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molSimplify
Index
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Z
A
ACM() (molSimplify.Classes.mol3D.mol3D method)
ACM_axis() (molSimplify.Classes.mol3D.mol3D method)
add_bond() (molSimplify.Classes.mol3D.mol3D method)
add_custom_path() (molSimplify.Classes.globalvars.globalvars method)
addAtom() (molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.monomer3D.monomer3D method)
align_dent1_lig() (in module molSimplify.Scripts.structgen)
align_dent2_catom2_coarse() (in module molSimplify.Scripts.structgen)
align_dent2_catom2_refined() (in module molSimplify.Scripts.structgen)
align_dent2_lig() (in module molSimplify.Scripts.structgen)
align_dent3_lig() (in module molSimplify.Scripts.structgen)
align_lig_centersym() (in module molSimplify.Scripts.structgen)
align_linear_pi_lig() (in module molSimplify.Scripts.structgen)
align_payload_to_multi_site() (in module molSimplify.Scripts.cellbuilder)
align_pi_ring_lig() (in module molSimplify.Scripts.structgen)
alignmol() (molSimplify.Classes.mol3D.mol3D method)
alignPtoaxis() (in module molSimplify.Scripts.geometry)
aligntoaxis() (in module molSimplify.Scripts.geometry)
aligntoaxis2() (in module molSimplify.Scripts.geometry)
amass() (molSimplify.Classes.globalvars.globalvars method)
append_descriptor_derivatives() (in module molSimplify.Informatics.lacRACAssemble)
append_descriptors() (in module molSimplify.Informatics.lacRACAssemble)
apply_ffopt() (molSimplify.Classes.mol3D.mol3D method)
apply_ffopt_list_constraints() (molSimplify.Classes.mol3D.mol3D method)
apply_plane_to_point() (in module molSimplify.Scripts.cellbuilder_tools)
args_parser_retrain() (in module molSimplify.Scripts.inparse)
aromatic_charge() (molSimplify.Classes.mol3D.mol3D method)
assign_graph_from_net() (molSimplify.Classes.mol3D.mol3D method)
atom3D (class in molSimplify.Classes.atom3D)
atom_only_autocorrelation() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
atom_only_autocorrelation_derivative() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
atom_only_deltametric() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
atom_only_deltametric_derivative() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
atom_only_ratiometric() (in module molSimplify.Informatics.autocorrelation)
atom_only_summetric() (in module molSimplify.Informatics.autocorrelation)
autoChooseConf() (molSimplify.Classes.protein3D.protein3D method)
autocorrelation() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
autocorrelation_catoms() (in module molSimplify.Informatics.autocorrelation)
autocorrelation_derivative() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
axes_angle_align() (in module molSimplify.Scripts.cellbuilder)
B
bbcombs_mononuc() (molSimplify.Classes.globalvars.globalvars method)
BCM() (molSimplify.Classes.mol3D.mol3D method)
BCM_opt() (molSimplify.Classes.mol3D.mol3D method)
best_fit_plane() (in module molSimplify.Scripts.geometry)
bondsdict() (molSimplify.Classes.globalvars.globalvars method)
C
calcCharges() (molSimplify.Classes.mol3D.mol3D method)
cell_ffopt() (in module molSimplify.Scripts.cellbuilder_tools)
center_of_sym() (in module molSimplify.Scripts.cellbuilder_tools)
centered_align_coord() (in module molSimplify.Scripts.cellbuilder)
centermass() (molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.monomer3D.monomer3D method)
(molSimplify.Classes.protein3D.protein3D method)
centersym() (molSimplify.Classes.mol3D.mol3D method)
centroid() (in module molSimplify.Scripts.rmsd)
(molSimplify.Classes.monomer3D.monomer3D method)
change_basis() (in module molSimplify.Scripts.cellbuilder_tools)
check_angle_linear() (molSimplify.Classes.mol3D.mol3D method)
check_rotate_linear_lig() (in module molSimplify.Scripts.structgen)
check_rotate_symm_lig() (in module molSimplify.Scripts.structgen)
check_top_layer_correct() (in module molSimplify.Scripts.cellbuilder_tools)
checkcolinear() (in module molSimplify.Scripts.geometry)
checkinput() (in module molSimplify.Scripts.inparse)
checkplanar() (in module molSimplify.Scripts.geometry)
checkTrue() (in module molSimplify.Scripts.inparse)
choose_best_site() (in module molSimplify.Scripts.cellbuilder)
choose_nearest_neighbour() (in module molSimplify.Scripts.cellbuilder)
cleanBonds() (molSimplify.Classes.mol3D.mol3D method)
cleaninput() (in module molSimplify.Scripts.inparse)
closest_H_2_metal() (molSimplify.Classes.mol3D.mol3D method)
closest_torus_point() (in module molSimplify.Scripts.cellbuilder_tools)
cmrotate() (in module molSimplify.Scripts.geometry)
combine() (molSimplify.Classes.mol3D.mol3D method)
combine_multi_aligned_payload_with_cell() (in module molSimplify.Scripts.cellbuilder)
concave_hull() (in module molSimplify.Scripts.cellbuilder)
connectivity_match() (in module molSimplify.Scripts.geometry)
construct_property_vector() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
convert2mol3D() (molSimplify.Classes.mol3D.mol3D method)
convert2OBMol() (molSimplify.Classes.mol3D.mol3D method)
convert2OBMol2() (molSimplify.Classes.mol3D.mol3D method)
convexhull() (molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.protein3D.protein3D method)
coords() (molSimplify.Classes.atom3D.atom3D method)
(molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.monomer3D.monomer3D method)
coordsvect() (molSimplify.Classes.mol3D.mol3D method)
copymol3D() (molSimplify.Classes.mol3D.mol3D method)
CosRule() (in module molSimplify.Scripts.distgeom)
count_atoms() (molSimplify.Classes.mol3D.mol3D method)
count_electrons() (molSimplify.Classes.mol3D.mol3D method)
count_nonH_atoms() (molSimplify.Classes.mol3D.mol3D method)
count_specific_atoms() (molSimplify.Classes.mol3D.mol3D method)
countAAs() (molSimplify.Classes.protein3D.protein3D method)
create_mol_with_inds() (molSimplify.Classes.mol3D.mol3D method)
createMolecularGraph() (molSimplify.Classes.mol3D.mol3D method)
cut_cell_to_index() (in module molSimplify.Scripts.cellbuilder)
D
d_fix() (in module molSimplify.Scripts.cellbuilder)
deleteatom() (molSimplify.Classes.mol3D.mol3D method)
deleteatoms() (molSimplify.Classes.mol3D.mol3D method)
deleteHs() (molSimplify.Classes.mol3D.mol3D method)
deltametric() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
deltametric_catoms() (in module molSimplify.Informatics.autocorrelation)
deltametric_derivative() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
deserialize_json() (in module molSimplify.Scripts.inparse)
dict_check_processing() (molSimplify.Classes.mol3D.mol3D method)
dihedral() (in module molSimplify.Scripts.geometry)
distance() (in module molSimplify.Scripts.geometry)
(molSimplify.Classes.atom3D.atom3D method)
(molSimplify.Classes.mol3D.mol3D method)
distance_2d_torus() (in module molSimplify.Scripts.cellbuilder_tools)
distance_2d_torus_next_only() (in module molSimplify.Scripts.cellbuilder_tools)
distance_zw() (in module molSimplify.Scripts.cellbuilder_tools)
distancev() (molSimplify.Classes.atom3D.atom3D method)
DistErr() (in module molSimplify.Scripts.distgeom)
DistErrGrad() (in module molSimplify.Scripts.distgeom)
distortbackbone() (in module molSimplify.Scripts.structgen)
draw_svg() (molSimplify.Classes.mol3D.mol3D method)
E
elementsbynum() (molSimplify.Classes.globalvars.globalvars method)
endict() (molSimplify.Classes.globalvars.globalvars method)
evaluate_basis_coefficients() (in module molSimplify.Scripts.cellbuilder_tools)
F
fetch_pdb() (molSimplify.Classes.protein3D.protein3D method)
ffopt() (in module molSimplify.Scripts.structgen)
find_all_surface_atoms() (in module molSimplify.Scripts.cellbuilder_tools)
find_atom() (molSimplify.Classes.mol3D.mol3D method)
find_extents() (in module molSimplify.Scripts.cellbuilder_tools)
find_extents_cv() (in module molSimplify.Scripts.cellbuilder_tools)
find_ligand_autocorrelation_derivatives_oct() (in module molSimplify.Informatics.autocorrelation)
find_ligand_autocorrelations_oct() (in module molSimplify.Informatics.autocorrelation)
find_ligand_autocorrs_and_deltametrics_oct_dimers() (in module molSimplify.Informatics.autocorrelation)
find_ligand_deltametric_derivatives_oct() (in module molSimplify.Informatics.autocorrelation)
find_ligand_deltametrics_oct() (in module molSimplify.Informatics.autocorrelation)
find_mc_eq_ax_autocorrelation_oct() (in module molSimplify.Informatics.autocorrelation)
find_mc_eq_ax_deltametrics_oct() (in module molSimplify.Informatics.autocorrelation)
find_metal() (molSimplify.Classes.mol2D.Mol2D method)
findAA() (molSimplify.Classes.protein3D.protein3D method)
findAtom() (molSimplify.Classes.protein3D.protein3D method)
findAtomsbySymbol() (molSimplify.Classes.mol3D.mol3D method)
findcloseMetal() (molSimplify.Classes.mol3D.mol3D method)
findMetal() (molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.protein3D.protein3D method)
findshape() (in module molSimplify.Scripts.distgeom)
findsmarts() (in module molSimplify.Scripts.structgen)
findsubMol() (molSimplify.Classes.mol3D.mol3D method)
force_field_relax_with_slab() (in module molSimplify.Scripts.cellbuilder)
fractionate_points_by_plane() (in module molSimplify.Scripts.cellbuilder_tools)
freeze_bottom_n_layers() (in module molSimplify.Scripts.cellbuilder_tools)
freeze_under_layer() (in module molSimplify.Scripts.cellbuilder_tools)
freezeatom() (molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.protein3D.protein3D method)
freezeatoms() (molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.protein3D.protein3D method)
from_mol2_file() (molSimplify.Classes.mol2D.Mol2D class method)
from_mol_file() (molSimplify.Classes.mol2D.Mol2D class method)
from_smiles() (molSimplify.Classes.mol2D.Mol2D class method)
(molSimplify.Classes.mol3D.mol3D class method)
full_autocorrelation() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
full_autocorrelation_derivative() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
G
gamgen() (in module molSimplify.Scripts.qcgen)
generate_all_ligand_autocorrelation_derivatives() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_all_ligand_autocorrelations() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_all_ligand_autocorrs_and_deltametrics_dimers() (in module molSimplify.Informatics.autocorrelation)
generate_all_ligand_deltametric_derivatives() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_all_ligand_deltametrics() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_all_ligand_misc() (in module molSimplify.Informatics.lacRACAssemble)
generate_atomonly_autocorrelation_derivatives() (in module molSimplify.Informatics.autocorrelation)
generate_atomonly_autocorrelations() (in module molSimplify.Informatics.autocorrelation)
generate_atomonly_deltametric_derivatives() (in module molSimplify.Informatics.autocorrelation)
generate_atomonly_deltametrics() (in module molSimplify.Informatics.autocorrelation)
generate_full_complex_autocorrelation_derivatives() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_full_complex_autocorrelations() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_full_complex_coulomb_autocorrelations() (in module molSimplify.Informatics.autocorrelation)
generate_mc_eq_ax_autocorrelation() (in module molSimplify.Informatics.autocorrelation)
generate_mc_eq_ax_deltametrics() (in module molSimplify.Informatics.autocorrelation)
generate_metal_autocorrelation_derivatives() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_metal_autocorrelations() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_metal_deltametric_derivatives() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_metal_deltametrics() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_metal_ox_autocorrelation_derivatives() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_metal_ox_autocorrelations() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_metal_ox_deltametric_derivatives() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_metal_ox_deltametrics() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
generate_metal_ox_eff_autocorrelations() (in module molSimplify.Informatics.autocorrelation)
generate_metal_ox_eff_deltametrics() (in module molSimplify.Informatics.autocorrelation)
generate_multiatom_autocorrelations() (in module molSimplify.Informatics.autocorrelation)
generate_multiatom_deltametrics() (in module molSimplify.Informatics.autocorrelation)
generate_multimetal_autocorrelations() (in module molSimplify.Informatics.autocorrelation)
generate_multimetal_deltametrics() (in module molSimplify.Informatics.autocorrelation)
generate_report() (in module molSimplify.Scripts.structgen)
geo_check_dictionary() (molSimplify.Classes.globalvars.globalvars method)
geo_dict_initialization() (molSimplify.Classes.mol3D.mol3D method)
geo_maxatomdist() (molSimplify.Classes.mol3D.mol3D method)
geo_rmsd() (molSimplify.Classes.mol3D.mol3D method)
Get3Eigs() (in module molSimplify.Scripts.distgeom)
get_all_angle_refs() (molSimplify.Classes.globalvars.globalvars method)
get_all_geometries() (molSimplify.Classes.globalvars.globalvars method)
get_basis_coefficients() (in module molSimplify.Scripts.cellbuilder_tools)
get_batoms() (in module molSimplify.Scripts.structgen)
get_bo_dict_from_inds() (molSimplify.Classes.mol3D.mol3D method)
get_descriptor_derivatives() (in module molSimplify.Informatics.lacRACAssemble)
get_descriptor_vector() (in module molSimplify.Informatics.lacRACAssemble)
get_fcs() (molSimplify.Classes.mol3D.mol3D method)
get_features() (molSimplify.Classes.mol3D.mol3D method)
get_first_shell() (molSimplify.Classes.mol3D.mol3D method)
get_geometry_type() (molSimplify.Classes.mol3D.mol3D method)
get_geometry_type_old() (molSimplify.Classes.mol3D.mol3D method)
get_linear_angle() (molSimplify.Classes.mol3D.mol3D method)
get_MLdist() (in module molSimplify.Scripts.structgen)
get_MLdist_database() (in module molSimplify.Scripts.structgen)
get_mol_graph_det() (molSimplify.Classes.mol3D.mol3D method)
get_num_coord_metal() (molSimplify.Classes.mol3D.mol3D method)
get_octetrule_charge() (molSimplify.Classes.mol3D.mol3D method)
get_smiles() (molSimplify.Classes.mol3D.mol3D method)
get_smilesOBmol_charge() (molSimplify.Classes.mol3D.mol3D method)
get_submol_noHs() (molSimplify.Classes.mol3D.mol3D method)
get_symmetry_denticity() (molSimplify.Classes.mol3D.mol3D method)
getAllAAs() (molSimplify.Classes.globalvars.globalvars method)
getAngle() (molSimplify.Classes.mol3D.mol3D method)
getAtom() (molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.protein3D.protein3D method)
getAtomCoords() (molSimplify.Classes.mol3D.mol3D method)
getAtoms() (molSimplify.Classes.mol3D.mol3D method)
getAtomTypes() (molSimplify.Classes.mol3D.mol3D method)
getAtomwithinds() (molSimplify.Classes.mol3D.mol3D method)
getAtomwithSyms() (molSimplify.Classes.mol3D.mol3D method)
getbackbcombsall() (in module molSimplify.Scripts.structgen)
getBondCutoff() (molSimplify.Classes.mol3D.mol3D method)
getBondedAtoms() (molSimplify.Classes.mol3D.mol3D method)
getBondedAtomsBOMatrix() (molSimplify.Classes.mol3D.mol3D method)
getBondedAtomsBOMatrixAug() (molSimplify.Classes.mol3D.mol3D method)
getBondedAtomsByCoordNo() (molSimplify.Classes.mol3D.mol3D method)
getBondedAtomsByThreshold() (molSimplify.Classes.mol3D.mol3D method)
getBondedAtomsH() (molSimplify.Classes.mol3D.mol3D method)
getBondedAtomsnotH() (molSimplify.Classes.mol3D.mol3D method)
getBondedAtomsOct() (molSimplify.Classes.mol3D.mol3D method)
getBondedAtomsSmart() (molSimplify.Classes.mol3D.mol3D method)
getBoundMols() (molSimplify.Classes.protein3D.protein3D method)
GetBoundsMatrices() (in module molSimplify.Scripts.distgeom)
getChain() (molSimplify.Classes.protein3D.protein3D method)
getClosestAtom() (molSimplify.Classes.mol3D.mol3D method)
getClosestAtomlist() (molSimplify.Classes.mol3D.mol3D method)
getClosestAtomnoHs() (molSimplify.Classes.mol3D.mol3D method)
GetCMDists() (in module molSimplify.Scripts.distgeom)
GetConf() (in module molSimplify.Scripts.distgeom)
getconnection() (in module molSimplify.Scripts.structgen)
getDistToMetal() (molSimplify.Classes.mol3D.mol3D method)
getFarAtom() (molSimplify.Classes.mol3D.mol3D method)
getfarAtomdir() (molSimplify.Classes.mol3D.mol3D method)
getfragmentlists() (molSimplify.Classes.mol3D.mol3D method)
getGreek() (molSimplify.Classes.monomer3D.monomer3D method)
getHs() (molSimplify.Classes.mol3D.mol3D method)
getHsbyAtom() (molSimplify.Classes.mol3D.mol3D method)
getHsbyIndex() (molSimplify.Classes.mol3D.mol3D method)
getIndex() (molSimplify.Classes.protein3D.protein3D method)
GetMetricMatrix() (in module molSimplify.Scripts.distgeom)
getMissingAAs() (molSimplify.Classes.protein3D.protein3D method)
getMissingAtoms() (molSimplify.Classes.protein3D.protein3D method)
getMLBondLengths() (molSimplify.Classes.mol3D.mol3D method)
getMolecule() (molSimplify.Classes.protein3D.protein3D method)
getNumAtoms() (molSimplify.Classes.mol3D.mol3D method)
getnupdateb() (in module molSimplify.Scripts.structgen)
getOBMol() (molSimplify.Classes.mol3D.mol3D method)
getPeptideAtoms() (molSimplify.Classes.monomer3D.monomer3D method)
getPointu() (in module molSimplify.Scripts.geometry)
globalvars (class in molSimplify.Classes.globalvars)
graph_determinant() (molSimplify.Classes.mol2D.Mol2D method)
graph_hash() (molSimplify.Classes.mol2D.Mol2D method)
graph_hash_edge_attr() (molSimplify.Classes.mol2D.Mol2D method)
groups() (molSimplify.Classes.globalvars.globalvars method)
H
hungarian() (in module molSimplify.Scripts.rmsd)
I
identify() (molSimplify.Classes.monomer3D.monomer3D method)
import_from_cif() (in module molSimplify.Scripts.cellbuilder_tools)
init_ANN() (in module molSimplify.Scripts.structgen)
init_ligand() (in module molSimplify.Scripts.structgen)
init_template() (in module molSimplify.Scripts.structgen)
initialize() (molSimplify.Classes.mol3D.mol3D method)
inverseCosRule() (in module molSimplify.Scripts.distgeom)
is_edge_compound() (molSimplify.Classes.mol3D.mol3D method)
is_linear_ligand() (molSimplify.Classes.mol3D.mol3D method)
is_number() (in module molSimplify.Scripts.inparse)
is_sandwich_compound() (molSimplify.Classes.mol3D.mol3D method)
ismetal() (molSimplify.Classes.atom3D.atom3D method)
IsOct() (molSimplify.Classes.mol3D.mol3D method)
isPristine() (molSimplify.Classes.mol3D.mol3D method)
IsStructure() (molSimplify.Classes.mol3D.mol3D method)
K
kabsch() (in module molSimplify.Scripts.geometry)
(in module molSimplify.Scripts.rmsd)
kabsch_rmsd() (in module molSimplify.Scripts.rmsd)
kabsch_rotate() (in module molSimplify.Scripts.rmsd)
L
layer_density_in_3D() (in module molSimplify.Informatics.autocorrelation)
ligand_comp_org() (molSimplify.Classes.mol3D.mol3D method)
M
make_formula() (molSimplify.Classes.mol3D.mol3D method)
makeQ() (in module molSimplify.Scripts.rmsd)
makeW() (in module molSimplify.Scripts.rmsd)
match_lig_list() (molSimplify.Classes.mol3D.mol3D method)
maxatomdist() (molSimplify.Classes.mol3D.mol3D method)
maxatomdist_nonH() (molSimplify.Classes.mol3D.mol3D method)
maxdist() (molSimplify.Classes.mol3D.mol3D method)
mcomplex() (in module molSimplify.Scripts.structgen)
mdistance() (in module molSimplify.Scripts.cellbuilder_tools)
meanabsdev() (molSimplify.Classes.mol3D.mol3D method)
metal_only_autocorrelation() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
metal_only_autocorrelation_derivative() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
metal_only_deltametric() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
metal_only_deltametric_derivative() (in module molSimplify.Informatics.autocorrelation)
(in module molSimplify.Informatics.lacRACAssemble)
metal_only_layer_density() (in module molSimplify.Informatics.autocorrelation)
metalslist() (molSimplify.Classes.globalvars.globalvars method)
Metrize() (in module molSimplify.Scripts.distgeom)
midpt() (in module molSimplify.Scripts.geometry)
mindist() (molSimplify.Classes.mol3D.mol3D method)
mindistmol() (molSimplify.Classes.mol3D.mol3D method)
mindistnonH() (molSimplify.Classes.mol3D.mol3D method)
mindisttopoint() (molSimplify.Classes.mol3D.mol3D method)
mlpgen() (in module molSimplify.Scripts.qcgen)
modifybackbonep() (in module molSimplify.Scripts.structgen)
module
molSimplify.Classes.atom3D
molSimplify.Classes.globalvars
molSimplify.Classes.mol2D
molSimplify.Classes.mol3D
molSimplify.Classes.monomer3D
molSimplify.Classes.protein3D
molSimplify.Classes.rundiag
molSimplify.Informatics.autocorrelation
molSimplify.Informatics.lacRACAssemble
molSimplify.Scripts.cellbuilder
molSimplify.Scripts.cellbuilder_tools
molSimplify.Scripts.distgeom
molSimplify.Scripts.generator
molSimplify.Scripts.geometry
molSimplify.Scripts.inparse
molSimplify.Scripts.periodic_QE
molSimplify.Scripts.qcgen
molSimplify.Scripts.rmsd
molSimplify.Scripts.structgen
Mol2D (class in molSimplify.Classes.mol2D)
mol3D (class in molSimplify.Classes.mol3D)
molcbasis() (in module molSimplify.Scripts.qcgen)
molcfrozens() (in module molSimplify.Scripts.qcgen)
molcgen() (in module molSimplify.Scripts.qcgen)
molcnactels() (in module molSimplify.Scripts.qcgen)
molcras2s() (in module molSimplify.Scripts.qcgen)
molcwrt() (in module molSimplify.Scripts.qcgen)
molecule_placement_supervisor() (in module molSimplify.Scripts.cellbuilder)
mols_symbols() (molSimplify.Classes.mol3D.mol3D method)
molSimplify.Classes.atom3D
module
molSimplify.Classes.globalvars
module
molSimplify.Classes.mol2D
module
molSimplify.Classes.mol3D
module
molSimplify.Classes.monomer3D
module
molSimplify.Classes.protein3D
module
molSimplify.Classes.rundiag
module
molSimplify.Informatics.autocorrelation
module
molSimplify.Informatics.lacRACAssemble
module
molSimplify.Scripts.cellbuilder
module
molSimplify.Scripts.cellbuilder_tools
module
molSimplify.Scripts.distgeom
module
molSimplify.Scripts.generator
module
molSimplify.Scripts.geometry
module
molSimplify.Scripts.inparse
module
molSimplify.Scripts.periodic_QE
module
molSimplify.Scripts.qcgen
module
molSimplify.Scripts.rmsd
module
molSimplify.Scripts.structgen
module
molsize() (molSimplify.Classes.mol3D.mol3D method)
monomer3D (class in molSimplify.Classes.monomer3D)
multialign_objective_function() (in module molSimplify.Scripts.cellbuilder)
multiatom_only_autocorrelation() (in module molSimplify.Informatics.autocorrelation)
multiatom_only_deltametric() (in module molSimplify.Informatics.autocorrelation)
multigamgen() (in module molSimplify.Scripts.qcgen)
multimetal_only_autocorrelation() (in module molSimplify.Informatics.autocorrelation)
multimetal_only_deltametric() (in module molSimplify.Informatics.autocorrelation)
multimolcgen() (in module molSimplify.Scripts.qcgen)
multiogen() (in module molSimplify.Scripts.qcgen)
multiqgen() (in module molSimplify.Scripts.qcgen)
multitcgen() (in module molSimplify.Scripts.qcgen)
mutate() (molSimplify.Classes.atom3D.atom3D method)
mybash() (in module molSimplify.Classes.globalvars)
N
norm() (in module molSimplify.Scripts.geometry)
normalize() (in module molSimplify.Scripts.geometry)
normalize_vector() (in module molSimplify.Scripts.cellbuilder_tools)
numRings() (molSimplify.Classes.mol3D.mol3D method)
O
oct_comp() (molSimplify.Classes.mol3D.mol3D method)
Oct_inspection() (molSimplify.Classes.mol3D.mol3D method)
ogen() (in module molSimplify.Scripts.qcgen)
ogenwrt() (in module molSimplify.Scripts.qcgen)
openbabel_ffopt() (in module molSimplify.Scripts.structgen)
overlapcheck() (molSimplify.Classes.mol3D.mol3D method)
P
parseall() (in module molSimplify.Scripts.inparse)
parseCLI() (in module molSimplify.Scripts.inparse)
parseinputfile() (in module molSimplify.Scripts.inparse)
parseinputs_advanced() (in module molSimplify.Scripts.inparse)
parseinputs_autocorr() (in module molSimplify.Scripts.inparse)
parseinputs_basic() (in module molSimplify.Scripts.inparse)
parseinputs_binding() (in module molSimplify.Scripts.inparse)
parseinputs_chainb() (in module molSimplify.Scripts.inparse)
parseinputs_customcore() (in module molSimplify.Scripts.inparse)
parseinputs_db() (in module molSimplify.Scripts.inparse)
parseinputs_inputgen() (in module molSimplify.Scripts.inparse)
parseinputs_ligdict() (in module molSimplify.Scripts.inparse)
parseinputs_naming() (in module molSimplify.Scripts.inparse)
parseinputs_postproc() (in module molSimplify.Scripts.inparse)
parseinputs_random() (in module molSimplify.Scripts.inparse)
parseinputs_slabgen() (in module molSimplify.Scripts.inparse)
parseinputs_tsgen() (in module molSimplify.Scripts.inparse)
periodic_2d_distance() (in module molSimplify.Scripts.cellbuilder_tools)
periodic_mindist() (in module molSimplify.Scripts.cellbuilder_tools)
periodic_selfdist() (in module molSimplify.Scripts.cellbuilder_tools)
periods() (molSimplify.Classes.globalvars.globalvars method)
pmrotate() (in module molSimplify.Scripts.geometry)
point_in_box() (in module molSimplify.Scripts.cellbuilder_tools)
PointRotateAxis() (in module molSimplify.Scripts.geometry)
PointRotateMat() (in module molSimplify.Scripts.geometry)
PointRotateSph() (in module molSimplify.Scripts.geometry)
points_below_plane() (in module molSimplify.Scripts.cellbuilder_tools)
PointTranslateSph() (in module molSimplify.Scripts.geometry)
PointTranslateSphgivenphi() (in module molSimplify.Scripts.geometry)
PointTranslateSphgivenr() (in module molSimplify.Scripts.geometry)
PointTranslatetoPSph() (in module molSimplify.Scripts.geometry)
polarizability() (molSimplify.Classes.globalvars.globalvars method)
populateBOMatrix() (molSimplify.Classes.mol3D.mol3D method)
populateBOMatrixAug() (molSimplify.Classes.mol3D.mol3D method)
print_geo_dict() (molSimplify.Classes.mol3D.mol3D method)
printxyz() (molSimplify.Classes.mol3D.mol3D method)
protate() (in module molSimplify.Scripts.geometry)
protateref() (in module molSimplify.Scripts.geometry)
protein3D (class in molSimplify.Classes.protein3D)
Q
qgen() (in module molSimplify.Scripts.qcgen)
quaternion_rmsd() (in module molSimplify.Scripts.rmsd)
quaternion_rotate() (in module molSimplify.Scripts.rmsd)
quaternion_transform() (in module molSimplify.Scripts.rmsd)
R
ratiometric() (in module molSimplify.Informatics.autocorrelation)
RCAngle() (molSimplify.Classes.mol3D.mol3D method)
RCDistance() (molSimplify.Classes.mol3D.mol3D method)
read_bo_from_mol() (molSimplify.Classes.mol3D.mol3D method)
read_bonder_order() (molSimplify.Classes.mol3D.mol3D method)
read_charge() (molSimplify.Classes.mol3D.mol3D method)
read_smiles() (molSimplify.Classes.mol3D.mol3D method)
readfrommol2() (molSimplify.Classes.mol3D.mol3D method)
readfrompdb() (molSimplify.Classes.protein3D.protein3D method)
readfromstring() (molSimplify.Classes.mol3D.mol3D method)
readfromtxt() (molSimplify.Classes.mol3D.mol3D method)
readfromxyz() (molSimplify.Classes.mol3D.mol3D method)
readMetaData() (molSimplify.Classes.protein3D.protein3D method)
reflect_through_plane() (in module molSimplify.Scripts.geometry)
ReflectPlane() (in module molSimplify.Scripts.geometry)
reorder_distance() (in module molSimplify.Scripts.rmsd)
reorder_hungarian() (in module molSimplify.Scripts.rmsd)
resetBondOBMol() (molSimplify.Classes.mol3D.mol3D method)
returnxyz() (molSimplify.Classes.mol3D.mol3D method)
rigorous_rmsd() (in module molSimplify.Scripts.rmsd)
rmsd() (in module molSimplify.Scripts.rmsd)
(molSimplify.Classes.mol3D.mol3D method)
rmsd_nonH() (molSimplify.Classes.mol3D.mol3D method)
rmsd_reorder_rotate() (in module molSimplify.Scripts.rmsd)
rotate_around_axis() (in module molSimplify.Scripts.geometry)
rotate_catom_fix_Hs() (in module molSimplify.Scripts.structgen)
rotate_catoms_fix_Hs() (in module molSimplify.Scripts.structgen)
rotate_mat() (in module molSimplify.Scripts.geometry)
rotate_MLaxis_minimize_steric() (in module molSimplify.Scripts.structgen)
rotateRef() (in module molSimplify.Scripts.geometry)
rotation_objective_func() (in module molSimplify.Scripts.structgen)
rotation_params() (in module molSimplify.Scripts.geometry)
run_diag (class in molSimplify.Classes.rundiag)
S
sanitycheck() (molSimplify.Classes.mol3D.mol3D method)
sanitycheckCSD() (molSimplify.Classes.mol3D.mol3D method)
SaveConf() (in module molSimplify.Scripts.distgeom)
set_ANN() (molSimplify.Classes.rundiag.run_diag method)
set_dict_bl() (molSimplify.Classes.rundiag.run_diag method)
set_mol() (molSimplify.Classes.rundiag.run_diag method)
set_sanity() (molSimplify.Classes.rundiag.run_diag method)
setAAs() (molSimplify.Classes.protein3D.protein3D method)
setAtoms() (molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.protein3D.protein3D method)
setBonds() (molSimplify.Classes.monomer3D.monomer3D method)
(molSimplify.Classes.protein3D.protein3D method)
setCentroid() (molSimplify.Classes.protein3D.protein3D method)
setChains() (molSimplify.Classes.protein3D.protein3D method)
setcmdistance() (in module molSimplify.Scripts.geometry)
setConf() (molSimplify.Classes.protein3D.protein3D method)
setcoords() (molSimplify.Classes.atom3D.atom3D method)
setDataCompleteness() (molSimplify.Classes.protein3D.protein3D method)
setEDIA() (molSimplify.Classes.atom3D.atom3D method)
setEDIAScores() (molSimplify.Classes.protein3D.protein3D method)
setHetmols() (molSimplify.Classes.protein3D.protein3D method)
setIndices() (molSimplify.Classes.protein3D.protein3D method)
setLoc() (molSimplify.Classes.mol3D.mol3D method)
(molSimplify.Classes.monomer3D.monomer3D method)
setMissingAAs() (molSimplify.Classes.protein3D.protein3D method)
setMissingAtoms() (molSimplify.Classes.protein3D.protein3D method)
setNext() (molSimplify.Classes.monomer3D.monomer3D method)
setPDBCode() (molSimplify.Classes.protein3D.protein3D method)
setPdistance() (in module molSimplify.Scripts.geometry)
setPdistanceu() (in module molSimplify.Scripts.geometry)
setPrev() (molSimplify.Classes.monomer3D.monomer3D method)
setR() (molSimplify.Classes.protein3D.protein3D method)
setRfree() (molSimplify.Classes.protein3D.protein3D method)
setRSRZ() (molSimplify.Classes.protein3D.protein3D method)
setTwinL() (molSimplify.Classes.protein3D.protein3D method)
setTwinL2() (molSimplify.Classes.protein3D.protein3D method)
shave__type() (in module molSimplify.Scripts.cellbuilder_tools)
shave_surface_layer() (in module molSimplify.Scripts.cellbuilder_tools)
shave_under_layer() (in module molSimplify.Scripts.cellbuilder_tools)
slab_module_supervisor() (in module molSimplify.Scripts.cellbuilder)
smartreorderligs() (in module molSimplify.Scripts.structgen)
staggered2_align_coord() (in module molSimplify.Scripts.cellbuilder)
startgen() (in module molSimplify.Scripts.generator)
startgen_pythonic() (in module molSimplify.Scripts.generator)
stripAtoms() (molSimplify.Classes.protein3D.protein3D method)
stripHetMol() (molSimplify.Classes.protein3D.protein3D method)
structgen() (in module molSimplify.Scripts.structgen)
Structure_inspection() (molSimplify.Classes.mol3D.mol3D method)
summetric() (in module molSimplify.Informatics.autocorrelation)
surface_center() (in module molSimplify.Scripts.cellbuilder)
symbol() (molSimplify.Classes.atom3D.atom3D method)
symvect() (molSimplify.Classes.mol3D.mol3D method)
T
tcgen() (in module molSimplify.Scripts.qcgen)
test_case() (in module molSimplify.Scripts.rmsd)
testmatplotlib() (molSimplify.Classes.globalvars.globalvars method)
testTF() (molSimplify.Classes.globalvars.globalvars method)
threshold_basis() (in module molSimplify.Scripts.cellbuilder_tools)
threshold_vector() (in module molSimplify.Scripts.cellbuilder_tools)
tracked_merge() (in module molSimplify.Scripts.cellbuilder)
translate() (molSimplify.Classes.atom3D.atom3D method)
(molSimplify.Classes.mol3D.mol3D method)
Triangle() (in module molSimplify.Scripts.distgeom)
tribonddict() (molSimplify.Classes.globalvars.globalvars method)
typevect() (molSimplify.Classes.mol3D.mol3D method)
U
unit_to_super() (in module molSimplify.Scripts.cellbuilder)
V
vdwrad() (molSimplify.Classes.globalvars.globalvars method)
vecangle() (in module molSimplify.Scripts.geometry)
vecdiff() (in module molSimplify.Scripts.geometry)
W
write_periodic_mol3d_to_qe() (in module molSimplify.Scripts.periodic_QE)
write_report() (molSimplify.Classes.rundiag.run_diag method)
writegxyz() (molSimplify.Classes.mol3D.mol3D method)
writemol2() (molSimplify.Classes.mol3D.mol3D method)
writemxyz() (molSimplify.Classes.mol3D.mol3D method)
writenumberedxyz() (molSimplify.Classes.mol3D.mol3D method)
writesepxyz() (molSimplify.Classes.mol3D.mol3D method)
writexyz() (molSimplify.Classes.mol3D.mol3D method)
X
xgcd() (in module molSimplify.Scripts.cellbuilder_tools)
xtb_opt() (in module molSimplify.Scripts.structgen)
xyz2gxyz() (in module molSimplify.Scripts.qcgen)
Z
zero_x() (in module molSimplify.Scripts.cellbuilder_tools)
zero_y() (in module molSimplify.Scripts.cellbuilder_tools)
zero_z() (in module molSimplify.Scripts.cellbuilder_tools)
zero_z_csm() (in module molSimplify.Scripts.cellbuilder_tools)
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