def test_file_pdb_to_parmed_Structure():
molsys = msm.demo['T4 lysozyme L99A']['181l.pdb']
molsys = msm.convert(molsys, to_form='parmed.Structure')
form = msm.get_form(molsys)
assert 'parmed.Structure' == form
def test_get_28():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
names = msm.get(molsys, target='entity', indices=0, name=True)
true_names = np.array(['TRIOSEPHOSPHATE ISOMERASE'], dtype=object)
assert np.all(names == true_names)
def test_get_30():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
n_molecules = msm.get(molsys, target='entity', indices=1, n_molecules=True)
true_n_molecules = [165]
assert np.all(n_molecules == true_n_molecules)
def test_get_1():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.get(molsys, target='atom', indices=[32, 33, 34], name=True)
true_output = np.array(['N', 'CA', 'C'], dtype=object)
assert np.all(output == true_output)
def test_get_15():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
atom_names = msm.get(molsys, target='atom', indices=[0, 1, 2], name=True)
true_atom_names = np.array(['N', 'CA', 'C'], dtype=object)
assert np.all(atom_names == true_atom_names)
import pytest
from molsysmt.multitool import get_form as get_form
from molsysmt import get
from molsysmt import convert
dict_tests = {
'pdb': 'data/1tcd.pdb',
'pdb:id': 'pdb:1tcd',
'molsysmt.MolSys': convert('data/1tcd.pdb', to_form='molsysmt.MolSys'),
'molsysmt.Topology': convert('data/1tcd.pdb', to_form='molsysmt.Topology'),
'openmm.Topology': convert('data/1tcd.pdb', to_form='openmm.Topology'),
'openmm.Modeller': convert('data/1tcd.pdb', to_form='openmm.Modeller'),
'openmm.PDBFile': convert('data/1tcd.pdb', to_form='openmm.PDBFile'),
'pdbfixer.PDBFixer': convert('data/1tcd.pdb', to_form='pdbfixer.PDBFixer'),
'mdtraj.Topology': convert('data/1tcd.pdb', to_form='mdtraj.Topology'),
'mdtraj.Trajectory': convert('data/1tcd.pdb', to_form='mdtraj.Trajectory')
}
id_names = []
args = []
for expected, item in dict_tests.items():
id_names.append(expected)
args.append((item, expected))
@pytest.mark.parametrize("item,expected", args, ids=id_names)
def test_1(item, expected):
assert get_form(item) == expected
def test_extract_1():
molsys = msm.demo['T4 lysozyme L99A']['181l.msmpk']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
molsys = msm.extract(molsys, selection='molecule_type=="small molecule"')
output = msm.is_composed_of(molsys, small_molecules=2)
assert output == True
def test_is_composed_of_1():
molsys = msm.convert(msm.demo['chicken villin HP35']['solvated.msmpk'],
to_form='molsysmt.MolSys')
output = msm.is_composed_of(molsys, proteins=True)
assert output == False
from molsysmt import convert
import numpy as np
import pickle
with open('data/1tcd.pickle', 'rb') as f:
expected_values = pickle.load(f)
args = [
# 'data/1tcd.pdb',
# convert('data/1tcd.pdb', to_form='molsysmt.MolSys'),
# convert('data/1tcd.pdb', to_form='molsysmt.Topology'),
# convert('data/1tcd.pdb', to_form='openmm.Topology'),
# convert('data/1tcd.pdb', to_form='openmm.Modeller'),
# convert('data/1tcd.pdb', to_form='openmm.PDBFile'),
# convert('data/1tcd.pdb', to_form='pdbfixer.PDBFixer'),
convert('data/1tcd.pdb', to_form='mdtraj.Topology'),
convert('data/1tcd.pdb', to_form='mdtraj.Trajectory')
]
# Component
@pytest.mark.parametrize("item", args, ids=get_form)
def test_atom_index_from_component_1(item):
output = get(item, target='component', atom_index=True)
assert np.all(
np.all(
output[ii] == expected_values['atom_index_from_component_1'][ii])
for ii in range(output.shape[0]))
def test_is_composed_of_4():
molsys = msm.convert(msm.demo['chicken villin HP35']['solvated.msmpk'],
to_form='molsysmt.MolSys')
molsys = msm.extract(molsys, selection='molecule_type=="peptide"')
output = msm.is_composed_of(molsys, peptides=1)
assert output == True
def test_is_composed_of_5():
molsys = msm.convert(msm.demo['chicken villin HP35']['solvated.msmpk'],
to_form='molsysmt.MolSys')
molsys = msm.extract(molsys, selection='molecule_type=="protein"')
output = msm.is_composed_of(molsys, proteins=1, waters=2, ions=2)
assert output == False
def test_is_composed_of_3():
molsys = msm.convert(msm.demo['chicken villin HP35']['solvated.msmpk'],
to_form='molsysmt.MolSys')
output = msm.is_composed_of(molsys, peptides=1, waters=True, ions=True)
assert output == True
def test_file_xyznpy_to_XYZ():
molsys = msm.demo['4 particles']['traj.xyznpy']
molsys = msm.convert(molsys, to_form='XYZ')
check = ('XYZ' == msm.get_form(molsys))
assert check
np.float32) * unit.nanometers / unit.picosecond
potential_energy = np.zeros([n_saving_periods],
np.float32) * unit.kilocalories_per_mole
kinetic_energy = np.zeros([n_saving_periods],
np.float32) * unit.kilocalories_per_mole
box = np.zeros([n_saving_periods, 3, 3], np.float32) * unit.nanometers
state = context.getState(getPositions=True, getVelocities=True, getEnergy=True)
time[0] = state.getTime()
position[0] = state.getPositions()
velocity[0] = state.getVelocities()
kinetic_energy[0] = state.getKineticEnergy()
potential_energy[0] = state.getPotentialEnergy()
box[0] = state.getPeriodicBoxVectors()
for ii in tqdm(range(n_saving_periods)):
context.getIntegrator().step(n_steps_per_saving_period)
state = context.getState(getPositions=True,
getVelocities=True,
getEnergy=True)
time[ii] = state.getTime()
position[ii] = state.getPositions()
velocity[ii] = state.getVelocities()
kinetic_energy[ii] = state.getKineticEnergy()
potential_energy[ii] = state.getPotentialEnergy()
box[ii] = state.getPeriodicBoxVectors()
trajdict = {'time': time, 'coordinates': position, 'box': box}
msm.convert(trajdict, to_form='traj.trjpk')
def test_contains_1():
molsys = msm.convert(msm.demo['T4 lysozyme L99A']['181l.pdb'],
to_form='molsysmt.MolSys')
output = msm.contains(molsys, waters=True)
assert output == True
def from_top(item, atom_indices='all', structure_indices='all'):
from molsysmt import convert
return convert(item, to_form='mdtraj.Topology', selection=atom_indices)
import molsysmt as msm
import numpy as np
from pathlib import Path
import os
# purge
print('Removing old files...')
files_to_be_purged = ['vacuum.pdb', 'vacuum.msmpk']
for filename in files_to_be_purged:
if os.path.isfile(filename):
os.remove(filename)
molsys = msm.build.build_peptide(['TyrGlyGlyPheMet',{'forcefield':'AMBER14', 'implicit_solvent':'OBC1'}])
_ = msm.convert(molsys, to_form='vacuum.msmpk')
_ = msm.convert(molsys, to_form='vacuum.pdb')
del(molsys)
def __init__(self,
forcefield='AMBER14',
implicit_solvent='OBC1',
solute_dielectric=1.0,
solvent_dielectric=78.3,
implicit_solvent_kappa=0.0 / unit.nanometer,
implicit_solvent_salt_conc=0.0 * unit.mole / unit.liter,
constraints='h_bonds',
hydrogen_mass=None):
"""Creating a new instance of AlanineTetrapeptideImplicitSolvent
...
Parameters
----------
forcefield: xxx
XXX
constraints: app.Hbonds
XXX
hydrogen_mass: None
XXX
Examples
--------
>>> from uibcdf_test_systems.systems import AlanineTetrapeptideImplicitSolvent
>>> from simtk import unit
>>> dialanine = AlanineTetrapeptideImplicitSolvent(forcefield='xxx')
Notes
-----
See `corresponding documentation in the user guide regarding this class
<../../systems/tetraalanine.html>`_.
"""
# Parameters
self.parameters = {}
self.parameters['forcefield'] = forcefield
self.parameters['implicit_solvent'] = implicit_solvent
self.parameters['solute_dielectric'] = solute_dielectric
self.parameters['solvent_dielectric'] = solvent_dielectric
self.parameters['implicit_solvent_kappa'] = implicit_solvent_kappa
self.parameters[
'implicit_solvent_salt_conc'] = implicit_solvent_salt_conc
self.parameters['constraints'] = constraints
self.parameters['hydrogen_mass'] = hydrogen_mass
# openmm.Modeller
from molsysmt import convert
from .files import alanine_tetrapeptide
file_pdb = alanine_tetrapeptide['vacuum.pdb']
item_modeller = convert(file_pdb, to_form='openmm.Modeller')
# OpenMM topology
self.topology = item_modeller.topology
# Coordinates
self.coordinates = item_modeller.positions
# OpenMM system
self.system = convert(
item_modeller,
to_form='openmm.System',
forcefield=forcefield,
constraints=constraints,
hydrogen_mass=hydrogen_mass,
non_bonded_method='no_cutoff',
implicit_solvent=implicit_solvent,
solute_dielectric=solute_dielectric,
solvent_dielectric=solvent_dielectric,
implicit_solvent_kappa=implicit_solvent_kappa,
implicit_solvent_salt_conc=implicit_solvent_salt_conc)
import openmm as mm
from openmm import app
from openmm import unit
from sys import stdout
from mdtraj.reporters import HDF5Reporter
# purge
print('Removing old files...')
files_to_be_purged = ['181l.pdb', '181l.mmtf', '1l17.pdb', '1l17.mmtf']
for filename in files_to_be_purged:
if os.path.isfile(filename):
os.remove(filename)
# 181l pdb, mmtf, msmpk files
print('Protein Data Bank files...')
msm.convert('pdb_id:181l', to_form='181l.pdb')
msm.convert('pdb_id:181l', to_form='181l.mmtf')
msm.convert('pdb_id:181l', to_form='181l.msmpk')
# 1l17 pdb, mmtf, msmpk files
print('Protein Data Bank files...')
msm.convert('pdb_id:1l17', to_form='1l17.pdb')
msm.convert('pdb_id:1l17', to_form='1l17.mmtf')
msm.convert('pdb_id:1l17', to_form='1l17.msmpk')
# vacuum
#print('Vacuum system in msmpk file...')
#molsys = msm.convert('pdb_id:181l', to_form='molsysmt.MolSys')
#molsys = msm.build.remove_solvent(molsys)
#molsys = msm.build.remove_hydrogens(molsys)
#molsys = msm.build.add_terminal_cappings(molsys, N_terminal='ACE', C_terminal='NME')
def __init__(self,
forcefield='AMBER14',
constraints='h_bonds',
hydrogen_mass=None):
"""XXX
A new test system is returned with the openmm system of particles in an external double
well potential.
Parameters
----------
forcefield: xxx
XXX
constraints: app.Hbonds
XXX
hydrogen_mass: None
XXX
Examples
--------
>>> from uibcdf_test_systems.systems import AlanineTetrapeptideVacuum
>>> from simtk import unit
>>> dialanine = AlanineTetrapeptideVacuum(forcefield='xxx')
Notes
-----
See `corresponding documentation in the user guide regarding this class
<../../systems/tetraalanine.html>`_.
"""
# Parameters
self.parameters = {}
self.parameters['forcefield'] = forcefield
self.parameters['constraints'] = constraints
self.parameters['hydrogen_mass'] = hydrogen_mass
# openmm.Modeller
from molsysmt import convert
from .files import alanine_tetrapeptide
file_pdb = alanine_tetrapeptide['vacuum.pdb']
item_modeller = convert(file_pdb, to_form='openmm.Modeller')
# OpenMM topology
self.topology = item_modeller.topology
# Coordinates
self.coordinates = item_modeller.positions
# OpenMM system
self.system = convert(item_modeller,
to_form='openmm.System',
forcefield=forcefield,
constraints=constraints,
hydrogen_mass=hydrogen_mass,
implicit_solvent=None,
non_bonded_method='no_cutoff')
from mdtraj.reporters import HDF5Reporter
# purge
print('Removing old files...')
files_to_be_purged = [
'1vii.pdb', '1vii.mmtf', 'villin_hp35_vacuum.msmpk',
'villin_hp35_solvated.msmpk', 'villin_hp35_solvated.dcd',
'villin_hp35_solvated.h5', 'villin_hp35_solvated_last.pdb'
]
for filename in files_to_be_purged:
if os.path.isfile(filename):
os.remove(filename)
# 1vii pdb and mmtf files
print('Protein Data Bank files...')
msm.convert('pdbid:1vii', to_form='1vii.pdb')
msm.convert('pdbid:1vii', to_form='1vii.mmtf')
# vacuum
print('Vacuum system in msmpk file...')
molsys = msm.convert('pdbid:1vii', to_form='molsysmt.MolSys')
molsys = msm.build.remove_hydrogens(molsys)
molsys = msm.build.add_terminal_cappings(molsys,
N_terminal='ACE',
C_terminal='NME')
molsys = msm.build.add_hydrogens(molsys, pH=7.4)
_ = msm.convert(molsys, to_form='villin_hp35_vacuum.msmpk')
# solvated
print('Solvated system in msmpk file...')
molsys = msm.build.solvate(
def __init__(self,
forcefield='AMBER14',
water_model='TIP3P',
rigid_water=True,
constraints='h_bonds',
hydrogen_mass=None,
non_bonded_method='PME',
non_bonded_cutoff=10.0 * unit.angstroms,
switch_distance=8.5 * unit.angstroms,
use_dispersion_correction=True,
ewald_error_tolerance=1.0e-5):
"""Creating a new instance of AlanineTetrapeptideExplicitSolvent
Parameters
----------
forcefield: xxx
XXX
constraints: app.Hbonds
XXX
hydrogen_mass: None
XXX
Examples
--------
>>> from uibcdf_test_systems.systems import AlanineTetrapeptideExplicitSolvent
>>> from simtk import unit
>>> dialanine = AlanineTetrapeptideExplicitSolvent()
Notes
-----
See `corresponding documentation in the user guide regarding this class
<../../systems/tetraalanine.html>`_.
"""
# openmm.Modeller
from molsysmt import convert
from .files import alanine_tetrapeptide
file_pdb = alanine_tetrapeptide['octahedral_14.pdb']
item_modeller = convert(file_pdb, to_form='openmm.Modeller')
# OpenMM topology
self.topology = item_modeller.topology
# Coordinates
self.coordinates = item_modeller.positions
# OpenMM system
self.system = convert(
item_modeller,
to_form='openmm.System',
forcefield=forcefield,
water_model=water_model,
rigid_water=rigid_water,
constraints=constraints,
hydrogen_mass=hydrogen_mass,
non_bonded_method=non_bonded_method,
non_bonded_cutoff=non_bonded_cutoff,
switch_distance=switch_distance,
use_dispersion_correction=use_dispersion_correction,
ewald_error_tolerance=ewald_error_tolerance)
def test_get_11():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
n_chains = msm.get(molsys, target='atom', n_chains=True)
assert n_chains == 4
def test_file_h5_to_molsysmt_Topology_and_molsysmt_Structures():
molsys = msm.demo['pentalanine']['traj.h5']
molsys = msm.convert(molsys,
to_form=['molsysmt.Topology', 'molsysmt.Trajectory'])
form = msm.get_form(molsys)
assert ['molsysmt.Topology', 'molsysmt.Trajectory'] == form
def test_get_19():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
ids = msm.get(molsys, target='group', indices=[0, 1, 2], id=True)
true_ids = np.array([4, 5, 6])
assert np.all(ids == true_ids)
def test_contains_5():
molsys = msm.convert(msm.demo['T4 lysozyme L99A']['181l.pdb'],
to_form='molsysmt.MolSys')
output = msm.contains(molsys, proteins=True, lipids=False)
assert output == True
def test_get_29():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
types = msm.get(molsys, target='entity', indices=1, type=True)
true_types = np.array(['water'], dtype=object)
assert np.all(types == true_types)
def test_contains_7():
molsys = msm.convert(msm.demo['T4 lysozyme L99A']['181l.pdb'],
to_form='molsysmt.MolSys')
output = msm.contains(molsys, small_molecules=3, ions=2)
assert output == False
def test_get_38():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
n_ions = msm.get(molsys, target='system', n_ions=True)
assert n_ions == 0
def test_file_pdb_to_pdbfixer_PDBFixer():
molsys = msm.demo['T4 lysozyme L99A']['181l.pdb']
molsys = msm.convert(molsys, to_form='pdbfixer.PDBFixer')
form = msm.get_form(molsys)
assert 'pdbfixer.PDBFixer' == form
