biopython Bio.PDB FAQ

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Biopython
Bio.PDB module FAQ
1,Focuses
on working with crystal structure biological macromolecules.
2,Well
tested. Nearly 5500 structures from PDB—all seemed to be parsed
correctly
3,Really
fast!
4,Not
directly supported for molecular graphics. But there are quite a few
python-based solutions. You can use Pymol or BTW.
http://pymol.sourceforge.net
5,USAGE:
a,        importing
Bio.PDB :       
>>>from
Bio.PDB import *
b,        input/output
create
a structure object from a PDB file:

create
        a PDBParser object:       
        >>>parser=PDBParser()
       

• create
          a structure object from a PDB file:
          >>>structure=parser.get_structure('DOG',
          '1LKE.pdb')
         
         
  create
  a structure object from an mmCIF file
  
• create
          an MMCIFParser object:
          >>>parser=MMCIFParser()
         
• create
          a structure object from the mmCIF file
          >>>structure=parser.get_structure('DOG','1LKE.cif')
  some
  more level access to an mmCIF file
  you
  can create a python dict that maps all mmCIF tags. If there are
  multiple values, the tag is mapped into a list of values.
  >>>mmcif_dict=MMCIF2Dict('1LKE.cif')
  eg:get
  solvent content from an mmCIF file:
  >>>sc=mmcif_dict('_exptl_crystal.density_percent_sol']
  eg:get
  the list of the y coordinates of all atoms:
  >>>y_list=mmcif_dict['_atom_site.Cartn_y']
  Return
  to parsing the PDB header
  >>>resolution=structure.header['resolution']
  >>>keywords=structure.header['keywords']
  The
  available keys : name, head, deposition_date, release_date,
  structure_method, resolution, structure_reference, journal_reference,
  author, compound
  The
  dict can also be created without creating a Structure object
  >>>file=open(filename,
  'r')
  >>>header_dict=parse_pdb_header(file)
  >>>file.close()
  Download
  structure from the PDB:
  >>>pdb1=PDBList()
  >>>pdb1.retrieve_pdb_file('1LKE')
  The
  PDBList class can also be used
  >>>python
  PDBList.py 1LKE
  you
  must in that directory, of course!
  Try
  to download the entire PDB if necessary
  >>>python
  PDBList.py all /data/pdb
  >>>>>>python
  PDBList.py all /data/pdb -d
  Adding
  the -d option will store all files in the same directory. It's not a
  good choice! Otherwise, they are sorted into PDB-style rectories
  according to their PDB   ID's.
  Keep
  a local copy of the PDB up-to-date using PDBList.py object
  >>>p1=PDBList(pdb='
  /data/pdb')
  >>>p1.update_pdb()
  Use
  the PDBIO class for writing PDB files
  eg:
  saving a structure
  >>>io=PDBIO()
  >>>io.set_structure(s)
  >>>io.save('out.pdb')
  You
  can't write mmCIF files
  the
  overall layout of a structure object:
  SMCRA(structure/model/chain/residue/atom)
  A
  structure consists of models/ A model consists of chains
  A
  chain consists of residues / A residue consists of atoms
  Navigate
  through a structure object:
  >>>p=PDBParser()
  >>>structure=p.get_structure('X',
  'pdb1fat.ent')
  >>>for
  model in structure:
          for
  chain in model:
                  for
  residue in chain:
                          for
  atom in residue:
                                  print
  atom
  some
  other shortcuts:
  >>>#
  iterate over all atoms in a structure
  >>>for
  atom in structure.get_atoms():
          print
  atom
  >>>#
  iterate over all residues in a model
  >>>for
  residue in model.get_residues():
          print
  residue
  structures,
  models, chains, residues, atoms are called Entities in Biopython.
  You
  can always get a parent Entity from a child Entity, eg:
  >>>residue=atom.get_parent()
  >>>chain=residue.get_parent()
  you
  can also test whether an Entity has a certain child use has_it method
  You
  can do that a bit more conveniently
  >>>atoms=structure.get_atoms()
  >>>residue=structure.get_residues()
  >>>atoms=chain.get_atoms()
  简单的说，它们(结构，模块，链，残基，原子）是一个范围问题。你可以从上级中抽取下级内容。也可以综合下级找上级（父子关系）
  >>>#
  get all residues from a structure
  >>>res_list=Selection.unfold_entities(structure,
  'R')
  >>>#
  get all atoms from a chain
  >>>atom_list=Selection.unfold_entities(chain,
  'A')
  A=atom,
  R=residue, C=chain, M=model, S=structure
  也可以跨级操作：
  >>>residue_list=Selection.unfold_entities(atom_list,
  'R')
  >>>chain_list=Selection.unfold_entities(atom_list,'C')
  Extract
  a specific Atom/Residue/Chain/Model from a structure:
  just
  use nest structure as list:
  >>>model=structure[0]
  >>>chain=model['A']
  >>>residue=chain[100]
  >>>atom=residue['CA']
  >>>atom=structure
  [0] ['A'] [100] ['CA']
  Model
  id: an integer which denotes the rank of the model in the
  PDB/mmCIF file.
  The
  model is starts at 0. Crystal structure generally have one model
  id(0), while NMR files usually have more
  Chain
  id: specified in the file, a single
  character(typically a letter)
  Residue
  id: complicated, due to the clumsy
  PDB format. A residue id is a tuple with three elements:
          1,the
  hetero-flag: 'H_' plus the name of the hetero-residue, eg. 'H_GLC',
  or 'W' in the case of a water molecule.
          2,
  sequence identifier in the chain, eg. 100
          3,
  insertion code: eg. 'A'. The insertion code is sometimes used to
  preserve a certain desirable residue numbering scheme
  hetero-flag
  and insertion code can be blank:
  >>>#
  full id
  >>>residue=chain[('
  ', 100, ' ')]
  >>>#
  shortcut id
  >>>residue=chain[100]
  atom
  id: the atom name. Eg: 'CA'
  In
  PDB files, a space can be part of an atom name.
  calcium—'CA..'
  , to distinguish from C alpha atom '.CA.'
  Disorder
  handle
  two
  views: the atom and the residue point of view
                  disordered
  atoms and residues are stored in special objects that behave as if
  there is no disorder