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Pydoc: module nefTools

nefTools

index

FIX

Functions

addOneDistanceRestraint(cat, selPairs, index, id, target_value, lower_limit, upper_limit, weight=1, XplorNIH_label=''): Given a list of pairs of atom selections, add a restraint to cat,
an input CifCategory.
Returns a tuple of (id,index,cat)

distanceRestraintHeader(name, comments=None, origin=None): Return a tuple of (commentStr,, cif.Cif) appropriate for a distance
restraint list with the specified name, where commentStr is a string
appropriate to place in a NEF file, and origin is a description of the
source of these distance restraints.

genHeader(datablockName='test1', cif=None): Generate boilerplate header fields for NEF entries. Return as a valid
NEF string.

genMolecularSystem(selection='all'): Return a string containing a nef_molecular_system saveframe valid for the
specified selection.

getBlock(nef, blockType='', nefRestraintName=None): Given an object nef, returned by nefTools.readNEF, get the block
of given type named nefRestraintName. If there's a
single block of this type, its name need not be specified.

An abbreviated form of nefRestraintName can be used for the case when
it begins with the blockType string followed by _STRING, in which
case only STRING need be specified.

getBlockNames(nef, blockType): Return a list of names of the given blockType.

getBlocksOfType(nef, blockType): Return a list of key,block pairs of the given blockType, where blockType
specifies either sf_category name, or a shorthand for this given
in the catPrefixes dictionary.

nefComment(oneOrMoreComment): Return a string properly formatted for one or more lines of comment
in the NEF format (lines should begin with the '# ' string.

nefShifts(nef, name=None, verbose=True): Read chemical shift data from the global NEF cif.Cif
object, which must have been previously populated by calling readNEF().

Returns a list of two-membered lists:
[chemical shift value, selection string, err]

readNEF(filenameOrString, initPSF=True, makeDisulfideBond=True): Read NEF data from file or string into an internal data
structure. The returned object is a cif.Cif object. If the
initPSF argument is True, all PSF information is generated from
the NEF data. If filenameOrString contains a newline, it is interpreted
as a string containing a NEF record, otherwise it is considered to be
a filename.

The makeDisulfideBond argument is passed through as the bond argument to
psfGen.addDisulfideBond funcion.

seqFromNEF(pdbRecord=None, cifData=None, useSeqres=False, processBiomt=False, failIfInsertion=-1): Return a list of list of sequences for an input record in mmCIF format-
True.

shiftsFromList(list, name): Return a formatted NEF record for the chemical shifts in the input list
as a string with the specified saveframe name.

The list argument should be a sequence of (val, sel) or (val,err,sel),
where val is the chemical shift value, err is the chemical shift error,
and sel is an atomSel.AtomSel specifying which atoms the shift value
corresponds to.

The resulting NEF record is sorted by the atoms order in the PSF.

shifts_writeNEF(name, shiftsBlock): Given a name, generate a full save set name by prepending the shifts
catPrefix,

Then return a formatted NEF record from the input shiftsBlock.

Data
		catPrefixes = {'dihedral': 'nef_dihedral_restraint_list', 'distance': 'nef_distance_restraint_list', 'rdc': 'nef_rdc_restraint_list', 'shifts': 'nef_chemical_shift_list', 'spectrum': 'nef_nmr_spectrum'} peaksPrefix = 'nef_nmr_spectrum_' shiftsPrefix = 'nef_chemical_shift_list_'