org.jmol.modelsetbio
public class AminoPolymer extends AlphaPolymer
Field Summary | |
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boolean | hasOAtoms |
short[] | mainchainHbondOffsets |
static float | maxHbondAlphaDistance |
static float | maxHbondAlphaDistance2 |
short[] | min1Energies |
short[] | min1Indexes |
short[] | min2Energies |
short[] | min2Indexes |
static float | minimumHbondDistance2 |
static double | QConst |
Constructor Summary | |
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AminoPolymer(Monomer[] monomers) |
Method Summary | |
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void | bondAminoHydrogen(int indexDonor, Point3f hydrogenPoint, BitSet bsA, BitSet bsB) |
int | calcHbondEnergy(Atom nitrogen, Point3f nitrogenPoint, Point3f hydrogenPoint, AminoMonomer target) |
void | calcHydrogenBonds(BitSet bsA, BitSet bsB) |
protected boolean | calcPhiPsiAngles() |
void | calcPhiPsiAngles(AminoMonomer leadingResidue, AminoMonomer trailingResidue) |
void | calcProteinMainchainHydrogenBonds(BitSet bsA, BitSet bsB) |
void | calculateStructures() |
boolean | checkWingAtoms() |
void | createResidueHydrogenBond(int indexAminoGroup, int indexCarbonylGroup, BitSet bsA, BitSet bsB) |
void | freeze() |
void | getPdbData(char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten) |
boolean | hasWingPoints() |
void | initializeHbondDataStructures() |
static boolean | isHelix(float psi, float phi) |
static boolean | isSheet(float psi, float phi) |
static boolean | isTurn(float psi, float phi) |
Parameters: psi N-C-CA-N torsion for NEXT group phi C-CA-N-C torsion for THIS group
Returns: whether this corresponds to a helix