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CGExplore documentation

CGExplore

  • Recipes
    • 1. Minimal model genetic algorithm
    • 2. Minimal model structure prediction
    • 3. Genetic algorithm-driven graph exploration
    • 4. Atomistic structure prediction
    • 5. Four component structure prediction
    • 6. Target optimisation
    • 7. Reproducing stk graphs
  • First paper example
  • Structure prediction
    • Available graphs
  • Systems optimisation
  • Sharing with collaborators
  • Molecular
  • OpenMM Interface
  • Forcefields
  • Terms
  • Analysis
  • Executables
  • Topologies
  • Atomistic tools
  • Utilities

Modules:

  • Modules
    • cgexplore
      • cgexplore.analysis
        • cgexplore.analysis.GeomMeasure
        • cgexplore.analysis.ShapeMeasure
        • cgexplore.analysis.known_shape_vectors
      • cgexplore.atomistic
        • cgexplore.atomistic.Crest
        • cgexplore.atomistic.cgx_optimisation_sequence
        • cgexplore.atomistic.extract_ditopic_ensemble
        • cgexplore.atomistic.get_ditopic_aligned_bb
        • cgexplore.atomistic.run_conformer_analysis
      • cgexplore.forcefields
        • cgexplore.forcefields.AssignedSystem
        • cgexplore.forcefields.ForceField
        • cgexplore.forcefields.ForceFieldLibrary
        • cgexplore.forcefields.MartiniForceField
        • cgexplore.forcefields.MartiniForceFieldLibrary
        • cgexplore.forcefields.MartiniSystem
        • cgexplore.forcefields.MartiniTopology
        • cgexplore.forcefields.cosine_periodic_angle_force
        • cgexplore.forcefields.custom_excluded_volume_force
        • cgexplore.forcefields.custom_lennard_jones_force
        • cgexplore.forcefields.get_martini_mass_by_type
      • cgexplore.molecular
        • cgexplore.molecular.BeadLibrary
        • cgexplore.molecular.CgBead
        • cgexplore.molecular.Conformer
        • cgexplore.molecular.Ensemble
        • cgexplore.molecular.FourC0Arm
        • cgexplore.molecular.FourC1Arm
        • cgexplore.molecular.GeneratedPrecursor
        • cgexplore.molecular.LinearPrecursor
        • cgexplore.molecular.Precursor
        • cgexplore.molecular.PrecursorGenerator
        • cgexplore.molecular.Single
        • cgexplore.molecular.SixBead
        • cgexplore.molecular.SpindryConformer
        • cgexplore.molecular.SquarePrecursor
        • cgexplore.molecular.StericSevenBead
        • cgexplore.molecular.StericSixBead
        • cgexplore.molecular.StericTwoC1Arm
        • cgexplore.molecular.ThreeC0Arm
        • cgexplore.molecular.ThreeC1Arm
        • cgexplore.molecular.ThreeC2Arm
        • cgexplore.molecular.Timestep
        • cgexplore.molecular.TrianglePrecursor
        • cgexplore.molecular.TwoC0Arm
        • cgexplore.molecular.TwoC1Arm
        • cgexplore.molecular.TwoC2Arm
        • cgexplore.molecular.TwoC3Arm
        • cgexplore.molecular.VaBene
        • cgexplore.molecular.VaBeneGenerator
        • cgexplore.molecular.check_fit
        • cgexplore.molecular.periodic_table
        • cgexplore.molecular.spd_to_stk
        • cgexplore.molecular.string_to_atom_number
      • cgexplore.optimisation
        • cgexplore.optimisation.CGOMMDynamics
        • cgexplore.optimisation.CGOMMOptimizer
        • cgexplore.optimisation.CGOMMSinglePoint
        • cgexplore.optimisation.OMMTrajectory
      • cgexplore.scram
        • cgexplore.scram.Configuration
        • cgexplore.scram.ConfiguredCode
        • cgexplore.scram.TopologyCode
        • cgexplore.scram.TopologyIterator
        • cgexplore.scram.VertexAlignment
        • cgexplore.scram.get_bb_va_topology_code_graph
        • cgexplore.scram.get_regraphed_molecule
        • cgexplore.scram.get_stk_topology_code
        • cgexplore.scram.get_vertex_alignments
        • cgexplore.scram.get_vertexset_molecule
        • cgexplore.scram.graph_optimise_cage
        • cgexplore.scram.optimise_cage
        • cgexplore.scram.optimise_from_files
        • cgexplore.scram.passes_graph_bb_va_iso
        • cgexplore.scram.points_on_sphere
        • cgexplore.scram.target_optimisation
        • cgexplore.scram.try_except_construction
      • cgexplore.systems_optimisation
        • cgexplore.systems_optimisation.Chromosome
        • cgexplore.systems_optimisation.ChromosomeGenerator
        • cgexplore.systems_optimisation.FitnessCalculator
        • cgexplore.systems_optimisation.Generation
        • cgexplore.systems_optimisation.StructureCalculator
        • cgexplore.systems_optimisation.define_angle
        • cgexplore.systems_optimisation.define_bond
        • cgexplore.systems_optimisation.define_cosine_angle
        • cgexplore.systems_optimisation.define_lennardjones
        • cgexplore.systems_optimisation.define_nonbonded
        • cgexplore.systems_optimisation.define_pyramid_angle
        • cgexplore.systems_optimisation.define_torsion
        • cgexplore.systems_optimisation.element_from_type
        • cgexplore.systems_optimisation.get_forcefield_from_dict
        • cgexplore.systems_optimisation.get_neighbour_library
        • cgexplore.systems_optimisation.merge_definer_dicts
        • cgexplore.systems_optimisation.yield_near_models
      • cgexplore.terms
        • cgexplore.terms.Angle
        • cgexplore.terms.Bond
        • cgexplore.terms.CosineAngle
        • cgexplore.terms.FoundAngle
        • cgexplore.terms.FoundTorsion
        • cgexplore.terms.MartiniAngleRange
        • cgexplore.terms.MartiniBondRange
        • cgexplore.terms.MartiniTorsionRange
        • cgexplore.terms.Nonbonded
        • cgexplore.terms.PyramidAngleRange
        • cgexplore.terms.TargetAngle
        • cgexplore.terms.TargetAngleRange
        • cgexplore.terms.TargetBond
        • cgexplore.terms.TargetBondRange
        • cgexplore.terms.TargetCosineAngle
        • cgexplore.terms.TargetCosineAngleRange
        • cgexplore.terms.TargetMartiniAngle
        • cgexplore.terms.TargetMartiniBond
        • cgexplore.terms.TargetMartiniTorsion
        • cgexplore.terms.TargetNonbonded
        • cgexplore.terms.TargetNonbondedRange
        • cgexplore.terms.TargetPyramidAngle
        • cgexplore.terms.TargetTorsion
        • cgexplore.terms.TargetTorsionRange
        • cgexplore.terms.Torsion
        • cgexplore.terms.find_angles
        • cgexplore.terms.find_torsions
      • cgexplore.topologies
        • cgexplore.topologies.CGM12L24
        • cgexplore.topologies.CGM4L8
        • cgexplore.topologies.CustomTopology
        • cgexplore.topologies.M4L82
        • cgexplore.topologies.M6L122
        • cgexplore.topologies.M8L162
        • cgexplore.topologies.UnalignedM1L2
        • cgexplore.topologies.stoich_map
      • cgexplore.utilities
        • cgexplore.utilities.AtomliteDatabase
        • cgexplore.utilities.Pymol
        • cgexplore.utilities.add_structure_to_ax
        • cgexplore.utilities.add_text_to_ax
        • cgexplore.utilities.check_directory
        • cgexplore.utilities.convert_pyramid_angle
        • cgexplore.utilities.draw_pie
        • cgexplore.utilities.extract_property
        • cgexplore.utilities.get_energy_per_bb
        • cgexplore.utilities.get_supramolecule
        • cgexplore.utilities.get_unforced_supramolecule
        • cgexplore.utilities.optimise_ligand
        • cgexplore.utilities.rattle
        • cgexplore.utilities.rmsd_checker
        • cgexplore.utilities.run_constrained_optimisation
        • cgexplore.utilities.run_optimisation
        • cgexplore.utilities.run_soft_md_cycle
        • cgexplore.utilities.shift_beads
        • cgexplore.utilities.soften_forcefield
        • cgexplore.utilities.write_chemiscope_json
        • cgexplore.utilities.yield_near_models
        • cgexplore.utilities.yield_shifted_models
        • cgexplore.utilities.ForceFieldUnavailableError
        • cgexplore.utilities.ForceFieldUnitError
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AtomisticΒΆ

A package of the classes for handling atomistic systems in cgexplore.

  • atomistic module

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