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BALL
1.4.79
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BALL
1.4.79
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#include <BALL/STRUCTURE/nucleotideMapping.h>
Public Types | |
| typedef std::pair< const std::string, const std::string > | Alignment |
Public Member Functions | |
| NucleotideMapping () | |
Accessors | |
| Chain * | getFirstStrand () const |
| Chain * | getSecondStrand () const |
| Residue * | firstToSecond (Residue *a) const |
| Residue * | secondToFirst (Residue *b) const |
Static Public Member Functions | |
Factory methods | |
| static NucleotideMapping | assignNaively (Chain &a, Chain &b, unsigned int offset_a=0, unsigned int offset_b=0) |
| static NucleotideMapping | assignFromDistances (Chain &a, Chain &b) |
| static NucleotideMapping | assignFromAlignment (Chain &a, Chain &b, const Alignment &alignment) |
This class defines the mapping between complementary bases in to strands of DNA. Ideally this should be tightly coupled with NucleicAcid, however as this is currently broken this class has to do the job. This also explains why a Chain is required as an input.
Definition at line 21 of file nucleotideMapping.h.
| typedef std::pair<const std::string, const std::string> BALL::NucleotideMapping::Alignment |
Definition at line 24 of file nucleotideMapping.h.
| BALL::NucleotideMapping::NucleotideMapping | ( | ) |
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Construct a NucleotideMapping given a sequence alignment of the strands. Note that residue names are not actually checked, but rather any pair of characters different from '-' are considered as an instruction to align the next bases. E.g: for the sequences ATGC and TCCG this would be a valid input:
*-*** **-**
Also the alignment does not need to cover the full length of the sequences. The assignment process simply stops when the end of the alignment is reached.
| a | The first nucleic acid, it is assumed that it is available in 5' -> 3' order. |
| b | The second nucleic acid, it is assumed that it is available in 5' -> 3' order. |
| alignment | A pair of strings defining the mapping between the two strands. it may only consist of the characters forming the respective abbreviation of the bases and '-' for gaps. |
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This method tries to reconstruct the base complementarity information by looking at the atom distances between the two nucleic acids. Äote that this can fail if the strands are strongly deformed.
| a | The first nucleic acid, it is assumed that it is available in 5' -> 3' order. |
| b | The second nucleic acid, it is assumed that it is available in 5' -> 3' order. |
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This method constructs a Nucleotide mapping by simply assuming, that the first base on the 5' end of a is complementary to the first base on the 3' end of b.
| a | The first nucleic acid, it is assumed that it is available in 5' -> 3' order. |
| b | The second nucleic acid, it is assumed that it is available in 5' -> 3' order. |
| offset_a | start matching at the base in strand a with index offset_a instead of 0 |
| offset_b | start matching at the base in strand b with index offset_b instead of 0 |
Given a nucleotide a located in the first strand. This method returns the nucleotide complementary to a located in the second strand. First and second refers to the order the strands were passed in at creation time.
| Chain* BALL::NucleotideMapping::getFirstStrand | ( | ) | const |
Get a pointer to the first DNA strand
| Chain* BALL::NucleotideMapping::getSecondStrand | ( | ) | const |
Get a pointer to the second DNA strand
Given a nucleotide b located in the second strand. This method returns the nucleotide complementary to b located in the first strand. First and second refers to the order the strands were passed in at creation time.
1.8.7