oslModelCmp ( model1,  model2 )

Compare two model-part-only OSL identifiers

oslResAtomCmp ( ra1,  ra2 )

Compare two residue-and-atom OSL identifiers

chimeraLabel (
        item,
        showModel=None,
        modelName=0,
        style=None,
        diffWith=None,
        bondSep="-",
        )

Return preferred chimera label for atom/bond/residue/molecule

showModel controls whether the model ID is part of the label If the value type is boolean, then the model is shown if the value is true. If the value is None, then the model is shown if there are multiple models, otherwise the model is omitted.

modelName controls whether the model name is part of the label. Has no effect if atom specs are being returned.

diffWith can either be a string or of the same type as 'item'; the returned label will not include any leading components that are the same as those in diffWith

style controls whether the label uses atom specs or quasi- English-like contents. It is either simple, osl, or None. If None, then the user's preferences controls the contents.

bondSep controls the text separator between parts of a bond when using English-like contents.

simplifyPath ( path )

parseResID ( resID )

Break a residue ID into sequence/insert code/chain

oslAtomCmp ( atom1,  atom2 )

Compare two atom-only OSL identifiers

bonds ( atomList,  internal=1 )

isProtein ( model )

Is the given model a protein?

getPseudoBondGroup (
        category,
        modelID=-1,
        associateWith=[],
        hidden=1,
        )

get a pseudobond group regardless of whether it already exists

This is utility function to perform the commonly-desired task of getting a pseudobond group whether or not it already exists. If the group does exist, that group is returned. Otherwise, the group is created, added to the open models, and returned.

modelID is the model ID to open the group in. If you use a negative number other than -1, then the PseudoBondGroup panel will not allow that group to be closed. associateWith is a list of models that the pseudobond group is closely associated with. If any of those models are closed, then the pseudobond group will also be closed. hidden indicates that the group shouldn't normally appear in the list of open models (and Model Panel; will still appear in Pseudobond Panel)

principalAtom ( res )

return the chain trace atom of a residue, if any

stringToAttr (
        string,
        prefix="",
        style="underscore",
        collapse=True,
        )

convert an arbitrary string into a legal Python identifier

string is the string to convert

prefix is a string to prepend to the result (the style will control whether the prefix is followed by an underscore or capital letter)

style controls the handling of illegal characters: 'underscore': replace them with underscores 'caps': omit them and capitalize the next letter

if style is underscore, then collapse controls whether consecutive underscores are collapsed into one

if there is no prefix and the string begins with a digit, an underscore will be prepended

getAtoms ( atomContainer )

polymorphic function to get an atom list from various things

atomSearchTree ( atomContainer,  sepVal=5.0 )

return an AdaptiveTree for spatially searching for atoms

atomContainer is a Molecule, Residue, Sequence, or list of atoms

sepVal is the sepVal parameter passed to the AdaptiveTree constructor (see CGLutil.AdaptiveTree)

returns the populated AdaptiveTree

displayResPart (
        residues,
        trace=0,
        backbone=0,
        other=0,
        side=0,
        add=0,
        skipIsolated=1,
        )

oslCmp ( osl1,  osl2 )

Compare two full OSL identifiers

oslResCmp ( res1,  res2 )

Compare two residue-only OSL identifiers