Set the spin systems of a peak’s resonances to have sequential connectivity according to sequence offsets. Sequence offsets for HN(CO)CA would be (None,-1,None), for H,C,N dims
Nmr.Peak, List of Int (Nmr.ResonanceGroupProb.sequenceOffset)
List of Nmr.ResonanceGroups
Add the resonances assigned to given peaks to a spin system. Makes a new spin system if none exists for the resonances Multiple spin systems will be merged, if present, for resonances upon confirmation
List of Nmr.Peaks
Nmr.ResonanceGroup
Add a resonance to a given spin system
Nmr.ResonanceGroup, Nmr.Resonance
List of Nmr.Resonances (belonging to the spin system)
Give the position in PPM for a peak dimension
Nmr.PeakDim
Float (ppm)
Determine if a pair of resonances are assigned to a potentially prochiral pair of atoms.
Nmr.Resonance, Nmr.Resonance
Boolean
Assign a resonance to given atom sets via a resonanceSet (optionally specified) Checks ensure that the resonance ends up in the correct spin system
List of Nmr.AtomSets, Nmr.Resonance, Nmr.ResonanceSet
Nmr.ResonanceSet
Assigns a given peak dimension to a given resonance, via a given peakDim contribution if specified and assign the resonance to atom sets if specified
Nmr.PeakDimContrib
Assign a resonance to a peak dimension, via a specified peakDimContrib if needed. Assigns a new resonance if none is input. Can also specify a set of peakContribs (grouped assigment possibilities) that the assignment relates to.
Nmr.PeakDimContrib
Changes the assignment of a resonance to a given residue if an appropriately named atom set can be found for the resonance’s assignName.
Nmr.Resonance, Nmr.Residue
None
Sets the assign names for a resonance according to given AtomSets or atom names without performing a real assignment. If no atom sets or assign names are given then all typing information is removed.
Nmr.Resonance, List of Nmr.AtomSets or None, List of Words or NOne
None
Connect a given spin system to a residue. Resonances in the spin system are assigned where possible. Also used to disconnect from a residue if Residue is None. Optionally merge spin systems assigned to same residue, given warning.
Nmr.ResonanceGroup, Nmr.Residue, Boolean, Boolean
Nmr.ResonanceGroup
Assigns a spin system to a given type of possible residue
Nmr.ResonanceGroup, Word(Molecule.MolResidue.ccpCode), Word(Molecule.MolResidue.molType)
None
Set a tentative/provisional/trial assignment from a resonance to the input atoms. Optionally set weight of the tentative assignment.
List of Nmr.AtomSets, Nmr.Resonance, Float, Boolean
None
Set a tentative/provisional/trial residue assignments for a given spin system. Optionally set weight of the tentative assignment.
Nmr.ResonanceGroup, List of MolSystem.Residues, Float, Boolean
List of Nmr.ResidueProbs
Calculates the value and error for a given shift based upon the peaks to which its resonance is assigned. Also sets links to appropriate peaks and peak dims. Optional float to scale simulated peak contributions (normally so that they have much less influence)
Nmr.Shift, Float
Float (shift.value)
Clear a peak dimension of any or a specified peakDim contribution Recalculates shifts of the resonances involved
Nmr.PeakDim, Nmr.PeakDimContrib
None
Remove a resonance’s peak dim contributions present in a specified list of peaks or all peaks in project (if peak=None)
Nmr.Resonance, List of Nmr.Peaks
None
Remove sequential links for a spin system. A sequence offset may be specified otherwise all sequential links are removed.
Nmr.ResonanceGroup, Int
None
Disconnects a resonance from any assigned atomSets. Option to remove previous assignment atom names
Nmr.Resonance
None
Find a spin system sequentially connected to the input one with given sequence offset.
Nmr.ResonanceGroup, Int
Nmr.ResonanceGroup
Find spin systems sequentially connected to the input one with given sequence offset.
Nmr.ResonanceGroup, Int .. describe:: Output
Nmr.ResonanceGroup
Finds the first shift in a shiftList for the specified atom.
MolSystem.Atom, Nmr.ShiftList
Nmr.Shift
For peakDim give the NMR shifts within a tolerance (which may be specified) of its position in a given set of ranges with options if the peakDim position might be aliased and to find only shifts with resonances assigned to atoms. Obeys molSystem assignments for atom linked peaks - these must match the peakDim’s experiment molSystems. Option to pas in an alternative ppm value if the main peakDim value is not to be used (e.g. reduced dimensionality MQ etc).
Nmr.PeakDim, List of Tuples (Float, Float) Float, Boolean, Boolean, Float
List of Nmr.Shifts
For a dataDimRef give the NMR shifts within a tolerance (which may be specified) to a given position with an option to find only shifts with resonances assigned to atoms
Nmr.DataDimRef, Float, Float, Boolean
List of Nmr.Shifts
Find the resonance set, if any, that connects a resonance to given atomSets Or that is shared between atomSets
Nmr.Resonance, List of Nmr.AtomSets
Nmr.ResonanceSet
Find the spin system in which a resonance resides makes a new spin system if none is found
Nmr.Resonance
Nmr.ResonanceGroup
Give all the aliased/unaliased positions of a peakDim either in a specified shift range or the full range for the dimension type. Units for the shift ranges are ppm. Note this function uses the peakDim.realValue, i.e. center of couplings for main assignment. Use the PeakBasic version if the actual extremum location should be used. Optional ppm argument if main position is not the one to be considered, e.g. in reduced dimensionality or MQ.
Nmr.PeakDim, List of (Tuples of Floats (MinShift,MaxShift) )
List of Floats (Nmr.PeakDim.positions)
Deterimine if an ambigous prochiral resonance (non-stereospecifically assigned) Has an “a” label or a “b” label. “a” is reserved for the upfield proton and any other nulceus bound to it.
Nmr.Resonance
Character
Gives the shifts that an atom set may be assigned to in a specified shift list or the first shift list in the project if none is specified.
Nmr.AtomSet, Nmr.ShiftList
List of Nmr.Shifts
Find all resonances that have a single bond connection to the input resonance Option to recalculate given assignment status (e.g. if something changes) Option to specify peakDimContribs to search
Nmr.Resonance, Boolean, List of Nmr.PeakDimContribs
List of Nmr.Resonances
Give the min and max possible chem shifts for a spectrums data dim based on set min/max epDim frequencies or full spec with
Nmr.FreqDataDim
List of Floats
Give the name for a fixedResonance, based upon a normal resonance
Nmr.Resonance
String
Find any resonance that may have a single bond connetion to the input resonance Option to specify the isotope type
Nmr.Resonance, Nmr.Resonance.isotopeCode
Nmr.Rssonance
Give a tupe of string identifiers for a peakDim indicating, chain, residue and atomic assignment
Nmr.PeakDim
3-Tuple of Words
Give the min and max possible chem shifts for a peak dim based on set min/max epDim frequencies or full spec with
Nmr.PeakDim
List of Floats
Gives the position in PPM for a given peak dimension
Nmr.PeakDim
Float (ppm)
Find the resonances (for a given atom type if specified) assigned to a given residue
Nmr.Residue, Word (ChemComp.ChemAtom.elementSymbol)
List of Nmr.Resonances
Give a tupe of string identifiers for a resonance indicating, chain, residue and atomic assignment
Nmr.Resonance
Tuple of Words (MolSystem.Chain.code, MolSystem.Residue identifier, Nmr.Resonance identifier)
Get the fraction of labelling for a given resonance’s assignment or make a guess if it is atom typed and in a residue typed spin system. Can work with a reference isotopomer scheme or a labeled mixture.
Nmr.Resonance, ChemComLabel.LabelingScheme or LabeledMolecule.LabeledMixture
Float
Find, if any exists, the molecular system associated with a given resonance by virtue of a direct assignment or spin system link.
Nmr.Resonance
Nmr.MolSystem or None
Generate a name for a resonance or fixedResonance based upon its assignment
Nmr.Resonance or NmrConstraint.FixedResonance
String
Get the fraction of a pair of resonances both being labelled given a labelling scheme. Considers individual isotopomers if the resonances are bound within the same residue. Can work with a reference isotopomer scheme or a labeled mixture.
Nmr.Resonance, Nmr.Resonance, ChemComLabel.LabelingScheme or LabeledMolecule.LabeledMixture
Float
Find the residue, if any, to which a resonance is assigned via atomSets etc
Nmr.Resonance
Nmr.Residue or None
Get any sequential spin system links (resonanceGroupProbs). An optional sequence offset may be specified.
Nmr.ResonanceGroup, Int
List of Nmr.ResonanceGroupProbs
Get all the shift lists associated with an NMR project.
Nmr.NmrProject
Nmr.ShiftList
Find a ChemComps that spin system is assigned to, or tentatively assigned to.
Nmr.ResonanceGroup
list of MolSystem.Residue. Contains no duplicates
Find a residues that spin system is assigned to, or tentatively assigned to.
Nmr.ResonanceGroup
list of MolSystem.Residue. Contains no duplicates
Get all the synthetic shift lists associated with an NMR project.
Nmr.NmrProject
Nmr.ShiftList
Initialise a resonance. If the resonance is assigned it is placed in a spin system if appropriate and its assignName is set. Optional argument to set whether merging spin systems is allowed. Typically this is not allowed upon load, but is allowed when assigning within Analysis.
Nmr.Resonance, Boolean
None
Determines if an atom is assigned to any resonances, with an optional argument to check if the resonances are linked to peaks.
MolSystem.Atom
Boolean
Determines if an NMR chain has any atoms in its residues that are assigned to resonances
Nmr.Chain
Boolean
Check to make sure a resonance to peakDim assignment obeys experimental onbond relationshps.
Nmr.PeakDim, Nmr.Resonance, Nmr.DataSource
String (warning message) or None
Determines if a peak is assigned, ether fully or partially
Peak, Boolean
Boolean
Determines if an NMR residue has any atoms that are assigned to resonances
MolSystem.Residue
Boolean
Determine whether a chemical shift value is contained within one of the input ranges.
Float (Nmr.Shift.value), List of Tuples of Floats (min, max range bounds)
Boolean
Give the name of a given set of atoms for GUIs
List of Nmr.AtomSets
Word
Makes an annotation string for a given peak dimension according to its assignment status
Nmr.PeakDim
String (Nmr.PeakDim.annotation)
Give the name of a resonance for GUIs. Either full identifier or just the atom type name (if any), Option to force the display of atom assignements set doAtoms to Ture/False
Nmr.Resonance, Boolean, Boolean
Word
Make a sequential link with a give offset between two spin systems. Assigning A to B with a delta of 1 assumes B is C-terminal/upstream of A
Nmr.ResonanceGroup, Nmr.ResonanceGroup, Int
Nmr.ResonanceGroupProb
Merge two resonances and their shifts into one
Nmr.Resonance, Nmr.Resonance
Nmr.Resonance
Merge the resonances from two spin systems into one spin system
Nmr.ResonanceGroup, Nmr.ResonanceGroup
Nmr.ResonanceGroup
Make a peakDim to resonance assignment via a PeakDimContrib. Optional argument to specify which PeakContrib assignment possibilities the peakDim assignment relates to.
Nmr.PeakDim, Nmr.Resonance, List of Nmr.PeakContribs
Nmr.PeakDimContrib
Make a new resonance in a given project. Sets initial isotopeCode. Uses the current NMR project.
Project, Word (Resonance.isotopeCode)
Nmr.Resonance
Make a new spin system for a project
Project
Nmr.ResonanceGroup (spin system)
Propogates approprate assignments across a group of peaks e.g. to spead F1 F3 assignments to a column of peaks in the same spin system. If a refPeak is present it will not be affected but its assignments will be used instead of the assignments from the other peaks. cleanNonRef Boolean option is used when there is a reference peak so that the non-reference peaks may be cleaned prior to propagation. Optional argument to pass in the tolerences for each dimension. Note peaks can be of different dimensions, but if you pass in tolerances, tolerances map 1:1 to peak.sortedPeakDims()
List of Nmr.Peaks, Nmr.Peak, Boolean, Dict of Resonance.isotopeCode:Float, Boolean
None
Remove the notification calls to automatically update annotations and quick shift lookups when assignments change.
None
None
Remove a resonance from a given spin system
Nmr.ResonanceGroup, Nmr.Resonance
None
Sets the MolSystem.Molsystem for all experiments with assignments to a given resonance and/or the experiment for a given peakDim Displays a warning if an assignment is made outside an experiment’s list of molSystems.
MolSystem.Residue, Nmr.PeakDim, Nmr.Resonance
Boolean
Sets up a list of lists of shifts for a shift list accessed by shift.value: quicker than searching all
Nmr.Shift
None
Set a resonance’s assign names based on a refExpDimRef to which it is assigned. Currently limited to CO, CA, CB, HA.
Nmr.Resonance, NmrExpPrototype.RefExpDimRef
None
Set up the notification calls to automatically update annotations and quick shift lookups when assignments change.
None
None
Split assignments that were once thought to be from one resonance into assignments from two.
Nmr.Resonance
Nmr.Resonance
If a resonance is assigned to a prociral centre in a stereospecific manner, change the assignment to the other prochiral atom set. Automatically swaps over any other resonance that may be assigned to the other prochiral option. If the makeAmbiguous option is True then the unambiougously assigned resonances are changed to ambigous assignments by assigning resonances to both prochiral options.
Nmr.Resonance, Boolean
None
Swaps the resonances for as pair of spin systems. Spin systen assignments updates according to resonance assignments
Nmr.ResonanceGroup, Nmr.ResonanceGroup
None
Recalculate the values for all shifts in a shift list given peak assignments
Nmr.ShiftList
None
Refresh an AtomSetMapping according to the current assignment status. AtomSets optionally passed into increase speed
Analysis.AtomSetMapping, List of Nmr.AtomSets
None
Updates annotation string for the peak dimension of a given contribution according to its assignment status
Nmr.PeakDimContrib
None
Update the shifts of resonances assigned to a given dim of peaks of a given spectrum. Required if the spectrum data dims chem shift weighting changes.
Analysis.AnalysisDataDim
None
Update the shifts of resonances assigned to a peakDim if that peakDim changes
Nmr.PeakDim
None
Update the shifts of resonances assigned to a peak. Required if the peak’s figure of merit changes
Nmr.Peak
None
Update the annotations for the peaks assigned to a residues resonances
MolSystem.Residue
None
Update the annotations for the peaks assigned to a resonances within a spin system that has a tentative assignment.
Nmr.ResidueProb
None
Update the shift values (and error) for a given resonance given assignment to a given peak dimension. The shift list is approriate to the peakDim’s experiment. Note that shift to peak and shift to peak dim links are also set.
Nmr.Resonance, Nmr.PeakDim
None
Update the annotations for the peaks assigned to a given resonance
Nmr.Resonance
None
Update the annotations for the peaks assigned to a resonances within a spin system.
Nmr.ResidueProb
None
Update the annotations for the peaks assigned to a resonanceSet’s resonances
Nmr.ResonanceSet
None