Convert an OPTIMADE structure, in the format of
StructureResource
to a PDB file or PDBx/mmCIF file (Protein Data Bank).
For more information on the file formats, see
this FAQ page
from the wwPDB website.
Note
These conversion functions are inspired heavily by the similar conversion
functions in the ASE library.
See here (PDB)
and here (PDBx/mmCIF) for the original ASE code.
For more information on the ASE library, see their documentation.
These conversion functions both rely on the NumPy library.
Warning
Currently, the PDBx/mmCIF conversion function is not parsing as a complete PDBx/mmCIF file.
get_pdb(optimade_structure)
Write Protein Data Bank (PDB) structure in the old PDB format from OPTIMADE structure.
Parameters:
Returns:
| Type |
Description |
str
|
A PDB file as a single Python str object.
|
Source code in optimade/adapters/structures/proteindatabank.py
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280 | def get_pdb(
optimade_structure: OptimadeStructure,
) -> str:
"""Write Protein Data Bank (PDB) structure in the old PDB format from OPTIMADE structure.
Parameters:
optimade_structure: OPTIMADE structure.
Returns:
A PDB file as a single Python `str` object.
"""
if globals().get("np", None) is None:
warn(NUMPY_NOT_FOUND, AdapterPackageNotFound)
return None # type: ignore[return-value]
pdb = ""
attributes = optimade_structure.attributes
rotation = None
if valid_lattice_vector(attributes.lattice_vectors): # type: ignore[arg-type]
currentcell = np.asarray(attributes.lattice_vectors)
cellpar = cell_to_cellpar(currentcell)
exportedcell = cellpar_to_cell(cellpar)
rotation = np.linalg.solve(currentcell, exportedcell)
# Setting Z-value = 1 and using P1 since we have all atoms defined explicitly
Z = 1
spacegroup = "P 1"
pdb += (
f"CRYST1{cellpar[0]:9.3f}{cellpar[1]:9.3f}{cellpar[2]:8.3f}"
f"{cellpar[3]:7.2f}{cellpar[4]:7.2f}{cellpar[5]:7.2f} {spacegroup:11s}{Z:4d}\n"
)
for i, vector in enumerate(scaled_cell(currentcell)):
pdb += f"SCALE{i + 1} {vector[0]:10.6f}{vector[1]:10.6f}{vector[2]:10.6f} {0:10.5f}\n"
# There is a limit of 5 digit numbers in this field.
pdb_maxnum = 100000
bfactor = 1.0
pdb += "MODEL 1\n"
species: dict[str, OptimadeStructureSpecies] = {
species.name: species
for species in attributes.species # type:ignore[union-attr]
}
sites = np.asarray(attributes.cartesian_site_positions)
if rotation is not None:
sites = sites.dot(rotation)
for site_number in range(attributes.nsites): # type: ignore[arg-type]
species_name = attributes.species_at_sites[site_number] # type: ignore[index]
site = sites[site_number]
current_species = species[species_name]
for index, symbol in enumerate(current_species.chemical_symbols):
if symbol == "vacancy":
continue
label = species_name
if len(current_species.chemical_symbols) > 1:
if (
"vacancy" in current_species.chemical_symbols
and len(current_species.chemical_symbols) == 2
):
pass
else:
label = f"{symbol}{index + 1}"
pdb += (
f"ATOM {site_number % pdb_maxnum:5d} {label:4} MOL 1 "
f"{site[0]:8.3f}{site[1]:8.3f}{site[2]:8.3f}"
f"{current_species.concentration[index]:6.2f}"
f"{bfactor:6.2f} {symbol.upper():2} \n"
)
pdb += "ENDMDL\n"
return pdb
|
get_pdbx_mmcif(optimade_structure)
Write Protein Data Bank (PDB) structure in the PDBx/mmCIF format from OPTIMADE structure.
Warning
The result of this function can currently not be parsed as a complete PDBx/mmCIF file.
Parameters:
Return
A modern PDBx/mmCIF file as a single Python str object.
Source code in optimade/adapters/structures/proteindatabank.py
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197 | def get_pdbx_mmcif(
optimade_structure: OptimadeStructure,
) -> str:
"""Write Protein Data Bank (PDB) structure in the PDBx/mmCIF format from OPTIMADE structure.
Warning:
The result of this function can currently not be parsed as a complete PDBx/mmCIF file.
Parameters:
optimade_structure: OPTIMADE structure.
Return:
A modern PDBx/mmCIF file as a single Python `str` object.
"""
if globals().get("np", None) is None:
warn(NUMPY_NOT_FOUND, AdapterPackageNotFound)
return None # type: ignore[return-value]
cif = """#
# Created from an OPTIMADE structure.
#
# See https://www.optimade.org and/or
# https://github.com/Materials-Consortia/OPTIMADE for more information.
#
# CIF 2.0 format, specifically mmCIF (PDBx).
# See http://mmcif.wwpdb.org for more information.
#
"""
entry_id = f"{optimade_structure.type}{optimade_structure.id}"
cif += f"data_{entry_id}\n_entry.id {entry_id}\n#\n"
attributes = optimade_structure.attributes
# Do this only if there's three non-zero lattice vectors
if valid_lattice_vector(attributes.lattice_vectors): # type: ignore[arg-type]
a_vector, b_vector, c_vector, alpha, beta, gamma = cell_to_cellpar(
attributes.lattice_vectors # type: ignore[arg-type]
)
cif += (
f"_cell.entry_id {entry_id}\n"
f"_cell.length_a {a_vector:g}\n"
f"_cell.length_b {b_vector:g}\n"
f"_cell.length_c {c_vector:g}\n"
f"_cell.angle_alpha {alpha:g}\n"
f"_cell.angle_beta {beta:g}\n"
f"_cell.angle_gamma {gamma:g}\n"
"_cell.Z_PDB 1\n#\n"
)
cif += (
f"_symmetry.entry_id {entry_id}\n"
"_symmetry.space_group_name_H-M 'P 1'\n"
"_symmetry.Int_Tables_number 1\n#\n"
)
# Since some structure viewers are having issues with cartesian coordinates,
# we calculate the fractional coordinates if this is a 3D structure and we have all the necessary information.
if not hasattr(attributes, "fractional_site_positions"):
attributes.fractional_site_positions = fractional_coordinates(
cell=attributes.lattice_vectors, # type: ignore[arg-type]
cartesian_positions=attributes.cartesian_site_positions, # type: ignore[arg-type]
)
# NOTE: The following lines are perhaps needed to create a "valid" PDBx/mmCIF file.
# However, at the same time, the information here is "default" and will for all structures "at this moment in time"
# be the same. I.e., no information is gained by adding this now.
# If it is found that they indeed are needed to create a "valid" PDBx/mmCIF file, they should be included in the output.
# cif += (
# "loop_\n"
# "_struct_asym.id\n"
# "_struct_asym.entity_id\n"
# "A 1\n#\n" # At this point, not using this feature.
# )
# cif += (
# "loop_\n"
# "_chem_comp.id\n"
# "X\n#\n" # At this point, not using this feature.
# )
# cif += (
# "loop_\n"
# "_entity.id\n"
# "1\n#\n" # At this point, not using this feature.
# )
# NOTE: This is otherwise a bit ahead of its time, since this OPTIMADE property is part of an open PR.
# See https://github.com/Materials-Consortia/OPTIMADE/pull/206
coord_type = (
"fract" if hasattr(attributes, "fractional_site_positions") else "Cartn"
)
cif += (
"loop_\n"
"_atom_site.group_PDB\n" # Always "ATOM"
"_atom_site.id\n" # number (1-counting)
"_atom_site.type_symbol\n" # species.chemical_symbols
"_atom_site.label_atom_id\n" # species.checmical_symbols symbol + number
# For these next keys, see the comment above.
# "_atom_site.label_asym_id\n" # Will be set to "A" _struct_asym.id above
# "_atom_site.label_comp_id\n" # Will be set to "X" _chem_comp.id above
# "_atom_site.label_entity_id\n" # Will be set to "1" _entity.id above
# "_atom_site.label_seq_id\n"
"_atom_site.occupancy\n" # species.concentration
f"_atom_site.{coord_type}_x\n" # cartesian_site_positions
f"_atom_site.{coord_type}_y\n" # cartesian_site_positions
f"_atom_site.{coord_type}_z\n" # cartesian_site_positions
"_atom_site.thermal_displace_type\n" # Set to 'Biso'
"_atom_site.B_iso_or_equiv\n" # Set to 1.0:f
)
if coord_type == "fract":
sites = attributes.fractional_site_positions
else:
sites = attributes.cartesian_site_positions
species: dict[str, OptimadeStructureSpecies] = {
species.name: species
for species in attributes.species # type: ignore[union-attr]
}
for site_number in range(attributes.nsites): # type: ignore[arg-type]
species_name = attributes.species_at_sites[site_number] # type: ignore[index]
site = sites[site_number]
current_species = species[species_name]
for index, symbol in enumerate(current_species.chemical_symbols):
if symbol == "vacancy":
continue
label = f"{species_name.upper()}{site_number + 1}"
if len(current_species.chemical_symbols) > 1:
if (
"vacancy" in current_species.chemical_symbols
and len(current_species.chemical_symbols) == 2
):
pass
else:
label = f"{symbol.upper()}{index + 1}"
cif += (
f"ATOM {site_number + 1:5d} {symbol} {label:8} "
f"{current_species.concentration[index]:6.4f} {site[0]:8.5f} "
f"{site[1]:8.5f} {site[2]:8.5f} {'Biso':4} {'1.000':6}\n"
)
return cif
|