dcdfile

Editer:Mogu
Version:0.0.1dev
environment:Pyton3.5.1

contants

  • DcdHeadr: defines dcd-headers structure.
  • Dcd: reads dcd-files.

referance

  • Author:Naoto Hori, https://github.com/naotohori/
  • Author:mash-ito, https://github.com/mash-it/

Note

python3: supporting that str is utf-8 type. We need to write [b”sgring”].

class cafepy.files.dcdfile.DcdHeader[source]

contans the structure of dcd-file header information. This class only is used by DCD class. Don’t directly use this class in your script.

Self.nset:
Self.istart:
Self.nstep_save:
 
Self.nstep:
Self.nunit_real:
 
Self.delta:
Self.title:
Self.tempk:
Self.lunit2mp:
Self.nmp_real:
Self.bsize:
Self.tstep:
class cafepy.files.dcdfile.DCD(filename)[source]

reads a DCD(binary) file which is an output from CafeMol Software. DCD-files contans coordinates of atoms with binary formart.

import cafepy.files.DCD

dcd = DCD('test.dcd')
# you can get a coordinate with list format.
print(dcd[0])
_pick_data()[source]

return binary data between ‘integer’ and ‘integer’. ‘integer’ indicates the number of bytes

openFile(filename, mode='r')
read(filename)

read [pdb, dcd, index] files. This function define reading type from files suffix. you need to set a proper suffix with filename.

Inputs:filename(str)
Returns:class [DCD, PDB, Index]