ConstraintBasic

ccpnmr.analysis.core.ConstraintBasic.copyFixedResonance(fixedResonance, nmrConstraintStore)

Make an equivalent fixed resonance in the input constraint store

Input

NmrConstraint.FixedResonance, Nmr.NmrConstraintStore

Output

NmrConstraint.FixedResonance

ccpnmr.analysis.core.ConstraintBasic.exportAriaTbl(constraints, fileName)

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)

Input

List of NmrConstraint.DistanceConstraints, String (export file name)

Output

None

ccpnmr.analysis.core.ConstraintBasic.getConstraintAtoms(constraint)

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.

Input

NmrConstraint.AbstractConstraint

Output

List of List of List of MolSystem.Atoms

ccpnmr.analysis.core.ConstraintBasic.getConstraintStoreResonances(nmrConstraintStore, makeUnassignedResonances=True)

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.

Input

Nmr.NmrConstraintStore, Boolean

Output

List of Nmr.Resonances

ccpnmr.analysis.core.ConstraintBasic.getDistancesFromIntensity(noeClasses, value)

Get constraining distances appropriate to a given NOE intensity value using a distance relation table.

Input

List of Tuples of Floats (relative NOE intensity, target dist, min dist, max dist), Float (NOE intensity/average for peak list)

Output

Float, Float, Float (targetValue, upperLimit, lowerLimit)

ccpnmr.analysis.core.ConstraintBasic.getFixedAtomSet(nmrConstraintStore, atoms)

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.

Input

Nmr.NmrConstraintStore, List of MolSystem.Atoms

Output

NmrConstraint.FixedAtomSet

ccpnmr.analysis.core.ConstraintBasic.getFixedResonance(nmrConstraintStore, resonance)

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.

Input

Nmr.NmrConstraintStore, Nmr.Resonance

Output

NmrConsraints.FixedResonance

ccpnmr.analysis.core.ConstraintBasic.getIntensityDistanceTable(spectrum)

For a given spectrum ind or get a default table of NOE intensity to constraint distance relations.

Input

Nmr.DataSource

Output

List of Tuples of Floats (relative NOE intensity, target dist, min dist, max dist)

ccpnmr.analysis.core.ConstraintBasic.getJCouplingsFromConstraint(jCouplingConstraint, jCouplingList)

The the J couplings associated with a J coupling constraint

Input

NmrConstraint.JCouplingConstraint, Nmr.JCouplingList

Output

List of Nmr.JCouplings

ccpnmr.analysis.core.ConstraintBasic.getMeanPeakIntensity(peaks, intensityType='volume')

Calculate the mean of the unsigned intensities of input peaks. Also sets peak.intensityValue on-the-fly attribute for quick access by Analysis.

Input

List of Nmr.Peaks, String (Nmr.PeakIntensity.intensityType)

Output

Float

ccpnmr.analysis.core.ConstraintBasic.getNoeDistance(intensity, params)

Get target, minimum and maximum distance for an NOE intensity Given ISPA parameters, erros and limits

Input

Float, 6 List of Floats

Output

Float, Float, Float

ccpnmr.analysis.core.ConstraintBasic.getPeakDimTolerance(peakDim, minTol, maxTol, multiplier)

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.

Input

Nmr.PeakDim, Float, Float, Float (Nmr,PeakDim.lineWidth to tolerance factor)

Output

Float (PPM tolerance)

ccpnmr.analysis.core.ConstraintBasic.getStructureViolations(constraintList, structure, violationList=None)

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)

Input

NmrConstraint.ConstraintList, MolStructure.StructureEnsemble

Output

NmrConstraint.ViolationList

ccpnmr.analysis.core.ConstraintBasic.isResidueInRange(residue, residueRanges, dataDim)

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).

Input

MolSystem.Residue, List of (List of Nmr.DataDims, MolSystem.Chain, MolSystem.Residue, MolSystem.Residue), Nmr.DataDim

Output

Boolean

ccpnmr.analysis.core.ConstraintBasic.makeAmbigDistConstraints(peakList, tolerances, chemShiftRanges, constraintSet=None, testOnly=False, labelling=None, minLabelFraction=0.10000000000000001, distanceFunction=None, residueRanges=None, minMerit=0.0, progressBar=None, intensityType='volume', ignoreDiagonals=True, doAliasing=True, structure=None, maxDist=None, scale=None, params=None, peakCategories=None)

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

Input

.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)

Output

NmrConstraint.DistanceConstraintList

ccpnmr.analysis.core.ConstraintBasic.makeDistConstraints(peakList, constraintSet=None, intensityType='volume', distanceFunction=None, normalise=True, labelling=None, params=None, residueRanges=None, minMerit=0.0, scale=None, normalisationType=None)

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.

Input

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)

Output

NmrConstraint.DistanceConstraintList

ccpnmr.analysis.core.ConstraintBasic.makeFixedResonance(nmrConstraintStore, resonance)

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.

Input

Nmr.NmrConstraintStore, Nmr.Resonance

Output

NmrConsraints.FixedResonance

ccpnmr.analysis.core.ConstraintBasic.makeNmrConstraintStore(nmrProject)

Make a new NMR constraint top object for a project which will contain constraints and violations.

Input

Nmr.NmrProject

Output

Nmr.NmrConstraintStore

ccpnmr.analysis.core.ConstraintBasic.makePeaksFromConstraints(constraints, spectrum=None)

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.

Input

List of NmrConstraint.DistanceConstraints, Nmr.DataSource

Output

List of Nmr.Peaks

ccpnmr.analysis.core.ConstraintBasic.makeStructureGeneration(structure, constraintSet=None, generationType='denovo')

Make a structure generation object to group structures together

Input

MolSystem.StructureEnsemble, Nmr.NmrConstraintStore

Output

Nmr.StructureGeneration

ccpnmr.analysis.core.ConstraintBasic.mergeConstraintLists(constraintListA, constraintListB)

Merge two constraint lists from a constraint set into one.

Input

NmrConstraint.ConstraintList, NmrConstraint.ConstraintList

Output

NmrConstraint.ConstraintList

ccpnmr.analysis.core.ConstraintBasic.mergeDuplicateConstraints(constraintList)

Merge redundant constraints in a constraint list (constraining the same resonances)

Input

NmrConstraint.ConstraintList

Output

NmrConstraint.ConstraintList

ccpnmr.analysis.core.ConstraintBasic.moveConstraintToList(constraint, constraintList)
Move a constraint to a different constraint list and take care of any

violations.

Input

NmrConstraint.Constraint, NmrConstraint.ConstraintList

Output

NmrConstraint.Constraint

ccpnmr.analysis.core.ConstraintBasic.splitConstraintListAmbigUnambig(constraintList)

Spit a constraint list into two lists according to whether constraints are ambigous or unambiguous.

Input

NmrConstraint.ConstraintList

Output

NmrConstraint.ConstraintList, NmrConstraint.ConstraintList

ccpnmr.analysis.core.ConstraintBasic.splitConstraintListViol(constraintList, violationList=None)

Spit a constraint list into two lists according to whether constraints show a violation (in th einput violation list).

Input

NmrConstraint.ConstraintList, NmrConstraint.ViolationList

Output

NmrConstraint.ConstraintList, NmrConstraint.ConstraintList

ccpnmr.analysis.core.ConstraintBasic.updateDistConstraintFromPeakAssign(constraint)

Update the items/contributions of a distance constraint given any new assignments to the peak from which it was originally derived.

Input

List of NmrConstraint.DistanceConstraint

Output

None

ccpnmr.analysis.core.ConstraintBasic.updateFixedResonance(fResonance, resonance=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.

Input

NmrConstraint.FixedResonance, Nmr.Resonance

Output

None

ccpnmr.analysis.core.ConstraintBasic.updatePeaksFromConstraints(constraints, replace=False)

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.

Input

List of NmrConstraint.DistanceConstraints, Boolean

Output

None

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