run_csymmatch # Gives pdb with oriented model create copy of csymmatch pdb with residue numbering matching native and rename chain to X concatenate the native and reformatted csymmatch pdb run ncont to generate contacts parse ncont file to generate map & analyse whether placed bits match and what type of structure they are
Rio[source]¶Bases: object
Foo
calcAllAtom(contactData)[source]¶Calculate the All Atom data using the origin and data saved previously
findOrigin(nativePdbInfo=None, mrPdbInfo=None, resSeqMap=None, origins=None, allAtom=False, workdir='/home/docs/checkouts/readthedocs.org/user_builds/ample/checkouts/latest/docs')[source]¶Find the origin using the maximum number of contacts as metric
helixFromContacts(contacts, dsspLog, minContig=2, maxGap=3)[source]¶Return the sequence of the longest contiguous helix from the given contact data
source is the native, target the model
Get start and stop indices of all contiguous chunks - we can match multiple chains in the model, but any match must be within a single native chain - the source can increment or decrement - the model only ever increments (ncont “sort target inc” argument) - matches can be in-register or out-of-register, but for finding the longest chunk we don’t care
startstop = [ (10,15), (17, 34), (38, 50) ]
# Loop through all chunks, and if any two have a gap of < mingap, join the indices together.
# Get the indices of the largest chunk
# Get the corresponding AA sequence
helixFromPdbs(origin, mrPdb, nativePdb, nativeChain, dsspLog, workdir='/home/docs/checkouts/readthedocs.org/user_builds/ample/checkouts/latest/docs')[source]¶This is a wrapper to generate the info and resSeqMap objects needed by score Origin
parseNcontLog(contactData, logfile=None, clean_up=True)[source]¶Lines are of format /1/B/1042(MET). / CA [ C]: /1/b/ 988(GLU). / CA [ C]: 1.09 223 X-1/2,Y-1/2,Z