Useful manipulations on PDB files
residueSequenceMap(refPdb=None, targetPdb=None)[source]¶Bases: object
Class for handling mapping between model and native residue indices.
Methods
fromInfo([refInfo, refChainID, targetInfo, …]) |
Create a map from 2 info objects |
read_pdb(pdb) |
Get sequence as string of 1AA |
ref2target(refResSeq) |
Return the target resSeq for the given reference resSeq. |
refIncomparable([cAlphaMask, bbMask]) |
Return a list of the resSeq in the reference that cannot be compared to the target. |
resSeqMatch() |
Return true if the residue numbering between the model and native over the aligned region is the same |
target2ref(targetResSeq) |
Return the referece resSeq for the given target resSeq. |
targetIncomparable([cAlphaMask, bbMask]) |
Return a list of the resSeq in the target that cannot be compared to the reference. |
| calc_map |
fromInfo(refInfo=None, refChainID=None, targetInfo=None, targetChainID=None, modelIdx=0)[source]¶Create a map from 2 info objects
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)