def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
from molsysmt.pbc import box_vectors_from_box_lengths_and_angles
if structure_indices is 'all':
structure_indices = _np.arange(get_n_structures_from_system(item))
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
box_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
frame_hdf5 = item.read(n_frames=size)
cell_lengths = frame_hdf5.cell_lengths
cell_angles = frame_hdf5.cell_angles
box = box_vectors_from_box_lengths_and_angles(
cell_lengths * _puw.unit('nm'), cell_angles * _puw.unit('degrees'))
box_list.append(_puw.get_value(box))
box = _np.concatenate(box_list)
del (box_list)
box = box.astype('float64')
box = box * _puw.unit('nm')
box = _puw.standardize(box)
return box
def get_time_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
if structure_indices is 'all':
n_structures = get_n_structures_from_system(item)
structure_indices = np.arange(n_structures)
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
time_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
_, time, _, _ = item.read(n_frames=size)
time_list.append(time)
time = _np.concatenate(time_list)
del (time_list)
time = time.astype('float64')
time = time * _puw.unit('ps')
time = _puw.standardize(time)
return time
def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
if structure_indices is 'all':
n_structures = get_n_structures_from_system(item)
structure_indices = np.arange(n_structures)
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
box_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
_, _, _, box = item.read(n_frames=size)
box_list.append(box)
box = np.concatenate(box_list)
del (box_list)
box = box.astype('float64')
box = box * _puw.unit(item.distance_unit)
box = _puw.standardize(box)
return box
def test_get_contacts_from_molsysmt_MolSys_2():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys')
CA_atoms_chain_0 = msm.get(molsys, selection="atom_name=='CA' and chain_index==0", atom_index=True)
CA_atoms_chain_1 = msm.get(molsys, selection="atom_name=='CA' and chain_index==1", atom_index=True)
contact_map = msm.structure.get_contacts(molsys, selection=CA_atoms_chain_0, selection_2=CA_atoms_chain_1,
threshold=1.2*puw.unit('nm'))
check_shape_1 = ((1, 248, 249)==contact_map.shape)
check_value_1 = np.all(np.array([False, False, False, False, True, False, False, True, False, False])==contact_map[0,48,40:50])
assert check_shape_1 and check_value_1
def get_box_from_system(item, indices='all', structure_indices='all'):
from molsysmt.pbc import box_vectors_from_box_lengths_and_angles
_, _, cell_lengths, cell_angles = item.read()
if cell_lengths is not None:
cell_lengths = cell_lengths*puw.unit(item.distance_unit)
cell_angles = cell_angles*puw.unit('degrees')
box = box_vectors_from_box_lengths_and_angles(cell_lengths, cell_angles)
if structure_indices is not 'all':
box = box[structure_indices,:,:]
box = puw.standardize(box)
else:
box = None
return box
def box_shape_from_box_vectors(box):
from molsysmt.pbc.box_shape_from_box_angles import box_shape_from_box_angles
if box is None:
return None
else:
tmp_box = np.asfortranarray(puw.get_value(box), dtype='float64')
n_structures = tmp_box.shape[0]
angles = libbox.angles_box(tmp_box, n_structures) * puw.unit('degrees')
return box_shape_from_box_angles(angles)
def get_time_from_system(item, indices='all', structure_indices='all'):
_, time, _, _ = item.read()
time = time*puw.unit('ps')
if structure_indices is not 'all':
time = time[structure_indices]*picoseconds
time = puw.standardize(time)
return time
def get_coordinates_from_atom(item, indices='all', structure_indices='all'):
xyz = item.positions
if structure_indices is not 'all':
xyz = xyz[structure_indices, :, :]
if indices is not 'all':
xyz = xyz[:, indices, :]
xyz = xyz * puw.unit(item.distance_unit)
xyz = puw.standardize(xyz)
return xyz
def test_get_contacts_from_molsysmt_MolSys_3():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys')
atoms_in_residues_chain_0 = msm.get(molsys, target='group',
selection="molecule_type=='protein' and chain_index==0", atom_index=True)
atoms_in_residues_chain_1 = msm.get(molsys, target='group',
selection="molecule_type=='protein' and chain_index==1", atom_index=True)
contact_map = msm.structure.get_contacts(molsys,
groups_of_atoms=atoms_in_residues_chain_0, group_behavior='geometric_center',
groups_of_atoms_2=atoms_in_residues_chain_1, group_behavior_2='geometric_center',
threshold=1.2*puw.unit('nm'))
check_shape_1 = ((1, 248, 249)==contact_map.shape)
check_value_1 = np.all(np.array([False, False, False, False, True, False, False, True, False, False])==contact_map[0,48,40:50])
assert check_shape_1 and check_value_1
def get_box_lengths_from_system(item, indices='all', structure_indices='all'):
cell_lengths = item.unitcell_lengths
if cell_lengths is not None:
cell_lengths = cell_lengths * puw.unit(item.distance_unit)
if structure_indices is not 'all':
cell_lengths = cell_lengths[structure_indices]
cell_lengths = puw.standardize(cell_lengths)
else:
cell_lengths = None
return cell_lengths
def get_box_angles_from_system(item, indices='all', structure_indices='all'):
cell_angles = item.unitcell_angles
if cell_lengths is not None:
cell_angles = cell_angles * puw.unit('degrees')
if structure_indices is not 'all':
cell_angles = cell_angles[structure_indices]
cell_angles = puw.standardize(cell_angles)
else:
cell_angles = None
return cell_angles
def is_XYZ(item):
output = False
if puw.is_quantity(item):
if puw.compatibility(item, puw.unit('nm')):
shape = np.shape(item)
if len(shape) == 3 and shape[-1] == 3:
output = True
elif len(shape) == 2 and shape[-1] == 3:
output = True
elif len(shape) == 1 and shape[-1] == 3:
output = True
return output
def get_coordinates_from_atom(item,
indices='all',
structure_indices='all',
check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
if structure_indices is 'all':
n_structures = get_n_structures_from_system(item)
structure_indices = _np.arange(n_structures)
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
xyz_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
if indices is 'all':
xyz, _, _, _ = item.read(n_structures=size)
else:
xyz, _, _, _ = item.read(n_structures=size, atom_indices=indices)
xyz_list.append(xyz)
xyz = _np.concatenate(xyz_list)
del (xyz_list)
xyz = xyz.astype('float64')
xyz = xyz * _puw.unit(item.distance_unit)
xyz = _puw.standardize(xyz)
return xyz
def test_get_neighbors_from_molsysmt_MolSys_7():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
atoms_in_residues_chain_0 = msm.get(
molsys,
target='group',
selection="molecule_type=='protein' and chain_index==0",
atom_index=True)
atoms_in_residues_chain_1 = msm.get(
molsys,
target='group',
selection="molecule_type=='protein' and chain_index==1",
atom_index=True)
neighbors, distances = msm.structure.get_neighbors(
molsys,
groups_of_atoms=atoms_in_residues_chain_0,
group_behavior='geometric_center',
groups_of_atoms_2=atoms_in_residues_chain_1,
group_behavior_2='geometric_center',
threshold=1.2 * puw.unit('nanometers'))
check_n_contacts = (18 == len(neighbors[0, 11]))
assert check_n_contacts
def mass(molecular_system, target='atom', selection='all'):
from molsysmt.basic import get
from molsysmt.physico_chemical_properties.atoms.mass import physical, units
from molsysmt._private._digestion import digest_target
target = digest_target(target)
values = physical
output = []
if target == 'atom':
atom_types = get(molecular_system,
target=target,
selection=selection,
atom_type=True)
for ii in atom_types:
output.append(values[ii.capitalize()])
elif target in ['group', 'component', 'molecule', 'chain', 'entity']:
atom_types_in_target = get(molecular_system,
target=target,
selection=selection,
atom_type=True)
for aux in atom_types_in_target:
output.append(np.sum([values[ii.capitalize()] for ii in aux]))
elif target == 'system':
atom_types_in_target = get(molecular_system,
target='atom',
selection='all',
atom_type=True)
output.append(
np.sum([values[ii.capitalize()] for ii in atom_types_in_target]))
if target == 'system':
output = output[0] * puw.unit(units)
else:
output = puw.quantity(np.array(output), units)
return output
import molsysmt as msm
from molsysmt import puw
import numpy as np
from pathlib import Path
import os
# Removing all msmpk files
for xyznpy_file in Path('.').glob('*.xyznpy'):
os.remove(xyznpy)
# New xyznpy files
molecular_system = np.zeros([3, 4, 3], dtype='float64') * puw.unit('nm')
molecular_system[0, 0, :] = [0, 2, -1] * puw.unit('nm')
molecular_system[1, 0, :] = [1, 2, -1] * puw.unit('nm')
molecular_system[2, 0, :] = [0, 2, -1] * puw.unit('nm')
molecular_system[0, 1, :] = [-1, 1, 1] * puw.unit('nm')
molecular_system[1, 1, :] = [-1, 0, 1] * puw.unit('nm')
molecular_system[2, 1, :] = [0, 0, 1] * puw.unit('nm')
molecular_system[0, 2, :] = [-2, 0, 1] * puw.unit('nm')
molecular_system[1, 2, :] = [-2, 0, 0] * puw.unit('nm')
molecular_system[2, 2, :] = [-1, 1, 0] * puw.unit('nm')
molecular_system[0, 3, :] = [-2, -2, -2] * puw.unit('nm')
molecular_system[1, 3, :] = [0, 0, 0] * puw.unit('nm')
molecular_system[2, 3, :] = [2, 2, 2] * puw.unit('nm')
msm.convert(molecular_system, to_form='traj.xyznpy')
def set_dihedral_angles(molecular_system,
quartets=None,
angles=None,
blocks=None,
structure_indices='all',
pbc=True,
in_place=False,
engine='MolSysMT',
check=True):
if check:
from molsysmt.tools.molecular_system import is_molecular_system
if not is_molecular_system(molecular_system):
raise MolecularSystemNeededError()
from molsysmt.topology.get_covalent_blocks import get_covalent_blocks
structure_indices = digest_structure_indices(structure_indices)
if type(quartets) in [list, tuple]:
quartets = np.array(quartets, dtype=int)
elif type(quartets) is np.ndarray:
pass
else:
raise ValueError
shape = quartets.shape
if len(shape) == 1:
if shape[0] == 4:
quartets = quartets.reshape([1, 4])
else:
raise ValueError
elif len(shape) == 2:
if shape[1] != 4:
raise ValueError
else:
raise ValueError
n_atoms = get(molecular_system, target='system', n_atoms=True, check=False)
n_quartets = quartets.shape[0]
n_structures = get(molecular_system,
target='system',
structure_indices=structure_indices,
n_structures=True,
check=False)
angles_units = puw.get_unit(angles)
angles_value = puw.get_value(angles)
if type(angles_value) in [float]:
if (n_quartets == 1 and n_structures == 1):
angles_value = np.array([[angles_value]], dtype=float)
else:
raise ValueError(
"angles do not match the number of frames and quartets")
elif type(angles_value) in [list, tuple]:
angles_value = np.array(angles_value, dtype=float)
elif type(angles_value) is np.ndarray:
pass
else:
raise ValueError
shape = angles_value.shape
if len(shape) == 1:
angles_value = angles_value.reshape([n_structures, n_quartets])
angles = angles_value * angles_units
if engine == 'MolSysMT':
if blocks is None:
blocks = []
for quartet in quartets:
tmp_blocks = get_covalent_blocks(
molecular_system,
remove_bonds=[quartet[1], quartet[2]],
check=False)
blocks.append(tmp_blocks)
coordinates = get(molecular_system,
target='system',
structure_indices=structure_indices,
coordinates=True,
check=False)
if pbc:
box, box_shape = get(molecular_system,
target='system',
structure_indices=structure_indices,
box=True,
box_shape=True,
check=False)
if box_shape is None:
raise ValueError(
"The system has no PBC box. The input argument 'pbc' can not be True."
)
orthogonal = 0
if box_shape is None:
orthogonal = 1
elif box_shape == 'cubic':
orthogonal = 1
else:
orthogonal = 1
box = np.zeros([n_structures, 3, 3]) * puw.unit('nm')
length_units = puw.unit(coordinates)
box = np.asfortranarray(puw.get_value(box, to_unit=length_units),
dtype='float64')
coordinates = np.asfortranarray(puw.get_value(coordinates),
dtype='float64')
angles = np.asfortranarray(puw.get_value(angles), dtype='float64')
aux_blocks = []
aux_atoms_per_block = []
for block in blocks:
aux_atoms_per_block.append(len(block[1]))
aux_blocks.append(list(block[1]))
aux_blocks = np.ravel(aux_blocks)
aux_atoms_per_block = np.array(aux_atoms_per_block, dtype=int)
libgeometry.set_dihedral_angles(coordinates, box, orthogonal, int(pbc),
quartets, angles, aux_blocks,
aux_atoms_per_block, n_quartets,
n_atoms, n_structures,
aux_blocks.shape[0])
coordinates = np.ascontiguousarray(coordinates) * length_units
if in_place:
return set(molecular_system,
target='system',
coordinates=coordinates,
structure_indices=structure_indices,
check=False)
else:
tmp_molecular_system = copy(molecular_system, check=False)
set(tmp_molecular_system,
target='system',
coordinates=coordinates,
structure_indices=structure_indices,
check=False)
return tmp_molecular_system
else:
raise NotImplementedError
def get_dihedral_angles(molecular_system,
dihedral_angle=None,
selection='all',
quartets=None,
structure_indices='all',
syntaxis='MolSysMT',
pbc=False,
check=True):
if check:
from molsysmt.tools.molecular_system import is_molecular_system
if not is_molecular_system(molecular_system):
raise MolecularSystemNeededError()
structure_indices = digest_structure_indices(structure_indices)
if quartets is None:
quartets = get_covalent_dihedral_quartets(
molecular_system,
dihedral_angle=dihedral_angle,
selection=selection,
syntaxis=syntaxis)
elif type(quartets) in [list, tuple]:
quartets = np.array(quartets, dtype=int)
elif type(quartets) is np.ndarray:
pass
else:
raise ValueError
shape = quartets.shape
if len(shape) == 1:
if shape[0] == 4:
quartets = quartets.reshape([1, 4])
else:
raise ValueError
elif len(shape) == 2:
if shape[1] != 4:
raise ValueError
else:
raise ValueError
coordinates = get(molecular_system,
target='system',
structure_indices=structure_indices,
coordinates=True)
n_angles = quartets.shape[0]
n_structures = coordinates.shape[0]
n_atoms = coordinates.shape[1]
if pbc:
box, box_shape = get(molecular_system,
target='system',
structure_indices=structure_indices,
box=True,
box_shape=True)
if box_shape is None:
raise ValueError(
"The system has no PBC box. The input argument 'pbc' can not be True."
)
orthogonal = 0
if box_shape is None:
orthogonal = 1
elif box_shape == 'cubic':
orthogonal = 1
else:
orthogonal = 1
box = np.zeros([n_structures, 3, 3]) * puw.unit('nm')
box = np.asfortranarray(puw.get_value(box, to_unit='nm'), dtype='float64')
coordinates = np.asfortranarray(puw.get_value(coordinates, to_unit='nm'),
dtype='float64')
angles = libgeometry.dihedral_angles(coordinates, box, orthogonal,
int(pbc), quartets, n_angles, n_atoms,
n_structures)
angles = np.ascontiguousarray(angles) * puw.unit('degrees')
return angles
def charge(molecular_system,
target='group',
selection='all',
type=None,
engine='OpenMM'):
from molsysmt._private._digestion import digest_engine, digest_target
engine = digest_engine(engine)
target = digest_target(target)
if type in ['physical_pH7', 'collantes']:
from molsysmt.basic import get
from molsysmt.physico_chemical_properties.groups.charge import units
if type == 'physical_pH7':
from molsysmt.physico_chemical_properties.groups.charge import physical_pH7 as values, units
elif type == 'collantes':
from molsysmt.physico_chemical_properties.groups.charge import collantes as values, units
else:
raise NotImplementedError()
output = []
if target == 'atom':
raise ValueError(
'Only targets bigger than, or equal to, groups are allowed when type is "physical_pH7" or "collantes"'
)
elif target == 'group':
group_names = get(molecular_system,
target=target,
selection=selection,
group_name=True)
for ii in group_names:
output.append(values[ii.upper()])
elif target in ['component', 'molecule', 'chain', 'entity']:
group_names = get(molecular_system,
target=target,
selection=selection,
group_name=True)
for aux in group_names:
output.append(np.sum([values[ii.upper()] for ii in aux]))
elif target == 'system':
group_names = get(molecular_system,
target='group',
selection='all',
group_names=True)
output.append(np.sum([values[ii.upper()] for ii in group_names]))
if target == 'system':
output = output[0] * puw.unit(units)
else:
output = puw.quantity(np.array(output), units)
else:
from molsysmt._private._digestion import digest_molecular_system
from molsysmt.basic import get, convert, get_form
molecular_system = digest_molecular_system(molecular_system)
if engine == 'OpenMM':
from openmm import NonbondedForce
openmm_system = convert(molecular_system, to_form='openmm.System')
output = []
if target == 'atom':
atom_indices = get(molecular_system,
target=target,
selection=selection,
atom_index=True)
for force_index in range(openmm_system.getNumForces()):
force = openmm_system.getForce(force_index)
if isinstance(force, NonbondedForce):
for index in atom_indices:
output.append(
force.getParticleParameters(
int(index))[0]._value)
output = np.array(output, dtype=float).round(4) * puw.unit('e')
elif target in [
'group', 'component', 'chain', 'molecule', 'entity'
]:
atom_indices = get(molecular_system,
target=target,
selection=selection,
atom_index=True)
for force_index in range(openmm_system.getNumForces()):
force = openmm_system.getForce(force_index)
if isinstance(force, NonbondedForce):
for atom_list in atom_indices:
var_aux = 0.0
for index in atom_list:
var_aux += force.getParticleParameters(
int(index))[0]._value
output.append(var_aux)
output = np.array(output, dtype=float).round(4) * puw.unit('e')
elif target == 'system':
atom_indices = get(molecular_system,
target='atom',
selection='all',
index=True)
var_aux = 0.0
for force_index in range(openmm_system.getNumForces()):
force = openmm_system.getForce(force_index)
if isinstance(force, NonbondedForce):
for index in atom_indices:
var_aux += force.getParticleParameters(
int(index))[0]._value
output = np.round(var_aux, 4) * puw.unit('e')
else:
raise NotImplementedError
return output