def get_mass(item, atom_indices, forcefield=['AMBER99SB-ILDN', 'TIP3P']):
from molsysmt import get_form
form_in = get_form(item)
mass = []
if form_in in ["openmm.Modeller", "openmm.System", "pdbfixer.PDBFixer"]:
if form_in in ["openmm.Modeller", "pdbfixer.PDBFixer"]:
from openmm.app import ForceField
forcefield_openmm = _digest_forcefields(forcefield)
system = ForceField(*forcefield_openmm).createSystem(item.topology)
elif form_in == "openmm.System":
system = item
atom_indices = set(atom_indices)
for particle_index in range(system.getNumParticles()):
if particle_index in atom_indices:
mass.append(system.getParticleMass(particle_index))
return mass
else:
raise NotImplementedError
def get_net_mass(item, atom_indices, forcefield=['AMBER99SB-ILDN', 'TIP3P']):
from molsysmt import get_form
form_in = get_form(item)
if form_in in ["openmm.Modeller", "openmm.System", "pdbfixer.PDBFixer"]:
if form_in in ["openmm.Modeller", "pdbfixer.PDBFixer"]:
from openmm.app import ForceField
forcefield_openmm = _digest_forcefields(forcefield)
system = ForceField(*forcefield_openmm).createSystem(item.topology)
elif form_in == "openmm.System":
system = item
atom_indices = set(atom_indices)
net_mass = 0.0 * _unit.amu
for particle_index in range(system.getNumParticles()):
if particle_index in atom_indices:
net_mass += system.getParticleMass(particle_index)
return net_mass.in_units_of(
_unit.gram / _unit.mole) / _unit.AVOGADRO_CONSTANT_NA
else:
raise NotImplementedError
def replace_HETATM_by_ATOM_in_terminal_cappings(molecular_system):
from molsysmt import get_form
form_in = get_form(molecular_system)
if form_in == 'string:pdb':
tmp_molecular_system = re.sub(
r'HETATM+(\s+\d+\s+\w+\s+(ACE||NME)+\s+\w+\s)', r'ATOM \1',
molecular_system)
elif form_in == 'file:pdb':
with open(molecular_system, 'r+') as f:
text = f.read()
out = re.sub(r'HETATM+(\s+\d+\s+\w+\s+(ACE||NME)+\s+\w+\s)',
r'ATOM \1', text)
f.seek(0)
f.write(out)
f.truncate()
tmp_molecular_system = molecular_system
return tmp_molecular_system
def test_file_gro_to_mdtraj_Trajectory():
import warnings
warnings.filterwarnings('ignore')
molsys = msm.demo['nglview']['1u19.gro']
molsys = msm.convert(molsys, to_form='mdtraj.Trajectory')
warnings.resetwarnings()
form = msm.get_form(molsys)
assert 'mdtraj.Trajectory' == form
def test_convert_file_gro_and_file_xtc_to_molsysmt_MolSys():
import warnings
warnings.filterwarnings('ignore')
molsys_1 = msm.demo['nglview']['1u19.gro']
molsys_2 = msm.demo['nglview']['1u19.xtc']
molsys = msm.convert([molsys_1, molsys_2], to_form='molsysmt.MolSys')
warnings.resetwarnings()
form = msm.get_form(molsys)
assert 'molsysmt.MolSys'==form
def test_string_pdb_text_to_openmm_Topology():
molsys = msm.convert(msm.demo['T4 lysozyme L99A']['181l.pdb'],
to_form='string:pdb_text')
molsys = msm.convert(molsys,
to_form='openmm.Topology',
selection='molecule_type=="protein"')
is_composed_of = msm.is_composed_of(molsys, proteins=1)
form = msm.get_form(molsys)
assert ('openmm.Topology' == form) and (is_composed_of == True)
def test_view_molsyst_MolSys_with_NLGView_1():
import nglview as nv
molsys = msm.demo['T4 lysozyme L99A']['181l.pdb']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
molsys_2 = nv.show_molsysmt(molsys)
check = ('nglview.NGLWidget'==msm.get_form(molsys_2))
check_n_elements = msm.compare(molsys, molsys_2, comparison='n_elements')
check_n_molecules = msm.compare(molsys, molsys_2, comparison='n_molecules')
check_n_structures = msm.compare(molsys, molsys_2, comparison='n_structures')
assert check and check_n_elements and check_n_molecules and check_n_structures
def test_file_msmpk_to_nglview_NGLWidget():
molsys = msm.demo['T4 lysozyme L99A']['vacuum.msmpk']
molsys_ref = msm.convert(molsys, to_form='molsysmt.MolSys')
molsys = msm.convert(molsys, to_form='nglview.NGLWidget')
check = ('nglview.NGLWidget' == msm.get_form(molsys))
check_n_elements = msm.compare(molsys, molsys_ref, comparison='n_elements')
check_n_molecules = msm.compare(molsys,
molsys_ref,
comparison='n_molecules')
check_n_structures = msm.compare(molsys,
molsys_ref,
comparison='n_structures')
assert check and check_n_elements and check_n_molecules and check_n_structures
def test_merge_molsysmt_MolSys_1():
molsys_1 = msm.convert(msm.demo['proline dipeptide']['vacuum.msmpk'],
to_form='molsysmt.MolSys')
molsys_2 = msm.convert(msm.demo['valine dipeptide']['vacuum.msmpk'],
to_form='molsysmt.MolSys')
molsys_3 = msm.convert(msm.demo['lysine dipeptide']['vacuum.msmpk'],
to_form='molsysmt.MolSys')
n_atoms_1 = msm.get(molsys_1, target='system', n_atoms=True)
n_atoms_2 = msm.get(molsys_2, target='system', n_atoms=True)
n_atoms_3 = msm.get(molsys_3, target='system', n_atoms=True)
molsys = msm.merge([molsys_1, molsys_2, molsys_3])
n_atoms, n_structures = msm.get(molsys,
target='system',
n_atoms=True,
n_structures=True)
check = ('molsysmt.MolSys' == msm.get_form(molsys))
check_n_atoms = (n_atoms == n_atoms_1 + n_atoms_2 + n_atoms_3)
check_n_structures = (n_structures == 1)
assert check and check_n_atoms and check_n_structures
def get_degrees_of_freedom(item, forcefield=['AMBER99SB-ILDN', 'TIP3P']):
from molsysmt import get_form
form_in = get_form(item)
if form_in in ["openmm.Modeller", "openmm.System", "pdbfixer.PDBFixer"]:
if form_in in ["openmm.Modeller", "pdbfixer.PDBFixer"]:
from openmm.app import ForceField
forcefield_openmm = _digest_forcefields(forcefield)
system = ForceField(*forcefield_openmm).createSystem(item.topology)
elif form_in == "openmm.System":
system = item
return 3 * system.getNumParticles() - system.getNumConstraints()
else:
raise NotImplementedError
def add(self,
item,
selection='all',
structure_indices='all',
syntaxis='MolSysMT'):
from molsysmt import convert, get_form, select
if get_form(item) != 'molsysmt.MolSys':
tmp_item = convert(item,
selection=selection,
structure_indices=structure_indices,
to_form='molsysmt.MolSys',
syntaxis=syntaxis)
self.topology.add(tmp_item.topology)
self.structures.add(tmp_item.trajectory)
else:
atom_indices = select(item, selection=selection, syntaxis=syntaxis)
self.topology.add(item.topology, selection=atom_indices)
self.structures.add(item.structures,
selection=atom_indices,
structure_indices=structure_indices)
def test_append_structures_molsysmt_MolSys():
molsys_1 = msm.convert(msm.demo['proline dipeptide']['vacuum.msmpk'],
to_form='molsysmt.MolSys')
molsys_2 = msm.structure.translate(
molsys_1, translation='[0.1, 0.1, 0.1] nanometers')
molsys_3 = msm.structure.translate(
molsys_1, translation='[0.2, 0.2, 0.2] nanometers')
n_atoms_1, n_structures_1 = msm.get(molsys_1,
target='system',
n_atoms=True,
n_structures=True)
n_structures_2 = msm.get(molsys_2, target='system', n_structures=True)
n_structures_3 = msm.get(molsys_3, target='system', n_structures=True)
msm.append_structures(molsys_1, [molsys_2, molsys_3])
n_atoms, n_structures = msm.get(molsys_1,
target='system',
n_atoms=True,
n_structures=True)
check = ('molsysmt.MolSys' == msm.get_form(molsys_1))
check_n_atoms = (n_atoms == n_atoms_1)
check_n_structures = (n_structures == n_structures_1 + n_structures_2 +
n_structures_3)
assert check and check_n_atoms and check_n_structures
def test_string_pdb_text_2():
fff=open(msm.demo['T4 lysozyme L99A']['181l.pdb'],'r')
molsys = fff.read()
fff.close()
output = msm.get_form(molsys)
assert output == 'string:pdb_text'
def test_string_pdb_text():
molsys = msm.demo['benzamidine']['benzamidine.pdb']
molsys = msm.convert(molsys, 'string:pdb_text')
molsys = 'pdb_text:'+molsys
output = msm.get_form(molsys)
assert output == 'string:pdb_text'
def test_string_aminoacids1_automatic_detection():
molsys = 'ALYDERRRT'
output = msm.get_form(molsys)
assert output == 'string:aminoacids1'
def test_string_aminoacids1():
molsys = 'aminoacids1:ALYDERRRT'
output = msm.get_form(molsys)
assert output == 'string:aminoacids1'
def test_string_aminoacids3_automatic_detection():
molsys = 'ACEALAGLYVALNME'
output = msm.get_form(molsys)
assert output == 'string:aminoacids3'
def test_molsysmt_MolSys():
molsys = msm.demo['chicken villin HP35']['vacuum.msmpk']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
output = msm.get_form(molsys)
assert output == 'molsysmt.MolSys'
def test_file_mmtf_to_molsysmt_MolSys_2():
molsys = msm.demo['chicken villin HP35']['1vii.mmtf']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
form = msm.get_form(molsys)
assert 'molsysmt.MolSys' == form
def test_string_pdb_automatic_detection():
molsys = msm.demo['benzamidine']['benzamidine.pdb']
molsys = msm.convert(molsys, 'string:pdb_text')
output = msm.get_form(molsys)
assert output == 'string:pdb_text'
def test_file_xyznpy():
molsys = msm.demo['4 particles']['traj.xyznpy']
output = msm.get_form(molsys)
assert output == 'file:xyznpy'
def test_file_inpcrd_prmtop():
molsys1 = msm.demo['pentalanine']['pentalanine.inpcrd']
molsys2 = msm.demo['pentalanine']['pentalanine.prmtop']
output = msm.get_form([molsys1, molsys2])
assert output == ['file:inpcrd', 'file:prmtop']
def test_file_mmtf():
molsys = msm.demo['chicken villin HP35']['1vii.mmtf']
output = msm.get_form(molsys)
assert output == 'file:mmtf'
def test_nglview_NGLWidget():
molsys = msm.demo['chicken villin HP35']['vacuum.msmpk']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
molsys = msm.view(molsys)
output = msm.get_form(molsys)
assert output == 'nglview.NGLWidget'
def test_class_XYZ():
molsys = np.zeros(shape=[10,4,3])*msm.puw.unit('nanometers')
output = msm.get_form(molsys)
assert output == 'XYZ'
def test_string_pdb_id():
molsys = 'pdb_id:1VII'
output = msm.get_form(molsys)
assert output == 'string:pdb_id'
def test_file_mmtf_to_molsysmt_MolSys_1():
molsys = msm.demo['T4 lysozyme L99A']['181l.mmtf']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
form = msm.get_form(molsys)
assert 'molsysmt.MolSys' == form
def test_string_pdb_id_automatic_detection():
molsys = '1VII'
output = msm.get_form(molsys)
assert output == 'string:pdb_id'
def test_file_msmpk():
molsys = msm.demo['chicken villin HP35']['vacuum.msmpk']
output = msm.get_form(molsys)
assert output == 'file:msmpk'
def test_string_aminoacids3():
molsys = 'aminoacids3:ACEALAGLYVALNME'
output = msm.get_form(molsys)
assert output == 'string:aminoacids3'
