Merge pull request #57 from MatteoLacki/github_issue_56_fastas

Added docs and another function on C++ side.

Author: michalsta

IsoSpec++/fasta.h

@@ -30,6 +30,11 @@ extern const double aa_elem_probabilities[19];
 
 extern const int aa_symbol_to_elem_counts[256*6];
 
+//! Count elemental composition of an unmodificed sequence of amino acids, resulting in CHNOSSe counts.
+/*!
+    WARNING!!! This function does not add the terminating H and OH groups, resulting in a residue backbone skeleton formula.
+    If you don't know what that means, you should probably be using parse_fasta_full function.
+*/
 inline void parse_fasta(const char* fasta, int atomCounts[6])
 {
     memset(atomCounts, 0, sizeof(decltype(atomCounts[0]))*6);
@@ -42,4 +47,21 @@ inline void parse_fasta(const char* fasta, int atomCounts[6])
     }
 }
 
+//! Turn an input FASTA aminoacid sequence into atom counts, in CHNOSSe order.
+/*!
+    Unlike parse_fasta, this function includes the H and OH groups at the N- and C- termini of the skeleton, resulting in a formula of a full (inert) molecule.
+*/
+inline void parse_fasta_full(const char* fasta, int atomCounts[6])
+{
+    parse_fasta(fasta, atomCounts)
+    // Add terminal water (H2O) for either precursor or fragment.
+    const int H_INDEX = 1; // Indexing: 0=C, 1=H, 2=N, 3=O, 4=S, 5=Se
+    const int O_INDEX = 3;
+
+    atomCounts[H_INDEX] += 2;
+    atomCounts[O_INDEX] += 1;
+}
+
+
+
 }  // namespace IsoSpec