Package ffx.potential.bonded

Class PolymerUtils

java.lang.Object
ffx.potential.bonded.PolymerUtils
public class PolymerUtils extends Object
Utilities for creating polymers.
Since:
1.0
Author:
Michael Schnieders

  • Constructor Details

    • PolymerUtils

      public PolymerUtils()

  • Method Details

    • assignAtomTypes

      public static List<Bond> assignAtomTypes(MolecularAssembly molecularAssembly, PDBFilter.PDBFileStandard fileStandard)
      Assign force field atoms types to common chemistries using "biotype" records.
      Parameters:
      molecularAssembly - MolecularAssembly to operate on.
      fileStandard - PDB file standard to follow.
      Returns:
      A List of created bonds.

    • buildDisulfideBonds

      public static void buildDisulfideBonds(List<Bond> ssBondList, MolecularAssembly molecularAssembly, List<Bond> bondList)
      Assign parameters to disulfide bonds.
      Parameters:
      ssBondList - List of SSBOND records.
      molecularAssembly - MolecularAssembly to operate on.
      bondList - Add new SS-Bonds to this list.

    • buildMissingResidues

      public static int buildMissingResidues(int xyzIndex, MolecularAssembly molecularAssembly, Map<Character,String[]> seqres, Map<Character,int[]> dbref)
      Currently builds missing internal loops based on information in DBREF and SEQRES records.

      Known limitations include: 1) No building n- and c-terminal loops. 2) No support for DBREF1 or DBREF2 records. 3) Incomplete optimization scheme to position the loops.

      Parameters:
      xyzIndex - XYZ index to begin from.
      molecularAssembly - MolecularAssembly to operate on.
      seqres - Map of SEQRES entries.
      dbref - Map of DBREF entries.
      Returns:
      xyzIndex updated based on built atoms.

    • findChainBreaks

      public static List<List<Residue>> findChainBreaks(List<Residue> residues, double cutoff)

    • locateDisulfideBonds

      public static List<Bond> locateDisulfideBonds(List<String> ssbonds, MolecularAssembly molecularAssembly, Map<String,String> pdbToNewResMap)
      Locate disulfide bonds based on SSBOND records.
      Parameters:
      ssbonds - List of SSBOND records.
      molecularAssembly - The MolecularAssembly to operate on.
      pdbToNewResMap - Maps chainIDResNumInsCode to renumbered chainIDResNum. For example, residue 52A in chain C might be renumbered to residue 53, and mapped as "C52A" to "C53".
      Returns:
      A List of Bond instances for SS-Bonds.

    • resolvePolymerLinks

      public static void resolvePolymerLinks(List<MSNode> molecules, MolecularAssembly molecularAssembly, List<Bond> bondList)
      Resolves links between polymeric hetero groups; presently only functional for cyclic molecules.
      Parameters:
      molecules - List of Molecules in the molecular assembly.
      molecularAssembly - MolecularAssembly to operate on.
      bondList - Add created bonds to this list.