def get_covalent_chains(molecular_system,
chain=None,
selection='all',
syntaxis='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_bondgraph import get_bondgraph
if selection is 'all':
mask = None
else:
mask = select(molecular_system,
selection=selection,
syntaxis=syntaxis,
check=False)
chain_atom_indices = []
for sel_in_chain in chain:
atom_indices = select(molecular_system,
selection=sel_in_chain,
mask=mask)
chain_atom_indices.append(atom_indices)
atom_indices = np.sort(np.unique(np.concatenate(chain_atom_indices)))
graph = get_bondgraph(molecular_system,
selection=atom_indices,
nodes_name='atom_index',
check=False)
n_slaves = len(chain_atom_indices)
output = [[ii] for ii in chain_atom_indices[0]]
for slave_index in range(n_slaves):
chain_atom_indices[slave_index] = set(chain_atom_indices[slave_index])
for slave_index in range(1, n_slaves):
slave_preindex = slave_index - 1
tmp_output = output.copy()
output = []
for chain in tmp_output:
for ii in graph.neighbors(chain[slave_preindex]):
if ii in chain_atom_indices[slave_index]:
new_chain = chain.copy()
new_chain.append(ii)
output.append(new_chain)
del (graph)
return np.array(output, dtype=int)
def get_bondgraph(molecular_system, nodes_name='atom_index', selection='all', syntaxis='MolSysMT',
to_form='networkx.Graph', check=True):
# tengo que incluir la forma NetworkX para convertir.
# en el caso de convert, lo que obtengo es una red con el nombre de los nodos dado por la
# con el indice de atomo empezando por cero (todavía no lo he decidido)
# el caso de este método es que nos da un grafo con los nodos nombrados según
# nodes_name en ['atom_index', 'short_string', 'long_string']
if check:
from molsysmt.tools.molecular_system import is_molecular_system
if not is_molecular_system(molecular_system):
raise MolecularSystemNeededError()
tmp_molecular_system = None
to_form = digest_to_form(to_form)
if to_form == 'networkx.Graph':
G = Graph()
if nodes_name is 'atom_index':
atom_indices, bonded_atoms = get(molecular_system, target='atom', selection=selection,
syntaxis=syntaxis, atom_index=True,
inner_bonded_atoms=True, check=False)
G.add_nodes_from(atom_indices)
G.add_edges_from(bonded_atoms)
else:
raise NotImplementedError
tmp_molecular_system = G
else:
raise NotImplementedError
return tmp_molecular_system
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 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_covalent_dihedral_quartets(molecular_system,
dihedral_angle=None,
with_blocks=False,
selection='all',
syntaxis='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
from molsysmt.topology.get_covalent_chains import get_covalent_chains
if dihedral_angle is not None:
if dihedral_angle == 'phi':
chain = [
'atom_name=="C"', 'atom_name=="N"', 'atom_name=="CA"',
'atom_name=="C"'
]
elif dihedral_angle == 'psi':
chain = [
'atom_name=="N"', 'atom_name=="CA"', 'atom_name=="C"',
'atom_name=="N"'
]
elif dihedral_angle == 'omega':
chain = [
'atom_name==["CA","CH3"]', 'atom_name=="C"', 'atom_name=="N"',
'atom_name==["CA","CH3"]'
]
elif dihedral_angle == 'chi1':
chain = [
'atom_name=="N"', 'atom_name=="CA"', 'atom_name=="CB"',
'atom_name==["CG","CG1","OG","OG1","SG"]'
] # flexible but PRO
elif dihedral_angle == 'chi2':
chain = [
'atom_name=="CA"', 'atom_name=="CB"',
'atom_name==["CG","CG1"]',
'atom_name==["CD","CD1","SD","OD1","ND1"]'
] # flexible but PRO
elif dihedral_angle == 'chi3':
chain = [
'atom_name=="CB"', 'atom_name=="CG"', 'atom_name==["CD","SD"]',
'atom_name==["NE","OE1","CE"]'
]
elif dihedral_angle == 'chi4':
chain = [
'atom_name=="CG"', 'atom_name=="CD"', 'atom_name==["NE","CE"]',
'atom_name==["CZ","NZ"]'
]
elif dihedral_angle == 'chi5':
chain = [
'atom_name=="CD"', 'atom_name=="NE"', 'atom_name=="CZ"',
'atom_name=="NH1"'
]
elif dihedral_angle == 'phi-psi':
tmp_phi = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='phi',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_psi = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='psi',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
if not with_blocks:
tmp_angs = [ii for ii in [tmp_phi, tmp_psi] if ii.shape[0] > 0]
tmp_angs = np.vstack(tmp_angs)
return tmp_angs
else:
tmp_angs = [
ii for ii in [tmp_phi[0], tmp_psi[0]] if ii.shape[0] > 0
]
tmp_angs = np.vstack(tmp_angs)
tmp_blocks = [
ii for ii in [tmp_phi[1], tmp_psi[1]] if ii.shape[0] > 0
]
tmp_blocks = np.vstack(tmp_blocks)
return tmp_angs, tmp_blocks
elif dihedral_angle == 'phi-psi-omega':
tmp_phi = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='phi',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_psi = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='psi',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_omega = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='omega',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
if not with_blocks:
tmp_angs = [
ii for ii in [tmp_phi, tmp_psi, tmp_omega]
if ii.shape[0] > 0
]
tmp_angs = np.vstack(tmp_angs)
return tmp_angs
else:
tmp_angs = [
ii for ii in [tmp_phi[0], tmp_psi[0], tmp_omega[0]]
if ii.shape[0] > 0
]
tmp_angs = np.vstack(tmp_angs)
tmp_blocks = [
ii for ii in [tmp_phi[1], tmp_psi[1], tmp_omega[1]]
if ii.shape[0] > 0
]
tmp_blocks = np.vstack(tmp_blocks)
return tmp_angs, tmp_blocks
elif dihedral_angle == 'all':
tmp_phi = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='phi',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_psi = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='psi',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_omega = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='omega',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_chi1 = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='chi1',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_chi2 = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='chi2',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_chi3 = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='chi3',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_chi4 = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='chi4',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
tmp_chi5 = get_covalent_dihedral_quartets(molecular_system,
dihedral_angle='chi5',
with_blocks=with_blocks,
selection=selection,
syntaxis=syntaxis,
check=False)
if not with_blocks:
tmp_angs = [
ii for ii in [
tmp_phi, tmp_psi, tmp_omega, tmp_chi1, tmp_chi2,
tmp_chi3, tmp_chi4, tmp_chi5
] if ii.shape[0] > 0
]
tmp_angs = np.vstack(tmp_angs)
return tmp_angs
else:
tmp_angs = [
ii for ii in [
tmp_phi[0], tmp_psi[0], tmp_omega[0], tmp_chi1[0],
tmp_chi2[0], tmp_chi3[0], tmp_chi4[0], tmp_chi5[0]
] if ii.shape[0] > 0
]
tmp_angs = np.vstack(tmp_angs)
tmp_blocks = [
ii for ii in [
tmp_phi[1], tmp_psi[1], tmp_omega[1], tmp_chi1[1],
tmp_chi2[1], tmp_chi3[1], tmp_chi4[1], tmp_chi5[1]
] if ii.shape[0] > 0
]
tmp_blocks = np.vstack(tmp_blocks)
return tmp_angs, tmp_blocks
else:
raise ValueError
quartets = get_covalent_chains(molecular_system,
chain=chain,
selection=selection,
syntaxis=syntaxis,
check=False)
if with_blocks:
n_quartets = quartets.shape[0]
blocks = []
for quartet_index in range(n_quartets):
quartet = quartets[quartet_index]
component_index = get(molecular_system,
target='atom',
indices=quartet[1],
component_index=True,
check=False)[0]
component_atom_indices = get(molecular_system,
target='component',
indices=component_index,
atom_index=True,
check=False)[0]
tmp_blocks = get_covalent_blocks(
molecular_system,
remove_bonds=[quartet[1], quartet[2]],
output_form='sets',
check=False)
blocks_in_component = []
for block in tmp_blocks:
if block.issubset(component_atom_indices):
blocks_in_component.append(block)
blocks.append(blocks_in_component)
return quartets, np.array(blocks)
else:
return quartets