`ovo.core.utils.residue_selection`¶

Module Contents¶

Classes¶

`ContigSegment`	Class for annotating a segment of the structure.
`MappedContigSegment`	Class for annotating a segment of the structure with mapping to input structure numbering.

Functions¶

`from_residues_to_segments`	Convert a list of residues [3,4,5,6,9,10,…] into a list of segments [3-6,9-10,…].
`from_residues_to_hotspots`	Convert a chain_id (i.e. A) and list of residues [3,4,…] into list of hotspots [A3, A4, …].
`parse_selections`	Input: a JSON-encoded representation of the selections that looks like this {“sequenceSelections”:[{“chainId”:”A”,”residues”:[10,11,12,13,15,16,17,18,19,20”]}]} Outputs list o segments [“A10-13”, “A15-20”]
`get_chains_and_contigs`
`from_hotspots_to_segments`
`from_segments_to_hotspots`	Convert a list of segments [“A3-5”,”A9-10”,…] to a STRING of hotspots “A3,A4,A5,A9,A10”.
`from_contig_to_residues`	Convert a str chain_segment / contig “A3-5/A9-10” to a list of residues [3,4,5,9,10].
`from_residues_to_chain_breaks`
`parse_partial_diffusion_binder_contig`	Get binder length and DESIGNED segments from binder contig as they correspond to positions in binder chain A
`create_partial_diffusion_binder_contig`	Create a new binder contig for partial diffusion from the designed segments and old binder contig
`_parse_range`
`parse_contig_for_input_structure`	Parse contig string and return segment annotations mapping to the INPUT structure numbering
`split_subcontig`	Split a single-chain subcontig into list of segments (not including the trailing /0)
`parse_contig_for_output_structure`	Parse contig string and return segment annotations mapping to our standardized RFdiffusion OUTPUT structure numbering.

API¶

ovo.core.utils.residue_selection.from_residues_to_segments(chain_id: str, residues: list[int], start_res: int | None = None, end_res: int | None = None) → list[str]¶

Convert a list of residues [3,4,5,6,9,10,…] into a list of segments [3-6,9-10,…].

Args: chain_id (str): Required. The chain ID. residues (list[int]): Required. A list of residues. start_res (int, optional): The start residue. If specified, trims residues from start_res. Defaults to None. end_res (int, optional): The end residue. If specified, trims residues to end_res. Defaults to None.

Returns: list(str): A list of segments, i.e. [3-6,9-10,…]

ovo.core.utils.residue_selection.from_residues_to_hotspots(chain_id: str, residues: list[int])¶: Convert a chain_id (i.e. A) and list of residues [3,4,…] into list of hotspots [A3, A4, …].

ovo.core.utils.residue_selection.parse_selections(selections: str) → list[str]¶: Input: a JSON-encoded representation of the selections that looks like this {“sequenceSelections”:[{“chainId”:”A”,”residues”:[10,11,12,13,15,16,17,18,19,20”]}]} Outputs list o segments [“A10-13”, “A15-20”]

ovo.core.utils.residue_selection.get_chains_and_contigs(pdb_str: str | None) → Dict[str, str] | None¶

ovo.core.utils.residue_selection.from_hotspots_to_segments(hotspots: str) → list[str] | None¶

ovo.core.utils.residue_selection.from_segments_to_hotspots(segments: list[str] | None) → str¶: Convert a list of segments [“A3-5”,”A9-10”,…] to a STRING of hotspots “A3,A4,A5,A9,A10”.

ovo.core.utils.residue_selection.from_contig_to_residues(chain_segment: str | None) → list[int] | None¶: Convert a str chain_segment / contig “A3-5/A9-10” to a list of residues [3,4,5,9,10].

ovo.core.utils.residue_selection.from_residues_to_chain_breaks(residues: list[int]) → List[str] | None¶

ovo.core.utils.residue_selection.parse_partial_diffusion_binder_contig(binder_contig: str) → tuple[int, list[str]]¶

Get binder length and DESIGNED segments from binder contig as they correspond to positions in binder chain A

default case for a peptide of 12 residues is simply binder_contig=”12-12” turned into [“A1-12”] or when redesigning only A1 and A3-7 in a peptide of 12 residues, this would be binder_contig=”1-1/A2-2/5-5/A8-12” turned into [“A1-1”, “A3-7”]

Parameters:: binder_contig – binder contig, e.g. 12-12 or 1-1/A2-2/5-5/A8-12
Returns:: binder length (int) and list of designed segments (list of str, e.g. [“A1-1”, “A3-7”])

ovo.core.utils.residue_selection.create_partial_diffusion_binder_contig(redesigned_segments: list[str], binder_length: int) → str¶

Create a new binder contig for partial diffusion from the designed segments and old binder contig

default case for a peptide of 12 residues: redesigned_segments=[] -> binder_contig=”12-12” or when redesigning only A1 and A3-7 in a peptide of 12 residues, redesigned_segments=[“A1-1”, “A3-7”] -> binder_contig=”1-1/A2-2/5-5/A8-12”

Parameters:

redesigned_segments – list of designed segments (list of str, e.g. [“A1-1”, “A3-7”])
binder_length – length of binder (int)

Returns:

new binder contig (str)

class ovo.core.utils.residue_selection.ContigSegment¶

Class for annotating a segment of the structure.

Parameters:

start – Starting residue number of the segment (inclusive).
end – Ending residue number of the segment (inclusive).
chain – Chain ID of the segment.
color – Color of the segment in hex format (e.g. “0x00ff00”), optional.
start_label – Label to show at the start of the segment, optional.
middle_label – Label to show in the middle of the segment, optional.
end_label – Label to show at the end of the segment, optional.

start: int¶: None

end: int¶: None

chain: str¶: None

color: str | None¶: None

start_label: str¶: None

middle_label: str¶: None

end_label: str¶: None

class ovo.core.utils.residue_selection.MappedContigSegment¶

Bases: ovo.core.utils.residue_selection.ContigSegment

Class for annotating a segment of the structure with mapping to input structure numbering.

In addition to ContigSegment fields, also includes:

Parameters:

input_start – Starting residue number of the segment in the input structure (inclusive).
input_end – Ending residue number of the segment in the input structure (inclusive).
input_chain – Chain ID of the segment in the input structure.

input_start: int | None¶: None

input_end: int | None¶: None

input_chain: str | None¶: None

ovo.core.utils.residue_selection._parse_range(range_str: str) → tuple[int, int]¶

ovo.core.utils.residue_selection.parse_contig_for_input_structure(contig: str, include_generated: bool = False) → list[ovo.core.utils.residue_selection.ContigSegment]¶

Parse contig string and return segment annotations mapping to the INPUT structure numbering

By default, includes only fixed segments (originating from input structure).

Parameters:

contig – contig string, e.g. “A1-5/A6-10 B1-8” or “A1-5/5-10 B1-8”
include_generated – include generated segments (e.g. 5-10) in the output, defaults to False. Note that generated segments will have start, end, and chain set to None!

ovo.core.utils.residue_selection.split_subcontig(subcontig: str) → list[str]¶

Split a single-chain subcontig into list of segments (not including the trailing /0)

Given “A1-5/5-10/A11-15/0”, returns [“A1-5”, “5-10”, “A11-15”]

ovo.core.utils.residue_selection.parse_contig_for_output_structure(contig: str) → list[ovo.core.utils.residue_selection.MappedContigSegment]¶

Parse contig string and return segment annotations mapping to our standardized RFdiffusion OUTPUT structure numbering.

See standardize_pdb.py script inside rfdiffusion pipeline.

Assumptions:

The “subcontigs” in the contig (split by whitespace) are ordered same as the chains in the output structure (contigs with generated segments come first, then contigs with only fixed segments)
Generated segments should be “resolved”, meaning that they should have same start and end in the range (5-5, not 5-10)
Chains that contain any RFdiffusion-generated segments are renumbered starting from 1 in the output structure, and they are in chains A, B, … in order of appearance (in case of multiple generated chains, typically just A)
Fixed chains (with no designed segments) are numbered same as in the input structure, and assigned remaining chains B, C, etc. in order of appearance

ovo.core.utils.residue_selection¶

Module Contents¶

Classes¶

Functions¶

API¶

`ovo.core.utils.residue_selection`¶