PDB - read and write pdb format¶
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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
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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,resname,resid,x,y,z,alpha,beta,segid,element (lists of type int,str,str,int,float,float,float,float,float,str,str)