ample.util.residue_map module

Useful manipulations on PDB files

class residueSequenceMap(refPdb=None, targetPdb=None)[source]

Bases: object

Class for handling mapping between model and native residue indices.

calc_map(nativePdb, modelPdb)[source]
fromInfo(refInfo=None, refChainID=None, targetInfo=None, targetChainID=None, modelIdx=0)[source]

Create a map from 2 info objects

read_pdb(pdb)[source]

Get sequence as string of 1AA get list of matching resSeq

ref2target(refResSeq)[source]

Return the target resSeq for the given reference resSeq. This will calculate a resSeq in the target if there isn’t one.

refIncomparable(cAlphaMask=True, bbMask=False)[source]

Return a list of the resSeq in the reference that cannot be compared to the target. This includes any where there isn’t a corresponding residue in the target, or there isn’t a c-alpha or backbone atom in either (if cAlphaMask or bbMask is set)

resSeqMatch()[source]

Return true if the residue numbering between the model and native over the aligned region is the same

target2ref(targetResSeq)[source]

Return the referece resSeq for the given target resSeq. This will calculate a resSeq in the reference if there isn’t one.

targetIncomparable(cAlphaMask=True, bbMask=False)[source]

Return a list of the resSeq in the target that cannot be compared to the reference. This includes any where there isn’t a corresponding residue in the reference, or there isn’t a c-alpha or backbone atom in either (if cAlphaMask or bbMask is set)