Modifier and Type | Class and Description |
---|---|
class |
Strand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
Modifier and Type | Method and Description |
---|---|
IStrand |
Strand.clone() |
IStrand |
BioPolymer.getStrand(String cName)
Retrieves a Monomer object by specifying its name.
|
Modifier and Type | Method and Description |
---|---|
Map<String,IStrand> |
BioPolymer.getStrands() |
Modifier and Type | Method and Description |
---|---|
void |
BioPolymer.addAtom(IAtom oAtom,
IMonomer oMonomer,
IStrand oStrand)
Adds the atom to a specified Strand and a specified Monomer.
|
void |
BioPolymer.addAtom(IAtom oAtom,
IStrand oStrand)
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugStrand
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IStrand |
DebugStrand.clone()
Clones this
IChemObject . |
IStrand |
DebugBioPolymer.getStrand(String cName)
Retrieves a Monomer object by specifying its name.
|
Modifier and Type | Method and Description |
---|---|
Map<String,IStrand> |
DebugBioPolymer.getStrands()
Returns a Map containing the strands in the Polymer.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugBioPolymer.addAtom(IAtom oAtom,
IMonomer oMonomer,
IStrand oStrand)
Adds the atom to a specified Strand and a specified Monomer.
|
void |
DebugBioPolymer.addAtom(IAtom oAtom,
IStrand oStrand)
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
|
Modifier and Type | Method and Description |
---|---|
IStrand |
IStrand.clone()
Returns a deep clone of this IChemObject.
|
IStrand |
IBioPolymer.getStrand(String cName)
Retrieve a Monomer object by specifying its name.
|
Modifier and Type | Method and Description |
---|---|
Map<String,IStrand> |
IBioPolymer.getStrands()
Returns a Map containing the strands in the Polymer.
|
Modifier and Type | Method and Description |
---|---|
void |
IBioPolymer.addAtom(IAtom oAtom,
IMonomer oMonomer,
IStrand oStrand)
Adds the atom to a specified Strand and a specified Monomer.
|
void |
IBioPolymer.addAtom(IAtom oAtom,
IStrand oStrand)
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
|
void |
IPDBPolymer.addAtom(IPDBAtom oAtom,
IMonomer oMonomer,
IStrand oStrand)
Adds the atom to a specified Strand and a specified Monomer.
|
Modifier and Type | Field and Description |
---|---|
protected IStrand |
CMLCoreModule.currentStrand |
Modifier and Type | Class and Description |
---|---|
class |
PDBStrand
An entry in the PDB database.
|
Modifier and Type | Method and Description |
---|---|
void |
PDBPolymer.addAtom(IPDBAtom oAtom,
IMonomer oMonomer,
IStrand oStrand)
Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
|
Modifier and Type | Method and Description |
---|---|
IStrand |
Strand.clone() |
IStrand |
BioPolymer.getStrand(String cName)
Retrieves a Monomer object by specifying its name.
|
Modifier and Type | Method and Description |
---|---|
Map<String,IStrand> |
BioPolymer.getStrands() |
Modifier and Type | Method and Description |
---|---|
void |
BioPolymer.addAtom(IAtom oAtom,
IMonomer oMonomer,
IStrand oStrand)
Adds the atom to a specified Strand and a specified Monomer.
|
void |
BioPolymer.addAtom(IAtom oAtom,
IStrand oStrand)
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
|
void |
PDBPolymer.addAtom(IPDBAtom oAtom,
IMonomer oMonomer,
IStrand oStrand)
Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
|
Modifier and Type | Method and Description |
---|---|
static IBioPolymer |
ProteinBuilderTool.addAminoAcidAtCTerminus(IBioPolymer protein,
IAminoAcid aaToAdd,
IStrand strand,
IAminoAcid aaToAddTo)
Builds a protein by connecting a new amino acid at the C-terminus of the
given strand.
|
static IBioPolymer |
ProteinBuilderTool.addAminoAcidAtNTerminus(IBioPolymer protein,
IAminoAcid aaToAdd,
IStrand strand,
IAminoAcid aaToAddTo)
Builds a protein by connecting a new amino acid at the N-terminus of the
given strand.
|
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