mmLib.Structure.Chain

Package mmLib :: Module Structure :: Class Chain

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Class Chain

object --+    
         |    
   Segment --+
             |
            Chain

Chain objects conatain a ordered list of Fragment objects.

Method Summary
	`__init__(self, model_id, chain_id, **args)`
	`__deepcopy__(self, memo)` Implements the copy module deepcopy() protocol.
	`__str__(self)`
	`add_fragment(self, fragment, delay_sort)` Adds a Fragment instance to the Chain.
	`construct_segment(self)` Constructs a new Segment object so that it has a valid .chain reference.
	`construct_sequence_list(self)` Constructs and returns a list with the 3-letter residue codes for the polymer sequence.
	`get_fragment_sequence_index(self, seq_index)`
	`iter_sequence(self)` Iterates over all 3-letter residue codes for the polymer sequence.
	`remove_fragment(self, fragment)` Remove the Fragment from the Chain.
	`remove_sequence(self)` Removes the current sequence mapping.
	`sequence_one_letter_code(self)` Return the one letter code representation of the sequence as a string.
	`set_chain_id(self, chain_id)` Sets a new ID for the Chain, updating the chain_id for all objects in the Structure hierarchy.
	`set_sequence(self, sequence_list)` The sequence_list is a list of 3-letter residue name codes which define the polymer sequence for the chain.
Inherited from Segment
	`__contains__(self, fragment_idx)` Checks for Fragment objects, or the fragment_id string.
	`__ge__(self, other)` Greator than or equal to operator based on chain_id.
	`__getitem__(self, fragment_idx)` Retrieve a Fragment within the Segment.
	`__gt__(self, other)` Greator than operator based on chain_id.
	`__iter__(self)` Iterate all Fragments contained in the Segment.
	`__le__(self, other)` Less than or equal operator based on chain_id.
	`__len__(self)` Return the number of Fragments in the Segment.
	`__lt__(self, other)` Less than operator based on the chain_id.
	`add_atom(self, atom, delay_sort)` Adds a Atom.
	`calc_sequence(self)` Attempts to calculate the residue sequence contained in the Segment object.
	`construct_sub_segment(self, start_frag_id, stop_frag_id)` Construct and return a sub-Segment between start_frag_id and stop_frag_id.
	`count_all_atoms(self)`
	`count_amino_acids(self)` Counts the number of AminoAcidResidue objects.
	`count_atoms(self)`
	`count_fragments(self)` Return the number of Fragment objects.
	`count_non_standard_residues(self)` Counts all non-standard residues in the Segment.
	`count_nucleic_acids(self)` Counts the number of NucleicAcidResidue objects.
	`count_standard_residues(self)` Counts the number of stardard residues in the Segment objects.
	`count_waters(self)` Counts all waters in the Segment.
	`get_chain(self)` Returns the Chain object this Segment is part of.
	`get_fragment(self, fragment_id)` Returns the PDB fragment uniquely identified by its fragment_id.
	`get_model(self)` Returns the parent Model object.
	`get_structure(self)` Returns the parent Structure object.
	`has_amino_acids(self)` Returns True if the Segment contains any AminoAcidResidue objects.
	`has_non_standard_residues(self)` Returns True if there are non-standard residues in the Segment.
	`has_nucleic_acids(self)` Returns True if the Segment contains any NucleicAcidResidue objects.
	`has_standard_residues(self)` Returns True if the Segment contains standard residues as defined by the PDB.
	`has_waters(self)` Returns True if there are waters in the Segment.
	`index(self, fragment)` Return the 0-based index of the Framgent in the segment list.
	`iter_all_atoms(self)` Performs a in-order iteration of all atoms in the Segment, including alternate conformations.
	`iter_amino_acids(self)` Same as iter_fragments(), but only iterates over AminoAcidResidue objects.
	`iter_atoms(self)` Iterates over all Atom objects within the Segment using the default conformation set in the parent Structure.
	`iter_bonds(self)` Iterates over all Bond objects attached to Atom objects within the Segment.
	`iter_fragments(self)` Iterates over all Fragment objects.
	`iter_non_standard_residues(self)` Iterates over non-standard residues in the segment, as defined by the PDB.
	`iter_nucleic_acids(self)` Same as iter_fragments(), but only iterates over NucleicAcidResidue objects.
	`iter_standard_residues(self)` Iterates over standard residues in the Segment, as defined by the PDB.
	`iter_waters(self)` Iterate over all waters in the Segment.
	`remove_atom(self, atom)` Removes a Atom object.
	`sort(self)` Sort the Fragments in the Segment into proper order.
Inherited from object
	`__delattr__(...)` x.__delattr__('name') <==> del x.name
	`__getattribute__(...)` x.__getattribute__('name') <==> x.name
	`__hash__(x)` x.__hash__() <==> hash(x)
	`__reduce__(...)` helper for pickle
	`__reduce_ex__(...)` helper for pickle
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value
Inherited from type
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T

Method Details

deepcopy(self, memo)

Implements the copy module deepcopy() protocol.

Overrides:: mmLib.Structure.Segment.__deepcopy__

add_fragment(self, fragment, delay_sort=False)

Adds a Fragment instance to the Chain. If delay_sort is True, then the fragment is not inserted in the proper position within the chain.

Overrides:: mmLib.Structure.Segment.add_fragment

construct_segment(self)

Constructs a new Segment object so that it has a valid .chain reference.

Overrides:: mmLib.Structure.Segment.construct_segment

construct_sequence_list(self)

Constructs and returns a list with the 3-letter residue codes for the polymer sequence.

iter_sequence(self)

Iterates over all 3-letter residue codes for the polymer sequence.

remove_fragment(self, fragment)

Remove the Fragment from the Chain.

Overrides:: mmLib.Structure.Segment.remove_fragment

remove_sequence(self)

Removes the current sequence mapping.

sequence_one_letter_code(self)

Return the one letter code representation of the sequence as a string.

set_chain_id(self, chain_id)

Sets a new ID for the Chain, updating the chain_id for all objects in the Structure hierarchy.

set_sequence(self, sequence_list)

The sequence_list is a list of 3-letter residue name codes which define the polymer sequence for the chain. Setting the sequence attempts to map the sequence codes to Fragment objects.

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