ample.util.reforigin module¶

class ReforiginRmsd(workdir=None, cAlphaOnly=True)[source]¶

Bases: object

Class to use reforigin to determine how well the model was placed.

calculate(refpdb=None, targetpdb=None, outpdb=None, DMAX=100)[source]¶

getRmsd(nativePdbInfo=None, placedPdbInfo=None, refModelPdbInfo=None, workdir=None, cAlphaOnly=True)[source]¶

For now just save lowest rmsd - can look at collecting more nativeInfo later

Currently we assume we are only given one model and that it has already been standardised.

preparePlacedPdb(placedPdb=None, placedChainID=None, nativeChainID=None, resSeqMap=None)[source]¶

Use pdbcur to: - extract chain to compare - strip down to CA/BB - remove any atoms that cannot be compared to the native