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## Chain.filter() -- check if this chain passes all criteria

`filter(structure_types='structure', minimal_resolution=99.0, minimal_chain_length=30, max_nonstdres=10, chop_nonstd_termini=True, minimal_stdres=30)`

> This checks the chain with various criteria, and returns `True` only if all of them are met. This is useful in combination with Chain.write() to produce sequences of chains. See also model.make_chains().

> structure_types refers to the experimental method used to determine the structure. The following types are recognized: 'structureX' for X-ray, 'structureN' for NMR and 'structureM' for model, 'structureE' for electron microscopy, 'structureF' for fiber diffraction, 'structureU' for neutron diffraction, 'structure' for any structure.

> chop_nonstd_termini, if set, removes a single non-standard residue (if present) from each terminus of the chain. This is done before the chain length criteria below are considered.

> minimal_resolution refers to the cut-off value of the experimental resolution of the structure. Structures with resolutions larger than this threshold are not accepted.

> minimal_chain_length refers to the lower limit of the chain length. Chains whose lengths are smaller than this value are not accepted.

> max_nonstdres sets the maximum limit of non-standard residues that is tolerated.

> minimal_stdres sets the minimum number of standard residues that are required to process the chain. Chains that don't have at least this number of standard residues are not accepted.

Example: examples/commands/make_chains.py

      # Example for: chain.filter(), chain.write()

      # This will read a PDB file (segment), and write out all of its chains
      # satisfying the listed conditions into separate alignment files in the
      # PIR format.

      from modeller import *

      env = environ()
      mdl = model(env, file='../atom_files/pdb1lzd.ent')
      for c in mdl.chains:
          if c.filter(minimal_chain_length=30, minimal_resolution=2.0,
                      minimal_stdres=30, chop_nonstd_termini=True,
                      structure_types='structureN structureX'):
              filename = '1lzd%s.chn' % c.name
              print "Wrote out", filename
              atom_file, align_code = c.atom_file_and_code(filename)
              c.write(filename, atom_file, align_code, format='PIR',
                      chop_nonstd_termini=True)

Next: Chain.write() write Up: The Chain class: a Previous: Chain.atoms all Contents Index