Package biana :: Package BianaObjects :: Module PDB' :: Class PDB

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Class PDB

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Instance Methods

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__init__(self, name, resolution=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

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_get_dssp_results(self)
Executes the program dssp to get the accessibility

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_get_sorted_chains(self)
Returns a list with the chain names sorted

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_get_sorted_residues(self, chain_name)

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_parse_dssp_results(self, fp)

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add_atom(self, chain_name, residue_num, residue_type=None, atomObject=None)
Atom object can be None in order to indicate that it must be added a residue but no atoms information

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add_residue(self, chain_name, residue_num=0, atoms_initial_list=[], residue_type=None, hssp_conservation=None, hssp_entropy=None, hssp_exposure=None, hssp_norm_entropy=None, hssp_variability=None, dssp=None, residue_object=None)
To add residue. source code

filter_residues(self, binary_list)
Returns a new PDB object with the residues filtered by binary_list

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get_accessibility(self, chain_name)

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get_chain_names(self)

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get_chain_num_atoms(self, chain_name)

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get_conservation(self, chain_name)

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get_contacting_pairs_indices(self, pdb2, chains1, chains2, type='min', cutoff=5.0)
Returns the indices!!! Not the residue nums!!!! source code

get_distances(self, pdb2, chains1, chains2, type='min', fragments1=None, fragments2=None)
"type" can be "min", "mean", "ca" or "cb" source code

get_dssp(self, chain_name)

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get_dssp_accessibility(self, chain_name)

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get_dssp_as_horiz(self, chain_name)
Returns the dssp result in psi-pred nomenclature

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get_dssp_ss(self, chain_name)

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get_entropy(self, chain_name)

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get_in_pdb_format(self)
Gets a string with the pdb atoms in PDB format

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get_name(self)

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get_norm_entropy(self, chain_name)

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get_num_atoms(self)

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get_num_residues(self, chain_name=None)

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get_pdb_summary(self)

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get_rel_dssp_accessibility(self, chain_name)

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get_residues(self, chain_name)

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get_sequence(self, chain_name=None)
Returns a dictionary with chains as keys and sequence string as values

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get_variability(self, chain_name)

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safe_traceback(self)

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set_resolution(self, resolution)

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

Static Methods

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read_pdb_file(pdbFile, fragments=[], merge_fragments=False, chain_value='A')
merge_fragments is used to reenumerate residues in fragments and consider all the fragments as a single chain source code

Properties

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Inherited from object: __class__

Method Details

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init(self, name, resolution=None)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

add_residue(self, chain_name, residue_num=0, atoms_initial_list=`[]`, residue_type=None, hssp_conservation=None, hssp_entropy=None, hssp_exposure=None, hssp_norm_entropy=None, hssp_variability=None, dssp=None, residue_object=None)

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To add residue. Chain_name is mandatory always. residue_num and atoms_initial_list are mandatory only if residue_object is not specified

if residue_object is specified, the rest of parameters except chain_name are not used

filter_residues(self, binary_list)

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Returns a new PDB object with the residues filtered by binary_list

The PDB must contain a single chain

get_distances(self, pdb2, chains1, chains2, type=`'min'`, fragments1=None, fragments2=None)

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"type" can be "min", "mean", "ca" or "cb"

"fragments" is used to determine which fragments are going to be used to calculate distances
            TODO!!!

For the moment, it returns a dictionary with the wcm of the different chain combinations

read_pdb_file(pdbFile, fragments=`[]`, merge_fragments=False, chain_value=`'A'`)
Static Method

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merge_fragments is used to reenumerate residues in fragments and consider all the fragments as a single chain

"chain_value" is used only when merging fragments

Class PDB

__init__(self, name, resolution=None) (Constructor)

add_residue(self, chain_name, residue_num=0, atoms_initial_list=[], residue_type=None, hssp_conservation=None, hssp_entropy=None, hssp_exposure=None, hssp_norm_entropy=None, hssp_variability=None, dssp=None, residue_object=None)

filter_residues(self, binary_list)

get_distances(self, pdb2, chains1, chains2, type='min', fragments1=None, fragments2=None)

read_pdb_file(pdbFile, fragments=[], merge_fragments=False, chain_value='A') Static Method

init(self, name, resolution=None)
(Constructor)

add_residue(self, chain_name, residue_num=0, atoms_initial_list=`[]`, residue_type=None, hssp_conservation=None, hssp_entropy=None, hssp_exposure=None, hssp_norm_entropy=None, hssp_variability=None, dssp=None, residue_object=None)

get_distances(self, pdb2, chains1, chains2, type=`'min'`, fragments1=None, fragments2=None)

read_pdb_file(pdbFile, fragments=`[]`, merge_fragments=False, chain_value=`'A'`)
Static Method