pdbfile

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

PDB: reading PDB(Protein data Bank)-files.

class cafepy.files.pdbfile.PDB(filename, *args, **kwargs)[source]

Reading a PDB(Protein Data Bank) file which is an output from CafeMol Software. This class returns coordinates as list format. Please check examples below.

Note

This class only read ATOM line.

from cafepy.files import PDB

pdb = PDB('test.pdb')
print(pdb[0])
# you can get the 1th atom xyz coordinate.

pdb.close()
get()[source]
Input:None
Returns:pdb data as list format
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]
readATOM()[source]

read ATOM line. In future, I will support all record.

Pdb_record:contains pdb records as list structure.
_format:provides atom line format.
class cafepy.files.pdbfile.CGPDB(filename, *args, **kwargs)[source]

Reading a Coarse-Grained PDB(Protein Data Bank) file which is an output from CafeMol Software.

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]