crops.core.ops module¶

Core operations (renumber, crop, split) are defined here.

crop_pdb(instr, inseq, original_id=True)[source]¶

Return modified gemmi.Structure without specified elements.

Parameters:	instr (`gemmi.Structure`) – Gemmi structure. inseq (`crops.elements.sequences.oligoseq`) – Input previously-cropped-sequence. original_id (bool, optional) – If True, it will keep residue ids alligned to original sequence, defaults to True.
Returns:	Cropped structure.
Return type:	`gemmi.Structure`

crop_seq(inseq, segments, cut_type, terms=False)[source]¶

Return modified crops.elements.sequences.sequence without specified elements.

Parameters:	inseq (`crops.elements.sequences.sequence`) – Input sequence. segments (`crops.elements.intervals.intinterval`) – Input preservation interval. cut_type (str) – Additional header information. terms (bool, optional) – If True, only terminal ends are removed, defaults to False.
Raises:	ValueError – If intervals given lie out of the sequence.
Returns:	Cropped sequence.
Return type:	`crops.elements.sequences.sequence`

get_sequence_alignment(sequence_1, sequence_2, mode='global', open_gap_score=-11, extend_gap_score=-2)[source]¶

Perform a sequence alignment using Needleman-Wunsch algorithm.

Return alignment_dict:
Parameters:	sequence_1 (str) – First input sequence. sequence_2 (str) – Second input sequence. mode (str, optional) – Alignment mode, defaults to ‘global’. open_gap_score (int, optional) – Opening gap penalty, defaults to -11. extend_gap_score (int, optional) – Extension gap penalty, defaults to -2.
	Dictionary with the residue mapping between both input sequences.
Rtype alignment_dict:
	dict [int, int]

renumber_pdb(inseq, instr, seqback=False, remove_ligands=False)[source]¶

Return modified gemmi.Structure with new residue numbers.

Parameters:	inseq (`crops.elements.sequences.oligoseq`) – Input sequence. instr (`gemmi.Structure`) – Gemmi structure. seqback (bool, optional) – If True, it additionally returns the `crops.elements.sequences.oligoseq` with the gaps found in the structure, defaults to False. remove_ligands (bool, optional) – If True, use `gemmi.Structure.remove_ligands_and_waters()` and `gemmi.Structure.remove_empty_chains()` prior to operation, defaults to False.
Return instr:	Renumbered structure.
Rtype instr:	`gemmi.Structure`
Return inseq:	Sequence with extra information about gaps, only if seqback is True.
Rtype inseq:	`crops.elements.sequences.oligoseq`

renumber_pdb_needleman(inseq, instr, seqback=False, remove_ligands=False)[source]¶

Return modified gemmi.Structure with new residue numbers. It uses Needleman-Wunsch algorithm to perform the sequence alignment.

Parameters:	inseq (`crops.elements.sequences.oligoseq`) – Input sequence. instr (`gemmi.Structure`) – Gemmi structure. seqback (bool, optional) – If True, it additionally returns the `crops.elements.sequences.oligoseq` with the gaps found in the structure, defaults to False. remove_ligands (bool, optional) – If True, use `gemmi.Structure.remove_ligands_and_waters()` and `gemmi.Structure.remove_empty_chains()` prior to operation, defaults to False.
Return instr:	Renumbered structure.
Rtype instr:	`gemmi.Structure`
Return inseq:	Sequence with extra information about gaps, only if seqback is True.
Rtype inseq:	`crops.elements.sequences.oligoseq`