pdb_cpp package

Subpackages

Submodules

pdb_cpp.TMalign module

Python wrappers around the TM-align / secondary-structure core.

pdb_cpp.TMalign.compute_secondary_structure(coor, **kwargs)[source]

Compute secondary structure using the TM-align core.

You should cite the original TM-align paper if you use this function: Zhang, Y., & Skolnick, J. NAR (2005).

Parameters:

coorCoor: The Coor object containing the protein structure.
**kwargsdict: Additional keyword arguments for the compute_SS function.

Returns:

list: List of per-chain secondary-structure dictionaries per model.

pdb_cpp.alignment module

Sequence-alignment convenience wrappers.

The compiled core implements the actual alignment algorithms; this module keeps the Python surface small and provides packaged defaults such as BLOSUM62.

pdb_cpp.alignment.align_chain_permutation(coor_1, coor_2, back_names=None, matrix_file=None, frame_ref=0)[source]

Align structures by permuting chain order and selecting the best RMSD.

Parameters:

coor_1Coor: First coordinate object.
coor_2Coor: Second coordinate object.
back_nameslist[str], optional: Backbone atom names to use.
matrix_filestr, optional: Path to the scoring matrix file. If None, uses packaged BLOSUM62.
frame_refint, optional: Reference frame index in coor_2.

Returns:

tuple: RMSD list and index mappings from the best permutation.

pdb_cpp.alignment.align_seq(seq1, seq2, gap_cost=-11, gap_ext=-1, matrix_file=None)[source]

Align two sequences using a simple scoring system.

Parameters:

seq1str: First sequence.
seq2str: Second sequence.
gap_costint, optional: Cost for opening a gap.
gap_extint, optional: Cost for extending a gap.
matrix_filestr, optional: Path to the scoring matrix file. If None, uses packaged BLOSUM62.

Returns:

tuple: Tuple containing the aligned sequences (seq1, seq2) and score.

pdb_cpp.alignment.print_align_seq(seq_1, seq_2, line_len=80)[source]

Print the aligned sequences with a fixed line length.

Parameters:

seq_1str: First sequence.
seq_2str: Second sequence.
line_lenint, optional: Length of each output line.

Returns:

None

pdb_cpp.cli_dockq module

Command-line interface for DockQ scoring.

This module turns the analysis helpers into a small CLI that can print either human-readable reports or JSON output.

pdb_cpp.cli_dockq.main(argv: list[str] | None = None) → int[source]: Run the DockQ command-line interface.

pdb_cpp.core module

class pdb_cpp.core.Alignment_cpp

Bases: pybind11_object

Attributes:

score: Alignment score
seq1: Aligned sequence 1
seq2: Aligned sequence 2

property score: Alignment score

property seq1: Aligned sequence 1

property seq2: Aligned sequence 2

class pdb_cpp.core.Coor(coor_in=None, pdb_id=None, format='', rcsb_structure='asymmetric_unit', assembly_id=1, cache_dir=None, force_download=False)

Bases: pybind11_object

Attributes:

active_model
alterloc_str
beta
chain
chain_str
conect
elem_str
insertres_str
len: Return the number of atoms in the selection.
model_num: Return the number of models in the selection.
models: Return all models of the selection.
name
name_str
num
occ
resid
resname
resname_str
uniq_resid
x
xyz
y
z

Methods

`add_Model`(self, arg0)
`clear`(self)
`get_Models`(self, arg0)
`get_aa_DL_seq`(self[, gap_in_seq, frame])	Get amino-acid sequences with D-residues encoded as lowercase
`get_aa_na_seq`(self[, gap_in_seq, frame])	Get amino-acid and nucleic-acid sequences per chain
`get_aa_seq`(self[, gap_in_seq, frame])	Get amino-acid sequences per chain
`get_aa_sequences`(self[, gap_in_seq, frame])	Get the amino acid sequence, optionally including gaps and specifying a frame index
`get_aa_sequences_dl`(self[, gap_in_seq, frame])	Get the amino acid sequence with D-residues encoded as lowercase
`get_all_Models`(self)
`get_alterloc`(self[, frame])
`get_beta`(self[, frame])
`get_chain`(self[, frame])
`get_elem`(self[, frame])
`get_index_select`(self, selection[, frame])	Get indices of atoms based on a selection string and an optional frame index
`get_insertres`(self[, frame])
`get_name`(self[, frame])
`get_num`(self[, frame])
`get_occ`(self[, frame])
`get_resid`(self[, frame])
`get_resname`(self[, frame])
`get_uniq_chain`(self)
`get_uniq_chain_str`(self)
`get_uniqresid`(self[, frame])
`get_x`(self[, frame])
`get_y`(self[, frame])
`get_z`(self[, frame])
`model_size`(self)
`read`(self, filename[, format])	Read a structure file; format can be 'pdb', 'cif', 'pqr', or 'gro' (default: infer from extension)
`remove_incomplete_backbone_residues`(self[, ...])	Remove residues with incomplete backbone atoms
`select_atoms`(self, selection[, frame])	Select atoms based on a selection string and an optional frame index
`select_bool_index`(self, arg0)
`set_alterloc`(self, arg0, arg1)
`set_beta`(self, arg0, arg1)
`set_chain`(self, arg0, arg1)
`set_elem`(self, arg0, arg1)
`set_insertres`(self, arg0, arg1)
`set_name`(self, arg0, arg1)
`set_num`(self, arg0, arg1)
`set_occ`(self, arg0, arg1)
`set_resid`(self, arg0, arg1)
`set_resname`(self, arg0, arg1)
`set_uniqresid`(self, arg0, arg1)
`set_x`(self, arg0, arg1)
`set_y`(self, arg0, arg1)
`set_z`(self, arg0, arg1)
`size`(self)
`write`(self, arg0)

property active_model

add_Model(self: pdb_cpp.core.Coor, arg0: pdb_cpp.core.Model) → None

property alterloc_str

property beta

property chain

property chain_str

clear(self: pdb_cpp.core.Coor) → None

property conect

property elem_str

get_Models(self: pdb_cpp.core.Coor, arg0: int) → pdb_cpp.core.Model

get_aa_DL_seq(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → dict[str, str]: Get amino-acid sequences with D-residues encoded as lowercase

get_aa_na_seq(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → dict[str, str]: Get amino-acid and nucleic-acid sequences per chain

get_aa_seq(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → dict[str, str]: Get amino-acid sequences per chain

get_aa_sequences(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → list[str]: Get the amino acid sequence, optionally including gaps and specifying a frame index

get_aa_sequences_dl(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → list[str]: Get the amino acid sequence with D-residues encoded as lowercase

get_all_Models(self: pdb_cpp.core.Coor) → list[pdb_cpp.core.Model]

get_alterloc(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(2)]]

get_beta(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_chain(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(2)]]

get_elem(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(5)]]

get_index_select(self: pdb_cpp.core.Coor, selection: str, frame: int = 0) → list[int]: Get indices of atoms based on a selection string and an optional frame index

get_insertres(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(2)]]

get_name(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(5)]]

get_num(self: pdb_cpp.core.Coor, frame: int = 0) → list[int]

get_occ(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_resid(self: pdb_cpp.core.Coor, frame: int = 0) → list[int]

get_resname(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(5)]]

get_uniq_chain(self: pdb_cpp.core.Coor) → list[Annotated[list[str], FixedSize(2)]]

get_uniq_chain_str(self: pdb_cpp.core.Coor) → list[str]

get_uniqresid(self: pdb_cpp.core.Coor, frame: int = 0) → list[int]

get_x(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_y(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_z(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

property insertres_str

property len

Return the number of atoms in the selection.

Returns:

int: Number of atoms.

property model_num

Return the number of models in the selection.

Returns:

int: Number of models.

model_size(self: pdb_cpp.core.Coor) → int

property models

Return all models of the selection.

Returns:

list[Model]: List of models.

property name

property name_str

property num

property occ

read(self: pdb_cpp.core.Coor, filename: str, format: str = '') → bool: Read a structure file; format can be ‘pdb’, ‘cif’, ‘pqr’, or ‘gro’ (default: infer from extension)

remove_incomplete_backbone_residues(self: pdb_cpp.core.Coor, back_atom: list[str] = ['CA', 'C', 'N', 'O']) → pdb_cpp.core.Coor: Remove residues with incomplete backbone atoms

property resid

property resname

property resname_str

select_atoms(self: pdb_cpp.core.Coor, selection: str, frame: int = 0) → pdb_cpp.core.Coor: Select atoms based on a selection string and an optional frame index

select_bool_index(self: pdb_cpp.core.Coor, arg0: list[bool]) → pdb_cpp.core.Coor

set_alterloc(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_beta(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_chain(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_elem(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_insertres(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_name(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_num(self: pdb_cpp.core.Coor, arg0: int, arg1: int) → None

set_occ(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_resid(self: pdb_cpp.core.Coor, arg0: int, arg1: int) → None

set_resname(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_uniqresid(self: pdb_cpp.core.Coor, arg0: int, arg1: int) → None

set_x(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_y(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_z(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

size(self: pdb_cpp.core.Coor) → int

property uniq_resid

write(self: pdb_cpp.core.Coor, arg0: str) → bool

property x

property xyz

property y

property z

class pdb_cpp.core.HBond

Bases: pybind11_object

Attributes:

acceptor_chain
acceptor_name
acceptor_resid
acceptor_resname
acceptor_xyz
angle_DHA
dist_DA
dist_HA
donor_chain
donor_h_name
donor_h_xyz
donor_heavy_name
donor_heavy_xyz
donor_resid
donor_resname

property acceptor_chain

property acceptor_name

property acceptor_resid

property acceptor_resname

property acceptor_xyz

property angle_DHA

property dist_DA

property dist_HA

property donor_chain

property donor_h_name

property donor_h_xyz

property donor_heavy_name

property donor_heavy_xyz

property donor_resid

property donor_resname

class pdb_cpp.core.Model

Bases: pybind11_object

Attributes:

alterloc_str
beta
chain
chain_str
elem_str
insertres_str
len: Return the number of atoms in the selection.
name
name_str
num
occ
resid
resname
resname_str
uniq_resid
x
xyz
y
z

Methods

`addAtom`(self, arg0, arg1, arg2, arg3, arg4, ...)
`clear`(self)
`get_alterloc`(self)
`get_beta`(self)
`get_centroid`(args, *kwargs)	Overloaded function.
`get_chain`(self)
`get_elem`(self)
`get_field`(self)
`get_insertres`(self)
`get_name`(self)
`get_num`(self)
`get_occ`(self)
`get_resid`(self)
`get_resname`(self)
`get_uniqresid`(self)
`get_x`(self)
`get_y`(self)
`get_z`(self)
`select_atoms`(self, arg0)
`set_alterloc`(self, arg0, arg1)
`set_beta`(self, arg0, arg1)
`set_chain`(self, arg0, arg1)
`set_elem`(self, arg0, arg1)
`set_insertres`(self, arg0, arg1)
`set_name`(self, arg0, arg1)
`set_num`(self, arg0, arg1)
`set_occ`(self, arg0, arg1)
`set_resid`(self, arg0, arg1)
`set_resname`(self, arg0, arg1)
`set_uniqresid`(self, arg0, arg1)
`set_x`(self, arg0, arg1)
`set_y`(self, arg0, arg1)
`set_z`(self, arg0, arg1)
`size`(self)

addAtom(self: pdb_cpp.core.Model, arg0: int, arg1: Annotated[list[str], FixedSize(5)], arg2: Annotated[list[str], FixedSize(5)], arg3: int, arg4: Annotated[list[str], FixedSize(2)], arg5: float, arg6: float, arg7: float, arg8: float, arg9: float, arg10: Annotated[list[str], FixedSize(2)], arg11: Annotated[list[str], FixedSize(5)], arg12: Annotated[list[str], FixedSize(2)], arg13: bool, arg14: int) → bool

property alterloc_str

property beta

property chain

property chain_str

clear(self: pdb_cpp.core.Model) → None

property elem_str

get_alterloc(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(2)]]

get_beta(self: pdb_cpp.core.Model) → list[float]

get_centroid(*args, **kwargs)

Overloaded function.

get_centroid(self: pdb_cpp.core.Model) -> Annotated[list[float], FixedSize(3)]

Calculate centroid of all atoms in the model

get_centroid(self: pdb_cpp.core.Model, indices: list[int]) -> Annotated[list[float], FixedSize(3)]

Calculate centroid of atoms at specified indices

get_chain(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(2)]]

get_elem(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(5)]]

get_field(self: pdb_cpp.core.Model) → list[bool]

get_insertres(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(2)]]

get_name(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(5)]]

get_num(self: pdb_cpp.core.Model) → list[int]

get_occ(self: pdb_cpp.core.Model) → list[float]

get_resid(self: pdb_cpp.core.Model) → list[int]

get_resname(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(5)]]

get_uniqresid(self: pdb_cpp.core.Model) → list[int]

get_x(self: pdb_cpp.core.Model) → list[float]

get_y(self: pdb_cpp.core.Model) → list[float]

get_z(self: pdb_cpp.core.Model) → list[float]

property insertres_str

property len

Return the number of atoms in the selection.

Returns:

int: Number of atoms.

property name

property name_str

property num

property occ

property resid

property resname

property resname_str

select_atoms(self: pdb_cpp.core.Model, arg0: str) → list[bool]

set_alterloc(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_beta(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

set_chain(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_elem(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_insertres(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_name(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_num(self: pdb_cpp.core.Model, arg0: int, arg1: int) → None

set_occ(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

set_resid(self: pdb_cpp.core.Model, arg0: int, arg1: int) → None

set_resname(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_uniqresid(self: pdb_cpp.core.Model, arg0: int, arg1: int) → None

set_x(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

set_y(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

set_z(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

size(self: pdb_cpp.core.Model) → int

property uniq_resid

property x

property xyz

property y

property z

class pdb_cpp.core.TMalignResult

Bases: pybind11_object

Attributes:

L_ali
Liden
TM1
TM2
TM_ali
rmsd
rotation
seqM
seqxA
seqyA
translation

property L_ali

property Liden

property TM1

property TM2

property TM_ali

property rmsd

property rotation

property seqM

property seqxA

property seqyA

property translation

pdb_cpp.core.align_chain_permutation(coor_1: pdb_cpp.core.Coor, coor_2: pdb_cpp.core.Coor, back_names: list[str] = ['C', 'N', 'O', 'CA'], matrix_file: str = '', frame_ref: int = 0) → tuple[list[float], tuple[list[int], list[int]]]: Align structures by permuting chain order and selecting the best RMSD.

pdb_cpp.core.align_index_based(coor_1: pdb_cpp.core.Coor, coor_2: pdb_cpp.core.Coor, index_1: list[int], index_2: list[int], frame_ref: int = 0) → tuple[list[float], list[int], list[int]]: Align two coordinate structures using pre-computed atom index pairs, skipping the sequence-alignment step. Accepts non-sequential / non-contiguous index lists. Returns (rmsds, index_1, index_2).

pdb_cpp.core.align_seq_based(coor_1: pdb_cpp.core.Coor, coor_2: pdb_cpp.core.Coor, chain_1: list[str] = ['A'], chain_2: list[str] = ['A'], back_names: list[str] = ['C', 'N', 'O', 'CA'], matrix_file: str = '', frame_ref: int = 0) → tuple[list[float], list[int], list[int]]: Align two coordinate structures using sequence based alignment

pdb_cpp.core.compute_SS(coor: pdb_cpp.core.Coor, gap_in_seq: bool = False) → list[list[str]]: Compute secondary structure for all models in a Coor object

pdb_cpp.core.compute_dihedrals(pts: numpy.ndarray[numpy.float32]) → numpy.ndarray[numpy.float32]

Compute all consecutive dihedral angles from an ordered (N, 3) float array.

Parameters:

ptsndarray, shape (N, 3): Ordered 3-D coordinates (e.g. consecutive CA positions).

Returns:

ndarray, shape (N-3,): Dihedral angles in degrees. Returns an empty array when N < 4.

pdb_cpp.core.compute_hbonds(donor_model: pdb_cpp.core.Model, acceptor_model: pdb_cpp.core.Model, full_model: pdb_cpp.core.Model, dist_DA_cutoff: float = 3.5, dist_HA_cutoff: float = 2.5, angle_cutoff: float = 90.0) → list[pdb_cpp.core.HBond]

Compute hydrogen bonds between two selections using Baker & Hubbard geometric criteria.

Parameters:

donor_modelModel: Model containing potential donor atoms (a subselection of a frame).
acceptor_modelModel: Model containing potential acceptor atoms (a subselection of a frame).
full_modelModel: The complete frame used to reconstruct backbone N-H positions.
dist_DA_cutofffloat, optional: Maximum donor-heavy to acceptor distance in Å (default 3.5).
dist_HA_cutofffloat, optional: Maximum hydrogen to acceptor distance in Å (default 2.5).
angle_cutofffloat, optional: Minimum D-H···A angle in degrees (default 90).

Returns:

list[HBond]: List of detected hydrogen bonds with full geometry information.

pdb_cpp.core.compute_sasa(model: pdb_cpp.core.Model, probe_radius: float = 1.399999976158142, n_points: int = 960, include_hydrogen: bool = False, by_atom: bool = False) → dict: Compute solvent-accessible surface area for one Model with a Shrake-Rupley sampler

pdb_cpp.core.coor_align(coor_1: pdb_cpp.core.Coor, coor_2: pdb_cpp.core.Coor, index_1: list[int], index_2: list[int], frame_ref: int = 0) → None: Align two coordinate structures using quaternion-based rotation

pdb_cpp.core.distance_matrix(xyz_a: numpy.ndarray[numpy.float32], xyz_b: numpy.ndarray[numpy.float32]) → numpy.ndarray[numpy.float32]: Compute a pairwise distance matrix between two coordinate sets

pdb_cpp.core.get_common_atoms(coor_1: pdb_cpp.core.Coor, coor_2: pdb_cpp.core.Coor, chain_1: list[str] = ['A'], chain_2: list[str] = ['A'], back_names: list[str] = ['C', 'N', 'O', 'CA'], matrix_file: str = '') → tuple[list[int], list[int]]: Get common atoms between two Coor objects based on sequence alignment

pdb_cpp.core.hy36decode(width: int, value: str) → int: Decode a hybrid-36 string with fixed width.

pdb_cpp.core.hy36encode(width: int, value: int) → str: Encode a number using hybrid-36 with fixed width.

pdb_cpp.core.rmsd(coor_1: pdb_cpp.core.Coor, coor_2: pdb_cpp.core.Coor, index_1: list[int], index_2: list[int], frame_ref: int = 0) → list[float]: Compute RMSD values for all models in coor_1 against one reference model in coor_2.

pdb_cpp.core.sequence_align(seq1: str, seq2: str, matrix_file: str = '', GAP_COST: int = -11, GAP_EXT: int = -1) → pdb_cpp.core.Alignment_cpp: Align two sequences using a substitution matrix and gap penalties

pdb_cpp.core.tmalign_ca(coor_1: pdb_cpp.core.Coor, coor_2: pdb_cpp.core.Coor, chain_1: list[str] = ['A'], chain_2: list[str] = ['A'], mm: int = 0, include_transform: bool = False) → pdb_cpp.core.TMalignResult: Align CA atoms of selected chains using the TM-align core from USalign

pdb_cpp.geom module

pdb_cpp.geom.apply_transform(coords, rotation, translation)[source]

Apply a rigid transform to 3D coordinates.

The transform follows $x’ = R x + t$ with row-wise coordinate arrays, implemented as coords @ R.T + t.

Parameters:

coordsarray-like, shape (N, 3): Input coordinates.
rotationarray-like, shape (3, 3): Rotation matrix.
translationarray-like, shape (3,): Translation vector.

Returns:

numpy.ndarray: Transformed coordinates with shape (N, 3).

pdb_cpp.geom.compute_dihedrals(pts: numpy.ndarray[numpy.float32]) → numpy.ndarray[numpy.float32]

Compute all consecutive dihedral angles from an ordered (N, 3) float array.

Parameters:

ptsndarray, shape (N, 3): Ordered 3-D coordinates (e.g. consecutive CA positions).

Returns:

ndarray, shape (N-3,): Dihedral angles in degrees. Returns an empty array when N < 4.

pdb_cpp.geom.distance_matrix(xyz_a: numpy.ndarray[numpy.float32], xyz_b: numpy.ndarray[numpy.float32]) → numpy.ndarray[numpy.float32]: Compute a pairwise distance matrix between two coordinate sets

pdb_cpp.rcsb module

Helpers for downloading and loading structures from the RCSB PDB.

pdb_cpp.rcsb.build_download_url(pdb_id, structure='asymmetric_unit', file_format='cif', assembly_id=1)[source]

Build an RCSB download URL for a structure file.

Parameters:

pdb_idstr: PDB identifier.
structurestr, default=”asymmetric_unit”: Either the deposited asymmetric unit or a biological assembly.
file_formatstr, default=”cif”: Download format. Supported values are "cif" and "pdb".
assembly_idint, default=1: Biological assembly identifier when structure is "biological_assembly".

Returns:

str: Download URL.

pdb_cpp.rcsb.download(*args, **kwargs)[source]: Alias for download_structure().

pdb_cpp.rcsb.download_structure(pdb_id, structure='asymmetric_unit', file_format='cif', assembly_id=1, cache_dir=None, force_download=False)[source]

Download and cache an RCSB structure file.

Parameters:

pdb_idstr: PDB identifier.
structurestr, default=”asymmetric_unit”: Either "asymmetric_unit" or "biological_assembly".
file_formatstr, default=”cif”: Download format. Supported values are "cif" and "pdb".
assembly_idint, default=1: Assembly identifier for biological assemblies.
cache_dirstr, optional: Cache directory. Defaults to a temporary directory managed by pdb_cpp.
force_downloadbool, default=False: Re-download the file even when it is already cached.

Returns:

str: Local path to the cached structure file.

pdb_cpp.rcsb.load(*args, **kwargs)[source]: Alias for load_structure().

pdb_cpp.rcsb.load_structure(pdb_id, structure='asymmetric_unit', file_format='cif', assembly_id=1, cache_dir=None, force_download=False)[source]: Download a structure from RCSB and return it as a Coor object.

pdb_cpp.select module

Selection helpers that wrap the coordinate-object methods.

pdb_cpp.select.remove_incomplete_backbone_residues(coor, back_atom=None)[source]

Remove residues with incomplete backbone atoms.

Parameters:

coorCoor: Coordinate object to clean.
back_atomlist[str], optional: Backbone atom names to require per residue.

Returns:

Coor: A new Coor object with incomplete residues removed.

pdb_cpp.sequence module

Thin wrappers around core sequence helpers.

class pdb_cpp.sequence.Coor(coor_in=None, pdb_id=None, format='', rcsb_structure='asymmetric_unit', assembly_id=1, cache_dir=None, force_download=False)

Bases: pybind11_object

Attributes:

active_model
alterloc_str
beta
chain
chain_str
conect
elem_str
insertres_str
len: Return the number of atoms in the selection.
model_num: Return the number of models in the selection.
models: Return all models of the selection.
name
name_str
num
occ
resid
resname
resname_str
uniq_resid
x
xyz
y
z

Methods

`add_Model`(self, arg0)
`clear`(self)
`get_Models`(self, arg0)
`get_aa_DL_seq`(self[, gap_in_seq, frame])	Get amino-acid sequences with D-residues encoded as lowercase
`get_aa_na_seq`(self[, gap_in_seq, frame])	Get amino-acid and nucleic-acid sequences per chain
`get_aa_seq`(self[, gap_in_seq, frame])	Get amino-acid sequences per chain
`get_aa_sequences`(self[, gap_in_seq, frame])	Get the amino acid sequence, optionally including gaps and specifying a frame index
`get_aa_sequences_dl`(self[, gap_in_seq, frame])	Get the amino acid sequence with D-residues encoded as lowercase
`get_all_Models`(self)
`get_alterloc`(self[, frame])
`get_beta`(self[, frame])
`get_chain`(self[, frame])
`get_elem`(self[, frame])
`get_index_select`(self, selection[, frame])	Get indices of atoms based on a selection string and an optional frame index
`get_insertres`(self[, frame])
`get_name`(self[, frame])
`get_num`(self[, frame])
`get_occ`(self[, frame])
`get_resid`(self[, frame])
`get_resname`(self[, frame])
`get_uniq_chain`(self)
`get_uniq_chain_str`(self)
`get_uniqresid`(self[, frame])
`get_x`(self[, frame])
`get_y`(self[, frame])
`get_z`(self[, frame])
`model_size`(self)
`read`(self, filename[, format])	Read a structure file; format can be 'pdb', 'cif', 'pqr', or 'gro' (default: infer from extension)
`remove_incomplete_backbone_residues`(self[, ...])	Remove residues with incomplete backbone atoms
`select_atoms`(self, selection[, frame])	Select atoms based on a selection string and an optional frame index
`select_bool_index`(self, arg0)
`set_alterloc`(self, arg0, arg1)
`set_beta`(self, arg0, arg1)
`set_chain`(self, arg0, arg1)
`set_elem`(self, arg0, arg1)
`set_insertres`(self, arg0, arg1)
`set_name`(self, arg0, arg1)
`set_num`(self, arg0, arg1)
`set_occ`(self, arg0, arg1)
`set_resid`(self, arg0, arg1)
`set_resname`(self, arg0, arg1)
`set_uniqresid`(self, arg0, arg1)
`set_x`(self, arg0, arg1)
`set_y`(self, arg0, arg1)
`set_z`(self, arg0, arg1)
`size`(self)
`write`(self, arg0)

property active_model

add_Model(self: pdb_cpp.core.Coor, arg0: pdb_cpp.core.Model) → None

property alterloc_str

property beta

property chain

property chain_str

clear(self: pdb_cpp.core.Coor) → None

property conect

property elem_str

get_Models(self: pdb_cpp.core.Coor, arg0: int) → pdb_cpp.core.Model

get_aa_DL_seq(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → dict[str, str]: Get amino-acid sequences with D-residues encoded as lowercase

get_aa_na_seq(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → dict[str, str]: Get amino-acid and nucleic-acid sequences per chain

get_aa_seq(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → dict[str, str]: Get amino-acid sequences per chain

get_aa_sequences(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → list[str]: Get the amino acid sequence, optionally including gaps and specifying a frame index

get_aa_sequences_dl(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → list[str]: Get the amino acid sequence with D-residues encoded as lowercase

get_all_Models(self: pdb_cpp.core.Coor) → list[pdb_cpp.core.Model]

get_alterloc(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(2)]]

get_beta(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_chain(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(2)]]

get_elem(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(5)]]

get_index_select(self: pdb_cpp.core.Coor, selection: str, frame: int = 0) → list[int]: Get indices of atoms based on a selection string and an optional frame index

get_insertres(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(2)]]

get_name(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(5)]]

get_num(self: pdb_cpp.core.Coor, frame: int = 0) → list[int]

get_occ(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_resid(self: pdb_cpp.core.Coor, frame: int = 0) → list[int]

get_resname(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(5)]]

get_uniq_chain(self: pdb_cpp.core.Coor) → list[Annotated[list[str], FixedSize(2)]]

get_uniq_chain_str(self: pdb_cpp.core.Coor) → list[str]

get_uniqresid(self: pdb_cpp.core.Coor, frame: int = 0) → list[int]

get_x(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_y(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_z(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

property insertres_str

property len

Return the number of atoms in the selection.

Returns:

int: Number of atoms.

property model_num

Return the number of models in the selection.

Returns:

int: Number of models.

model_size(self: pdb_cpp.core.Coor) → int

property models

Return all models of the selection.

Returns:

list[Model]: List of models.

property name

property name_str

property num

property occ

read(self: pdb_cpp.core.Coor, filename: str, format: str = '') → bool: Read a structure file; format can be ‘pdb’, ‘cif’, ‘pqr’, or ‘gro’ (default: infer from extension)

remove_incomplete_backbone_residues(self: pdb_cpp.core.Coor, back_atom: list[str] = ['CA', 'C', 'N', 'O']) → pdb_cpp.core.Coor: Remove residues with incomplete backbone atoms

property resid

property resname

property resname_str

select_atoms(self: pdb_cpp.core.Coor, selection: str, frame: int = 0) → pdb_cpp.core.Coor: Select atoms based on a selection string and an optional frame index

select_bool_index(self: pdb_cpp.core.Coor, arg0: list[bool]) → pdb_cpp.core.Coor

set_alterloc(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_beta(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_chain(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_elem(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_insertres(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_name(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_num(self: pdb_cpp.core.Coor, arg0: int, arg1: int) → None

set_occ(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_resid(self: pdb_cpp.core.Coor, arg0: int, arg1: int) → None

set_resname(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_uniqresid(self: pdb_cpp.core.Coor, arg0: int, arg1: int) → None

set_x(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_y(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_z(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

size(self: pdb_cpp.core.Coor) → int

property uniq_resid

write(self: pdb_cpp.core.Coor, arg0: str) → bool

property x

property xyz

property y

property z

pdb_cpp.sequence.get_aa_DL_seq(coor, gap_in_seq=True, frame=0)[source]

Return the amino acid sequence with D-residues in lowercase.

Parameters:

coorCoor: Coordinate object.
gap_in_seqbool, optional: Whether to insert gaps for missing residues.
frameint, optional: Frame index to use for the selection.

Returns:

dict: Mapping of chain ID to sequence.

pdb_cpp.sequence.get_aa_seq(coor, gap_in_seq=True, frame=0)[source]

Return the amino acid sequence of the selection.

Parameters:

coorCoor: Coordinate object.
gap_in_seqbool, optional: Whether to insert gaps for missing residues.
frameint, optional: Frame index to use for the selection.

Returns:

dict: Mapping of chain ID to sequence.

Module contents

Public package entry point for pdb_cpp.

Importing this module exposes the primary coordinate classes and loads the runtime patches that add Python-friendly helpers onto the C++ bindings.

class pdb_cpp.Coor(coor_in=None, pdb_id=None, format='', rcsb_structure='asymmetric_unit', assembly_id=1, cache_dir=None, force_download=False)

Bases: pybind11_object

Attributes:

active_model
alterloc_str
beta
chain
chain_str
conect
elem_str
insertres_str
len: Return the number of atoms in the selection.
model_num: Return the number of models in the selection.
models: Return all models of the selection.
name
name_str
num
occ
resid
resname
resname_str
uniq_resid
x
xyz
y
z

Methods

`add_Model`(self, arg0)
`clear`(self)
`get_Models`(self, arg0)
`get_aa_DL_seq`(self[, gap_in_seq, frame])	Get amino-acid sequences with D-residues encoded as lowercase
`get_aa_na_seq`(self[, gap_in_seq, frame])	Get amino-acid and nucleic-acid sequences per chain
`get_aa_seq`(self[, gap_in_seq, frame])	Get amino-acid sequences per chain
`get_aa_sequences`(self[, gap_in_seq, frame])	Get the amino acid sequence, optionally including gaps and specifying a frame index
`get_aa_sequences_dl`(self[, gap_in_seq, frame])	Get the amino acid sequence with D-residues encoded as lowercase
`get_all_Models`(self)
`get_alterloc`(self[, frame])
`get_beta`(self[, frame])
`get_chain`(self[, frame])
`get_elem`(self[, frame])
`get_index_select`(self, selection[, frame])	Get indices of atoms based on a selection string and an optional frame index
`get_insertres`(self[, frame])
`get_name`(self[, frame])
`get_num`(self[, frame])
`get_occ`(self[, frame])
`get_resid`(self[, frame])
`get_resname`(self[, frame])
`get_uniq_chain`(self)
`get_uniq_chain_str`(self)
`get_uniqresid`(self[, frame])
`get_x`(self[, frame])
`get_y`(self[, frame])
`get_z`(self[, frame])
`model_size`(self)
`read`(self, filename[, format])	Read a structure file; format can be 'pdb', 'cif', 'pqr', or 'gro' (default: infer from extension)
`remove_incomplete_backbone_residues`(self[, ...])	Remove residues with incomplete backbone atoms
`select_atoms`(self, selection[, frame])	Select atoms based on a selection string and an optional frame index
`select_bool_index`(self, arg0)
`set_alterloc`(self, arg0, arg1)
`set_beta`(self, arg0, arg1)
`set_chain`(self, arg0, arg1)
`set_elem`(self, arg0, arg1)
`set_insertres`(self, arg0, arg1)
`set_name`(self, arg0, arg1)
`set_num`(self, arg0, arg1)
`set_occ`(self, arg0, arg1)
`set_resid`(self, arg0, arg1)
`set_resname`(self, arg0, arg1)
`set_uniqresid`(self, arg0, arg1)
`set_x`(self, arg0, arg1)
`set_y`(self, arg0, arg1)
`set_z`(self, arg0, arg1)
`size`(self)
`write`(self, arg0)

property active_model

add_Model(self: pdb_cpp.core.Coor, arg0: pdb_cpp.core.Model) → None

property alterloc_str

property beta

property chain

property chain_str

clear(self: pdb_cpp.core.Coor) → None

property conect

property elem_str

get_Models(self: pdb_cpp.core.Coor, arg0: int) → pdb_cpp.core.Model

get_aa_DL_seq(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → dict[str, str]: Get amino-acid sequences with D-residues encoded as lowercase

get_aa_na_seq(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → dict[str, str]: Get amino-acid and nucleic-acid sequences per chain

get_aa_seq(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → dict[str, str]: Get amino-acid sequences per chain

get_aa_sequences(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → list[str]: Get the amino acid sequence, optionally including gaps and specifying a frame index

get_aa_sequences_dl(self: pdb_cpp.core.Coor, gap_in_seq: bool = True, frame: int = 0) → list[str]: Get the amino acid sequence with D-residues encoded as lowercase

get_all_Models(self: pdb_cpp.core.Coor) → list[pdb_cpp.core.Model]

get_alterloc(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(2)]]

get_beta(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_chain(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(2)]]

get_elem(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(5)]]

get_index_select(self: pdb_cpp.core.Coor, selection: str, frame: int = 0) → list[int]: Get indices of atoms based on a selection string and an optional frame index

get_insertres(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(2)]]

get_name(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(5)]]

get_num(self: pdb_cpp.core.Coor, frame: int = 0) → list[int]

get_occ(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_resid(self: pdb_cpp.core.Coor, frame: int = 0) → list[int]

get_resname(self: pdb_cpp.core.Coor, frame: int = 0) → list[Annotated[list[str], FixedSize(5)]]

get_uniq_chain(self: pdb_cpp.core.Coor) → list[Annotated[list[str], FixedSize(2)]]

get_uniq_chain_str(self: pdb_cpp.core.Coor) → list[str]

get_uniqresid(self: pdb_cpp.core.Coor, frame: int = 0) → list[int]

get_x(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_y(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

get_z(self: pdb_cpp.core.Coor, frame: int = 0) → list[float]

property insertres_str

property len

Return the number of atoms in the selection.

Returns:

int: Number of atoms.

property model_num

Return the number of models in the selection.

Returns:

int: Number of models.

model_size(self: pdb_cpp.core.Coor) → int

property models

Return all models of the selection.

Returns:

list[Model]: List of models.

property name

property name_str

property num

property occ

read(self: pdb_cpp.core.Coor, filename: str, format: str = '') → bool: Read a structure file; format can be ‘pdb’, ‘cif’, ‘pqr’, or ‘gro’ (default: infer from extension)

remove_incomplete_backbone_residues(self: pdb_cpp.core.Coor, back_atom: list[str] = ['CA', 'C', 'N', 'O']) → pdb_cpp.core.Coor: Remove residues with incomplete backbone atoms

property resid

property resname

property resname_str

select_atoms(self: pdb_cpp.core.Coor, selection: str, frame: int = 0) → pdb_cpp.core.Coor: Select atoms based on a selection string and an optional frame index

select_bool_index(self: pdb_cpp.core.Coor, arg0: list[bool]) → pdb_cpp.core.Coor

set_alterloc(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_beta(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_chain(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_elem(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_insertres(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_name(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_num(self: pdb_cpp.core.Coor, arg0: int, arg1: int) → None

set_occ(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_resid(self: pdb_cpp.core.Coor, arg0: int, arg1: int) → None

set_resname(self: pdb_cpp.core.Coor, arg0: int, arg1: str) → None

set_uniqresid(self: pdb_cpp.core.Coor, arg0: int, arg1: int) → None

set_x(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_y(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

set_z(self: pdb_cpp.core.Coor, arg0: int, arg1: float) → None

size(self: pdb_cpp.core.Coor) → int

property uniq_resid

write(self: pdb_cpp.core.Coor, arg0: str) → bool

property x

property xyz

property y

property z

class pdb_cpp.Model

Bases: pybind11_object

Attributes:

alterloc_str
beta
chain
chain_str
elem_str
insertres_str
len: Return the number of atoms in the selection.
name
name_str
num
occ
resid
resname
resname_str
uniq_resid
x
xyz
y
z

Methods

`addAtom`(self, arg0, arg1, arg2, arg3, arg4, ...)
`clear`(self)
`get_alterloc`(self)
`get_beta`(self)
`get_centroid`(args, *kwargs)	Overloaded function.
`get_chain`(self)
`get_elem`(self)
`get_field`(self)
`get_insertres`(self)
`get_name`(self)
`get_num`(self)
`get_occ`(self)
`get_resid`(self)
`get_resname`(self)
`get_uniqresid`(self)
`get_x`(self)
`get_y`(self)
`get_z`(self)
`select_atoms`(self, arg0)
`set_alterloc`(self, arg0, arg1)
`set_beta`(self, arg0, arg1)
`set_chain`(self, arg0, arg1)
`set_elem`(self, arg0, arg1)
`set_insertres`(self, arg0, arg1)
`set_name`(self, arg0, arg1)
`set_num`(self, arg0, arg1)
`set_occ`(self, arg0, arg1)
`set_resid`(self, arg0, arg1)
`set_resname`(self, arg0, arg1)
`set_uniqresid`(self, arg0, arg1)
`set_x`(self, arg0, arg1)
`set_y`(self, arg0, arg1)
`set_z`(self, arg0, arg1)
`size`(self)

addAtom(self: pdb_cpp.core.Model, arg0: int, arg1: Annotated[list[str], FixedSize(5)], arg2: Annotated[list[str], FixedSize(5)], arg3: int, arg4: Annotated[list[str], FixedSize(2)], arg5: float, arg6: float, arg7: float, arg8: float, arg9: float, arg10: Annotated[list[str], FixedSize(2)], arg11: Annotated[list[str], FixedSize(5)], arg12: Annotated[list[str], FixedSize(2)], arg13: bool, arg14: int) → bool

property alterloc_str

property beta

property chain

property chain_str

clear(self: pdb_cpp.core.Model) → None

property elem_str

get_alterloc(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(2)]]

get_beta(self: pdb_cpp.core.Model) → list[float]

get_centroid(*args, **kwargs)

Overloaded function.

get_centroid(self: pdb_cpp.core.Model) -> Annotated[list[float], FixedSize(3)]

Calculate centroid of all atoms in the model

get_centroid(self: pdb_cpp.core.Model, indices: list[int]) -> Annotated[list[float], FixedSize(3)]

Calculate centroid of atoms at specified indices

get_chain(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(2)]]

get_elem(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(5)]]

get_field(self: pdb_cpp.core.Model) → list[bool]

get_insertres(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(2)]]

get_name(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(5)]]

get_num(self: pdb_cpp.core.Model) → list[int]

get_occ(self: pdb_cpp.core.Model) → list[float]

get_resid(self: pdb_cpp.core.Model) → list[int]

get_resname(self: pdb_cpp.core.Model) → list[Annotated[list[str], FixedSize(5)]]

get_uniqresid(self: pdb_cpp.core.Model) → list[int]

get_x(self: pdb_cpp.core.Model) → list[float]

get_y(self: pdb_cpp.core.Model) → list[float]

get_z(self: pdb_cpp.core.Model) → list[float]

property insertres_str

property len

Return the number of atoms in the selection.

Returns:

int: Number of atoms.

property name

property name_str

property num

property occ

property resid

property resname

property resname_str

select_atoms(self: pdb_cpp.core.Model, arg0: str) → list[bool]

set_alterloc(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_beta(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

set_chain(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_elem(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_insertres(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_name(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_num(self: pdb_cpp.core.Model, arg0: int, arg1: int) → None

set_occ(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

set_resid(self: pdb_cpp.core.Model, arg0: int, arg1: int) → None

set_resname(self: pdb_cpp.core.Model, arg0: int, arg1: str) → None

set_uniqresid(self: pdb_cpp.core.Model, arg0: int, arg1: int) → None

set_x(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

set_y(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

set_z(self: pdb_cpp.core.Model, arg0: int, arg1: float) → None

size(self: pdb_cpp.core.Model) → int

property uniq_resid

property x

property xyz

property y

property z