Package edPDB :: Module cbook :: Class PDB

Class PDB

object --+
         |
        PDB

Class that represents a PDB file and allows extractions of interesting parts.

The structure itself is never changed. In order to extract sub-parts of a structure one selects these parts and writes them as new pdb file.

The advantage over a simple :program:`grep` is that you will be able to read any odd pdb file and you will also able to do things like :meth:`~edPDB.cbook.PDB.extract_protein` or :meth:`~edPDB.cbook.PDB.extract_lipids`.

Instance Methods

[hide private]

__init__(self, pdbname)
Load structure from file *pdbname*.

source code

write(self, filename, **kwargs)
Write pdbfile which includes or excludes residues.

source code

residues_by_resname(self, resnames, **kwargs)
Return a list of BioPDB residues that match *resnames*.

source code

residues_by_selection(self, selection)
Return a list of BioPDB residues that are selected by *selection*.

source code

extract_resnames(self, filename, resnames, **kwargs)
Write a pdb file with *resnames* extracted.

source code

extract_protein(self, filename, **kwargs)
Write a pdb file with the protein (i.e.

source code

extract_notprotein(self, filename, **kwargs)
Write a pdb file without any amino acids extracted.

source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, pdbname)
(Constructor)

source code

Load structure from file *pdbname*.

Overrides: object.__init__

write(self, filename, **kwargs)

source code

Write pdbfile which includes or excludes residues.

:Arguments:
    *filename*
        output pdb filename
    *inclusions*
        list of residues to include
    *exclusions*
        list of residues to exclude
    *chain*
        relabel the selection with a new chain identifier


 Residues must be BioPDB residues as returned by, for
 instance, :meth:`~edPDB.cbook.PDB.residues_by_resname`.

 .. Note:: Currently only either *inclusions* or *exclusions* can be
           supplied, not both.

residues_by_resname(self, resnames, **kwargs)

source code

Return a list of BioPDB residues that match *resnames*.

*resnames* can be a string or a list.

residues_by_selection(self, selection)

source code

Return a list of BioPDB residues that are selected by *selection*.

*selection* must be BioPDB.PDB.PDBIO.Select instance (see for example :class:`edPDB.xpdb.ProteinSelect`).

extract_protein(self, filename, **kwargs)

source code

Write a pdb file with the protein (i.e. all amino acids) extracted.

extract_lipids(self, filename, lipid_resnames=`'POPC|POPG|POPE|DMPC|DPPE|DOPE'`, **kwargs)

source code

Write a pdb file with the lipids extracted.

Note that resnames are also tried truncated to the first three characters, which means that POPE and POPG are identical and cannot be distinguished.

Class PDB

__init__(self, pdbname) (Constructor)

write(self, filename, **kwargs)

residues_by_resname(self, resnames, **kwargs)

residues_by_selection(self, selection)

extract_protein(self, filename, **kwargs)

extract_lipids(self, filename, lipid_resnames='POPC|POPG|POPE|DMPC|DPPE|DOPE', **kwargs)

init(self, pdbname)
(Constructor)

extract_lipids(self, filename, lipid_resnames=`'POPC|POPG|POPE|DMPC|DPPE|DOPE'`, **kwargs)