|
|
getBboneAtom
|
getBboneAtom ( res, atom_name )
find atom of type atom in residue res with
the highest occupancy value
|
|
|
reposLastO
|
reposLastO (
last_res,
last_bbone_ats,
atom_drawMode,
bond_drawMode,
)
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|
|
getBFactor
|
getBFactor ( mol )
|
|
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addNewC
|
addNewC (
last_bbone_ats,
new_res,
phi,
**kw,
)
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|
|
addNewCA
|
addNewCA (
last_bbone_ats,
new_res,
**kw,
)
|
|
|
addNewN
|
addNewN (
last_bbone_ats,
new_res,
**kw,
)
|
|
|
getPhiPsiVals
|
getPhiPsiVals ( conformation )
|
Exceptions
|
|
|
AddAAError, "Must specify both phi and psi values or neither"
AddAAError, "Conformation must be one of " "\"alpha\", \"abeta\", \"pbeta\", " " \"ext\" or \"phi,psi\""
|
|
|
|
getShortestPoint
|
getShortestPoint ( ref_point, point_list )
|
|
|
addAA
|
addAA (
residue_type,
residue_seq,
last_res,
conformation=None,
)
add an amino acid to a model.
|
Exceptions
|
|
|
AddAAError, val
AddAAError, "Couldn't find 'C' backbone atom of last residue"
AddAAError, "Couldn't find 'N' backbone atom of last residue"
AddAAError, "Couldn't find 'CA' backbone atom of last residue"
AddAAError, "Can only add to last residue."
AddAAError, "Can't add amino acid, model already contains residue with sequence '%s'." % residue_seq
AddAAError, "Residue sequence argument can contain at most one insertion character"
AddAAError, what
AddAAError, "Couldn't find 'O' backbone atom of last residue"
|
|
|
|
cleanUp
|
cleanUp (
mol,
new_res,
atoms,
)
|
|
|
pruneLastResidue
|
pruneLastResidue ( last_res )
|
Exceptions
|
|
|
AddAAError, "No suitable position to add new amino acid"
|
|
|
|
isLastRes
|
isLastRes ( res )
|
|
|
getLastResidue
|
getLastResidue ( after_res )
|
Exceptions
|
|
|
AddAAError, "Couldn't find valid residue based on atom spec \"%s\"" % after_res
AddAAError, "Too many residues specified: " "%s specifies %d residues" %( after_res, num_res_spec )
AddAAError, "Can only add to last residue!"
|
|
|
|
addNewOs
|
addNewOs (
new_res,
psi,
**kw,
)
|
|