Index

_

__init__() (hps.core.models method) (hps.core.system method) (hps.dynamics.Dynamics method)

_constructHeaders() (hps.reporter.hps_reporter.hpsReporter method), [1] _constructReportValues() (hps.reporter.hps_reporter.hpsReporter method), [1] _setParameters() (hps.core.system static method) (hps.core.system.system static method)

A

add_Wang_Frenkel_Forces() (hps.core.system.system method) addAshbaughHatchForces() (hps.core.system method) (hps.core.system.system method) addGaussianAngleForces() (hps.core.system.system method) addGaussianTorsionForces() (hps.core.system.system method) addHarmonicBondForces() (hps.core.system.system method) addParticles() (hps.core.system method) (hps.core.system.system method)

addSystemForces() (hps.core.system method) (hps.core.system.system method) addYukawaForces() (hps.core.system method) (hps.core.system.system method) ashbaugh_HatchForce (hps.core.system attribute) (hps.core.system.system attribute) atoms (hps.core.system attribute) (hps.core.system.system attribute)

B

bond() (hps.core.geometry.geometry static method) bonded_exclusions_index (hps.core.system attribute) (hps.core.system.system attribute) bonds (hps.core.system attribute) (hps.core.system.system attribute)

bonds_indexes (hps.core.system attribute) (hps.core.system.system attribute) box_dimension (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) buildHPSModel() (hps.core.models static method) (hps.core.models.models static method)

C

checkBondDistances() (hps.core.system method) (hps.core.system.system method) checkLargeForces() (hps.core.system method) (hps.core.system.system method)

checkpoint (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) createSystemObject() (hps.core.system method) (hps.core.system.system method)

D

device (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) dt (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) dumpForceFieldData() (hps.core.system method) (hps.core.system.system method)

dumpStructure() (hps.core.system method) (hps.core.system.system method) dumpTopology() (hps.core.system method) (hps.core.system.system method) Dynamics (class in hps.dynamics) (class in hps.dynamics.dynamics)

F

forceGroups (hps.core.system attribute) (hps.core.system.system attribute)

frequency_p (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute)

G

gaussianAngleForce (hps.core.system attribute) (hps.core.system.system attribute) gaussianTorsionForce (hps.core.system attribute) (hps.core.system.system attribute) geometry (class in hps.core.geometry) getAngles() (hps.core.system.system method)

getAtoms() (hps.core.system method) (hps.core.system.system method) getBonds() (hps.core.system method) (hps.core.system.system method) getCAlphaOnly() (hps.core.system.system method) getTorsions() (hps.core.system.system method)

H

harmonicBondForce (hps.core.system attribute) (hps.core.system.system attribute) hps module hps.core module hps.core.geometry module hps.core.models module hps.core.system module

hps.dynamics module hps.dynamics.dynamics module hps.parameters module hps.parameters.model_parameters module, [1] hps.reporter module, [1] hps.reporter.hps_reporter module, [1] hpsReporter (class in hps.reporter.hps_reporter), [1]

L

loadForcefieldFromFile() (hps.core.system method) (hps.core.system.system method)

M

md_steps (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) minimize (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) model (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) models (class in hps.core) (class in hps.core.models) module hps hps.core hps.core.geometry hps.core.models hps.core.system hps.dynamics hps.dynamics.dynamics hps.parameters hps.parameters.model_parameters, [1] hps.reporter, [1] hps.reporter.hps_reporter, [1]

N

n_angles (hps.core.system attribute) (hps.core.system.system attribute) n_atoms (hps.core.system attribute) (hps.core.system.system attribute) n_bonds (hps.core.system attribute) (hps.core.system.system attribute) n_torsions (hps.core.system attribute) (hps.core.system.system attribute)

nstcomm (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) nstlog (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) nstxout (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute)

P

parameters (in module hps.parameters.model_parameters), [1], [2] pbc (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) pcoupl (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) pdb_file (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute)

position2Array() (hps.core.geometry.geometry static method) ppn (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) protein_code (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute)

R

read_config() (hps.dynamics.Dynamics method) (hps.dynamics.dynamics.Dynamics method) readOpenMMReporterFile() (in module hps.reporter.hps_reporter), [1] ref_p (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) ref_t (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute)

restart (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) rf_sigma (hps.core.system attribute) (hps.core.system.system attribute) run() (hps.dynamics.dynamics.Dynamics method)

S

setBondForceConstants() (hps.core.system method) (hps.core.system.system method) setCAChargePerResidueType() (hps.core.system method) (hps.core.system.system method) setCAHPSPerResidueType() (hps.core.system method) (hps.core.system.system method) setCAIDPerResidueType() (hps.core.system.system method) setCAMassPerResidueType() (hps.core.system method) (hps.core.system.system method) setCARadiusPerResidueType() (hps.core.system method) (hps.core.system.system method) setParticlesCharge() (hps.core.system method) (hps.core.system.system method)

setParticlesHPS() (hps.core.system method) (hps.core.system.system method) setParticlesMass() (hps.core.system.system method) setParticlesRadii() (hps.core.system method) (hps.core.system.system method) setParticleTypeID() (hps.core.system.system method) structure (hps.core.system attribute) (hps.core.system.system attribute) system (class in hps.core) (class in hps.core.system) (hps.core.system attribute) (hps.core.system.system attribute)

T

tau_t (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute) tcoupl (hps.dynamics.Dynamics attribute) (hps.dynamics.dynamics.Dynamics attribute)

topology (hps.core.system attribute) (hps.core.system.system attribute)

Y

yukawaForce (hps.core.system attribute) (hps.core.system.system attribute)