PDB - read and write pdb format

espressopp.tools.pdbwrite(filename, system, molsize=4, append=False, typenames=None)

Writes a file in PDB format

Parameters:

• filename (string) – output file name

• system (espressopp System object) – espressopp system

• molsize (int) – if molsize>0, the molecule count is increased every molsize particles (default 4)

• append (bool) – if True, append to filename, other over-write filename (default False)

• typenames (dict, key=int, value=string) – dictionary used for mapping from espressopp’s integer particle types to the particle type strings written in a pdb file

espressopp.tools.pdbread(filename, natoms, header)

Reads one frame of a pdb format file

Parameters:

• filename (string) – input file name

• natoms (int) – number of atoms in pdf file

• header (int) – number of header lines to skip at start of file

Returns: index,atomname,locator,resname,resid,resseq,x,y,z,alpha,beta,segid,element (lists of type int,str,str,str,str,int,float,float,float,float,float,str,str)