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IMP Reference Guide
develop.63b38c487d,2024/12/25
The Integrative Modeling Platform
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A single entity in the system. More...
Inherits Entity.
A single entity in the system.
This contains information (such as database identifiers) specific to a particular sequence rather than a copy (for example, when modeling a homodimer, two AsymUnits will point to the same Entity).
This functions identically to the base ihm.Entity class, but it allows identifying residues by either the PMI numbering scheme (which is always contiguous starting at 1, covering the entire sequence in the FASTA files, or the IHM scheme (seq_id, which also starts at 1, but which only covers the modeled subset of the full sequence, with non-modeled N-terminal or C-terminal residues removed). The actual offset (which is the integer to be added to the IHM numbering to get PMI numbering, or equivalently the number of not-represented N-terminal residues in the PMI sequence) is available in the pmi_offset member.
If a UniProt accession was provided for the sequence (either when State.create_molecule() was called, or in the FASTA alignment file header) then that is available in the uniprot member, and can be added to the IHM system with the add_uniprot_reference method.
Public Member Functions | |
| def | add_uniprot_reference |
| Add UniProt accession (if available) to the IHM system. More... | |
| def | pmi_range |
| Return a range of IHM residues indexed using PMI numbering. More... | |
| def | pmi_residue |
| Return a single IHM residue indexed using PMI numbering. More... | |
| def IMP.pmi.mmcif.Entity.add_uniprot_reference | ( | self | ) |
Add UniProt accession (if available) to the IHM system.
If a UniProt accession was provided for the sequence (either when State.create_molecule() was called, or in the FASTA alignment file header), then look this up at the UniProt web site (requires network access) to get full information, and add it to the IHM system. The resulting reference object is returned. If the IMP and UniProt sequences are not identical, then this object may need to be modified by specifying an alignment and/or single-point mutations.
| def IMP.pmi.mmcif.Entity.pmi_range | ( | self, | |
| res_id_begin, | |||
| res_id_end | |||
| ) |
| def IMP.pmi.mmcif.Entity.pmi_residue | ( | self, | |
| res_id | |||
| ) |