Chemical shifts¶

ChemicalShifts is a tidy table of assigned chemical shifts — one row per atom — plus the operations you most often want on them: re-referencing, the chemical-shift index (CSI), and building peak lists.

Constructing¶

import makeshift as ms

# From a BMRB id (downloads + parses)
cs = ms.ChemicalShifts.from_bmrb(5363)

# From an already-parsed entry
entry = ms.NMRStarEntry.from_bmrb(5363)
cs = ms.ChemicalShifts.from_entry(entry)

Both constructors accept reref= and calc_csi= so you can correct referencing and compute CSI in one step:

cs = ms.ChemicalShifts.from_bmrb(4527, reref="lacs", calc_csi=True)

The table¶

cs.data

Column	Meaning
`Seq_ID`	Residue number
`Comp_ID`	Residue type (three-letter)
`Atom_ID`	Atom name
`Atom_type`	Element
`Val`	Shift (ppm)

After calc_csi=True (or cs.add_csi()), two more columns appear: csi_raw (secondary shift) and csi (the discretised ±1/0 index).

Re-referencing¶

cs.reref(method="panav")   # or "lacs"
cs.reref_offsets           # {'N': ..., 'CA': ..., 'CB': ..., ...}

The two methods and when to prefer each are covered in Re-referencing.

Chemical-shift index¶

cs.add_csi()   # adds csi_raw and csi columns in place; returns self

CSI compares each backbone shift to random-coil values to flag helix/strand propensity per residue — the basis PANAV uses to pick a reference distribution.

From shifts to peaks¶

peaks = cs.peaklist()                       # default amide HSQC
peaks = cs.peaklist(dims=[("H", "N")])      # explicit dimensions
peaks = cs.peaklist(entity_id=1)            # a specific entity

See Peak lists for the full set of dimension options and outputs.

Sequences¶

cs.sequences()          # one row per entity
cs.get_entry()          # the underlying NMRStarEntry, if built from one

Full API¶

See the ChemicalShifts reference.