Index

_

_abc_impl (ligandparam.stages.abstractstage.AbstractStage attribute) (ligandparam.stages.build_system.StageBuild attribute) (ligandparam.stages.charge.StageNormalizeCharge attribute) (ligandparam.stages.charge.StageUpdateCharge attribute) (ligandparam.stages.gaussian.StageGaussian attribute) (ligandparam.stages.gaussian.StageGaussianRotation attribute) (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute) (ligandparam.stages.initialize.StageInitialize attribute) (ligandparam.stages.leap.StageLeap attribute) (ligandparam.stages.parmchk.StageParmChk attribute) (ligandparam.stages.resp.StageLazyResp attribute) (ligandparam.stages.resp.StageMultiRespFit attribute) (ligandparam.stages.teststage.TestStage attribute) (ligandparam.stages.typematching.StageUpdate attribute) _add_output() (ligandparam.stages.abstractstage.AbstractStage method) _add_required() (ligandparam.stages.abstractstage.AbstractStage method) _append_stage() (ligandparam.stages.abstractstage.AbstractStage method) (ligandparam.stages.build_system.StageBuild method) (ligandparam.stages.charge.StageNormalizeCharge method) (ligandparam.stages.charge.StageUpdateCharge method) (ligandparam.stages.gaussian.StageGaussian method) (ligandparam.stages.gaussian.StageGaussianRotation method) (ligandparam.stages.gaussian.StageGaussiantoMol2 method) (ligandparam.stages.initialize.StageInitialize method) (ligandparam.stages.leap.StageLeap method) (ligandparam.stages.parmchk.StageParmChk method) (ligandparam.stages.resp.StageLazyResp method) (ligandparam.stages.resp.StageMultiRespFit method) (ligandparam.stages.teststage.TestStage method) (ligandparam.stages.typematching.StageUpdate method) _aq_build() (ligandparam.stages.build_system.StageBuild method) _check_required() (ligandparam.stages.abstractstage.AbstractStage method) _check_self() (ligandparam.stages.abstractstage.AbstractStage method)

_clean() (ligandparam.stages.abstractstage.AbstractStage method) (ligandparam.stages.build_system.StageBuild method) (ligandparam.stages.charge.StageNormalizeCharge method) (ligandparam.stages.charge.StageUpdateCharge method) (ligandparam.stages.gaussian.StageGaussian method) (ligandparam.stages.gaussian.StageGaussianRotation method) (ligandparam.stages.gaussian.StageGaussiantoMol2 method) (ligandparam.stages.initialize.StageInitialize method) (ligandparam.stages.leap.StageLeap method) (ligandparam.stages.parmchk.StageParmChk method) (ligandparam.stages.resp.StageLazyResp method) (ligandparam.stages.resp.StageMultiRespFit method) (ligandparam.stages.teststage.TestStage method) (ligandparam.stages.typematching.StageUpdate method) _execute() (ligandparam.stages.abstractstage.AbstractStage method) (ligandparam.stages.build_system.StageBuild method) (ligandparam.stages.charge.StageNormalizeCharge method) (ligandparam.stages.charge.StageUpdateCharge method) (ligandparam.stages.gaussian.StageGaussian method) (ligandparam.stages.gaussian.StageGaussianRotation method) (ligandparam.stages.gaussian.StageGaussiantoMol2 method) (ligandparam.stages.initialize.StageInitialize method) (ligandparam.stages.leap.StageLeap method) (ligandparam.stages.parmchk.StageParmChk method) (ligandparam.stages.resp.StageLazyResp method) (ligandparam.stages.resp.StageMultiRespFit method) (ligandparam.stages.teststage.TestStage method) (ligandparam.stages.typematching.StageUpdate method) _gas_build() (ligandparam.stages.build_system.StageBuild method) _generate_implied() (ligandparam.stages.abstractstage.AbstractStage method) _parse_inputoptions() (ligandparam.stages.abstractstage.AbstractStage method) _print_rotation() (ligandparam.stages.gaussian.StageGaussianRotation method) _print_status() (ligandparam.stages.gaussian.StageGaussianRotation method) _target_build() (ligandparam.stages.build_system.StageBuild method)

A

AbstractStage (class in ligandparam.stages.abstractstage) add_block() (ligandparam.io.gaussianIO.GaussianWriter method) add_fragment() (ligandparam.multiresp.parmhelper.FragmentedSys method) add_group_restraint() (ligandparam.multiresp.endstate.EndState method) add_leaprc() (ligandparam.io.leapIO.LeapWriter method) add_line() (ligandparam.io.leapIO.LeapWriter method) add_mm() (ligandparam.multiresp.parmhelper.FragmentedSys method) add_state() (ligandparam.multiresp.residueresp.ResidueResp method) Add_TempChange() (ligandparam.multiresp.mdinutils.Mdin method) AmberCmd (class in ligandparam.multiresp.mdinutils) append() (ligandparam.multiresp.intermolequiv.IntermolEquiv method)

append_esp() (ligandparam.multiresp.endstate.EndState method) append_esps() (ligandparam.multiresp.endstate.EndState method) append_stage() (ligandparam.stages.abstractstage.AbstractStage method) apply_backbone_restraint() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method) apply_equiv_hydrogens() (ligandparam.multiresp.residueresp.ResidueResp method) apply_equiv_nonbridge() (ligandparam.multiresp.residueresp.ResidueResp method) apply_nucleobase_restraint() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method) apply_sugar_restraint() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method)

B

BASH (class in ligandparam.multiresp.parmhelper)

BuildLigand (class in ligandparam.recipes.buildligand)

C

check_charge() (ligandparam.stages.charge.StageNormalizeCharge method) check_complete() (ligandparam.io.gaussianIO.GaussianReader method) check_overlaps() (ligandparam.multiresp.parmhelper.FragmentedSys method) check_target() (ligandparam.stages.build_system.StageBuild method) clean() (ligandparam.stages.abstractstage.AbstractStage method) clear_charge_data() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method)

CmdString() (ligandparam.multiresp.mdinutils.AmberCmd method) Computer (class in ligandparam.multiresp.parmhelper) Coordinates (class in ligandparam.io.coordinates) CopyParm() (in module ligandparam.multiresp.parmhelper) crd7 (ligandparam.multiresp.mdinutils.AmberCmd attribute)

D

default_options (ligandparam.stages.abstractstage.AbstractStage attribute) dipout (ligandparam.multiresp.mdinutils.AmberCmd attribute)

Disang1D (class in ligandparam.multiresp.mdinutils) Disang2D (class in ligandparam.multiresp.mdinutils)

E

EndState (class in ligandparam.multiresp.endstate)

exe (ligandparam.multiresp.mdinutils.AmberCmd attribute) execute() (ligandparam.stages.abstractstage.AbstractStage method)

F

find_fitidx() (ligandparam.multiresp.intermolequiv.RespMol method) Fragment (class in ligandparam.multiresp.parmhelper)

FragmentedSys (class in ligandparam.multiresp.parmhelper) FreeLigand (class in ligandparam.recipes.freeligand) funkify_residue_name() (ligandparam.multiresp.parmhelper.Fragment method)

G

GaussianInput (class in ligandparam.io.gaussianIO) GaussianReader (class in ligandparam.io.gaussianIO) GaussianWriter (class in ligandparam.io.gaussianIO) gen_leap() (ligandparam.io.leapIO.LeapWriter method) generate_block() (ligandparam.io.gaussianIO.GaussianInput method) get_array() (ligandparam.multiresp.parmhelper.Computer method) get_coef() (ligandparam.multiresp.parmhelper.Fragment method) get_coefs() (ligandparam.multiresp.parmhelper.FragmentedSys method) get_coordinates() (ligandparam.io.coordinates.Coordinates method) get_dvdl() (ligandparam.multiresp.parmhelper.FragmentedSys method) get_dvdl_coefs() (ligandparam.multiresp.parmhelper.FragmentedSys method) get_elements() (ligandparam.io.coordinates.Coordinates method) get_energy() (ligandparam.multiresp.parmhelper.FragmentedSys method) get_funkified_residue_name() (ligandparam.multiresp.parmhelper.Fragment method) get_mbar() (ligandparam.multiresp.parmhelper.FragmentedSys method) get_mdouts() (ligandparam.multiresp.endstate.EndState method) get_noshake_selection() (ligandparam.multiresp.parmhelper.FragmentedSys method) get_num_cores() (ligandparam.multiresp.parmhelper.Computer method) Get_Num_Ions() (ligandparam.stages.build_system.StageBuild method) get_resp_body() (ligandparam.multiresp.endstate.EndState method)

get_resp_header() (ligandparam.multiresp.endstate.EndState method) get_run_command() (ligandparam.io.gaussianIO.GaussianWriter method) get_selected_atoms() (ligandparam.multiresp.intermolequiv.RespMol method) get_selected_mmcharge_from_each_touched_residue() (ligandparam.multiresp.parmhelper.Fragment method) get_touched_residues() (ligandparam.multiresp.parmhelper.Fragment method) get_unique_atoms() (ligandparam.multiresp.intermolequiv.IntermolEquiv method) get_unique_atoms_from_state() (ligandparam.multiresp.intermolequiv.IntermolEquiv method) GetAtomsBondedToIdx() (in module ligandparam.multiresp.respfunctions) (ligandparam.multiresp.parmhelper.Fragment method) GetAvgStdDevAndErr() (in module ligandparam.multiresp.respfunctions) GetConnectionAtoms() (ligandparam.multiresp.parmhelper.Fragment method) GetEquivHydrogens() (in module ligandparam.multiresp.respfunctions) GetEquivNonbridgeOxygens() (in module ligandparam.multiresp.respfunctions) GetLinkPairs() (ligandparam.multiresp.parmhelper.Fragment method) GetMMBoundaryTerms() (ligandparam.multiresp.parmhelper.Fragment method) GetMMTermsForQMRegion() (ligandparam.multiresp.parmhelper.FragmentedSys method) GetMMTermsForQMRegionAsDict() (ligandparam.multiresp.parmhelper.FragmentedSys method) GetQMAtoms() (ligandparam.multiresp.parmhelper.FragmentedSys method) GetResidueNameFromAtomIdx() (in module ligandparam.multiresp.respfunctions) GetSelectedAtomIndices() (in module ligandparam.multiresp.parmhelper) GetSelectedResidueIndices() (in module ligandparam.multiresp.parmhelper)

H

has_ab_initio() (ligandparam.multiresp.parmhelper.FragmentedSys method)

I

IntermolEquiv (class in ligandparam.multiresp.intermolequiv)

L

LazyLigand (class in ligandparam.recipes.lazyligand) LeapWriter (class in ligandparam.io.leapIO) ligandparam.io.coordinates module ligandparam.io.gaussianIO module ligandparam.io.leapIO module ligandparam.multiresp.endstate module ligandparam.multiresp.functions module ligandparam.multiresp.intermolequiv module ligandparam.multiresp.mdinutils module ligandparam.multiresp.parmhelper module ligandparam.multiresp.residueresp module ligandparam.multiresp.respfunctions module ligandparam.recipes.buildligand module ligandparam.recipes.freeligand module

ligandparam.recipes.lazyligand module ligandparam.recipes.rnaligand module ligandparam.stages.abstractstage module ligandparam.stages.build_system module ligandparam.stages.charge module ligandparam.stages.gaussian module ligandparam.stages.initialize module ligandparam.stages.leap module ligandparam.stages.parmchk module ligandparam.stages.resp module ligandparam.stages.teststage module ligandparam.stages.typematching module list_files_in_directory() (ligandparam.stages.abstractstage.AbstractStage method) ListToSelection() (in module ligandparam.multiresp.parmhelper)

M

MakeNewMMBoundaryTerms() (ligandparam.multiresp.parmhelper.FragmentedSys method) MakeUniqueAngleParams() (in module ligandparam.multiresp.parmhelper) MakeUniqueBondParams() (in module ligandparam.multiresp.parmhelper) MakeUniqueDihedralParams() (in module ligandparam.multiresp.parmhelper) mdfrc (ligandparam.multiresp.mdinutils.AmberCmd attribute) Mdin (class in ligandparam.multiresp.mdinutils) mdin (ligandparam.multiresp.mdinutils.AmberCmd attribute) mdinfo (ligandparam.multiresp.mdinutils.AmberCmd attribute) mdout (ligandparam.multiresp.mdinutils.AmberCmd attribute) mdouts_to_pymbar() (ligandparam.multiresp.parmhelper.FragmentedSys method) module ligandparam.io.coordinates ligandparam.io.gaussianIO ligandparam.io.leapIO ligandparam.multiresp.endstate ligandparam.multiresp.functions ligandparam.multiresp.intermolequiv ligandparam.multiresp.mdinutils ligandparam.multiresp.parmhelper ligandparam.multiresp.residueresp ligandparam.multiresp.respfunctions ligandparam.recipes.buildligand ligandparam.recipes.freeligand ligandparam.recipes.lazyligand ligandparam.recipes.rnaligand ligandparam.stages.abstractstage ligandparam.stages.build_system ligandparam.stages.charge ligandparam.stages.gaussian ligandparam.stages.initialize ligandparam.stages.leap ligandparam.stages.parmchk ligandparam.stages.resp ligandparam.stages.teststage ligandparam.stages.typematching

Mol2Writer (class in ligandparam.io.coordinates) multimolecule_fit() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method)

N

nc (ligandparam.multiresp.mdinutils.AmberCmd attribute)

normalize() (ligandparam.stages.charge.StageNormalizeCharge method)

O

open() (ligandparam.multiresp.parmhelper.BASH method)

OpenParm() (in module ligandparam.multiresp.parmhelper)

P

parm7 (ligandparam.multiresp.mdinutils.AmberCmd attribute) perform_fit() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method) preserve_mm_charges_by_shifting() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method) preserve_residue_charges_by_shifting() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method)

print() (ligandparam.io.gaussianIO.GaussianInput method) (ligandparam.io.gaussianIO.GaussianWriter method) print_charge_differences() (ligandparam.stages.charge.StageNormalizeCharge method) print_docs() (ligandparam.stages.abstractstage.AbstractStage method) print_equiv() (ligandparam.multiresp.intermolequiv.IntermolEquiv method) print_resp() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method)

R

read_log() (ligandparam.io.gaussianIO.GaussianReader method) read_mdout() (ligandparam.multiresp.parmhelper.FragmentedSys method) read_next_resp() (ligandparam.multiresp.endstate.EndState method) read_respfile() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method) ReadGauEsp() (in module ligandparam.multiresp.respfunctions) ReadGauOutput() (in module ligandparam.multiresp.respfunctions) ReadNextRespCharges() (in module ligandparam.multiresp.respfunctions) ReadOrMakeGauEsp() (in module ligandparam.multiresp.respfunctions) redistribute_cores() (ligandparam.multiresp.parmhelper.FragmentedSys method) redistribute_residue_charges() (ligandparam.multiresp.parmhelper.Fragment method) (ligandparam.multiresp.parmhelper.FragmentedSys method)

refc (ligandparam.multiresp.mdinutils.AmberCmd attribute) remove_blank_lines() (ligandparam.stages.gaussian.StageGaussiantoMol2 method) remove_line() (ligandparam.io.leapIO.LeapWriter method) Remove_PDB_CONECT() (in module ligandparam.io.coordinates) ResidueResp (class in ligandparam.multiresp.residueresp) RespMol (class in ligandparam.multiresp.intermolequiv) RNALigand (class in ligandparam.recipes.rnaligand) rotate() (ligandparam.io.coordinates.Coordinates method) rst7 (ligandparam.multiresp.mdinutils.AmberCmd attribute) RunGauEsp() (in module ligandparam.multiresp.respfunctions)

S

Set_DLFIND() (ligandparam.multiresp.mdinutils.Mdin method) Set_DLFIND_Minimize() (ligandparam.multiresp.mdinutils.Mdin method) Set_DLFIND_TransitionState() (ligandparam.multiresp.mdinutils.Mdin method) Set_DumpFreq() (ligandparam.multiresp.mdinutils.Mdin method) set_equiv_atoms() (ligandparam.multiresp.endstate.EndState method) set_exclude() (ligandparam.multiresp.parmhelper.Computer method) set_mm_parm() (ligandparam.multiresp.parmhelper.FragmentedSys method) Set_NPT() (ligandparam.multiresp.mdinutils.Mdin method) Set_NVE() (ligandparam.multiresp.mdinutils.Mdin method) Set_NVT() (ligandparam.multiresp.mdinutils.Mdin method) Set_PrintFreq() (ligandparam.multiresp.mdinutils.Mdin method) Set_QMMM_AM1() (ligandparam.multiresp.mdinutils.Mdin method) Set_QMMM_PBE0() (ligandparam.multiresp.mdinutils.Mdin method) Set_Restart() (ligandparam.multiresp.mdinutils.Mdin method) SetBaseName() (ligandparam.multiresp.mdinutils.AmberCmd method) SetDefaults() (ligandparam.multiresp.mdinutils.AmberCmd method) SetGroupSize() (ligandparam.multiresp.mdinutils.AmberCmd method) setup() (ligandparam.recipes.buildligand.BuildLigand method) (ligandparam.recipes.freeligand.FreeLigand method) (ligandparam.recipes.lazyligand.LazyLigand method) (ligandparam.recipes.rnaligand.RNALigand method)

SimpleXYZ() (in module ligandparam.io.coordinates) sort() (ligandparam.multiresp.parmhelper.FragmentedSys method) StageBuild (class in ligandparam.stages.build_system) StageGaussian (class in ligandparam.stages.gaussian) StageGaussianRotation (class in ligandparam.stages.gaussian) StageGaussiantoMol2 (class in ligandparam.stages.gaussian) StageInitialize (class in ligandparam.stages.initialize) StageLazyResp (class in ligandparam.stages.resp) StageLeap (class in ligandparam.stages.leap) StageMultiRespFit (class in ligandparam.stages.resp) StageNormalizeCharge (class in ligandparam.stages.charge) StageParmChk (class in ligandparam.stages.parmchk) StageUpdate (class in ligandparam.stages.typematching) StageUpdateCharge (class in ligandparam.stages.charge) statisticalInefficiency() (in module ligandparam.multiresp.functions)

T

TestStage (class in ligandparam.stages.teststage)

U

unset_amberhome() (ligandparam.multiresp.parmhelper.Computer method)

update_coordinates() (ligandparam.io.coordinates.Coordinates method) use_gpu() (ligandparam.multiresp.parmhelper.Computer method)

W

write() (ligandparam.io.coordinates.Mol2Writer method) (ligandparam.io.gaussianIO.GaussianWriter method) (ligandparam.io.leapIO.LeapWriter method) write_array() (ligandparam.multiresp.parmhelper.Computer method) write_mdin() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.parmhelper.FragmentedSys method) (ligandparam.multiresp.residueresp.ResidueResp method) write_mm_optimization() (ligandparam.multiresp.parmhelper.FragmentedSys method) write_parm() (ligandparam.multiresp.parmhelper.FragmentedSys method)

write_rotation() (ligandparam.stages.gaussian.StageGaussianRotation method) WriteArray8() (in module ligandparam.multiresp.respfunctions) WriteDisang() (ligandparam.multiresp.mdinutils.Disang1D method) (ligandparam.multiresp.mdinutils.Disang2D method) WriteFitSh() (in module ligandparam.multiresp.functions) WriteFrcmodObj() (in module ligandparam.multiresp.functions) WriteLeapSh() (in module ligandparam.multiresp.functions) WriteMaskedFrcmod() (in module ligandparam.multiresp.functions) WriteMdin() (ligandparam.multiresp.mdinutils.Mdin method)