detectClash (
        testAtoms,
        interTest=True,
        clashThreshold=clashDef,
        hbondAllowance=hbondDef,
        assumedMaxVdw=2.1,
        bondSeparation=bondSepDef,
        intraRes=False,
        )

Detect steric clashes

testAtoms should be a list of atoms.

if interTest is True then non-bonded clashes between atoms in testAtoms and non-testAtoms atoms will be found. Otherwise non-bonded clashes within testAtoms atoms will be found. The "clash value" is the sum of the VDW radii minus the distance, keeping only the maximal clash (which must exceed clashThreshold).

hbondAllowance is how much the clash value is reduced if one atom is a donor and the other an acceptor.

Atom pairs are eliminated from consideration if they are less than or equal to bondSeparation bonds apart.

Intra-residue clashes are ignored unless intraRes is True.

Returns a dictionary keyed on atoms, with values that are dictionaries keyed on clashing atom with value being the clash value.

nukeGroup ()

cmdDetectClash (
        testAtoms,
        overlapCutoff=options [ CLASH_THRESHOLD ],
        hbondAllowance=options [ HBOND_ALLOWANCE ],
        interTest=True,
        setAttrs=options [ ACTION_ATTR ],
        selectClashes=options [ ACTION_SELECT ],
        colorClashes=options [ ACTION_COLOR ],
        clashColor=defColors [ CLASH_COLOR ],
        nonclashColor=defColors [ NONCLASH_COLOR ],
        makePseudobonds=options [ ACTION_PSEUDOBONDS ],
        pbColor=defColors [ PB_COLOR ],
        lineWidth=options [ PB_WIDTH ],
        bondSeparation=options [ BOND_SEPARATION ],
        saveFile=None,
        namingStyle=None,
        ignoreIntraRes=options [ IGNORE_INTRA_RES ],
        log=options [ ACTION_REPLYLOG ],
        )

ChimeraExtension.py

gui.py

prefs.py