import MAT
import TDA


# This will save the protein chains in batches as chains/0 chains/1 chains/2 ...
# Note 'chains/' directory must exist.
MAT.getChains(loadPath='pdbstyle-1.55/', savePath='chains/',SCOPEdir='dir.cla.scop.1.55.txt')
MAT.getChains(loadPath='pdbstyle-2.07/', savePath='chains/',SCOPEdir='dir.cla.scope.2.07-stable.txt')


# rangeTo is the number that the files under 'chains/' that we should process
# Note 'mats/' directory must exist.
MAT.getDistMs(loadPath='chains/',savePath='mats/',sparse=False,rangeTo=N)


#########################
# Cropped Dist M
#########################
#upToBatchNum is the number of files under 'mats/' that we should process
# Note 'croppedMats/' directory must exist along with the batch directories.
# mkdir croppedMats
# cd croppedMats
# mkdir {1..999}

MAT.splitMat(loadPath='mats/', savePath='croppedMats/',windowSize=100,upToBatchNum=N)

#########################
# Persistence Homology
#########################
#toRange is the number of files under 'mats/' that we should process
# Note 'barcodes/' directory must exist
TDA.genHoms(loadPath='mats/', savePath='barcodes/', toRange=N)


#rng is the number of files under 'mats/' that we should process
# Note 'barcodeImgs/' directory must exist along with the batch directories.
# mkdir barcodeImgs
# cd barcodeImgs
# mkdir {1..999}
TDA.getBcodeImgsSeparated(loadPath='barcodes/', savePath='barcodeImgs/',rng=N)