Conditions

class rfproteina.conditions.Hotspot

Bases: ConditionBase

Hotspot annotation for protein design.

name: ClassVar[str] = 'hotspot'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of bool

aliases: ClassVar[tuple[str, ...]] = ('C_HOT', 'mask_hotspot_1_atom')

default_value: ClassVar[Any] = False

enum: ClassVar[type[Enum] | None] = None

full_name: ClassVar[str] = 'condition_hotspot_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.RasaEnum(*values)

Bases: IntEnum

UNSPECIFIED = 0

BURIED = 1

INTERMEDIATE = 2

EXPOSED = 3

class rfproteina.conditions.Rasa

Bases: ConditionBase

Conditioning that provides binned RASA values to the model. Zero denotes no conditioning.

name: ClassVar[str] = 'rasa-binned'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of RasaEnum

aliases: ClassVar[tuple[str, ...]] = ('C_RAS',)

default_value: ClassVar[Any] = 0

classmethod mask_from_annotation(annotation: Int[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

enum

alias of RasaEnum

full_name: ClassVar[str] = 'condition_rasa-binned_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.HBondEnum(*values)

Bases: IntEnum

NONE = 0

DONOR = 1

ACCEPTOR = 2

BOTH = 3

class rfproteina.conditions.HydrogenBond

Bases: ConditionBase

Conditioning that provides hydrogen bond information (donor/acceptor) to the model.

name: ClassVar[str] = 'hbond'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of HBondEnum

aliases: ClassVar[tuple[str, ...]] = ('C_HB',)

default_value: ClassVar[Any] = 0

classmethod mask_from_annotation(annotation: Int[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

enum

alias of HBondEnum

full_name: ClassVar[str] = 'condition_hbond_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.PiStacking

Bases: ConditionBase

Conditioning for pi-stacking interactions.

name: ClassVar[str] = 'pistack'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of bool

aliases: ClassVar[tuple[str, ...]] = ('C_PISTACK', 'mask_pistack_1_atom')

default_value: ClassVar[Any] = False

enum: ClassVar[type[Enum] | None] = None

full_name: ClassVar[str] = 'condition_pistack_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.PiCationEnum(*values)

Bases: IntEnum

NONE = 0

AROMATIC = 1

CATION = 2

BOTH = 3

class rfproteina.conditions.PiCation

Bases: ConditionBase

Conditioning for pi-cation interactions (aromatic ring / cation role).

name: ClassVar[str] = 'pication'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of PiCationEnum

aliases: ClassVar[tuple[str, ...]] = ('C_PICATION',)

default_value: ClassVar[Any] = 0

classmethod mask_from_annotation(annotation: Int[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

enum

alias of PiCationEnum

full_name: ClassVar[str] = 'condition_pication_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.SaltBridgeEnum(*values)

Bases: IntEnum

NONE = 0

POSITIVE = 1

NEGATIVE = 2

class rfproteina.conditions.SaltBridge

Bases: ConditionBase

Conditioning for salt bridge interactions.

name: ClassVar[str] = 'saltbridge'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of SaltBridgeEnum

aliases: ClassVar[tuple[str, ...]] = ('C_SALT',)

default_value: ClassVar[Any] = 0

classmethod mask_from_annotation(annotation: Int[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

enum

alias of SaltBridgeEnum

full_name: ClassVar[str] = 'condition_saltbridge_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.Hydrophobic

Bases: ConditionBase

Conditioning for hydrophobic contacts.

name: ClassVar[str] = 'hydrophobic'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of bool

aliases: ClassVar[tuple[str, ...]] = ('C_HPHOB', 'mask_hydrophobic_1_atom')

default_value: ClassVar[Any] = False

enum: ClassVar[type[Enum] | None] = None

full_name: ClassVar[str] = 'condition_hydrophobic_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.MetalCoordEnum(*values)

Bases: IntEnum

NONE = 0

METAL = 1

COORDINATING = 2

class rfproteina.conditions.MetalCoordination

Bases: ConditionBase

Conditioning for metal coordination interactions.

name: ClassVar[str] = 'metal-coord'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of MetalCoordEnum

aliases: ClassVar[tuple[str, ...]] = ('C_MCOORD',)

default_value: ClassVar[Any] = 0

classmethod mask_from_annotation(annotation: Int[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

enum

alias of MetalCoordEnum

full_name: ClassVar[str] = 'condition_metal-coord_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.SecondaryStructure

Bases: ConditionBase

Conditioning that provides secondary structure information to the model.

name: ClassVar[str] = 'secondary-structure'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'residue'

dtype

alias of SSEnum

aliases: ClassVar[tuple[str, ...]] = ('C_SEC',)

default_value: ClassVar[Any] = 0

classmethod mask_from_annotation(annotation: Int[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

enum

alias of SSEnum

full_name: ClassVar[str] = 'condition_secondary-structure_1_residue'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.IndexGroup

Bases: ConditionBase

Indicates atoms within the same equivalence class of known index offsets.

Does not differentiate between globally indexed vs unindexed groups (that is annotated in C_IDX.mask). While the default annotation is monotonically increasing by one, this should not be expected to always hold.

Groups by molecule to ensure that all tokens of one molecule share a group even if they are not contiguous in the atom array.

name: ClassVar[str] = 'index-group'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'token'

dtype

alias of int

aliases: ClassVar[tuple[str, ...]] = ('C_IDXGRP',)

classmethod mask_from_annotation(annotation: Int[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

classmethod default_annotation(atom_array: AtomArray) → Int[ndarray, 'n_atoms']

Fill a system or one-body annotation, or override for structure-dependent/sparse defaults.

enum: ClassVar[type[Enum] | None] = None

full_name: ClassVar[str] = 'condition_index-group_1_token'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.CathLabel

Bases: ConditionBase

Conditioning that provides cath labels to the model. ‘x.x.x.x’ is null conditioning.

name: ClassVar[str] = 'cath-label'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'residue'

dtype

alias of str

aliases: ClassVar[tuple[str, ...]] = ('C_CATH',)

NULL_VALUE = 'x.x.x.x'

default_value: ClassVar[Any] = 'x.x.x.x'

classmethod mask_from_annotation(annotation: Shaped[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

classmethod default_annotation(atom_array: AtomArray) → Shaped[ndarray, 'n_atoms']

Fill a system or one-body annotation, or override for structure-dependent/sparse defaults.

enum: ClassVar[type[Enum] | None] = None

full_name: ClassVar[str] = 'condition_cath-label_1_residue'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.InternalCoordinate

Bases: ConditionBase

Materialized internal-coordinate payload for atoms in non-reserved coordinate groups.

C_CRDGRP is the source of truth for membership. These coordinates provide group-local structure without fixing the groups’ relative positions or orientations.

name: ClassVar[str] = 'InternalCoordinate'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of float

aliases: ClassVar[tuple[str, ...]] = ('C_INTCRD',)

default_value: ClassVar[Any] = nan

value_shape: ClassVar[tuple[int, ...]] = (3,)

classmethod mask_from_annotation(annotation: Float[ndarray, 'n_atoms 3']) → Bool[ndarray, 'n_atoms']

Report payload presence for the Condition API; do not use as group membership.

enum: ClassVar[type[Enum] | None] = None

full_name: ClassVar[str] = 'condition_InternalCoordinate_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.ChainCentroid

Bases: ConditionBase

Per-chain centroid xyz (Å, (n_atoms, 3)), broadcast per atom; NaN where unincluded.

name: ClassVar[str] = 'ChainCentroid'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of float

aliases: ClassVar[tuple[str, ...]] = ('C_CENTROID',)

default_value: ClassVar[Any] = nan

value_shape: ClassVar[tuple[int, ...]] = (3,)

classmethod mask_from_annotation(annotation: Float[ndarray, 'n_atoms 3']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

classmethod default_annotation(atom_array: AtomArray) → Float[ndarray, 'n_atoms 3']

Fill a system or one-body annotation, or override for structure-dependent/sparse defaults.

enum: ClassVar[type[Enum] | None] = None

full_name: ClassVar[str] = 'condition_ChainCentroid_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.CoordinateGroup

Bases: ConditionBase

Indicates atoms within the same equivalence class of known relative coordinates.

name: ClassVar[str] = 'CoordinateGroup'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'atom'

dtype

alias of int

aliases: ClassVar[tuple[str, ...]] = ('C_CRDGRP',)

KNOWN_ABSOLUTE_COORDS = 0

UNKNOWN_COORDS = -1

MAX_GROUP_ID = 32767

classmethod set_annotation(atom_array: AtomArray, array: Int[ndarray, 'n_atoms'], *, on_internal_coord_mismatch: Literal['raise', 'clear'] = 'raise') → None

Set membership, preserving saved targets for unchanged whole atom sets.

Parameters:

• atom_array – Structure to modify in place.

• array – New group IDs; pass a copy instead of mutating the existing annotation. IDs must be in [-1, 32767]. Group 0 must match absolute conditioning; modify C_CRD first.

• on_internal_coord_mismatch – Raise before writing if membership changes invalidate saved targets, or clear targets throughout affected groups with "clear". Whole-group renaming preserves targets under either policy.

classmethod mask_from_annotation(annotation: Int[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

classmethod is_internal(atom_array: AtomArray) → Bool[ndarray, 'n_atoms']

Return atoms assigned to a non-reserved internal-coordinate group.

classmethod default_annotation(atom_array: AtomArray) → Int[ndarray, 'n_atoms']

Fill a system or one-body annotation, or override for structure-dependent/sparse defaults.

enum: ClassVar[type[Enum] | None] = None

full_name: ClassVar[str] = 'condition_CoordinateGroup_1_atom'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.BasePairEnum(*values)

Bases: IntEnum

the Enum to hold int info corresponding to BasePair annotations

UNSPECIFIED = 0

PAIR = 1

LOOP = 2

class rfproteina.conditions.BasePair

Bases: ConditionBase

NA secondary-structure pair condition (residue semantics, 2-body sparse storage).

name: ClassVar[str] = 'basepair'

n_body: ClassVar[int] = 2

level: ClassVar[Level] = 'residue'

is_symmetric: ClassVar[bool] = True

dtype

alias of BasePairEnum

aliases: ClassVar[tuple[str, ...]] = ('C_BP',)

classmethod default_annotation(atom_array: AtomArray) → AnnotationList2D

Fill a system or one-body annotation, or override for structure-dependent/sparse defaults.

classmethod mask_from_annotation(annotation: AnnotationList2D) → AnnotationList2D

Derive this StandardAnnotation’s mask from its value annotation.

enum

alias of BasePairEnum

full_name: ClassVar[str] = 'condition_basepair_2_residue'

has_ground_truth: ClassVar[bool] = False

class rfproteina.conditions.NucleicSSState

Bases: ConditionBase

Per-residue NA secondary-structure state encoded with BasePairEnum.

name: ClassVar[str] = 'na-ss-state'

n_body: ClassVar[int] = 1

level: ClassVar[Level] = 'residue'

dtype

alias of BasePairEnum

aliases: ClassVar[tuple[str, ...]] = ('C_NA_SS_STATE',)

default_value: ClassVar[Any] = 0

classmethod mask_from_annotation(annotation: Int[ndarray, 'n_atoms']) → Bool[ndarray, 'n_atoms']

Derive this StandardAnnotation’s mask from its value annotation.

enum

alias of BasePairEnum

full_name: ClassVar[str] = 'condition_na-ss-state_1_residue'

has_ground_truth: ClassVar[bool] = False

is_symmetric: ClassVar[bool] = True

class rfproteina.conditions.SequenceProbability

Bases: ConditionBase

Base class for an explicitly specified unified sequence-token probability.

NaN leaves an identity unspecified; zero explicitly excludes it. Presence is derived from the stored value, including invalid infinities for validation.

token_name: ClassVar[str]

token_index: ClassVar[int]

alias_suffix: ClassVar[str]

default_value: ClassVar[Any] = nan

classmethod mask_from_annotation(annotation: ndarray) → ndarray

Derive this StandardAnnotation’s mask from its value annotation.

rfproteina.conditions.C_HOT

alias of Hotspot

rfproteina.conditions.C_RAS

alias of Rasa

rfproteina.conditions.C_SEC

alias of SecondaryStructure

rfproteina.conditions.C_HB

alias of HydrogenBond

rfproteina.conditions.C_PISTACK

alias of PiStacking

rfproteina.conditions.C_PICATION

alias of PiCation

rfproteina.conditions.C_SALT

alias of SaltBridge

rfproteina.conditions.C_HPHOB

alias of Hydrophobic

rfproteina.conditions.C_MCOORD

alias of MetalCoordination

rfproteina.conditions.C_IDXGRP

alias of IndexGroup

rfproteina.conditions.C_CATH

alias of CathLabel

rfproteina.conditions.C_INTCRD

alias of InternalCoordinate

rfproteina.conditions.C_CRDGRP

alias of CoordinateGroup

rfproteina.conditions.C_CENTROID

alias of ChainCentroid

rfproteina.conditions.C_BP

alias of BasePair

rfproteina.conditions.C_NA_SS_STATE

alias of NucleicSSState

rfproteina.conditions.C_SEQ_PROB_A

alias of ASequenceProbability

rfproteina.conditions.C_SEQ_PROB_ALA

alias of AlaSequenceProbability

rfproteina.conditions.C_SEQ_PROB_ARG

alias of ArgSequenceProbability

rfproteina.conditions.C_SEQ_PROB_ASN

alias of AsnSequenceProbability

rfproteina.conditions.C_SEQ_PROB_ASP

alias of AspSequenceProbability

rfproteina.conditions.C_SEQ_PROB_C

alias of CSequenceProbability

rfproteina.conditions.C_SEQ_PROB_CYS

alias of CysSequenceProbability

rfproteina.conditions.C_SEQ_PROB_DA

alias of DaSequenceProbability

rfproteina.conditions.C_SEQ_PROB_DC

alias of DcSequenceProbability

rfproteina.conditions.C_SEQ_PROB_DG

alias of DgSequenceProbability

rfproteina.conditions.C_SEQ_PROB_DT

alias of DtSequenceProbability

rfproteina.conditions.C_SEQ_PROB_G

alias of GSequenceProbability

rfproteina.conditions.C_SEQ_PROB_GLN

alias of GlnSequenceProbability

rfproteina.conditions.C_SEQ_PROB_GLU

alias of GluSequenceProbability

rfproteina.conditions.C_SEQ_PROB_GLY

alias of GlySequenceProbability

rfproteina.conditions.C_SEQ_PROB_HIS

alias of HisSequenceProbability

rfproteina.conditions.C_SEQ_PROB_ILE

alias of IleSequenceProbability

rfproteina.conditions.C_SEQ_PROB_LEU

alias of LeuSequenceProbability

rfproteina.conditions.C_SEQ_PROB_LYS

alias of LysSequenceProbability

rfproteina.conditions.C_SEQ_PROB_MET

alias of MetSequenceProbability

rfproteina.conditions.C_SEQ_PROB_PHE

alias of PheSequenceProbability

rfproteina.conditions.C_SEQ_PROB_PRO

alias of ProSequenceProbability

rfproteina.conditions.C_SEQ_PROB_SER

alias of SerSequenceProbability

rfproteina.conditions.C_SEQ_PROB_THR

alias of ThrSequenceProbability

rfproteina.conditions.C_SEQ_PROB_TRP

alias of TrpSequenceProbability

rfproteina.conditions.C_SEQ_PROB_TYR

alias of TyrSequenceProbability

rfproteina.conditions.C_SEQ_PROB_U

alias of USequenceProbability

rfproteina.conditions.C_SEQ_PROB_VAL

alias of ValSequenceProbability