Dertemine whether two atoms are bonded together .. describe:: Input
MolSystem.Atom, MolSystem.Atom
Boolean
Determine if two atoms have a connectivity that may be observable in a TOCSY experiment
MolSystem.Atom, MolSystem.atom
Boolean
Determine whether two resonances are assigned to directly bonded atoms
Nmr.Resonance, Nmr.Resonance
Boolean
Make a new molecule based upon the sequence of an existing ome .. describe:: Input
Molecule.Molecule
Molecule.Molecule
Assign residueB to an equivalent set of resonances as residueA Optional dictionary, keyed by experiment to specifiy which chain (should be parent of residueA or residueB or None - for both) an experiment’s peak assignments should go with.
MolSystem.Residue, MolSystem.Residue, Dict of Nmr.Experiment:MolSystem.Chain (or None)
None
Aligns two sequence strings (of one letter codes) - results are gapped with ‘-‘ .. describe:: Input
String, String, Dict of Dicts (homology score matrix), Int, Int, Int, Int
String, String (aligned & gapped sequence strings)
Nmr.Resonance
List of Nmr.Resonances
Find the mol system chain that best matches the input ccpCodes (like three letter codes). Useful for trying to match structures to existing molecular data. Optional argument to specify which chains cannot be matched.
4-List of MolSystem.Atoms
ChemComp.ChemTorsion
Get a list of atoms bound to a given atom.. .. describe:: Input
MolSystem.Atom
List of MolSystem.Atoms
MolSystem.Chain, MolSystem.Chain
List of List of [MolSystem.Residue or None]
Retrieve an NMR chemical shift reference atom record
Implementation.Project, Word (ChemAtom.name), Word (ChemComp.ccpCode), Word, (chemComp.molType), Word
Float
Word (Molecule.MolResidue.MolType), Implementation.Project
Return the min and max chemical shifts for a given atom type observed in the databases
ChemComp.ChemAtom, Float, Word
Float
MolSystem.Residue
MolSystem.Residue
Implementation.Project, String (ChemComp.molType or ‘all’)
List of Words (ChemComp.CcpCodes)
Get the minimum number of binds that connect two atoms. Stops at a specified limit (and returns None if not within it)
MolSystem.Atom, MolSystem.atom, Int
Int
Get the random coil chemical shift value of a chemAtom
ChemComp.ChemAtom
Float
Citation
Schwarzinger, S., Kroon, G. J. A., Foss, T. R., Chung, J., Wright, P. E., Dyson, H. J. “Sequence-Dependent Correlation of Random Coil NMR Chemical Shifts”, J. Am. Chem. Soc. 123, 2970-2978 (2001)
Values obtained from a GGXGG sequence pentapeptide.
MolSystem.Residue
Word
MolSystem.Residue
Analysis.ResidueMapping
Determine which atoms of a chem comp varient would give rise to observable resonances considering a given reference experiment and/or an isotope labelling scheme. Can specify minimum fraction of an isotope to consider something observable and the chemical elements which you are observing. Boolean option to match database min and max chemical shift bounds to atom sites, rather than randon coil shift values (default).
MolSystem.Residue, NmrExpPrototype.RefExperiment, ChemCompLabel.LabelingScheme or LabeledMolecule.LabeledMixture, Float, Boolean, List of Words
List of ChemComp.ChemAtoms
Match a sequence of residue ccpCodes to an existing chain and calculate the alignment score. .. describe:: Input
MolSystem.Chain, List of Words (MolSystem.Residue.ccpCodes)
List of 2-List of [Int or None, MolSystem.Residue or None], Float (score)
Word, Word (ChemElement.symbol)
Unicode Word
Sorts a list of atom names according to greek/sidechain order when letters are latinised .. describe:: Input
List of Strings
List of Strings (sorted)
Make atomSet and atomSetMapping for equivalent atoms
Word (AtomSet.name), List of MolSystem.Atoms, ChemComp.ChemAtomSet, Word (AtomSetMapping.mappingType)
Nmr.AtomSet
Make atomSetMapping given atomSets and mapping type .. describe:: Input
Analysis.AtomSetMapping
Make atom set mappings for multiple atom set selections .. describe:: Input
Analysis.AtomSetMapping
Convert atom or atomSet name into name for gui: e.g H becomes Hn .. describe:: Input
Word (Nmr.AtomSet.name), Word, Word
Word
Make a molSystemLink given two residues and the linkEnds to be joined .. describe:: Input
MolSystem.Residue, MolSystem.Residue, ChemComp.LinkEnd, ChemComp.LinkEnd
MolSystem.MolSystemLink
Convert a sterospecific atom name into a non-stereospecific one for a GUI .. describe:: Input
Word, Int (naming offset from start of alphabet)
Word
MolSystem.Residue, Boolean
None
MolSystem.Residue
None
MolSystem.Residue
None
Make unique identifier for a given residue type in a given chain location .. describe:: Input
MolSystem.Residue, List of ChemCmp.chemAtoms
Word
Moves a chain from one molSystem to another .. describe:: Input
MolSystem.Chain, MolSystem.MolSystem
None
Get a new molSystem for a project with a unique code. .. describe:: Input
Implementation.Project
MolSystem.MolSystem
- results are gapped with ‘-‘; first tries an exact substring match,
if that failts it then uses dynamicAlign
String, String, Dict of Dicts (homology score matrix), Int, Int, Int, Int
String, String (aligned & gapped sequence strings)
Transfer any atomic assignments from one chain to another where possible. .. describe:: Input
MolSystem.Chain, MolSystem.Chain
None
Move any atomic assignments from one residue to another where possible.
MolSystem.Residue, MolSystem.Residue
None