Rosetta 3.3
Classes | Functions | Variables
rosetta_py::io::pdb Namespace Reference

Classes

class  PdbRecord
class  Atom

Functions

def read_pdb_file
def write_pdb_file
def get_atoms
def get_het_atoms
def centroid
def translate
def rmsd
def bounding_box
def split_chains
def uniquify_chains
def standardize_atom_names
def sort_H_to_end

Variables

dictionary rosetta_to_pdb_names

Function Documentation

def rosetta_py::io::pdb::bounding_box (   atoms)
Calculates a simple bounding box as (xmin,xmax,ymin,ymax,zmin,zmax).
def rosetta_py::io::pdb::centroid (   atoms)
Returns an unweighted center-of-mass for the list of Atom objects as a tuple (x,y,z).
def rosetta_py::io::pdb::get_atoms (   records)
Simple function to fish out all ATOM and HETATM records.
def rosetta_py::io::pdb::get_het_atoms (   records)
Simple function to fish out all HETATM records.
def rosetta_py::io::pdb::read_pdb_file (   f)
Returns a list of PdbRecord objects.

f is either a file name or a file object.
def rosetta_py::io::pdb::rmsd (   atoms1,
  atoms2 
)
Calculates root-mean-square deviation without superposition
def rosetta_py::io::pdb::sort_H_to_end (   atoms)
In-place stable sort of hydrogens after all heavy atoms, like Rosetta
def rosetta_py::io::pdb::split_chains (   records)
Returns a list of lists of Atom objects, one for each chain.

Non-Atom records are not returned but are used to find chain breaks.
We take TER, END, and change of existing chain ID as signals of chain break.
Distances between residues are NOT checked.
We assume that if multiple models exist, they have already been split.
def rosetta_py::io::pdb::standardize_atom_names (   atoms,
  move_to_segid = True 
)
Converts Rosetta atom names to more normal PDB-like names.

If move_to_segid is True, the old names will overwrite the atom segid field.
def rosetta_py::io::pdb::translate (   atoms,
  x,
  y,
  z 
)
Translates the Atoms by the specified amounts.
def rosetta_py::io::pdb::uniquify_chains (   records)
Creates unique chain names (within each model) without regard to the original names.

Should operate on all PDB records, not just Atoms.
We take TER, END, and change of existing chain ID as signals of chain break.
Distances between residues are NOT checked.

TODO: This should be re-written to use split_models() and split_chains().
def rosetta_py::io::pdb::write_pdb_file (   f,
  records 
)
Writes a list of PdbRecord objects to file.

f is either a file name or a file object.

Variable Documentation

Initial value:
00001 {'CNH2':' C  ', 'COO ':' C  ', 'CH1 ':' C  ',
00002     'CH2 ':' C  ', 'CH3 ':' C  ', 'aroC':' C  ', 'Ntrp':' N  ', 'Nhis':' N  ',
00003     'NH2O':' N  ', 'Nlys':' N  ', 'Narg':' N  ', 'Npro':' N  ', 'OH  ':' O  ',
00004     'ONH2':' O  ', 'OOC ':' O  ', 'S   ':' S  ', 'Nbb ':' N  ', 'CAbb':' C  ',
00005     'CObb':' C  ', 'OCbb':' O  ', 'Hpol':' H  ', 'Hapo':' H  ', 'Haro':' H  ',
00006     'HNbb':' H  ', 'Phos':' P  '}
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