mmLib.Structure.Segment

Package mmLib :: Module Structure :: Class Segment

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Class Segment

object --+
         |
        Segment

Known Subclasses:: Chain

Segment objects are a container for Fragment objects, but are disaccociated with the Structure object hierarch. Chain objects are a subclass of Segment objects which are part of the Structure hierarchy.

Method Summary
	`__init__(self, model_id, chain_id, **args)`
	`__contains__(self, fragment_idx)` Checks for Fragment objects, or the fragment_id string.
	`__deepcopy__(self, memo)` Implements copy module protocol for deepcopy() operation.
	`__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.
	`__str__(self)`
	`add_atom(self, atom, delay_sort)` Adds a Atom.
	`add_fragment(self, fragment, delay_sort)` Adds a Fragment instance to the Segment.
	`calc_sequence(self)` Attempts to calculate the residue sequence contained in the Segment object.
	`construct_segment(self)` Constructs a new Segment object so that it has a valid .chain reference.
	`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.
	`remove_fragment(self, fragment)` Removes a Fragment object from the Segment.
	`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

contains(self, fragment_idx)
(In operator)

Checks for Fragment objects, or the fragment_id string.

deepcopy(self, memo)

Implements copy module protocol for deepcopy() operation.

ge(self, other)
(Greater-than-or-equals operator)

Greator than or equal to operator based on chain_id.

getitem(self, fragment_idx)
(Indexing operator)

Retrieve a Fragment within the Segment. This can take a integer index of the Fragment's position within the segment, the fragment_id string of the Fragment to retrieve, or a slice of the Segment to return a new Segment object containing the sliced subset of Fragments. If the slice values are fragment_id strings, then the Segment which is returned includes those Fragments. If the slice values are integers, then normal list slicing rules apply.

gt(self, other)
(Greater-than operator)

Greator than operator based on chain_id.

iter(self)

Iterate all Fragments contained in the Segment.

le(self, other)
(Less-than-or-equals operator)

Less than or equal operator based on chain_id.

len(self)
(Length operator)

Return the number of Fragments in the Segment.

lt(self, other)
(Less-than operator)

Less than operator based on the chain_id.

add_atom(self, atom, delay_sort=False)

Adds a Atom.

add_fragment(self, fragment, delay_sort=False)

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

calc_sequence(self)

Attempts to calculate the residue sequence contained in the Segment object. This is a simple algorithm: find the longest running sequence of the same bio-residue, and that's the sequence. Returns a list of 3-letter residues codes of the calculated sequence.

construct_segment(self)

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

construct_sub_segment(self, start_frag_id, stop_frag_id)

Construct and return a sub-Segment between start_frag_id and stop_frag_id. If start_frag_id is None, then the slice is taken from the beginning of this Segment, and if stop_frag_id is None it is taken to the end of this Segment.

count_amino_acids(self)

Counts the number of AminoAcidResidue objects.

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. Standard residues are AminoAcidResidue and NucliecAcidResiue 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. Standard residues are AminoAcidResidue and NucliecAcidResiue objects.

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. The iteration is performed in order according to the Fragment's position within the Segment object.

iter_non_standard_residues(self)

Iterates over non-standard residues in the segment, as defined by the PDB. Non-standard residues are anything which is not a amino or nucleic acid.

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. Standard residues are AminoAcidResidue and NucliecAcidResiue objects.

iter_waters(self)

Iterate over all waters in the Segment.

remove_atom(self, atom)

Removes a Atom object.

remove_fragment(self, fragment)

Removes a Fragment object from the Segment.

sort(self)

Sort the Fragments in the Segment into proper order.

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