Make an equivalent fixed resonance in the input constraint store
NmrConstraint.FixedResonance, Nmr.NmrConstraintStore
NmrConstraint.FixedResonance
Exports a constraint list to a file as an ARIA 1.x readable .tbl file (similar to CNS format). For proper CNS format use CcpNmr FormmatConverter. NBNB will expand restraisnt (A<->C) or B<->D) to (A or B)<->(C or D)
List of NmrConstraint.DistanceConstraints, String (export file name)
None
Get the atoms that may be assigned to the constrained resonances The outer most list is due to restraint ambiguity, the middle list is the list for different resonances and the inner list is for equivalent atoms.
NmrConstraint.AbstractConstraint
List of List of List of MolSystem.Atoms
Makes any missing resonances for assigned fixedResonances in an NmrConstraintStore with the option to also make new resonances for unassigned fixedResonances. Returns all the resonances linkable from the constraints in an NmrConstraintStore object.
Nmr.NmrConstraintStore, Boolean
List of Nmr.Resonances
Get constraining distances appropriate to a given NOE intensity value using a distance relation table.
List of Tuples of Floats (relative NOE intensity, target dist, min dist, max dist), Float (NOE intensity/average for peak list)
Float, Float, Float (targetValue, upperLimit, lowerLimit)
Finds or creates a fixed set of atoms that is used in an NMR constraint head object (equivalent to one NmrConstraint file). Creating fixed atom sets allows assignments to change but old constraints to be preserved.
Nmr.NmrConstraintStore, List of MolSystem.Atoms
NmrConstraint.FixedAtomSet
Find or create a fixed resonance for an NMR constraint top object equivalent to the input normal resonance. The fixed resonance will preserve assignment information at the time of constraint generation.
Nmr.NmrConstraintStore, Nmr.Resonance
NmrConsraints.FixedResonance
For a given spectrum ind or get a default table of NOE intensity to constraint distance relations.
Nmr.DataSource
List of Tuples of Floats (relative NOE intensity, target dist, min dist, max dist)
The the J couplings associated with a J coupling constraint
NmrConstraint.JCouplingConstraint, Nmr.JCouplingList
List of Nmr.JCouplings
Calculate the mean of the unsigned intensities of input peaks. Also sets peak.intensityValue on-the-fly attribute for quick access by Analysis.
List of Nmr.Peaks, String (Nmr.PeakIntensity.intensityType)
Float
Get target, minimum and maximum distance for an NOE intensity Given ISPA parameters, erros and limits
Float, 6 List of Floats
Float, Float, Float
Finds the shift matching tolerance for a peak dim based on its line width. Defaults to the minimum tolerance if no line width is present.
Nmr.PeakDim, Float, Float, Float (Nmr,PeakDim.lineWidth to tolerance factor)
Float (PPM tolerance)
Calculate the violated restraints in a restraint list given in input structure. Currently limited to distance and dihedral restraints. Option to add violations to a speficied violation list (otherwise a new one will be made)
NmrConstraint.ConstraintList, MolStructure.StructureEnsemble
NmrConstraint.ViolationList
Determine if a residue is in a residue range table for a given data dim. The range table lists residue bounds (first and last residue objects) for a chain appropriate to a list of data dims (often bonded).
MolSystem.Residue, List of (List of Nmr.DataDims, MolSystem.Chain, MolSystem.Residue, MolSystem.Residue), Nmr.DataDim
Boolean
Makes a constraint list with constraints by matching known shifts in given range and within specified tolerances to a NOESY peak list. Optional labelling scheme/mixture and labelling threshold to filter according to a given set of residue isotopomers. Constraints will be put in a new NMR constraint store object if none is specified. Peaks are catergorised into various lists. A structure and max distance can be used to filter contributions. The scale option is the value by which peak intensities are scaled for NOE table/function lookup. Params relate to the generic NOE distance function if neither these nor a distance function is specified a lookuptable is used
.PeakList (NOESY), List of (Nmr.DataDim, Float, Float, Float) (shift tolerances), List of (Nmr.DataDim, String (isotope code), Float, Float) (chem shift ranges) Nmr.NmrConstraintStore, Boolean (test only), ChemCompLabel.LabelingScheme or True (automatic from experiment MolLabel), Float, Function (to get distances from NOEs), Nmr.PeakIntensity.intensityType, List of (List of Nmr.DataDims, Nmr.Chain, Integer, Integer) (residue ranges), Float (min Peak.figOfMerit), ProgressBar (Analysis popup), Boolean, Boolean, MolStructure.StructureEnsemble, Float Float, List of Floats (distance function parameters) Dict (for Category Name:Lists of Nmr.Peaks)
NmrConstraint.DistanceConstraintList
Makes a constraint list with constraints based upon the assigned peaks within a NOESY peak list. Constraints will be put in a new NMR constraint head object if none is specified. An NOE intensity-to-distance function, minimum peak merit and allowed residue ranges may be input for the calculation. A normalising peak list can be specified to help calibrate the peak intensities according to the sensitivity of a corresponding root resonances. The scale option is the value by which peak intensities are scaled for NOE table/function lookup. Params relate to the generic NOE distance function if neither these nor a distance function is specified a lookuptable is used.
Nmr.PeakList (NOESY), Nmr.NmrConstraintStore, String (Nmr.PeakIntensity.intensityType) Function (to get constraining distances), Boolean ChemComLabel.LabelingScheme or True (automatic from experiment MolLabel), List of Floats (distance function parameters), List of (List of Nmr.DataDims, Nmr.Chain, Integer, Integer), Float (Nmr.Peak.figOfMerit), Float (baseline intensity)
NmrConstraint.DistanceConstraintList
Make a new fixed resonance for an NMR constraint top object based on a normal resonance. The fixed resonance will preserve assignment information at the time of constraint generation.
Nmr.NmrConstraintStore, Nmr.Resonance
NmrConsraints.FixedResonance
Make a new NMR constraint top object for a project which will contain constraints and violations.
Nmr.NmrProject
Nmr.NmrConstraintStore
Predict the occurence of a set of NOESY peaks from a list of constraints. This function attempts to use sister lists to the input restraints linked peaks unless an overring target spectrum is passed in. This function is ideal for visualising the NOE disambiguation of procedures like ARIA and CYANA.
List of NmrConstraint.DistanceConstraints, Nmr.DataSource
List of Nmr.Peaks
Make a structure generation object to group structures together
MolSystem.StructureEnsemble, Nmr.NmrConstraintStore
Nmr.StructureGeneration
Merge two constraint lists from a constraint set into one.
NmrConstraint.ConstraintList, NmrConstraint.ConstraintList
NmrConstraint.ConstraintList
Merge redundant constraints in a constraint list (constraining the same resonances)
NmrConstraint.ConstraintList
NmrConstraint.ConstraintList
Move a constraint to a different constraint list and take care of any
violations.
- Input
NmrConstraint.Constraint, NmrConstraint.ConstraintList
- Output
NmrConstraint.Constraint
Spit a constraint list into two lists according to whether constraints are ambigous or unambiguous.
NmrConstraint.ConstraintList
NmrConstraint.ConstraintList, NmrConstraint.ConstraintList
Spit a constraint list into two lists according to whether constraints show a violation (in th einput violation list).
NmrConstraint.ConstraintList, NmrConstraint.ViolationList
NmrConstraint.ConstraintList, NmrConstraint.ConstraintList
Update the items/contributions of a distance constraint given any new assignments to the peak from which it was originally derived.
List of NmrConstraint.DistanceConstraint
None
Update the atom assignments of a fixed resonance to reflect a connected Nmr.Resonance. Will not remove asslignments if Nmr.Resonance is missing of unassigned. A new Nmr.Resonance may optinally be specified.
NmrConstraint.FixedResonance, Nmr.Resonance
None
Update the assignments of the peaks that are linked to distance constraints of a constraint set, given changes to the constraint items. This function is ideal for visualising the NOE disambiguation of procedures like ARIA and CYANA. Option to replace any existing assignments; otherwise assignments will be added to.
List of NmrConstraint.DistanceConstraints, Boolean
None