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Packages that use Monomer | |
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org.strbio.mol | These classes represent objects or concepts useful to structural biologists. |
org.strbio.mol.lib | These classes represent conceptual objects used in structural biology algorithms. |
org.strbio.mol.lib.pred2ary | These classes represent conceptual objects used in the Pred2ary program, which are probably not very useful for other purposes. |
Uses of Monomer in org.strbio.mol |
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Subclasses of Monomer in org.strbio.mol | |
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class |
Nucleotide
Class to represent a single nucleotide Version 1.0, 8/17/01 - original version, based on org.strbio.mol.Residue |
class |
ProfRes
Class to represent a single residue in a protein with profile information. |
class |
ProfResPSI
Class to represent a single residue in a profile, with position specific information (PSI) added. |
class |
Residue
Class to represent a single residue in a protein. |
Methods in org.strbio.mol that return Monomer | |
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Monomer |
Polymer.firstMon()
Return first monomer if there is one, else null. |
Monomer[] |
Polymer.getMonomers()
get an array of the monomers. |
Monomer[] |
Polymer.getNonGapMonomers()
get an array of the valid non-gap monomers. |
Monomer[] |
Polymer.getValidNonGapMonomers()
get an array of the valid non-gap monomers. |
Monomer |
Polymer.lastMon()
Return last monomer if there is one, else null. |
Monomer |
Polymer.monomer(int n)
returns the N'th monomer in the sequence. |
Monomer |
ProfilePSI.newMonomer()
This returns a new ProfResPSI. |
Monomer |
Profile.newMonomer()
Profiles are made of ProfRes-type monomers. |
Monomer |
Protein.newMonomer()
This should return a new monomer of whatever type this polymer is made of (i.e. |
Monomer |
Polymer.newMonomer()
This should return a new monomer of whatever type this polymer is made of (i.e. |
Monomer |
ProfilePSI.newMonomer(char t)
This returns a new ProfResPSI. |
Monomer |
Profile.newMonomer(char t)
|
Monomer |
Protein.newMonomer(char t)
This should return a new monomer of whatever type this polymer is made of (i.e. |
Monomer |
Polymer.newMonomer(char t)
This should return a new monomer of whatever type this polymer is made of (i.e. |
Monomer |
ProfilePSI.newMonomer(java.lang.String s)
This returns a new ProfResPSI. |
Monomer |
Profile.newMonomer(java.lang.String s)
|
Monomer |
Protein.newMonomer(java.lang.String s)
This should return a new monomer of whatever type this polymer is made of (i.e. |
Monomer |
Polymer.newMonomer(java.lang.String s)
This should return a new monomer of whatever type this polymer is made of (i.e. |
protected Monomer |
Polymer.YAPFGetNextMonomer(int n)
Return the next non-gap residue with number 'n', or null if there is none. |
Methods in org.strbio.mol with parameters of type Monomer | |
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void |
Monomer.copyAtoms(Monomer q)
copy the atoms from another monomer. |
void |
ProfRes.copyDataFrom(Monomer q)
Copy another ProfRes. |
void |
ProfResPSI.copyDataFrom(Monomer q)
Copy another ProfResPSI. |
void |
Residue.copyDataFrom(Monomer q)
copy another residue, including the atoms. |
void |
Monomer.copyDataFrom(Monomer q)
copy another monomer, including the atoms. |
Constructors in org.strbio.mol with parameters of type Monomer | |
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Monomer(Monomer q)
copy another monomer, including the atoms. |
Uses of Monomer in org.strbio.mol.lib |
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Methods in org.strbio.mol.lib with parameters of type Monomer | |
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double |
ScoreUFSippl90.score(Monomer a,
Monomer b)
|
double |
ScoreSippl90.score(Monomer a,
Monomer b)
|
double |
ScoreScaledID.score(Monomer a,
Monomer b)
Returns EQUAL if monomer types are the same, otherwise NOTEQUAL. |
double |
ScoreReversePSIBlast.score(Monomer a,
Monomer b)
|
double |
ScorePredFreq.score(Monomer a,
Monomer b)
|
double |
ScorePred2ary.score(Monomer a,
Monomer b)
|
double |
ScorePhiPsi.score(Monomer a,
Monomer b)
|
double |
ScorePairwiseDistance.score(Monomer a,
Monomer b)
|
double |
ScorePSIBlast.score(Monomer a,
Monomer b)
|
double |
ScoreJDB10.score(Monomer a,
Monomer b)
|
double |
ScoreID.score(Monomer a,
Monomer b)
Returns EQUAL if residue types are the same, otherwise NOTEQUAL. |
double |
ScoreFischer.score(Monomer a,
Monomer b)
|
double |
ScoreDefay.score(Monomer a,
Monomer b)
|
double |
ScoreBlosum62.score(Monomer a,
Monomer b)
|
double |
ScoreAverageReversePSIBlast.score(Monomer a,
Monomer b)
|
double |
ScoreAveragePSIBlast.score(Monomer a,
Monomer b)
|
double |
ScoreAlphaTau.score(Monomer a,
Monomer b)
|
double |
Score2ary.score(Monomer a,
Monomer b)
|
double |
ScoreFunction.score(Monomer seqMon,
Monomer foldMon)
This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad. |
double |
ScoreList.totalScore(Monomer a,
Monomer b)
return the total score for a monomer pair, from all scoring functions at this point on. |
Uses of Monomer in org.strbio.mol.lib.pred2ary |
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Subclasses of Monomer in org.strbio.mol.lib.pred2ary | |
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class |
PCPRes
ProfRes with a couple extras useful for 2ary structure prediction. |
Methods in org.strbio.mol.lib.pred2ary that return Monomer | |
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Monomer |
PredClassProfile.newMonomer()
|
Monomer |
PredClassProfile.newMonomer(char t)
|
Monomer |
PredClassProfile.newMonomer(java.lang.String s)
|
Methods in org.strbio.mol.lib.pred2ary with parameters of type Monomer | |
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void |
PCPRes.copyDataFrom(Monomer q)
Copy another PCPRes. |
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