Index

_

_calcDistDCD() (cafepy.core.calc_distance.CalcDistance method) _calcDistPDB() (cafepy.core.calc_distance.CalcDistance method)

_pick_data() (cafepy.files.dcdfile.DCD method) _read() (cafepy.files.indexfile.Index method) (cafepy.files.ninfofile.Ninfo method)

C

CafeMemManager (class in cafepy.utils.cafepy_memory_manager) cafepy.core.calc_cmap (module) cafepy.core.calc_com (module) cafepy.core.calc_distance (module) cafepy.core.calc_qscore (module) cafepy.core.calc_rmsd (module) cafepy.core.calc_rmsf (module) cafepy.core.calc_superimpose (module) cafepy.files.cafeinpfile (module) cafepy.files.dcdfile (module) cafepy.files.file_io (module) cafepy.files.indexfile (module) cafepy.files.moviefile (module) cafepy.files.ninfofile (module) cafepy.files.pdbfile (module)

cafepy.files.psffile (module) cafepy.utils.cafepy_base (module) cafepy.utils.cafepy_error (module) cafepy.utils.cafepy_math (module) cafepy.utils.cafepy_memory_manager (module) cafepy.utils.cafepy_stdout (module) CafePyBase (class in cafepy.utils.cafepy_base) CafePyError (class in cafepy.utils.cafepy_error) CafepyStdout (class in cafepy.utils.cafepy_stdout) CalcCOM (class in cafepy.core.calc_com) CalcDistance (class in cafepy.core.calc_distance) CalcQscore (class in cafepy.core.calc_qscore) CGPDB (class in cafepy.files.pdbfile) cmdline (module) CmdLineError (class in cafepy.utils.cafepy_error)

D

DCD (class in cafepy.files.dcdfile)

DcdHeader (class in cafepy.files.dcdfile)

F

FileIO (class in cafepy.files.file_io)

FileTypeError (class in cafepy.utils.cafepy_error)

G

get() (cafepy.files.pdbfile.PDB method)

getIndex() (cafepy.core.calc_distance.CalcDistance method)

I

Index (class in cafepy.files.indexfile)

InputError (class in cafepy.utils.cafepy_error)

M

makePair() (cafepy.core.calc_distance.CalcDistance method)

Movie (class in cafepy.files.moviefile)

N

Ninfo (class in cafepy.files.ninfofile)

O

openFile() (cafepy.files.dcdfile.DCD method) (cafepy.files.file_io.FileIO method) (cafepy.files.indexfile.Index method) (cafepy.files.moviefile.Movie method) (cafepy.files.pdbfile.CGPDB method) (cafepy.files.pdbfile.PDB method) (cafepy.files.psffile.PSF method)

P

PDB (class in cafepy.files.pdbfile)

PSF (class in cafepy.files.psffile)

R

read() (cafepy.core.calc_com.CalcCOM method) (cafepy.core.calc_distance.CalcDistance method) (cafepy.core.calc_qscore.CalcQscore method) (cafepy.files.dcdfile.DCD method) (cafepy.files.moviefile.Movie method) (cafepy.files.pdbfile.CGPDB method) (cafepy.files.pdbfile.PDB method) (cafepy.utils.cafepy_base.CafePyBase method) readATOM() (cafepy.files.pdbfile.PDB method)

ReadingError (class in cafepy.utils.cafepy_error) run() (cafepy.core.calc_com.CalcCOM method) (cafepy.core.calc_distance.CalcDistance method)

S

scripts.cmdline (module)

Signal (class in cafepy.utils.cafepy_stdout)