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Imported modules
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import chimera
import operator
import os
import os.path
from string import atoi, find, split, digits
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Functions
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bonds
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bonds ( atomList, internal=1 )
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chimeraLabel
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chimeraLabel (
item,
showModel=None,
modelName=0,
style=None,
diffWith=None,
)
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
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displayResPart
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displayResPart (
residues,
trace=0,
backbone=0,
other=0,
side=0,
skipIsolated=1,
)
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getPseudoBondGroup
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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)
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isProtein
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isProtein ( model )
Is the given model a protein?
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oslAtomCmp
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oslAtomCmp ( atom1, atom2 )
Compare two atom-only OSL identifiers
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oslCmp
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oslCmp ( osl1, osl2 )
Compare two full OSL identifiers
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oslModelCmp
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oslModelCmp ( model1, model2 )
Compare two model-part-only OSL identifiers
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oslResAtomCmp
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oslResAtomCmp ( ra1, ra2 )
Compare two residue-and-atom OSL identifiers
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oslResCmp
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oslResCmp ( res1, res2 )
Compare two residue-only OSL identifiers
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parseResID
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parseResID ( resID )
Break a residue ID into sequence/insert code/chain
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principalAtom
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principalAtom ( res )
return the chain trace atom of a residue, if any
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simplifyPath
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simplifyPath ( path )
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