Index

_

__getitem__() (mchem.system.System method) __init__() (mchem.element.Element method) (mchem.forcefield.base.AtomType method) (mchem.forcefield.base.ForceField method) (mchem.forcefield.base.Generator method) (mchem.forcefield.generators.AmoebaAngleGenerator method) (mchem.forcefield.generators.AmoebaBondGenerator method) (mchem.forcefield.generators.AmoebaOutOfPlaneBendGenerator method) (mchem.forcefield.generators.AmoebaPiTorsionGenerator method) (mchem.forcefield.generators.AmoebaStretchBendGenerator method) (mchem.forcefield.generators.AmoebaTorsionTorsionGenerator method) (mchem.forcefield.generators.AmoebaUreyBradleyGenerator method) (mchem.forcefield.generators.AmoebaVdwGenerator method) (mchem.forcefield.generators.AnisotropicPolarizationGenerator method) (mchem.forcefield.generators.IsotropicPolarizationGenerator method) (mchem.forcefield.generators.MBUCBChargePenetrationGenerator method) (mchem.forcefield.generators.MBUCBChargeTransferGenerator method) (mchem.forcefield.generators.MultipoleGenerator method) (mchem.forcefield.generators.PeriodicTorsionGenerator method) (mchem.system.Box method) (mchem.system.System method) (mchem.template.ResidueTemplate method) (mchem.terms.base.TermList method) (mchem.terms.bonded.AmoebaAngle method) (mchem.terms.bonded.AmoebaAngleInPlane method) (mchem.terms.bonded.AmoebaAngleTorsion method) (mchem.terms.bonded.AmoebaBond method) (mchem.terms.bonded.AmoebaOutOfPlaneBend method) (mchem.terms.bonded.AmoebaPiTorsion method) (mchem.terms.bonded.AmoebaStretchBend method) (mchem.terms.bonded.AmoebaStretchTorsion method) (mchem.terms.bonded.AmoebaTorsionTorsion method) (mchem.terms.bonded.AmoebaTorsionTorsionGrid method) (mchem.terms.bonded.AmoebaUreyBradley method) (mchem.terms.bonded.CMAP method) (mchem.terms.bonded.CMAPTable method) (mchem.terms.bonded.HarmonicAngle method) (mchem.terms.bonded.HarmonicBond method) (mchem.terms.bonded.PeriodicTorsion method) (mchem.terms.nonbonded.AmoebaVdw147 method) (mchem.terms.nonbonded.AnisotropicPolarization method) (mchem.terms.nonbonded.IsotropicPolarization method) (mchem.terms.nonbonded.MBUCBChargePenetration method) (mchem.terms.nonbonded.MBUCBChargeTransfer method) (mchem.terms.nonbonded.Multipole method) (mchem.terms.nonbonded.PairList method) (mchem.terms.nonbonded.Particle method) (mchem.topology.Atom method) (mchem.topology.Bond method) (mchem.topology.BondedAtoms method) (mchem.topology.Residue method) (mchem.topology.Topology method)

A

a (mchem.system.Box attribute) addAngle() (mchem.forcefield.generators.AmoebaAngleGenerator method) addAtom() (mchem.topology.Residue method) addAtomToResidue() (mchem.topology.Topology method) addAtomType() (mchem.forcefield.base.ForceField method) addBond() (mchem.forcefield.generators.AmoebaBondGenerator method) (mchem.topology.Atom method) (mchem.topology.Topology method) addGenerator() (mchem.forcefield.base.ForceField method) addGeneratorWithClass() (mchem.forcefield.base.ForceField method) addMeta() (mchem.system.System method) addMultipole() (mchem.forcefield.generators.MultipoleGenerator method) addOutofPlaneBend() (mchem.forcefield.generators.AmoebaOutOfPlaneBendGenerator method) addParameterField() (mchem.forcefield.base.Generator method) addParameterWithAtomTypes() (mchem.forcefield.base.Generator method) addParameterWithSmirks() (mchem.forcefield.base.Generator method) addPiTorsion() (mchem.forcefield.generators.AmoebaPiTorsionGenerator method) addPolarize() (mchem.forcefield.generators.AnisotropicPolarizationGenerator method) (mchem.forcefield.generators.IsotropicPolarizationGenerator method) addProperTorsion() (mchem.forcefield.generators.PeriodicTorsionGenerator method) addResidue() (mchem.topology.Topology method) addTerm() (mchem.forcefield.generators.MBUCBChargePenetrationGenerator method) (mchem.forcefield.generators.MBUCBChargeTransferGenerator method) (mchem.system.System method) addTerms() (mchem.system.System method) addToPolarizationGroup() (mchem.topology.Atom method) addUreyBrad() (mchem.forcefield.generators.AmoebaUreyBradleyGenerator method) addVdw() (mchem.forcefield.generators.AmoebaVdwGenerator method) alpha (mchem.system.Box attribute) (mchem.terms.nonbonded.IsotropicPolarization attribute) (mchem.terms.nonbonded.MBUCBChargePenetration attribute) (mchem.terms.nonbonded.MBUCBChargeTransfer attribute) alphaxx (mchem.terms.nonbonded.AnisotropicPolarization attribute) alphaxy (mchem.terms.nonbonded.AnisotropicPolarization attribute) alphaxz (mchem.terms.nonbonded.AnisotropicPolarization attribute) alphayy (mchem.terms.nonbonded.AnisotropicPolarization attribute) alphayz (mchem.terms.nonbonded.AnisotropicPolarization attribute) alphazz (mchem.terms.nonbonded.AnisotropicPolarization attribute)

AmoebaAngle (class in mchem.terms.bonded) AmoebaAngleGenerator (class in mchem.forcefield.generators) AmoebaAngleInPlane (class in mchem.terms.bonded) AmoebaAngleTorsion (class in mchem.terms.bonded) AmoebaBond (class in mchem.terms.bonded) AmoebaBondGenerator (class in mchem.forcefield.generators) AmoebaOutOfPlaneBend (class in mchem.terms.bonded) AmoebaOutOfPlaneBendGenerator (class in mchem.forcefield.generators) AmoebaPiTorsion (class in mchem.terms.bonded) AmoebaPiTorsionGenerator (class in mchem.forcefield.generators) AmoebaStretchBend (class in mchem.terms.bonded) AmoebaStretchBendGenerator (class in mchem.forcefield.generators) AmoebaStretchTorsion (class in mchem.terms.bonded) AmoebaTorsionTorsion (class in mchem.terms.bonded) AmoebaTorsionTorsionGenerator (class in mchem.forcefield.generators) AmoebaTorsionTorsionGrid (class in mchem.terms.bonded) AmoebaUreyBradley (class in mchem.terms.bonded) AmoebaUreyBradleyGenerator (class in mchem.forcefield.generators) AmoebaVdw147 (class in mchem.terms.nonbonded) AmoebaVdwGenerator (class in mchem.forcefield.generators) angle1 (mchem.terms.bonded.AmoebaTorsionTorsionGrid attribute) angle2 (mchem.terms.bonded.AmoebaTorsionTorsionGrid attribute) AnisotropicPolarization (class in mchem.terms.nonbonded) AnisotropicPolarizationGenerator (class in mchem.forcefield.generators) append() (mchem.terms.base.TermList method) assignAtomTypes() (mchem.forcefield.base.ForceField method) assignIndex() (mchem.topology.Topology method) Atom (class in mchem.topology) atomClass (mchem.forcefield.base.AtomType attribute) (mchem.topology.Atom property) atomClasses (mchem.forcefield.base.ForceField attribute) atomicNum (mchem.element.Element attribute), [1] (mchem.topology.Atom property) atoms (mchem.topology.Residue property) atoms() (mchem.topology.Topology method) AtomType (class in mchem.forcefield.base) atomType (mchem.topology.Atom property) atomTypes (mchem.forcefield.base.ForceField attribute) axistype (mchem.terms.nonbonded.Multipole attribute)

B

b (mchem.system.Box attribute) (mchem.terms.nonbonded.MBUCBChargeTransfer attribute) b0 (mchem.terms.bonded.AmoebaBond attribute) (mchem.terms.bonded.HarmonicBond attribute) b01 (mchem.terms.bonded.AmoebaStretchBend attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) b02 (mchem.terms.bonded.AmoebaStretchBend attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) b03 (mchem.terms.bonded.AmoebaStretchTorsion attribute) beta (mchem.system.Box attribute) (mchem.terms.nonbonded.MBUCBChargePenetration attribute)

Bisector (mchem.terms.nonbonded.MultipoleAxisType attribute) Bond (class in mchem.topology) BondedAtoms (class in mchem.topology) bondedAtoms (mchem.topology.Atom property) (mchem.topology.Topology property) bonds (mchem.topology.Atom property) (mchem.topology.Topology property) Box (class in mchem.system) BoxShape (in module mchem.solvate)

C

c (mchem.system.Box attribute) c0 (mchem.terms.nonbonded.Multipole attribute) checkParameter() (mchem.forcefield.base.Generator method) close() (mchem.system.System method) cls (mchem.terms.base.TermList property) CMAP (class in mchem.terms.bonded) cmap (mchem.terms.bonded.CMAP attribute) CMAPTable (class in mchem.terms.bonded) connTable (mchem.topology.Topology property) coordinates (mchem.topology.Topology property) createSystem() (mchem.forcefield.base.ForceField method) createTerms() (mchem.forcefield.base.Generator method) (mchem.forcefield.generators.AmoebaAngleGenerator method) (mchem.forcefield.generators.AmoebaBondGenerator method) (mchem.forcefield.generators.AmoebaOutOfPlaneBendGenerator method) (mchem.forcefield.generators.AmoebaPiTorsionGenerator method) (mchem.forcefield.generators.AmoebaStretchBendGenerator method) (mchem.forcefield.generators.AmoebaTorsionTorsionGenerator method) (mchem.forcefield.generators.AmoebaUreyBradleyGenerator method) (mchem.forcefield.generators.AmoebaVdwGenerator method) (mchem.forcefield.generators.AnisotropicPolarizationGenerator method) (mchem.forcefield.generators.IsotropicPolarizationGenerator method) (mchem.forcefield.generators.MBUCBChargePenetrationGenerator method) (mchem.forcefield.generators.MBUCBChargeTransferGenerator method) (mchem.forcefield.generators.MultipoleGenerator method) (mchem.forcefield.generators.PeriodicTorsionGenerator method)

cubic (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) (mchem.terms.bonded.AmoebaBond attribute)

D

d (mchem.terms.nonbonded.MBUCBChargeTransfer attribute) data (mchem.system.System property)

dx (mchem.terms.nonbonded.Multipole attribute) dy (mchem.terms.nonbonded.Multipole attribute) dz (mchem.terms.nonbonded.Multipole attribute)

E

editable (mchem.topology.Topology property) Element (class in mchem.element) element (mchem.terms.nonbonded.Particle attribute) ene (mchem.terms.bonded.CMAPTable attribute) energy() (mchem.terms.nonbonded.PairList method) epsilon (mchem.terms.nonbonded.AmoebaVdw147 attribute) exportAtomTypeDefs() (mchem.forcefield.base.ForceField method)

exportAtomTypes() (mchem.forcefield.base.ForceField method) exportParameterToStr() (mchem.forcefield.base.Generator method) (mchem.forcefield.generators.AmoebaVdwGenerator method) (mchem.forcefield.generators.AnisotropicPolarizationGenerator method) (mchem.forcefield.generators.MBUCBChargePenetrationGenerator method) (mchem.forcefield.generators.MBUCBChargeTransferGenerator method) (mchem.forcefield.generators.MultipoleGenerator method) extend() (mchem.topology.BondedAtoms method)

F

f (mchem.terms.bonded.AmoebaTorsionTorsionGrid attribute) fc (mchem.terms.bonded.AmoebaOutOfPlaneBend attribute) (mchem.terms.bonded.AmoebaUreyBradley attribute) findAtomTypes() (mchem.forcefield.base.ForceField method)

float2str() (in module mchem.forcefield.base) ForceField (class in mchem.forcefield.base) fromDatabase() (mchem.system.System method) fromXMLData() (mchem.template.ResidueTemplate class method)

G

gamma (mchem.system.Box attribute) generateNeighbors() (mchem.topology.Atom method) generateTopologicalInfo() (mchem.topology.Atom method) (mchem.topology.Topology method) Generator (class in mchem.forcefield.base) generators (mchem.forcefield.base.ForceField property) getAtomType() (mchem.template.ResidueTemplate method) getAtomWithIdx() (mchem.topology.Topology method) getAtomWithName() (mchem.topology.Residue method) getGeneratorWithClass() (mchem.forcefield.base.ForceField method) getHighOrderNeighbors() (mchem.topology.Atom method) getMetadata() (mchem.forcefield.base.Generator method) getNeighbors() (mchem.topology.Atom method) getParameterIdxWithAtomType() (mchem.forcefield.base.Generator method)

getParameterIdxWithSmirks() (mchem.forcefield.base.Generator method) getParameters() (mchem.forcefield.base.ForceField method) (mchem.forcefield.base.Generator method) getParameterWithAtomType() (mchem.forcefield.base.Generator method) getParameterWithIdx() (mchem.forcefield.base.Generator method) getParameterWithSmirks() (mchem.forcefield.base.Generator method) getResidueWithIdx() (mchem.topology.Topology method) getTableNames() (mchem.system.System method) getTermsByName() (mchem.system.System method) getTopologicalInfo() (mchem.topology.Atom method) gridIdx (mchem.terms.bonded.AmoebaTorsionTorsion attribute) (mchem.terms.bonded.AmoebaTorsionTorsionGrid attribute) grp (mchem.terms.nonbonded.AnisotropicPolarization attribute) (mchem.terms.nonbonded.IsotropicPolarization attribute)

H

HarmonicAngle (class in mchem.terms.bonded) HarmonicBond (class in mchem.terms.bonded) hasResidue() (mchem.topology.Atom method)

hasTopology() (mchem.topology.Atom method) (mchem.topology.Bond method) (mchem.topology.Residue method)

I

idx (mchem.terms.nonbonded.AmoebaVdw147 attribute) (mchem.terms.nonbonded.AnisotropicPolarization attribute) (mchem.terms.nonbonded.IsotropicPolarization attribute) (mchem.terms.nonbonded.MBUCBChargePenetration attribute) (mchem.terms.nonbonded.MBUCBChargeTransfer attribute) (mchem.terms.nonbonded.Multipole attribute) (mchem.terms.nonbonded.Particle attribute) (mchem.topology.Atom property) (mchem.topology.Residue property)

insertResidue() (mchem.topology.Topology method) IsotropicPolarization (class in mchem.terms.nonbonded) IsotropicPolarizationGenerator (class in mchem.forcefield.generators)

K

k (mchem.terms.bonded.AmoebaPiTorsion attribute) k1 (mchem.terms.bonded.PeriodicTorsion attribute) k11 (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) k12 (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) k13 (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) k2 (mchem.terms.bonded.PeriodicTorsion attribute) k21 (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) k22 (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) k23 (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) k3 (mchem.terms.bonded.PeriodicTorsion attribute)

k31 (mchem.terms.bonded.AmoebaStretchTorsion attribute) k32 (mchem.terms.bonded.AmoebaStretchTorsion attribute) k33 (mchem.terms.bonded.AmoebaStretchTorsion attribute) k4 (mchem.terms.bonded.PeriodicTorsion attribute) k5 (mchem.terms.bonded.PeriodicTorsion attribute) k6 (mchem.terms.bonded.PeriodicTorsion attribute) kb (mchem.terms.bonded.AmoebaBond attribute) (mchem.terms.bonded.HarmonicBond attribute) kb1 (mchem.terms.bonded.AmoebaStretchBend attribute) kb2 (mchem.terms.bonded.AmoebaStretchBend attribute) kth (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) (mchem.terms.bonded.HarmonicAngle attribute) kx (mchem.terms.nonbonded.Multipole attribute) ky (mchem.terms.nonbonded.Multipole attribute) kz (mchem.terms.nonbonded.Multipole attribute)

L

LastAxisTypeIndex (mchem.terms.nonbonded.MultipoleAxisType attribute) load_pdb() (in module mchem.fileformats.pdb) loadAtomTypeDefs() (mchem.forcefield.base.ForceField method)

loadAtomTypes() (mchem.forcefield.base.ForceField method) loadForces() (mchem.forcefield.base.ForceField method) loadTemplateDefinitions() (in module mchem.template)

M

mass (mchem.element.Element attribute), [1] (mchem.terms.nonbonded.Particle attribute) (mchem.topology.Atom property) matchTemplate() (mchem.topology.Residue method) matchTemplates() (mchem.topology.Topology method) MBUCBChargePenetration (class in mchem.terms.nonbonded) MBUCBChargePenetrationGenerator (class in mchem.forcefield.generators) MBUCBChargeTransfer (class in mchem.terms.nonbonded) MBUCBChargeTransferGenerator (class in mchem.forcefield.generators) mchem.element module mchem.fileformats module mchem.fileformats.pdb module mchem.forcefield module mchem.forcefield.base module mchem.forcefield.generators module mchem.main module mchem.solvate module mchem.system module mchem.template module mchem.terms module

mchem.terms.base module mchem.terms.bonded module mchem.terms.nonbonded module mchem.topology module mchem.units module meta (mchem.system.System property) module mchem.element mchem.fileformats mchem.fileformats.pdb mchem.forcefield mchem.forcefield.base mchem.forcefield.generators mchem.main mchem.solvate mchem.system mchem.template mchem.terms mchem.terms.base mchem.terms.bonded mchem.terms.nonbonded mchem.topology mchem.units Multipole (class in mchem.terms.nonbonded) MultipoleAxisType (class in mchem.terms.nonbonded) MultipoleGenerator (class in mchem.forcefield.generators)

N

name (mchem.element.Element attribute), [1] (mchem.forcefield.base.AtomType attribute) (mchem.terms.nonbonded.Particle attribute) (mchem.topology.Atom property) (mchem.topology.Residue property) NoAxisType (mchem.terms.nonbonded.MultipoleAxisType attribute)

numAtoms (mchem.topology.Residue property) (mchem.topology.Topology property) numBonds (mchem.topology.Topology property) numParameters (mchem.forcefield.base.Generator property) numResidues (mchem.topology.Topology property) nx (mchem.terms.bonded.AmoebaTorsionTorsion attribute) ny (mchem.terms.bonded.AmoebaTorsionTorsion attribute)

P

p0 (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaBond attribute) (mchem.terms.bonded.AmoebaOutOfPlaneBend attribute) (mchem.terms.bonded.AmoebaPiTorsion attribute) (mchem.terms.bonded.AmoebaStretchBend attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) (mchem.terms.bonded.AmoebaTorsionTorsion attribute) (mchem.terms.bonded.AmoebaUreyBradley attribute) (mchem.terms.bonded.CMAP attribute) (mchem.terms.bonded.HarmonicAngle attribute) (mchem.terms.bonded.HarmonicBond attribute) (mchem.terms.bonded.PeriodicTorsion attribute) (mchem.terms.nonbonded.PairList attribute) p1 (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaBond attribute) (mchem.terms.bonded.AmoebaOutOfPlaneBend attribute) (mchem.terms.bonded.AmoebaPiTorsion attribute) (mchem.terms.bonded.AmoebaStretchBend attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) (mchem.terms.bonded.AmoebaTorsionTorsion attribute) (mchem.terms.bonded.AmoebaUreyBradley attribute) (mchem.terms.bonded.CMAP attribute) (mchem.terms.bonded.HarmonicAngle attribute) (mchem.terms.bonded.HarmonicBond attribute) (mchem.terms.bonded.PeriodicTorsion attribute) (mchem.terms.nonbonded.PairList attribute) p2 (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaOutOfPlaneBend attribute) (mchem.terms.bonded.AmoebaPiTorsion attribute) (mchem.terms.bonded.AmoebaStretchBend attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) (mchem.terms.bonded.AmoebaTorsionTorsion attribute) (mchem.terms.bonded.AmoebaUreyBradley attribute) (mchem.terms.bonded.CMAP attribute) (mchem.terms.bonded.HarmonicAngle attribute) (mchem.terms.bonded.PeriodicTorsion attribute) p3 (mchem.terms.bonded.AmoebaAngleInPlane attribute) (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaOutOfPlaneBend attribute) (mchem.terms.bonded.AmoebaPiTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) (mchem.terms.bonded.AmoebaTorsionTorsion attribute) (mchem.terms.bonded.CMAP attribute) (mchem.terms.bonded.PeriodicTorsion attribute) p4 (mchem.terms.bonded.AmoebaPiTorsion attribute) (mchem.terms.bonded.AmoebaTorsionTorsion attribute) (mchem.terms.bonded.CMAP attribute) p5 (mchem.terms.bonded.AmoebaPiTorsion attribute) (mchem.terms.bonded.CMAP attribute) p6 (mchem.terms.bonded.CMAP attribute) p7 (mchem.terms.bonded.CMAP attribute) PairList (class in mchem.terms.nonbonded) parametrized (mchem.topology.Atom property)

paramFields (mchem.forcefield.base.Generator property) paramIdx (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaBond attribute) (mchem.terms.bonded.AmoebaOutOfPlaneBend attribute) (mchem.terms.bonded.AmoebaPiTorsion attribute) (mchem.terms.bonded.AmoebaStretchBend attribute) (mchem.terms.bonded.AmoebaUreyBradley attribute) (mchem.terms.bonded.CMAPTable attribute) (mchem.terms.bonded.HarmonicAngle attribute) (mchem.terms.bonded.HarmonicBond attribute) (mchem.terms.bonded.PeriodicTorsion attribute) (mchem.terms.nonbonded.AmoebaVdw147 attribute) (mchem.terms.nonbonded.AnisotropicPolarization attribute) (mchem.terms.nonbonded.IsotropicPolarization attribute) (mchem.terms.nonbonded.MBUCBChargePenetration attribute) (mchem.terms.nonbonded.MBUCBChargeTransfer attribute) (mchem.terms.nonbonded.Multipole attribute) parentIdx (mchem.terms.nonbonded.AmoebaVdw147 attribute) parseElement() (mchem.forcefield.generators.AmoebaAngleGenerator static method) (mchem.forcefield.generators.AmoebaBondGenerator static method) (mchem.forcefield.generators.AmoebaOutOfPlaneBendGenerator static method) (mchem.forcefield.generators.AmoebaPiTorsionGenerator static method) (mchem.forcefield.generators.AmoebaStretchBendGenerator static method) (mchem.forcefield.generators.AmoebaTorsionTorsionGenerator static method) (mchem.forcefield.generators.AmoebaUreyBradleyGenerator static method) (mchem.forcefield.generators.AmoebaVdwGenerator static method) (mchem.forcefield.generators.AnisotropicPolarizationGenerator static method) (mchem.forcefield.generators.IsotropicPolarizationGenerator static method) (mchem.forcefield.generators.MBUCBChargePenetrationGenerator static method) (mchem.forcefield.generators.MBUCBChargeTransferGenerator static method) (mchem.forcefield.generators.MultipoleGenerator static method) (mchem.forcefield.generators.PeriodicTorsionGenerator static method) Particle (class in mchem.terms.nonbonded) pathsToBondedAtoms (mchem.topology.Atom property) pentic (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) PeriodicTorsion (class in mchem.terms.bonded) PeriodicTorsionGenerator (class in mchem.forcefield.generators) phase1 (mchem.terms.bonded.PeriodicTorsion attribute) phase2 (mchem.terms.bonded.PeriodicTorsion attribute) phase3 (mchem.terms.bonded.PeriodicTorsion attribute) phase4 (mchem.terms.bonded.PeriodicTorsion attribute) phase5 (mchem.terms.bonded.PeriodicTorsion attribute) phase6 (mchem.terms.bonded.PeriodicTorsion attribute) phi (mchem.terms.bonded.CMAPTable attribute) phi01 (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) phi02 (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) phi03 (mchem.terms.bonded.AmoebaAngleTorsion attribute) (mchem.terms.bonded.AmoebaStretchTorsion attribute) polarizationGroup (mchem.topology.Atom property) processDisulfideBond() (mchem.topology.Topology method) processFileNames() (mchem.forcefield.base.ForceField method) pruneBonds() (mchem.topology.Atom method) (mchem.topology.Topology method) psi (mchem.terms.bonded.CMAPTable attribute)

Q

quartic (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) (mchem.terms.bonded.AmoebaBond attribute) qxx (mchem.terms.nonbonded.Multipole attribute)

qxy (mchem.terms.nonbonded.Multipole attribute) qxz (mchem.terms.nonbonded.Multipole attribute) qyy (mchem.terms.nonbonded.Multipole attribute) qyz (mchem.terms.nonbonded.Multipole attribute) qzz (mchem.terms.nonbonded.Multipole attribute)

R

r0 (mchem.terms.bonded.AmoebaUreyBradley attribute) raise_exception() (mchem.forcefield.base.Generator method) read_pdb_box() (in module mchem.fileformats.pdb) reduction (mchem.terms.nonbonded.AmoebaVdw147 attribute) register_term_class() (in module mchem.system) removeAtom() (mchem.topology.Residue method) removeResidue() (mchem.topology.Topology method)

require_editable() (in module mchem.topology) require_noneditable() (in module mchem.topology) Residue (class in mchem.topology) residue (mchem.topology.Atom property) residues (mchem.topology.Topology property) ResidueTemplate (class in mchem.template) resname (mchem.terms.nonbonded.Particle attribute) resnum (mchem.terms.nonbonded.Particle attribute)

S

save() (mchem.forcefield.base.ForceField method) (mchem.system.System method) setAtomClass() (mchem.topology.Atom method) setAtomType() (mchem.template.ResidueTemplate method) (mchem.topology.Atom method) setAxisType() (mchem.forcefield.generators.MultipoleGenerator static method) setEditable() (mchem.topology.Topology method) setIdx() (mchem.topology.Atom method) (mchem.topology.Residue method) setMetadata() (mchem.forcefield.base.Generator method) setName() (mchem.topology.Atom method) (mchem.topology.Residue method) setParameterWithIdx() (mchem.forcefield.base.Generator method) setPolarizationGroup() (mchem.forcefield.generators.AnisotropicPolarizationGenerator method) (mchem.forcefield.generators.IsotropicPolarizationGenerator method) (mchem.topology.Atom method)

setPosition() (mchem.topology.Atom method) setResidue() (mchem.topology.Atom method) setStdName() (mchem.topology.Residue method) setTopology() (mchem.topology.Residue method) sextic (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) sigma (mchem.terms.nonbonded.AmoebaVdw147 attribute) solvate() (in module mchem.solvate) stdName (mchem.topology.Residue property) str2bool() (in module mchem.forcefield.base) str2float() (in module mchem.forcefield.base) str2int() (in module mchem.forcefield.base) symbol (mchem.element.Element attribute), [1] (mchem.topology.Atom property) System (class in mchem.system)

T

TermList (class in mchem.terms.base) th0 (mchem.terms.bonded.AmoebaAngle attribute) (mchem.terms.bonded.AmoebaAngleInPlane attribute) (mchem.terms.bonded.AmoebaStretchBend attribute) (mchem.terms.bonded.HarmonicAngle attribute) th01 (mchem.terms.bonded.AmoebaAngleTorsion attribute)

th02 (mchem.terms.bonded.AmoebaAngleTorsion attribute) thole (mchem.terms.nonbonded.AnisotropicPolarization attribute) (mchem.terms.nonbonded.IsotropicPolarization attribute) ThreeFold (mchem.terms.nonbonded.MultipoleAxisType attribute) Topology (class in mchem.topology) topology (mchem.topology.Atom property) (mchem.topology.Residue property)

U

updateParameters() (mchem.forcefield.base.ForceField method) (mchem.forcefield.base.Generator method)

V

vx (mchem.terms.nonbonded.Particle attribute)

vy (mchem.terms.nonbonded.Particle attribute) vz (mchem.terms.nonbonded.Particle attribute)

W

write_pdb() (in module mchem.fileformats.pdb)

X

xmlele2str() (in module mchem.forcefield.base) xx (mchem.terms.nonbonded.Particle attribute)

xy (mchem.terms.nonbonded.Particle attribute) xz (mchem.terms.nonbonded.Particle attribute)

Z

z (mchem.terms.nonbonded.MBUCBChargePenetration attribute) ZBisect (mchem.terms.nonbonded.MultipoleAxisType attribute)

ZOnly (mchem.terms.nonbonded.MultipoleAxisType attribute) ZThenX (mchem.terms.nonbonded.MultipoleAxisType attribute)