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Imported modules
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import chimera
from chimera import angle, dihedral, cross, Xform_xform, Coord
from chimera.bondGeom import bondPositions
from chimera.idatm import tetrahedral, planar, linear, single, typeInfo, geometry, substituents
from chimera.molEdit import addAtom, addDihedralAtom
from math import pi, cos, sin
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Functions
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formDihedral
getResInfo
swap
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formDihedral
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formDihedral (
resBud,
real1,
tmplRes,
a,
b,
)
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Exceptions
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AssertionError, "Can't form in-residue dihedral for" " %s of residue %s" %(bud, res.oslIdent() )
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getResInfo
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getResInfo ( res )
return a list of the fixed atoms of the residue, a list of
the fixed atoms that non-fixed atoms attach to, and whether
this residue is the start and/or end of a chain
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swap
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swap (
res,
newRes,
preserve=0,
)
change res into type newRes
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Exceptions
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AssertionError, "Atom %s of residue %s has no" " neighbors after pruning?!?" %(bud, res.oslIdent() )
AssertionError, "Can't determine atom type" " information for atom %s of residue %s" %(bud, res.oslIdent() )
AssertionError, "Can't disambiguate " "tetrahedral position by " "forming in-residue dihedral " "for %s of residue %s" %(bud, res.oslIdent() )
AssertionError, "Too many atoms bonded to %s of" " residue %s" %(bud, res.oslIdent() )
AssertionError, "Too many positions returned" " for atom %s of residue %s" %(bud, res.oslIdent() )
ValueError, "New residue type (%s) " "not compatible with starting residue type (%s)" %( newRes, res.type )
ValueError, "No connectivity template for residue '%s'" % newRes
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