Index

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_required() (ligandparam.stages.abstractstage.AbstractStage method) add_state() (ligandparam.multiresp.residueresp.ResidueResp method) Add_TempChange() (ligandparam.multiresp.mdinutils.Mdin method) additional_args (ligandparam.stages.initialize.StageInitialize attribute) alpha (ligandparam.stages.gaussian.StageGaussianRotation attribute) 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) atom_type (ligandparam.stages.charge.StageNormalizeCharge attribute) (ligandparam.stages.charge.StageUpdateCharge attribute) (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute) (ligandparam.stages.initialize.StageInitialize attribute)

B

BASH (class in ligandparam.multiresp.parmhelper)

beta (ligandparam.stages.gaussian.StageGaussianRotation attribute)

C

charge_column (ligandparam.stages.charge.StageUpdateCharge attribute) charge_model (ligandparam.stages.initialize.StageInitialize attribute) charge_source (ligandparam.stages.charge.StageUpdateCharge attribute) check_charge() (ligandparam.stages.charge.StageNormalizeCharge method) check_complete() (ligandparam.io.gaussianIO.GaussianReader method) check_overlaps() (ligandparam.multiresp.parmhelper.FragmentedSys 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) cwd (ligandparam.stages.abstractstage.AbstractStage attribute)

D

decimals (ligandparam.stages.charge.StageNormalizeCharge attribute) dipout (ligandparam.multiresp.mdinutils.AmberCmd attribute)

Disang1D (class in ligandparam.multiresp.mdinutils) Disang2D (class in ligandparam.multiresp.mdinutils) dry_run (ligandparam.stages.abstractstage.AbstractStage attribute)

E

EndState (class in ligandparam.multiresp.endstate) exe (ligandparam.multiresp.mdinutils.AmberCmd attribute) execute() (ligandparam.stages.abstractstage.AbstractStage method) (ligandparam.stages.charge.StageNormalizeCharge method) (ligandparam.stages.charge.StageUpdateCharge method) (ligandparam.stages.gaussian.GaussianMinimizeRESP method) (ligandparam.stages.gaussian.GaussianRESP 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.typematching.StageMatchAtomNames method) (ligandparam.stages.typematching.StageUpdate method)

F

find_fitidx() (ligandparam.multiresp.intermolequiv.RespMol method) force_gaussian_rerun (ligandparam.stages.gaussian.GaussianMinimizeRESP attribute) (ligandparam.stages.gaussian.GaussianRESP attribute) (ligandparam.stages.gaussian.StageGaussianRotation attribute) (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute)

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

G

gamma (ligandparam.stages.gaussian.StageGaussianRotation attribute) gaussian_cwd (ligandparam.stages.gaussian.GaussianMinimizeRESP attribute) (ligandparam.stages.gaussian.GaussianRESP attribute) (ligandparam.stages.gaussian.StageGaussianRotation attribute) (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute) GaussianInput (class in ligandparam.io.gaussianIO) GaussianMinimizeRESP (class in ligandparam.stages.gaussian) GaussianReader (class in ligandparam.io.gaussianIO) GaussianRESP (class in ligandparam.stages.gaussian) 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_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

in_com_template (ligandparam.stages.gaussian.StageGaussianRotation attribute) in_frcmod (ligandparam.stages.leap.StageLeap attribute) in_log (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute) in_mol2 (ligandparam.stages.charge.StageNormalizeCharge attribute) (ligandparam.stages.charge.StageUpdateCharge attribute) (ligandparam.stages.gaussian.GaussianMinimizeRESP attribute) (ligandparam.stages.gaussian.GaussianRESP attribute) (ligandparam.stages.gaussian.StageGaussianRotation attribute) (ligandparam.stages.leap.StageLeap attribute) (ligandparam.stages.parmchk.StageParmChk attribute)

in_pdb (ligandparam.stages.initialize.StageInitialize attribute) IntermolEquiv (class in ligandparam.multiresp.intermolequiv)

L

label (ligandparam.stages.gaussian.GaussianMinimizeRESP attribute) (ligandparam.stages.gaussian.GaussianRESP attribute) leaprc (ligandparam.stages.leap.StageLeap attribute) 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.stages.abstractstage 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.typematching module list_files_in_directory() (ligandparam.stages.abstractstage.AbstractStage method) ListToSelection() (in module ligandparam.multiresp.parmhelper) logger (ligandparam.stages.abstractstage.AbstractStage attribute)

M

main_input (ligandparam.stages.abstractstage.AbstractStage attribute) 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) mem (ligandparam.stages.abstractstage.AbstractStage attribute) minimize (ligandparam.stages.gaussian.GaussianMinimizeRESP attribute) 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.stages.abstractstage ligandparam.stages.charge ligandparam.stages.gaussian ligandparam.stages.initialize ligandparam.stages.leap ligandparam.stages.parmchk ligandparam.stages.resp ligandparam.stages.typematching

Mol2Writer (class in ligandparam.io.coordinates) molname (ligandparam.stages.leap.StageLeap attribute) multimolecule_fit() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method)

N

nc (ligandparam.multiresp.mdinutils.AmberCmd attribute) net_charge (ligandparam.stages.charge.StageNormalizeCharge attribute) (ligandparam.stages.charge.StageUpdateCharge attribute) (ligandparam.stages.gaussian.GaussianMinimizeRESP attribute) (ligandparam.stages.gaussian.GaussianRESP attribute) (ligandparam.stages.gaussian.StageGaussianRotation attribute) (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute) (ligandparam.stages.initialize.StageInitialize attribute) (ligandparam.stages.parmchk.StageParmChk attribute)

normalize() (ligandparam.stages.charge.StageNormalizeCharge method) nproc (ligandparam.stages.abstractstage.AbstractStage attribute)

O

open() (ligandparam.multiresp.parmhelper.BASH method) OpenParm() (in module ligandparam.multiresp.parmhelper) opt_theory (ligandparam.stages.gaussian.GaussianMinimizeRESP attribute) (ligandparam.stages.gaussian.StageGaussianRotation attribute) out_frcmod (ligandparam.stages.parmchk.StageParmChk attribute) out_gaussian_label (ligandparam.stages.gaussian.StageGaussianRotation attribute) out_gaussian_log (ligandparam.stages.gaussian.GaussianMinimizeRESP attribute) (ligandparam.stages.gaussian.GaussianRESP attribute)

out_lib (ligandparam.stages.leap.StageLeap attribute) out_mol2 (ligandparam.stages.charge.StageNormalizeCharge attribute) (ligandparam.stages.charge.StageUpdateCharge attribute) (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute) (ligandparam.stages.initialize.StageInitialize attribute) out_pdb (ligandparam.stages.leap.StageLeap attribute)

P

parm7 (ligandparam.multiresp.mdinutils.AmberCmd attribute) perform_fit() (ligandparam.multiresp.endstate.EndState method) (ligandparam.multiresp.residueresp.ResidueResp method) precision (ligandparam.stages.charge.StageNormalizeCharge attribute) 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_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) required (ligandparam.stages.abstractstage.AbstractStage attribute) ResidueResp (class in ligandparam.multiresp.residueresp) resp_theory (ligandparam.stages.gaussian.GaussianMinimizeRESP attribute) (ligandparam.stages.gaussian.GaussianRESP attribute) (ligandparam.stages.gaussian.StageGaussianRotation attribute) RespMol (class in ligandparam.multiresp.intermolequiv) rotate() (ligandparam.io.coordinates.Coordinates method) rst7 (ligandparam.multiresp.mdinutils.AmberCmd attribute) RunGauEsp() (in module ligandparam.multiresp.respfunctions)

S

secondary (ligandparam.stages.initialize.StageInitialize attribute) 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.stages.gaussian.GaussianMinimizeRESP method) (ligandparam.stages.gaussian.GaussianRESP method) (ligandparam.stages.gaussian.StageGaussianRotation method) (ligandparam.stages.gaussian.StageGaussiantoMol2 method) SimpleXYZ() (in module ligandparam.io.coordinates) sort() (ligandparam.multiresp.parmhelper.FragmentedSys method) stage_name (ligandparam.stages.abstractstage.AbstractStage attribute) 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) StageMatchAtomNames (class in ligandparam.stages.typematching) 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

temp1_mol2 (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute) temp2_mol2 (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute)

template_mol2 (ligandparam.stages.gaussian.StageGaussiantoMol2 attribute) tmp_mol2 (ligandparam.stages.charge.StageNormalizeCharge attribute) (ligandparam.stages.charge.StageUpdateCharge attribute)

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)

X

xyz (ligandparam.stages.gaussian.StageGaussianRotation attribute)