Import sequence format for RNA, DNA and PEPTIDES

[even1024]

Background
There is a requirement to have parsing of RNA, DNA, and peptide sequences.
These sequences represented as a plain strings with a combination of the following symbols:

for peptides:
A - Alanine
C - Cysteine
D - Aspartic Acid
E - Glutamic Acid
F - Phenylalanine
G - Glycine
H - Histidine
I - Isoleucine
K - Lysine
L - Leucine
M - Methionine
N - Asparagine
P - Proline
Q - Glutamine
R - Arginine
S - Serine
T - Threonine
V - Valine
W - Tryptophan
Y - Tyrosine

for RNA nucleotides:
A - AMP (Adenosine monophosphate)
C - CMP (Cytidine monophosphate)
G - GMP (Guanosine monophosphate)
U - UMP (Uridine monophosphate)
T - rTMP (Ribothymidine monophosphate)

for DNA nucleotides:
A - dAMP (Deoxyadenosine monophosphate)
C - dCMP (Deoxycytidine monophosphate)
G - dGMP (Deoxyguanosine monophosphate)
U - dUMP (Deoxyuridine monophosphate)
T - TMP (Thymidine monophosphate)

Sequence parser should split nucleotides into its components: phosphate, sugar and nucleobase as following:

For RNA case:
Input: <string> (of RNA letters)
Input Visualization (given just for better explanation):

Output: All supported indigo formats including ket format in JSON for Ketcher.
Output Visualization (given just for better explanation):

Algo: every RNA letter wrap into r(...)p i.e. A -> r(A)p, C -> r(C)p and so on

Example:
Input: "ACGU"
Output: r(A)p, r(C)p, r(G)p, r(U) (in ket format)

For DNA, case:
Input: <string> (of RNA letters)
Input Visualization:

Output: All supported indigo formats including ket format in JSON for Ketcher.
Output Visualization:

Algo: every RNA letter wrap into d(...)p i.e. A -> d(A)p, C -> d(C)p and so on

Example:
Input: "ACGT"
Output: d(A)p, d(C)p, d(G)p, d(T) (in ket format)

Please note that phosphate component "p" appears from the right side of an expanded nucleotide.
"r" - means ribose and "d"- deoxyribose.

Solution

1. Implement C++ class SequenceLoader in addition to the existing Indigo loaders for molecular formats.
2. Implement following functions for C API, where type can be one of "RNA", "DNA" or "PEPTIDE":

int indigoLoadSequence(int source, const char* type);
int indigoLoadSequenceFromString(const char* string,  const char* type);
int indigoLoadSequenceFromFile(const char* filename,  const char* type);
int indigoLoadSequenceFromBuffer(const char* buffer, int size,  const char* type);

3. Add language bindings for Python, Java, C#
   python binding functions:
   def loadSequence(self, input_string: string, sequence_type: string):
   def loadSequenceFromFile(self, input_file: string, sequence_type: string):

4. Add the following content types to WASM "loadMoleculeOrReaction" and Indigo service "convert" API:

chemical/x-rna-sequence, chemical/x-dna-sequence, chemical/x-peptide-sequence

5. Coordinates for monomers calculated according to the pictures above. Backbone monomers coordinates calculated from left to right. Branch monomers positioned under the sugars they connected to.