Python: package pasd

pasd

index

Stubs for future PASD NOE assignment support.

Package Contents

match
netfilter
noeTools

Functions

correctedSelection(resNum, resName, atomName): NMR-STAR formatted shift tables typically have three
types of atom name problems:

1.  Backbone amides are named H, rather than HN.

2.  methylenes are typically named H*2 and H*3 instead of
H*1 and H*2.  H*3 maps to H*2 and H*2 maps to H*1.

3.  Selections involving methyls usually only select one
of the three protons.

Returns an xplor selection with the atom name corrected/expanded
as necessary.

covalentNeighbors(atom, range): return list of atoms within range bonds of argument atom

findUnassignedAtoms(shiftList, flexibleRegion='', tclOutput=False, simulation=None, expectedNonassigned='\n (name o*) or \n (name c) or \n (name s*) or\n (resn thr and name hg1) or \n (resn ser and name hg) or \n (resn lys and (name hz* nz)) or \n (resn tyr and (name hh cg cz)) or \n (resn arg and (name he hh* cz nh* ne)) or\n (resn gln and name cd) or \n (resn glu and name cd) or \n (resn asn and name cg) or \n (resn asp and name cg) or\n (resn phe and name cg) or \n (resn trp and (name cg cd2 ce2)) or \n (resn his and name cg) or\n (resn pro and name n) or\n (name ht*)'): Given a list of shift entries, find atoms with no assignment

expectedNonassigned - default atoms which we don't expect to see
                      (exchangable protons, oxygens, sulfurs, or
                      heavyatoms with no attached protons)
flexibleRegion      - selection specifying atoms which we don't expect
                      to see due to flexibility.
tclOutput           - if True, return an informational string,
                      else return a named tuple with string member
                      message a list of atoms missingAtoms.

hasAssignmentWithinBondedNeighborhood(peak, range): Return True if the specified peak contains any assignments containing
a from/to pair separated by range bonds or fewer.

nefShifts(nef, name=None, verbose=True, tclOutput=False): 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]

peakAssignLikelihoodsFromStructs(structureData, peaks, violCutoff=0.5, sim=None): #
# Given a list of <filename, atomPosArray> pairs of converged structures
# and a list of peaks,
# use the coords to determine the likelihood of each peakAssignment
#
# Could be replaced with something that would calculate previous likelihood
# of any pair of ShiftAssignments, whether they're used in a PeakAssignment
# or not.
#

pipeShifts(pipe, verbose=True, tclOutput=False): Read chemical shift data from NMRPipe table format.

pipe is a string specifying either the path of the table or, directly, its
contents.

readSTAR(filename, addSaveSet=False): Read in the given NMR-STAR file and store the contents in the global
starData variable, which is returned.

If addSaveSet=True, wrap the contents of the file with the lines
save_dummy
  .
  .
  .
save_

removeBondedPeaks(pot, bondRange=2): Remove all peaks from the < pasdPot>.PASDPot argument pot which
contain any assignments with one or more from/to pair separated by
bondRange or few bonds.

sparkyPeaks(filename, noePot, fromProtonColumnName, toProtonColumnName, heightColumnName, fromHeavyatomColumnName=None, toHeavyatomColumnName=None, idColumnName=None, name=None, verbose=True, tclOutput=True): Read Sparky format into pasdPot.PASDPot

arguments:

  filename                - name of sparky file
  pasdPot                 - a PASDPot instance
  fromProtonColumnName    - string label for from- Proton
  toProtonColumnName      - string label for to- Proton
  fromHeavyatomColumnName - string label for from- heavyatom
  toHeavyatomColumnName   - string label for to- heavyatom
  heightColumnName        - string label for the height/intensity column.
                           Set this to None to use uniform weights.
  idColumnName            - string label for the column providing an
                           reference label. With a value of None, the
                           peaks are given integer ids, starting with 1.
  name                    - prefix to use for peak names. In PASD,
                            these must be different for each peaklist.
  verbose                 - whether to produce verbose output
  tclOutput               - If True, return a valid TCL list string

starPeaks(fromProtonColumnName, toProtonColumnName, fromHeavyatomColumnName=None, toHeavyatomColumnName=None, saveSet=None, tclOutput=True): Read nmr-star table for 3d experiments.

Specify NMR-STAR saveSet where the experimental data is located,
and the identities of labels for the dimensions of the experiment.
These names correspond to NMR-STAR items Spectral_dim.Dimension_name.

starShifts(useAmbiguityCodes=False, saveSet=None, verbose=False, segmentName=None, residOffset=0, defaultErr=0, tclOutput=True): Read chemical shift data from the global starData cif.Cif
object, which must have been previously populated by calling readStar().

If useAmbiguityCodes is True, some effort is made to obey the
included ambiguity codes.

Use a non-zero residOffset if the residue numbering in the shift table
differs from that in your PSF.

If the error (Val_err field) is not present in the STAR file, the
defaultErr value is used for all chemical shifts.

The return value is a sequence of tuples: (shift_val,selection,err).
However, if tclOutput=True, a string is returned containing valid
a TCL list of { val {selection} } elements.

structureMetrics(coordsByFilename, peaks, pasdPots, violCutoff=0.5, completenessWeight=0.0, inverseBound=4.0, inverseMethylCorrection=0.0, verbose=True, sim=None): Given a list of <filename, atomPosArray> pairs from grabPDBfiles,
check each one's violations of a given set of peaks
and return a list of the named tuple StructureMetrics for each structure.
This list is sorted by the structure's score.

updateUser(mess): Output the message to stdout if pasd.updateUser_enabled is set to
True.

xeasyShifts(filename, verbose=True, tclOutput=True, simulation=None, segmentName=None): Read XEASY format chemical shifts.

Data
		aveExp = 6 distanceBins = [(1.8, 2.7, 0.2), (1.8, 3.3, 0.5), (1.8, 5.0, 0.8), (1.8, 6.0, 1.0)] geminalAmbigTab = {'ALA': [], 'ARG': ['hb', 'hg', 'hd'], 'ASN': ['hb', 'hd2'], 'ASP': ['hb'], 'CYS': ['hb'], 'GLN': ['hb', 'hg', 'he2'], 'GLU': ['hb', 'hg'], 'GLY': ['ha'], 'HIS': ['hb'], 'ILE': ['hg1', 'cg1'], ...} longRangeResidCutoff = 6 mappings = [['', 'h', 'hn'], ['gly', 'ha3', 'ha2'], ['gly', 'ha2', 'ha1'], ['ile', 'hg13', 'hg12'], ['ile', 'hg12', 'hg11'], ['phe', 'hb3', 'hb2'], ['phe', 'hb2', 'hb1'], ['phe', 'cd', 'cd#'], ['phe', 'ce', 'ce#'], ['trp', 'hb3', 'hb2'], ['trp', 'hb2', 'hb1'], ['cys', 'hb3', 'hb2'], ['cys', 'hb2', 'hb1'], ['ser', 'hb3', 'hb2'], ['ser', 'hb2', 'hb1'], ['asn', 'hb3', 'hb2'], ['asn', 'hb2', 'hb1'], ['tyr', 'hb3', 'hb2'], ['tyr', 'hb2', 'hb1'], ['tyr', 'cd', 'cd#'], ...] nMono* = 1 updateUser_enabled = False