| ! | Bio.Chain, Bio.Protein.Chain |
| // | Bio.Chain, Bio.Protein.Chain |
| AA | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| AffineGap | |
| 1 (Type/Class) | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| 2 (Data Constructor) | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| AffineGap2 | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| AffineTransformable | Bio.Utils.Geometry |
| ALA | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Alanine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| align | Bio.Chain.Alignment |
| Alignable | Bio.Chain.Alignment.Type |
| alignment | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| AlignmentResult | |
| 1 (Type/Class) | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| 2 (Data Constructor) | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| AminoAcid | |
| 1 (Type/Class) | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| 2 (Data Constructor) | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| angle | |
| 1 (Function) | Bio.Utils.Geometry |
| 2 (Function) | Bio.Protein.Metric |
| ARG | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Arginine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| ASN | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| ASP | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Asparagine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| AsparticAcid | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| assocs | Bio.Chain, Bio.Protein.Chain |
| atom | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| atom' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| AtomType | Bio.Utils.IUPAC |
| BB | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBCA | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBCAT | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBCG | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBO | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBOCG | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBOR | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBORH | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBOT | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBOXTR | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBOXTRH | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BBT | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| BLOSUM62 | |
| 1 (Type/Class) | Bio.Chain.Alignment.Scoring |
| 2 (Data Constructor) | Bio.Chain.Alignment.Scoring |
| blosum62 | Bio.Chain.Alignment.Scoring |
| bounds | Bio.Chain, Bio.Protein.Chain |
| build | Bio.Protein.Chain.Builder |
| Buildable | Bio.Protein.Chain.Builder |
| C | Bio.Utils.IUPAC |
| c | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| c' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CA | Bio.Utils.IUPAC |
| ca | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| ca' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CB | Bio.Utils.IUPAC |
| cb | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CD | Bio.Utils.IUPAC |
| cd | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CD1 | Bio.Utils.IUPAC |
| cd1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CD2 | Bio.Utils.IUPAC |
| cd2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CE | Bio.Utils.IUPAC |
| ce | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CE1 | Bio.Utils.IUPAC |
| ce1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CE2 | Bio.Utils.IUPAC |
| ce2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CE3 | Bio.Utils.IUPAC |
| ce3 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CG | |
| 1 (Type/Class) | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| 2 (Data Constructor) | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| 3 (Data Constructor) | Bio.Utils.IUPAC |
| cg | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| cg' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CG1 | Bio.Utils.IUPAC |
| cg1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CG2 | Bio.Utils.IUPAC |
| cg2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CH2 | Bio.Utils.IUPAC |
| ch2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CH3 | Bio.Utils.IUPAC |
| Chain | Bio.Chain, Bio.Protein.Chain |
| chain | Bio.Chain, Bio.Protein.Chain |
| ChainLike | Bio.Chain, Bio.Protein.Chain |
| chi | Bio.Protein.Algebra |
| cNA | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| Complementary | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| cond | Bio.Chain.Alignment.Type |
| Conditions | |
| 1 (Type/Class) | Bio.Chain.Alignment.Type |
| 2 (Data Constructor) | Bio.Chain.Alignment.Type |
| Create | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid, Bio.Protein.AminoAcid |
| create | |
| 1 (Function) | Bio.Molecule |
| 2 (Function) | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| Createable | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| cross | Bio.Utils.Geometry |
| CYS | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Cysteine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CZ | Bio.Utils.IUPAC |
| cz | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CZ2 | Bio.Utils.IUPAC |
| cz2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| CZ3 | Bio.Utils.IUPAC |
| cz3 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| DA | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| DC | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| defDiag | Bio.Chain.Alignment.Algorithms |
| defStart | Bio.Chain.Alignment.Algorithms |
| defStop | Bio.Chain.Alignment.Algorithms |
| DELETE | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| Delete | Bio.Chain.Alignment.Type |
| deleteAt | Bio.Molecule |
| deleteCostExtend | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| deleteCostOpen | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| DG | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| difference | Bio.Chain.Alignment |
| difference' | Bio.Chain.Alignment |
| differenceGen | Bio.Chain.Alignment |
| differenceGen' | Bio.Chain.Alignment |
| dihedral | |
| 1 (Function) | Bio.Utils.Geometry |
| 2 (Function) | Bio.Protein.Metric |
| distance | |
| 1 (Function) | Bio.Utils.Geometry |
| 2 (Function) | Bio.Protein.Metric |
| DNA | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| doMove | Bio.Chain.Alignment.Type |
| dot | Bio.Utils.Geometry |
| DT | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| EditDistance | |
| 1 (Type/Class) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| 2 (Data Constructor) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| EditOp | Bio.Chain.Alignment.Type |
| eig3 | Bio.Utils.Matrix |
| empty | Bio.Molecule |
| Env | |
| 1 (Type/Class) | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| 2 (Data Constructor) | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| environment | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Epsilon | Bio.Utils.Geometry |
| fillInnerMatrix | Bio.Chain.Alignment.Algorithms |
| fromList | Bio.Chain, Bio.Protein.Chain |
| FromSymbol | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| fromSymbol | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| fromSymbolE | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| FromThreeSymbols | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| fromThreeSymbols | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| functionDec | Bio.Chain.Alignment.Scoring.TH |
| gapExtend | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| gapOpen | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| getBinDir | Paths_cobot |
| getChain | |
| 1 (Function) | Bio.Protein.Chain |
| 2 (Function) | Bio.NucleicAcid.Chain |
| getChains | Bio.Molecule |
| getDataDir | Paths_cobot |
| getDataFileName | Paths_cobot |
| getDynLibDir | Paths_cobot |
| getI | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| getJ | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| getLibDir | Paths_cobot |
| getLibexecDir | Paths_cobot |
| getSysconfDir | Paths_cobot |
| GLN | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| GlobalAlignment | |
| 1 (Type/Class) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| 2 (Data Constructor) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| GLU | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| GlutamicAcid | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Glutamine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| GLY | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Glycine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| H | |
| 1 (Type/Class) | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| 2 (Data Constructor) | Bio.Utils.IUPAC |
| HA | Bio.Utils.IUPAC |
| HA2 | Bio.Utils.IUPAC |
| HA3 | Bio.Utils.IUPAC |
| HasAtom | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| HasC | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| HasCA | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| HasN | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| HasO | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| HasOXT | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| HasRadical | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| HasRadicalType | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| HB | Bio.Utils.IUPAC |
| HB1 | Bio.Utils.IUPAC |
| HB2 | Bio.Utils.IUPAC |
| HB3 | Bio.Utils.IUPAC |
| HD | Bio.Utils.IUPAC |
| HD1 | Bio.Utils.IUPAC |
| HD11 | Bio.Utils.IUPAC |
| HD12 | Bio.Utils.IUPAC |
| HD13 | Bio.Utils.IUPAC |
| HD2 | Bio.Utils.IUPAC |
| HD21 | Bio.Utils.IUPAC |
| HD22 | Bio.Utils.IUPAC |
| HD23 | Bio.Utils.IUPAC |
| HD3 | Bio.Utils.IUPAC |
| HE | Bio.Utils.IUPAC |
| HE1 | Bio.Utils.IUPAC |
| HE2 | Bio.Utils.IUPAC |
| HE21 | Bio.Utils.IUPAC |
| HE22 | Bio.Utils.IUPAC |
| HE3 | Bio.Utils.IUPAC |
| HG | Bio.Utils.IUPAC |
| HG1 | Bio.Utils.IUPAC |
| HG11 | Bio.Utils.IUPAC |
| HG12 | Bio.Utils.IUPAC |
| HG13 | Bio.Utils.IUPAC |
| HG2 | Bio.Utils.IUPAC |
| HG21 | Bio.Utils.IUPAC |
| HG22 | Bio.Utils.IUPAC |
| HG23 | Bio.Utils.IUPAC |
| HG3 | Bio.Utils.IUPAC |
| HH | Bio.Utils.IUPAC |
| HH11 | Bio.Utils.IUPAC |
| HH12 | Bio.Utils.IUPAC |
| HH2 | Bio.Utils.IUPAC |
| HH21 | Bio.Utils.IUPAC |
| HH22 | Bio.Utils.IUPAC |
| HIS | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Histidine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| hydrogens | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| HZ | Bio.Utils.IUPAC |
| HZ1 | Bio.Utils.IUPAC |
| HZ2 | Bio.Utils.IUPAC |
| HZ3 | Bio.Utils.IUPAC |
| ILE | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| initB | Bio.Protein.Chain.Builder |
| INSERT | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| Insert | Bio.Chain.Alignment.Type |
| insertCostExtend | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| insertCostOpen | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| instDec | Bio.Chain.Alignment.Scoring.TH |
| isAffine | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| isDelete | Bio.Chain.Alignment.Type |
| IsGap | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| isInsert | Bio.Chain.Alignment.Type |
| isMatch | Bio.Chain.Alignment.Type |
| Isoleucine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| isStop | Bio.Chain.Alignment.Type |
| LEU | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Leucine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| loadMatrix | Bio.Chain.Alignment.Scoring.Loader, Bio.Chain.Alignment.Scoring |
| LocalAlignment | |
| 1 (Type/Class) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| 2 (Data Constructor) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| localStart | Bio.Chain.Alignment.Algorithms |
| localStop | Bio.Chain.Alignment.Algorithms |
| LYS | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Lysine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| MATCH | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| Match | Bio.Chain.Alignment.Type |
| Matrix | Bio.Chain.Alignment.Type |
| matrix | Bio.Chain.Alignment.Scoring.TH, Bio.Chain.Alignment.Scoring |
| matrixDec | Bio.Chain.Alignment.Scoring.TH |
| MET | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Methionine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Metricable | Bio.Protein.Metric |
| mkClause | Bio.Chain.Alignment.Scoring.TH |
| modify | Bio.Chain, Bio.Protein.Chain |
| modifyAfter | Bio.Chain, Bio.Protein.Chain |
| modifyBefore | Bio.Chain, Bio.Protein.Chain |
| Molecule | |
| 1 (Type/Class) | Bio.Molecule |
| 2 (Data Constructor) | Bio.Molecule |
| MoleculeLike | Bio.Molecule |
| Monomer | Bio.Protein.Chain.Builder |
| Move | Bio.Chain.Alignment.Type |
| move | Bio.Chain.Alignment.Algorithms |
| moveAffine | Bio.Chain.Alignment.Algorithms |
| moveSimple | Bio.Chain.Alignment.Algorithms |
| N | Bio.Utils.IUPAC |
| n | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| n' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| ND1 | Bio.Utils.IUPAC |
| nd1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| ND2 | Bio.Utils.IUPAC |
| nd2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| NE | Bio.Utils.IUPAC |
| ne | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| NE1 | Bio.Utils.IUPAC |
| ne1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| NE2 | Bio.Utils.IUPAC |
| ne2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| nearZero | Bio.Utils.Geometry |
| nextB | Bio.Protein.Chain.Builder |
| NH1 | Bio.Utils.IUPAC |
| nh1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| NH2 | Bio.Utils.IUPAC |
| nh2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| norm | Bio.Utils.Geometry |
| normalize | Bio.Utils.Geometry |
| NUC44 | |
| 1 (Type/Class) | Bio.Chain.Alignment.Scoring |
| 2 (Data Constructor) | Bio.Chain.Alignment.Scoring |
| nuc44 | Bio.Chain.Alignment.Scoring |
| NucleicAcidChain | |
| 1 (Type/Class) | Bio.NucleicAcid.Chain |
| 2 (Data Constructor) | Bio.NucleicAcid.Chain |
| nucleoIso | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| NZ | Bio.Utils.IUPAC |
| nz | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| O | Bio.Utils.IUPAC |
| o | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| o' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| OD1 | Bio.Utils.IUPAC |
| od1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| OD2 | Bio.Utils.IUPAC |
| od2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| OE1 | Bio.Utils.IUPAC |
| oe1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| OE2 | Bio.Utils.IUPAC |
| oe2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| OG | Bio.Utils.IUPAC |
| og | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| OG1 | Bio.Utils.IUPAC |
| og1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| OH | Bio.Utils.IUPAC |
| oh | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| omega | Bio.Protein.Algebra |
| Operation | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| OXT | |
| 1 (Type/Class) | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| 2 (Data Constructor) | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| 3 (Data Constructor) | Bio.Utils.IUPAC |
| oxt | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| oxt' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| PAM250 | |
| 1 (Type/Class) | Bio.Chain.Alignment.Scoring |
| 2 (Data Constructor) | Bio.Chain.Alignment.Scoring |
| pam250 | Bio.Chain.Alignment.Scoring |
| PHE | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Phenylalanine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| phi | Bio.Protein.Algebra |
| prettyAlignmment | Bio.Chain.Alignment |
| PRO | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Proline | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| ProteinChain | |
| 1 (Type/Class) | Bio.Protein.Chain |
| 2 (Data Constructor) | Bio.Protein.Chain |
| psi | Bio.Protein.Algebra |
| R | Bio.Utils.Geometry |
| RA | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| rad2rad | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Radical | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| radical | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| radical' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| RadicalType | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid, Bio.Protein.AminoAcid |
| radicalType | Bio.Protein.AminoAcid.Instances, Bio.Protein.AminoAcid |
| Ray | |
| 1 (Type/Class) | Bio.Utils.Geometry |
| 2 (Data Constructor) | Bio.Utils.Geometry |
| RC | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| rcNA | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| ReturnMetric | Bio.Protein.Metric |
| RG | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| RNA | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| rotate | Bio.Utils.Geometry |
| rotateR | Bio.Utils.Geometry |
| RU | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| score | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| scoreMatrix | Bio.Chain.Alignment.Type |
| Scoring | Bio.Chain.Alignment.Type |
| scoring | Bio.Chain.Alignment.Scoring.Loader, Bio.Chain.Alignment.Scoring |
| ScoringMatrix | Bio.Chain.Alignment.Scoring.Loader, Bio.Chain.Alignment.Scoring |
| SD | Bio.Utils.IUPAC |
| sd | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| semi | Bio.Chain.Alignment.Type |
| SemiglobalAlignment | |
| 1 (Type/Class) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| 2 (Data Constructor) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| semiStart | Bio.Chain.Alignment.Algorithms |
| sequence1 | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| sequence2 | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| SequenceAlignment | Bio.Chain.Alignment.Type |
| SER | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Serine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| set | Bio.Molecule |
| SG | Bio.Utils.IUPAC |
| sg | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| similarity | Bio.Chain.Alignment |
| similarity' | Bio.Chain.Alignment |
| similarityGen | Bio.Chain.Alignment |
| similarityGen' | Bio.Chain.Alignment |
| SimpleGap | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| SimpleGap2 | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| singleton | Bio.Molecule |
| Stop | Bio.Chain.Alignment.Type |
| substitute | Bio.Chain.Alignment.Algorithms |
| substituteED | Bio.Chain.Alignment.Algorithms |
| Substitution | Bio.Chain.Alignment.Scoring.TH |
| svd3 | Bio.Utils.Geometry |
| Symbol | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| symbol | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| THR | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| ThreeSymbols | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| threeSymbols | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| Threonine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| toDNA | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| toRNA | Bio.NucleicAcid.Nucleotide.Type, Bio.NucleicAcid.Nucleotide |
| traceStart | Bio.Chain.Alignment.Type |
| translate | Bio.Utils.Geometry |
| TRP | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Tryptophan | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| typeDec | Bio.Chain.Alignment.Scoring.TH |
| TYR | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Tyrosine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| unsafeRead | Bio.Chain, Bio.Protein.Chain |
| V3R | Bio.Utils.Geometry |
| VAL | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Valine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| version | Paths_cobot |
| viewAlignment | Bio.Chain.Alignment |
| zoRay | Bio.Utils.Geometry |
| _atom' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _c' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _ca' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cb | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cd | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cd1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cd2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _ce | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _ce1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _ce2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _ce3 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cg | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cg' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cg1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cg2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _ch2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cz | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cz2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _cz3 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _direction | Bio.Utils.Geometry |
| _environment | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _n' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _nd1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _nd2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _ne | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _ne1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _ne2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _nh1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _nh2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _nz | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _o' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _od1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _od2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _oe1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _oe2 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _og | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _og1 | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _oh | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _origin | Bio.Utils.Geometry |
| _oxt' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _radical' | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _sd | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| _sg | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |