Python find_all_magres示例

示例#1

文件： atoms_multifile.py 项目： ccp9-community/magres-format

import sys
from magres.format import MagresFile
from magres.utils import find_all_magres
from magres.atoms import MagresAtoms

magres_files = [MagresFile(f) for f in find_all_magres(sys.argv[1])]

atoms = MagresAtoms.load_magres(magres_files)

coupling_atom = atoms.get_species('C', 1)

# Set a bunch of arbitrary references for the magnetic shielding
atoms.set_reference('H', 100.0)
atoms.set_reference('C', 55.0)
atoms.set_reference('O', -2.0)

for atom in atoms:
  print atom, atom.efg.Cq, atom.ms.iso, atom.isc[coupling_atom].J_iso

示例#2

文件： absiscdev.py 项目： ccp9-community/magres-format

#!python
import sys
from magres.format import MagresFile, BadVersion
from magres.atoms import MagresAtoms
from magres.utils import find_all_magres

magres_files = []
for f in find_all_magres(sys.argv[1]):
  try:
    magres_files.append(MagresFile(f))
  except BadVersion:
    continue

s1 = sys.argv[2]
i1 = int(sys.argv[3])
s2 = sys.argv[4]
i2 = int(sys.argv[5])

tensor = 'isc'
if len(sys.argv) >= 7:
  tensor = sys.argv[6]

atoms = MagresAtoms.load_magres(magres_files)

atom1 = atoms.get_species(s1, i1)
atom2 = atoms.get_species(s2, i2)

if tensor == "isc_spin_total":
  K1 = atom1.isc_fc[atom2].K + atom1.isc_spin[atom2].K
  K2 = atom2.isc_fc[atom1].K + atom2.isc_spin[atom1].K
else:

示例#3

文件： compisc.py 项目： chemik22/magresview

#!/usr/bin/python
import sys
from numpy.linalg import det
from magres.format import MagresFile, BadVersion
from magres.atoms import MagresAtoms
from magres.utils import find_all_magres

magres_files = []
for f in find_all_magres(sys.argv[1]):
  try:
    magres_files.append(MagresFile(f))
  except BadVersion:
    continue

s1 = sys.argv[2]
i1 = int(sys.argv[3])
s2 = sys.argv[4]
i2 = int(sys.argv[5])

tensor = 'isc'
if len(sys.argv) >= 7:
  tensor = sys.argv[6]

atoms = MagresAtoms.load_magres(magres_files)

atom1 = atoms.get_species(s1, i1)
atom2 = atoms.get_species(s2, i2)

if tensor == "isc_spin_total":
  K1 = atom1.isc_fc[atom2].K + atom1.isc_spin[atom2].K
  K2 = atom2.isc_fc[atom1].K + atom2.isc_spin[atom1].K

示例#4

文件： atoms_multifile.py 项目： chemik22/magresview

import sys
from magres.format import MagresFile
from magres.utils import find_all_magres
from magres.atoms import MagresAtoms

magres_files = [MagresFile(f) for f in find_all_magres(sys.argv[1])]

atoms = MagresAtoms.load_magres(magres_files)

coupling_atom = atoms.get_species('C', 1)

# Set a bunch of arbitrary references for the magnetic shielding
atoms.set_reference('H', 100.0)
atoms.set_reference('C', 55.0)
atoms.set_reference('O', -2.0)

for atom in atoms:
    print atom, atom.efg.Cq, atom.ms.iso, atom.isc[coupling_atom].J_iso