chemik22/magresview

    omega = 3A(2|m| + 1)/hbar

  for all available transitions m->m+1

"""
import sys
import math
from magres.atoms import MagresAtoms
from magres.utils import load_all_magres
import magres.units as units

s = sys.argv[1]

atomss = []
for f in sys.argv[2:]:
  atomss += load_all_magres(f)

def frange(a, b, x):
  while a < b:
    yield a
    a += x

for atoms in atomss:
  print atoms.magres_file.path

  vals = []

  first = True

  for atom in atoms:
    if atom.species == s:

コード例 #6

ファイル: nqr.py プロジェクト: ccp9-community/magres-format

    omega = 3A(2|m| + 1)/hbar

  for all available transitions m->m+1

"""
import sys
import math
from magres.atoms import MagresAtoms
from magres.utils import load_all_magres
import magres.units as units

s = sys.argv[1]

atomss = []
for f in sys.argv[2:]:
  atomss += load_all_magres(f)

def frange(a, b, x):
  while a < b:
    yield a
    a += x

for atoms in atomss:
  print atoms.magres_file.path

  vals = []

  first = True

  for atom in atoms:
    if atom.species == s: