SYMBOL INDEX (1494 symbols across 154 files)

FILE: benchmark_distance.py
  function old_distance (line 6) | def old_distance(r1, r2):
  function new_distance (line 11) | def new_distance(r1, r2):
  function benchmark (line 14) | def benchmark():

FILE: molSimplify/Classes/atom3D.py
  class atom3D (line 13) | class atom3D:
    method __init__ (line 30) | def __init__(self,
    method __repr__ (line 100) | def __repr__(self):
    method coords (line 111) | def coords(self):
    method distance (line 125) | def distance(self, atom2):
    method distancev (line 145) | def distancev(self, atom2):
    method ismetal (line 165) | def ismetal(self, transition_metals_only=True, include_X=False) -> bool:
    method setcoords (line 187) | def setcoords(self, xyz):
    method symbol (line 207) | def symbol(self) -> str:
    method mutate (line 219) | def mutate(self, newType='C'):
    method translate (line 241) | def translate(self, dxyz):
    method setEDIA (line 254) | def setEDIA(self, score):

FILE: molSimplify/Classes/dft_obs.py
  class dft_observation (line 23) | class dft_observation:
    method __init__ (line 24) | def __init__(self, name, geopath):
    method sety (line 34) | def sety(self, y_value):
    method obtain_mol3d (line 37) | def obtain_mol3d(self):
    method get_coord (line 48) | def get_coord(self):
    method get_descriptor_vector (line 51) | def get_descriptor_vector(self, lig_only, simple, flag_name=False, lou...
    method append_descriptors (line 98) | def append_descriptors(self, list_of_names, list_of_props, prefix, suf...
  function write_descriptor_csv (line 113) | def write_descriptor_csv(list_of_runs):

FILE: molSimplify/Classes/globalvars.py
  function mybash (line 590) | def mybash(cmd):
  function get_version (line 613) | def get_version():
  class globalvars (line 625) | class globalvars(metaclass=Singleton):
    method __init__ (line 628) | def __init__(self):
    method amass (line 741) | def amass(self) -> Dict[str, Tuple[float, int, float, int]]:
    method polarizability (line 751) | def polarizability(self) -> Dict[str, float]:
    method tribonddict (line 761) | def tribonddict(self):
    method bondsdict (line 771) | def bondsdict(self):
    method elementsbynum (line 781) | def elementsbynum(self):
    method endict (line 791) | def endict(self):
    method vdwrad (line 801) | def vdwrad(self):
    method metalslist (line 811) | def metalslist(self, transition_metals_only=True, include_X=False):
    method groups (line 837) | def groups(self):
    method periods (line 847) | def periods(self):
    method geo_check_dictionary (line 857) | def geo_check_dictionary(self):
    method get_all_geometries (line 867) | def get_all_geometries(self):
    method get_all_angle_refs (line 877) | def get_all_angle_refs(self):
    method get_all_polyhedra (line 887) | def get_all_polyhedra(self):
    method add_custom_path (line 897) | def add_custom_path(self, path):
    method bbcombs_mononuc (line 909) | def bbcombs_mononuc(self):
    method testTF (line 961) | def testTF(self):
    method testmatplotlib (line 977) | def testmatplotlib(self):
    method getAllAAs (line 993) | def getAllAAs(self):

FILE: molSimplify/Classes/helpers.py
  function read_atom (line 13) | def read_atom(line):
  function makeMol (line 41) | def makeMol(a_dict, mols, conf, chains, prev_a_dict, bonds, aa=True):

FILE: molSimplify/Classes/ligand.py
  class ligand (line 17) | class ligand:
    method __init__ (line 35) | def __init__(self, master_mol, index_list, dent, read_lig=False):
    method __repr__ (line 71) | def __repr__(self):
    method obtain_mol3d (line 78) | def obtain_mol3d(self):
    method get_lig_mol2 (line 110) | def get_lig_mol2(self, transition_metals_only=True, inds=None, include...
    method percent_buried_vol (line 187) | def percent_buried_vol(self, radius=3.5, gridspec=0.1,
  function ligand_breakdown (line 266) | def ligand_breakdown(mol, BondedOct=False, silent=True, transition_metal...
  function ligand_assign_original (line 328) | def ligand_assign_original(mol, liglist, ligdents, ligcons, loud=False, ...
  function ligand_assign_consistent (line 762) | def ligand_assign_consistent(mol, liglist, ligdents, ligcons, loud=False,
  function ligand_assign_alleq (line 1951) | def ligand_assign_alleq(mol, liglist, ligdents, ligcons):
  function get_lig_symmetry (line 2000) | def get_lig_symmetry(mol, loud=False, htol=3):

FILE: molSimplify/Classes/mol2D.py
  class Mol2D (line 19) | class Mol2D(nx.Graph):
    method __repr__ (line 21) | def __repr__(self):
    method from_smiles (line 37) | def from_smiles(cls, smiles: str):
    method from_mol2_file (line 81) | def from_mol2_file(cls, filename):
    method from_mol_file (line 107) | def from_mol_file(cls, filename):
    method from_mol3d (line 132) | def from_mol3d(cls, mol3d: Mol3D):
    method graph_hash (line 145) | def graph_hash(self) -> str:
    method graph_hash_edge_attr (line 170) | def graph_hash_edge_attr(self) -> str:
    method graph_determinant (line 202) | def graph_determinant(self, return_string: bool = True) -> Union[str, ...
    method find_metal (line 252) | def find_metal(self, transition_metals_only: bool = True) -> List[int]:
    method find_simple_paths (line 282) | def find_simple_paths(self, source, sink, cutoff=None, constraints=None):
    method denticity_hapticity (line 308) | def denticity_hapticity(self, catoms):
  function substructure_search (line 356) | def substructure_search(
  function motif_counts_only (line 453) | def motif_counts_only(

FILE: molSimplify/Classes/mol3D.py
  class mol3D (line 237) | class mol3D:
    method __init__ (line 250) | def __init__(self, name='ABC', loc='', use_atom_specific_cutoffs=False):
    method __repr__ (line 325) | def __repr__(self):
    method ACM (line 328) | def ACM(self, idx1, idx2, idx3, angle):
    method ACM_axis (line 372) | def ACM_axis(self, idx1, idx2, axis, angle):
    method BCM (line 408) | def BCM(self, idx1, idx2, d):
    method BCM_opt (line 445) | def BCM_opt(self, idx1, idx2, d, ff='uff'):
    method IsOct (line 481) | def IsOct(self, init_mol=None, dict_check=False,
    method IsStructure (line 616) | def IsStructure(self, init_mol=None, dict_check=False,
    method Oct_inspection (line 733) | def Oct_inspection(self, init_mol=None, catoms_arr=None, dict_check=Fa...
    method RCAngle (line 838) | def RCAngle(self, idx1, idx2, idx3, anglei, anglef, angleint=1.0, writ...
    method RCDistance (line 894) | def RCDistance(self, idx1, idx2, disti, distf, distint=0.05, writegeo=...
    method Structure_inspection (line 948) | def Structure_inspection(self, init_mol=None, catoms_arr=None, num_coo...
    method addAtom (line 1054) | def addAtom(self, atom: atom3D, index: Optional[int] = None, auto_popu...
    method add_bond (line 1130) | def add_bond(self, idx1: int, idx2: int, bond_type: int) -> dict:
    method alignmol (line 1173) | def alignmol(self, atom1, atom2):
    method apply_ffopt (line 1190) | def apply_ffopt(self, constraints=False, ff='uff'):
    method apply_ffopt_list_constraints (line 1224) | def apply_ffopt_list_constraints(self, list_constraints=False, ff='uff'):
    method aromatic_charge (line 1259) | def aromatic_charge(self, bo_graph):
    method assign_graph_from_net (line 1284) | def assign_graph_from_net(self, path_to_net, return_graph=False):
    method calcCharges (line 1315) | def calcCharges(self, charge=0, method='QEq'):
    method centermass (line 1333) | def centermass(self):
    method centersym (line 1361) | def centersym(self):
    method check_angle_linear (line 1384) | def check_angle_linear(self, catoms_arr=None):
    method choose_atoms_to_move (line 1428) | def choose_atoms_to_move(self, ligands, swap_indices, catoms):
    method cleanBonds (line 1498) | def cleanBonds(self):
    method closest_H_2_metal (line 1510) | def closest_H_2_metal(self, delta=0):
    method combine (line 1551) | def combine(self, mol, bond_to_add=[], dirty=False):
    method continuous_shape_measure (line 1618) | def continuous_shape_measure(self, ideal_polyhedron):
    method convert2OBMol (line 1693) | def convert2OBMol(self, force_clean=False, ignoreX=False):
    method convert2OBMol2 (line 1739) | def convert2OBMol2(self, ignoreX=False):
    method convert2mol3D (line 1785) | def convert2mol3D(self):
    method convexhull (line 1808) | def convexhull(self):
    method coords (line 1830) | def coords(self, no_tabs=False):
    method coordsvect (line 1854) | def coordsvect(self):
    method copymol3D (line 1871) | def copymol3D(self, mol0):
    method count_atoms (line 1902) | def count_atoms(self, exclude=['H', 'h', 'x', 'X']):
    method count_electrons (line 1923) | def count_electrons(self, charge=0):
    method count_nonH_atoms (line 1944) | def count_nonH_atoms(self):
    method count_specific_atoms (line 1960) | def count_specific_atoms(self, atom_types=['x', 'X']):
    method createMolecularGraph (line 1981) | def createMolecularGraph(self, oct=True, strict_cutoff=False, catom_li...
    method create_mol_with_inds (line 2032) | def create_mol_with_inds(self, inds):
    method deleteHs (line 2066) | def deleteHs(self):
    method deleteatom (line 2077) | def deleteatom(self, atomIdx):
    method deleteatoms (line 2115) | def deleteatoms(self, Alist):
    method dev_from_ideal_geometry (line 2154) | def dev_from_ideal_geometry(self, ideal_polyhedron: np.ndarray) -> Tup...
    method dict_check_processing (line 2225) | def dict_check_processing(self, dict_check, num_coord=6, debug=False, ...
    method distance (line 2285) | def distance(self, mol):
    method draw_svg (line 2305) | def draw_svg(self, filename):
    method findAtomsbySymbol (line 2331) | def findAtomsbySymbol(self, sym: str) -> List[int]:
    method findMetal (line 2352) | def findMetal(self, transition_metals_only: bool = True,
    method findcloseMetal (line 2383) | def findcloseMetal(self, atom0):
    method findsubMol (line 2414) | def findsubMol(self, atom0, atomN, smart=False):
    method flip_symmetry (line 2465) | def flip_symmetry(self, verbose=True, max_allowed_dev=30, target_symme...
    method freezeatom (line 2864) | def freezeatom(self, atomIdx):
    method freezeatoms (line 2876) | def freezeatoms(self, Alist):
    method from_smiles (line 2891) | def from_smiles(cls, smiles, gen3d: bool = True):
    method geo_dict_initialization (line 2924) | def geo_dict_initialization(self):
    method geo_maxatomdist (line 2942) | def geo_maxatomdist(self, mol2):
    method geo_rmsd (line 2983) | def geo_rmsd(self, mol2):
    method getAngle (line 3025) | def getAngle(self, idx0, idx1, idx2):
    method getAtom (line 3053) | def getAtom(self, idx):
    method getAtomCoords (line 3070) | def getAtomCoords(self, idx):
    method getAtomTypes (line 3087) | def getAtomTypes(self):
    method getAtoms (line 3104) | def getAtoms(self):
    method getAtomwithSyms (line 3120) | def getAtomwithSyms(self, syms=['X'], return_index=False):
    method getAtomwithinds (line 3146) | def getAtomwithinds(self, inds):
    method getBondCutoff (line 3163) | def getBondCutoff(self, atom: atom3D, ratom: atom3D) -> float:
    method getBondedAtoms (line 3193) | def getBondedAtoms(self, idx: int) -> List[int]:
    method getBondedAtomsBOMatrix (line 3224) | def getBondedAtomsBOMatrix(self, idx):
    method getBondedAtomsBOMatrixAug (line 3248) | def getBondedAtomsBOMatrixAug(self, idx):
    method getBondedAtomsByCoordNo (line 3272) | def getBondedAtomsByCoordNo(self, idx, CoordNo=6):
    method getBondedAtomsByThreshold (line 3305) | def getBondedAtomsByThreshold(self, idx, threshold=1.15):
    method getBondedAtomsH (line 3347) | def getBondedAtomsH(self, idx):
    method getBondedAtomsOct (line 3377) | def getBondedAtomsOct(self, ind, CN=6, debug=False, flag_loose=False, ...
    method getBondedAtomsSmart (line 3508) | def getBondedAtomsSmart(self, idx, oct=False, strict_cutoff=False, cat...
    method getBondedAtomsnotH (line 3534) | def getBondedAtomsnotH(self, idx, metal_multiplier=1.35, nonmetal_mult...
    method getClosestAtom (line 3568) | def getClosestAtom(self, ratom):
    method getClosestAtomlist (line 3592) | def getClosestAtomlist(self, atom_idx, cdist=3.0):
    method getClosestAtomnoHs (line 3616) | def getClosestAtomnoHs(self, ratom):
    method getFarAtom (line 3640) | def getFarAtom(self, reference, atomtype=False):
    method getHs (line 3675) | def getHs(self):
    method getHsbyAtom (line 3691) | def getHsbyAtom(self, ratom):
    method getHsbyIndex (line 3714) | def getHsbyIndex(self, idx):
    method getMLBondLengths (line 3736) | def getMLBondLengths(self):
    method getNumAtoms (line 3763) | def getNumAtoms(self):
    method getOBMol (line 3775) | def getOBMol(self, fst, convtype, ffclean=False, gen3d=True):
    method get_bo_dict_from_inds (line 3818) | def get_bo_dict_from_inds(self, inds):
    method get_coordinate_array (line 3850) | def get_coordinate_array(self):
    method get_element_list (line 3874) | def get_element_list(self):
    method get_fcs (line 3894) | def get_fcs(self, strict_cutoff=False, catom_list=None, max6=True):
    method get_features (line 3921) | def get_features(self, lac=True, force_generate=False, eq_sym=False,
    method get_first_shell (line 4007) | def get_first_shell(self, check_hapticity=True):
    method get_geometry_type (line 4067) | def get_geometry_type(self, dict_check=False, angle_ref=False,
    method get_geometry_type_distance (line 4161) | def get_geometry_type_distance(
    method get_geometry_type_old (line 4262) | def get_geometry_type_old(self, dict_check=False, angle_ref=False, num...
    method get_graph (line 4400) | def get_graph(self):
    method get_graph_hash (line 4419) | def get_graph_hash(self, attributed_flag=True, oct=False, loud=True):
    method get_linear_angle (line 4466) | def get_linear_angle(self, ind):
    method get_mol_graph_det (line 4494) | def get_mol_graph_det(self, oct=True, use_bo_mat=False):
    method get_molecular_mass (line 4562) | def get_molecular_mass(self):
    method get_num_coord_metal (line 4589) | def get_num_coord_metal(self, debug=False, strict_cutoff=False, catom_...
    method get_octetrule_charge (line 4662) | def get_octetrule_charge(self, debug=False):
    method get_pair_distance (line 4728) | def get_pair_distance(self, idx1, idx2):
    method get_smiles (line 4748) | def get_smiles(self, canonicalize=False, use_mol2=False) -> str:
    method get_smilesOBmol_charge (line 4780) | def get_smilesOBmol_charge(self):
    method get_submol_noHs (line 4812) | def get_submol_noHs(self):
    method get_symmetry (line 4831) | def get_symmetry(self, verbose=True, max_allowed_dev=30, details=False):
    method get_symmetry_denticity (line 5044) | def get_symmetry_denticity(self, return_eq_catoms=False, BondedOct=Fal...
    method getfarAtomdir (line 5123) | def getfarAtomdir(self, uP):
    method getfragmentlists (line 5147) | def getfragmentlists(self):
    method graph_from_bodict (line 5182) | def graph_from_bodict(self, bo_dict):
    method initialize (line 5201) | def initialize(self):
    method isPristine (line 5214) | def isPristine(self, unbonded_min_dist=1.3, oct=False):
    method is_edge_compound (line 5261) | def is_edge_compound(self, transition_metals_only: bool = True) -> Tup...
    method is_linear_ligand (line 5309) | def is_linear_ligand(self, ind):
    method is_sandwich_compound (line 5358) | def is_sandwich_compound(self, transition_metals_only: bool = True
    method ligand_comp_org (line 5423) | def ligand_comp_org(self, init_mol, catoms_arr=None,
    method make_formula (line 5536) | def make_formula(self, latex=True, hill_system=False):
    method match_lig_list (line 5606) | def match_lig_list(self, init_mol, catoms_arr=None,
    method maxatomdist (line 5749) | def maxatomdist(self, mol2):
    method maxatomdist_nonH (line 5779) | def maxatomdist_nonH(self, mol2):
    method maxdist (line 5810) | def maxdist(self, mol):
    method meanabsdev (line 5832) | def meanabsdev(self, mol2):
    method mindist_legacy (line 5864) | def mindist_legacy(self, mol):
    method mindistmol (line 5886) | def mindistmol(self):
    method mindistnonH (line 5904) | def mindistnonH(self, mol):
    method mindisttopoint (line 5927) | def mindisttopoint(self, point):
    method mol3D_to_networkx (line 5949) | def mol3D_to_networkx(self,get_symbols:bool=True,get_bond_order:bool=T...
    method mols_symbols (line 5972) | def mols_symbols(self):
    method molsize (line 5984) | def molsize(self):
    method moments_of_inertia (line 6002) | def moments_of_inertia(self):
    method num_rings (line 6032) | def num_rings(self, index):
    method oct_comp (line 6068) | def oct_comp(self, angle_ref=False, catoms_arr=None, debug=False):
    method overlapcheck (line 6166) | def overlapcheck(self, mol, silence=False):
    method populateBOMatrix (line 6195) | def populateBOMatrix(self, bonddict=False, set_bo_mat=False):
    method populateBOMatrixAug (line 6234) | def populateBOMatrixAug(self):
    method principal_moments_of_inertia (line 6267) | def principal_moments_of_inertia(self, return_eigvecs=False):
    method print_geo_dict (line 6297) | def print_geo_dict(self):
    method printxyz (line 6320) | def printxyz(self):
    method read_bo_from_mol (line 6331) | def read_bo_from_mol(self, molfile):
    method read_bond_order (line 6339) | def read_bond_order(self, bofile):
    method read_charge (line 6380) | def read_charge(self, chargefile):
    method read_smiles (line 6402) | def read_smiles(self, smiles, ff="mmff94", steps=2500):
    method readfrommol (line 6448) | def readfrommol(self, filename):
    method readfrommol2 (line 6508) | def readfrommol2(self, filename, readstring=False):
    method readfromstring (line 6601) | def readfromstring(self, xyzstring):
    method readfromtxt (line 6638) | def readfromtxt(self, txt):
    method readfromxyz (line 6669) | def readfromxyz(self, filename: str, ligand_unique_id=False, read_fina...
    method reflect_coords (line 6748) | def reflect_coords(self, metal_coords, lig1_catom_coords, lig2_catom_c...
    method resetBondOBMol (line 6785) | def resetBondOBMol(self):
    method returnxyz (line 6800) | def returnxyz(self, no_tabs=False):
    method rmsd (line 6824) | def rmsd(self, mol2):
    method rmsd_nonH (line 6857) | def rmsd_nonH(self, mol2):
    method roland_combine (line 6888) | def roland_combine(self, mol, catoms, bond_to_add=[], dirty=False):
    method mindist (line 6962) | def mindist(self, mol, exclude1=[], exclude2=[]):
    method substruct_add (line 6992) | def substruct_add(self, dec, base_idx, sub_idx, force_field=True):
    method sanitycheck (line 7145) | def sanitycheck(self, silence=False, debug=False):
    method sanitycheckCSD (line 7193) | def sanitycheckCSD(self, oct=False, angle1=30, angle2=80, angle3=45, d...
    method setLoc (line 7271) | def setLoc(self, loc):
    method symvect (line 7283) | def symvect(self):
    method translate (line 7300) | def translate(self, dxyz):
    method typevect (line 7313) | def typevect(self):
    method writegxyz (line 7330) | def writegxyz(self, filename):
    method writemol (line 7350) | def writemol(self, filename):
    method new_writemol2 (line 7415) | def new_writemol2(
    method writemol2 (line 7543) | def writemol2(self, filename, writestring=False, ignoreX=False, force=...
    method writemol2_bodict (line 7650) | def writemol2_bodict(
    method writemxyz (line 7773) | def writemxyz(self, mol, filename, no_tabs=False):
    method writenumberedxyz (line 7802) | def writenumberedxyz(self, filename):
    method writesepxyz (line 7830) | def writesepxyz(self, mol, filename):
    method writexyz (line 7856) | def writexyz(self, filename, symbsonly=True, ignoreX=False,

FILE: molSimplify/Classes/monomer3D.py
  class monomer3D (line 9) | class monomer3D:
    method __init__ (line 15) | def __init__(self, three_lc='GLY', chain='undef', id=-1, occup=1.00, l...
    method __repr__ (line 46) | def __repr__(self):
    method identify (line 49) | def identify(self):
    method getGreek (line 67) | def getGreek(self, greek):
    method coords (line 87) | def coords(self):
    method centermass (line 102) | def centermass(self):
    method centroid (line 131) | def centroid(self):
    method setBonds (line 154) | def setBonds(self):
    method getPeptideAtoms (line 193) | def getPeptideAtoms(self):
    method setNext (line 203) | def setNext(self, next_aa):
    method setPrev (line 213) | def setPrev(self, prev_aa):
    method addAtom (line 223) | def addAtom(self, atom, index=None):
    method setLoc (line 245) | def setLoc(self, loc):

FILE: molSimplify/Classes/partialcharges.py
  function fpriority (line 9) | def fpriority(xyzf):
  function fsym (line 106) | def fsym(xyzf):
  function fvalency (line 122) | def fvalency(xyzf):
  function fcharge (line 138) | def fcharge(xyzf, charge):
  function scharge_ave (line 155) | def scharge_ave(xyzf, charge):
  function fdistance (line 178) | def fdistance(xyzf):
  function all_prop (line 196) | def all_prop(xyzf, charge):
  function features (line 208) | def features(xyzf, charge):

FILE: molSimplify/Classes/protein3D.py
  class protein3D (line 27) | class protein3D:
    method __init__ (line 34) | def __init__(self, pdbCode='undef'):
    method setAAs (line 82) | def setAAs(self, aas):
    method setAtoms (line 95) | def setAtoms(self, atoms):
    method setIndices (line 107) | def setIndices(self, a_ids):
    method setHetmols (line 118) | def setHetmols(self, hetmols):
    method setChains (line 131) | def setChains(self, chains):
    method setMissingAtoms (line 144) | def setMissingAtoms(self, missing_atoms):
    method setMissingAAs (line 156) | def setMissingAAs(self, missing_aas):
    method setConf (line 167) | def setConf(self, conf):
    method autoChooseConf (line 178) | def autoChooseConf(self):
    method setR (line 212) | def setR(self, R):
    method setRfree (line 223) | def setRfree(self, Rfree):
    method setRSRZ (line 234) | def setRSRZ(self, RSRZ):
    method getMissingAtoms (line 245) | def getMissingAtoms(self):
    method getMissingAAs (line 262) | def getMissingAAs(self):
    method countAAs (line 276) | def countAAs(self):
    method findAtom (line 290) | def findAtom(self, sym="X", aa=True):
    method findAA (line 335) | def findAA(self, three_lc="XAA"):
    method getChain (line 367) | def getChain(self, chain_id):
    method getMolecule (line 450) | def getMolecule(self, a_id, aas_only=False):
    method stripAtoms (line 497) | def stripAtoms(self, atoms_stripped):
    method stripHetMol (line 578) | def stripHetMol(self, hetmol):
    method findMetal (line 611) | def findMetal(self, transition_metals_only=True):
    method freezeatom (line 644) | def freezeatom(self, atomIdx):
    method freezeatoms (line 656) | def freezeatoms(self, Alist):
    method getAtom (line 670) | def getAtom(self, idx):
    method getIndex (line 687) | def getIndex(self, atom):
    method getBoundMols (line 708) | def getBoundMols(self, h_id, aas_only=False):
    method readfrompdb (line 734) | def readfrompdb(self, text):
    method fetch_pdb (line 915) | def fetch_pdb(self, pdbCode):
    method setBonds (line 942) | def setBonds(self, bonds):
    method readMetaData (line 956) | def readMetaData(self):
    method setDataCompleteness (line 1010) | def setDataCompleteness(self, DataCompleteness):
    method setTwinL (line 1021) | def setTwinL(self, TwinL):
    method setTwinL2 (line 1032) | def setTwinL2(self, TwinL2):
    method setEDIAScores (line 1043) | def setEDIAScores(self):
    method setPDBCode (line 1095) | def setPDBCode(self, pdbCode):
    method centermass (line 1106) | def centermass(self):
    method setCentroid (line 1132) | def setCentroid(self):
    method convexhull (line 1156) | def convexhull(self):

FILE: molSimplify/Classes/rundiag.py
  class run_diag (line 9) | class run_diag:
    method __init__ (line 15) | def __init__(self):
    method set_sanity (line 37) | def set_sanity(self, sanity, min_distance):
    method set_ANN (line 52) | def set_ANN(self, ANN_flag, ANN_reason=False, ANN_dict=False, catalysi...
    method set_dict_bl (line 84) | def set_dict_bl(self, dict_bl):
    method set_mol (line 97) | def set_mol(self, mol):
    method write_report (line 113) | def write_report(self, path):

FILE: molSimplify/Classes/voxelgrid.py
  class VoxelGrid (line 8) | class VoxelGrid:
    method __init__ (line 9) | def __init__(self, voxel_size=0.5, vdw_scale=0.9):
    method copy (line 22) | def copy(self):
    method get_clash_severity (line 31) | def get_clash_severity(self, coords_lig, elements_lig, coords_complex,...
    method _to_voxel_index (line 56) | def _to_voxel_index(self, coord):
    method _get_voxel_sphere_indices (line 59) | def _get_voxel_sphere_indices(self, center, radius):
    method add_atom (line 74) | def add_atom(self, element, coord, atom_id=None, group="complex"):
    method add_atoms (line 89) | def add_atoms(self, elements, coords, atom_ids=None, group="complex", ...
    method get_voxel_status (line 119) | def get_voxel_status(self, coord, radius):
    method has_cross_clash (line 135) | def has_cross_clash(self, coord, radius):
    method get_clashing_atoms (line 143) | def get_clashing_atoms(self, verbose=False):
    method get_clashing_ligand_atoms (line 168) | def get_clashing_ligand_atoms(self):
    method has_voxel_clash (line 171) | def has_voxel_clash(self):
  function plot_all_voxels (line 179) | def plot_all_voxels(
  function plot_voxels (line 267) | def plot_voxels(voxel_grid, group="both", mode="cube", size=50, silent=F...

FILE: molSimplify/Informatics/HFXsensitivity/measure_HFX_sensitivity_oxo_hat_reb_rel.py
  function measure_sensitivity (line 25) | def measure_sensitivity(path_to_csv, path_to_write=False, R2_cutoff=0.99...
  function measure_R2 (line 285) | def measure_R2(X, y):
  function CV_check (line 292) | def CV_check(X, y, name, prop, CV_tolerance, num_points):
  function R2_upon_elimination (line 322) | def R2_upon_elimination(X, y, name, prop, R2_cutoff, num_points):
  function slope_sign_check (line 360) | def slope_sign_check(X, y, name, prop, num_points):
  function main (line 425) | def main():

FILE: molSimplify/Informatics/HFXsensitivity/measure_HFX_stable.py
  function measure_sensitivity (line 24) | def measure_sensitivity(path_to_csv, path_to_write=False, prop='SSE', R2...
  function measure_R2 (line 223) | def measure_R2(X, y):
  function symmetry_class (line 229) | def symmetry_class(complex_name):
  function CV_check (line 243) | def CV_check(X, y, name, prop, CV_tolerance, R2_cutoff, num_points):
  function slope_sign_check (line 270) | def slope_sign_check(X, y, name, prop, num_points):
  function main (line 326) | def main():

FILE: molSimplify/Informatics/MOF/MOF_descriptors.py
  function get_primitive (line 59) | def get_primitive(data_path, write_path, occupancy_tolerance=1):
  function load_sbu_lc_descriptors (line 85) | def load_sbu_lc_descriptors(sbu_path: str) -> Tuple[str, pd.DataFrame, p...
  function gen_and_append_desc (line 114) | def gen_and_append_desc(
  function make_MOF_SBU_RACs (line 180) | def make_MOF_SBU_RACs(
  function make_MOF_linker_RACs (line 392) | def make_MOF_linker_RACs(
  function mkdir_if_absent (line 508) | def mkdir_if_absent(folder_paths):
  function make_file_if_absent (line 526) | def make_file_if_absent(path, filenames):
  function path_maker (line 547) | def path_maker(path):
  function failure_response (line 569) | def failure_response(path, failure_str):
  function bond_information_write (line 590) | def bond_information_write(linker_list, linker_anchors_superlist, adj_ma...
  function surrounded_sbu_gen (line 660) | def surrounded_sbu_gen(SBU_list, linker_list, sbu_path, molcif, adj_matr...
  function dist_mat_comp (line 831) | def dist_mat_comp(X):
  function detect_1D_rod (line 855) | def detect_1D_rod(molcif, all_atom_types, cpar, log_path, name, adj_matr...
  function get_MOF_descriptors (line 954) | def get_MOF_descriptors(

FILE: molSimplify/Informatics/MOF/MOF_functionalizer.py
  function functionalize_MOF (line 33) | def functionalize_MOF(cif_file,
  function first_functionalization (line 232) | def first_functionalization(molcif,
  function additional_functionalization (line 326) | def additional_functionalization(i,
  function apply_functionalization (line 451) | def apply_functionalization(molcif, all_atom_types, position_to_function...
  function analyze_linker (line 570) | def analyze_linker(cart_coords,
  function symmetry_check (line 619) | def symmetry_check(all_atom_types, fcoords, cell_v, precision=1):
  function linker_identification (line 661) | def linker_identification(linker_list, i, checked_list):
  function geo_dict_loader (line 699) | def geo_dict_loader():
  function vector_preparation (line 746) | def vector_preparation(connected_atom_types, neighbors_not_to_replace, l...
  function connecting_atom_functionalization (line 818) | def connecting_atom_functionalization(connection_atom_dict,
  function multiatomic_functionalization (line 854) | def multiatomic_functionalization(connection_atom_dict,
  function make_networkx_graph (line 945) | def make_networkx_graph(adj_matrix):
  function get_linkers (line 968) | def get_linkers(molcif, adj_matrix, all_atom_types):
  function connected_atoms_from_adjmat (line 1007) | def connected_atoms_from_adjmat(adj_matrix, index, all_atom_types):
  function check_support (line 1034) | def check_support(functional_group):
  function functionalize_MOF_at_indices (line 1060) | def functionalize_MOF_at_indices(cif_file, path2write, functional_group,...
  function functionalize_MOF_at_indices_mol3D_merge (line 1197) | def functionalize_MOF_at_indices_mol3D_merge(cif_file, path2write, funct...
  function alignment_objective (line 1367) | def alignment_objective(rotation_vector, molcif_clone, MOF_main_carbon_i...
  function post_functionalization_overlap_and_bonding_check (line 1429) | def post_functionalization_overlap_and_bonding_check(cell_v, all_atom_ty...
  function atom_deletion (line 1464) | def atom_deletion(cart_coords, all_atom_types, delete_list):
  function atom_addition (line 1504) | def atom_addition(extra_atom_types, final_atom_types, new_coord_list, ex...
  function DS_remover (line 1542) | def DS_remover(file_list):
  function mkdir_if_absent (line 1560) | def mkdir_if_absent(folder_path):
  function apply_monatomic_functionalization (line 1577) | def apply_monatomic_functionalization(molcif, all_atom_types, atom_to_re...
  function main (line 1594) | def main():

FILE: molSimplify/Informatics/MOF/MOF_functionalizer_v2.py
  function resource_filename (line 42) | def resource_filename(req_or_pkg: object, resource: str) -> str:
  function functionalize_MOF (line 53) | def functionalize_MOF(cif_file, path2write, functional_group = 'F', func...
  function first_functionalization (line 282) | def first_functionalization(cell_v, molcif,
  function additional_functionalization (line 377) | def additional_functionalization(cell_v, i,
  function apply_functionalization (line 518) | def apply_functionalization(cell_v, molcif, allatomtypes, position_to_fu...
  function functionalization_gram_schmidt (line 647) | def functionalization_gram_schmidt(molcif, geo_dict_loader_gram_schmidt,...
  function functional_group_rotation (line 711) | def functional_group_rotation(functional_group_coords, axis, rotation_an...
  function analyze_linker (line 724) | def analyze_linker(cart_coords,
  function symmetry_check (line 773) | def symmetry_check(allatomtypes, fcoords, cell_v, precision=1):
  function linker_identification (line 821) | def linker_identification(linker_list, i, checkedlist):
  function geo_dict_loader (line 859) | def geo_dict_loader():
  function vector_preparation (line 906) | def vector_preparation(connected_atom_types, neighbors_not_to_replace, l...
  function connecting_atom_functionalization (line 978) | def connecting_atom_functionalization(connection_atom_dict,
  function multiatomic_functionalization (line 1014) | def multiatomic_functionalization(connection_atom_dict,
  function make_networkx_graph (line 1120) | def make_networkx_graph(adj_matrix):
  function get_linkers (line 1143) | def get_linkers(molcif, adj_matrix, allatomtypes):
  function connected_atoms_from_adjmat (line 1185) | def connected_atoms_from_adjmat(adj_matrix, index, allatomtypes):
  function apply_monatomic_functionalization (line 1212) | def apply_monatomic_functionalization(molcif, allatomtypes, atom_to_repl...
  function check_support (line 1227) | def check_support(functional_group):
  function functionalize_MOF_at_indices (line 1255) | def functionalize_MOF_at_indices(cif_file, path2write, functional_group,...
  function functionalize_MOF_at_indices_mol3D_merge (line 1394) | def functionalize_MOF_at_indices_mol3D_merge(cif_file, path2write, funct...
  function alignment_objective (line 1567) | def alignment_objective(rotation_vector, molcif_clone, MOF_main_carbon_i...
  function post_functionalization_overlap_and_bonding_check (line 1631) | def post_functionalization_overlap_and_bonding_check(cell_v, all_atom_ty...
  function atom_deletion (line 1695) | def atom_deletion(cart_coords, allatomtypes, delete_list):
  function atom_addition (line 1735) | def atom_addition(extra_atom_types, final_atom_types, new_coord_list, ex...
  function DS_remover (line 1773) | def DS_remover(file_list):
  function mkdir_if_absent (line 1791) | def mkdir_if_absent(folder_path):
  function main (line 1810) | def main():

FILE: molSimplify/Informatics/MOF/PBC_functions.py
  function readcif (line 17) | def readcif(name, readstring=False):
  function compute_image_flag (line 131) | def compute_image_flag(cell, fcoord1, fcoord2):
  function linker_length (line 159) | def linker_length(adjmat, anchors):
  function slice_mat (line 191) | def slice_mat(mat, atoms):
  function ligand_detect (line 210) | def ligand_detect(cell, cart_coords, adj_mat, anchor_list):
  function XYZ_connected (line 256) | def XYZ_connected(cell, cart_coords, adj_mat):
  function writeXYZfcoords (line 308) | def writeXYZfcoords(filename, atoms, cell, fcoords):
  function writeXYZandGraph (line 335) | def writeXYZandGraph(filename, atoms, cell, fcoords, mol_graph):
  function returnXYZandGraph (line 366) | def returnXYZandGraph(filename, atoms, cell, fcoords, mol_graph):
  function writeXYZcoords (line 400) | def writeXYZcoords(filename, atoms, coords):
  function writeXYZcoords_withcomment (line 424) | def writeXYZcoords_withcomment(filename, atoms, coords, comment):
  function write2file (line 451) | def write2file(pt, fn, st):
  function write_cif (line 472) | def write_cif(fname, cellprm, fcoords, atom_labels):
  function mkcell (line 512) | def mkcell(cpar):
  function cell_to_cellpar (line 547) | def cell_to_cellpar(cell, radians=False):
  function findPaths (line 581) | def findPaths(G, u, n):
  function fractional2cart (line 608) | def fractional2cart(fcoords, cell):
  function frac_coord (line 627) | def frac_coord(coord, cell):
  function compute_distance_matrix (line 647) | def compute_distance_matrix(cell, cart_coords, num_cells=1):
  function position_nearest_atom (line 686) | def position_nearest_atom(cell, cart_coords, index_of_interest, num_cell...
  function make_graph_from_nodes_edges (line 739) | def make_graph_from_nodes_edges(nodes, edges, attribs):
  function make_supercell (line 763) | def make_supercell(cell, atoms, fcoords, exp_coeff):
  function compute_adj_matrix (line 811) | def compute_adj_matrix(distance_mat, all_atom_types, wiggle_room=1, hand...
  function get_closed_subgraph (line 899) | def get_closed_subgraph(linkers, SBU_list, adj_matrix):
  function include_extra_shells (line 962) | def include_extra_shells(SBU_lists, molcif, adjmat):
  function disorder_detector (line 995) | def disorder_detector(name):
  function remove_duplicate_atoms (line 1069) | def remove_duplicate_atoms(all_atom_types, fcoords):
  function remove_undesired_atoms (line 1098) | def remove_undesired_atoms(undesired_indices, all_atom_types, fcoords):
  function overlap_removal (line 1128) | def overlap_removal(cif_path, new_cif_path):
  function solvent_removal (line 1166) | def solvent_removal(cif_path, new_cif_path, wiggle_room=1):

FILE: molSimplify/Informatics/MOF/cluster_extraction.py
  function get_primitive (line 24) | def get_primitive(data_path, write_path):
  function make_MOF_SBU_RACs (line 39) | def make_MOF_SBU_RACs(SBU_list, SBU_subgraph, molcif, depth, name, cell,...
  function make_MOF_linker_RACs (line 111) | def make_MOF_linker_RACs(linker_list, linker_subgraphlist, molcif, depth...
  function get_MOF_descriptors (line 129) | def get_MOF_descriptors(data, depth, path=False, xyz_path = False):

FILE: molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
  function periodic_checker (line 28) | def periodic_checker(graph, coords):
  function branch (line 63) | def branch(molcif, main_paths, atoms_in_sbu, new_atoms=None):
  function identify_main_chain (line 104) | def identify_main_chain(temp_mol, link_list):
  function get_molcif_cycles_no_metal (line 165) | def get_molcif_cycles_no_metal(molcif):
  function breakdown_MOF (line 199) | def breakdown_MOF(SBU_list, SBU_subgraph, molcif, name, cell, anchoring_...
  function prepare_initial_SBU (line 504) | def prepare_initial_SBU(molcif, all_atom_types, metal_list, log_path, na...
  function identify_lc_atoms (line 552) | def identify_lc_atoms(molcif, remove_list, metal_list):
  function identify_short_linkers (line 605) | def identify_short_linkers(molcif, initial_SBU_list, initial_SBU_subgrap...
  function make_MOF_fragments (line 739) | def make_MOF_fragments(data, path, xyz_path):

FILE: molSimplify/Informatics/MOF/linker_rotation.py
  function rotate_around_axis (line 16) | def rotate_around_axis(axis, r, p, t):
  function linker_rotation (line 62) | def linker_rotation(molcif, fcoords, linker, rot_angle, cell_v, all_atom...
  function rotate_and_write (line 149) | def rotate_and_write(input_cif, path2write, rot_angle, is_degree=True):
  function main (line 215) | def main():

FILE: molSimplify/Informatics/Mol2Parser.py
  class Mol2Parser (line 4) | class Mol2Parser:
    method __init__ (line 8) | def __init__(self, mol2path):
    method build_BO_matrix (line 14) | def build_BO_matrix(self):
    method get_atoms (line 24) | def get_atoms(self):
    method get_connectivity (line 36) | def get_connectivity(self):

FILE: molSimplify/Informatics/RACassemble.py
  function assemble_connectivity_from_parts (line 41) | def assemble_connectivity_from_parts(metal_mol: mol3D, custom_ligand_dict):
  function get_descriptor_vector (line 93) | def get_descriptor_vector(this_complex, custom_ligand_dict=False,
  function get_rac155_graph_based (line 194) | def get_rac155_graph_based(this_complex, custom_ligand_dict=False, ox_mo...
  function get_descriptor_derivatives (line 217) | def get_descriptor_derivatives(this_complex, custom_ligand_dict=False, o...
  function create_OHE (line 320) | def create_OHE(metal: str,
  function append_descriptor_derivatives (line 365) | def append_descriptor_derivatives(descriptor_derivative_names, descripto...

FILE: molSimplify/Informatics/active_learning/expected_improvement.py
  function get_2D_pareto_indices (line 6) | def get_2D_pareto_indices(points: np.ndarray) -> np.ndarray:
  function get_2D_EI (line 38) | def get_2D_EI(pred_mean: np.ndarray, pred_std: np.ndarray,
  function get_2D_PI_and_centroid (line 77) | def get_2D_PI_and_centroid(pred_mean: np.ndarray, pred_std: np.ndarray,
  function get_2D_EHVI (line 203) | def get_2D_EHVI(pred_mean: np.ndarray, pred_std: np.ndarray,

FILE: molSimplify/Informatics/autocorrelation.py
  function append_descriptors (line 15) | def append_descriptors(descriptor_names, descriptors, list_of_names, lis...
  function append_descriptor_derivatives (line 70) | def append_descriptor_derivatives(descriptor_derivative_names, descripto...
  function autocorrelation (line 108) | def autocorrelation(mol, prop_vec, orig, d, oct=True, use_dist=False, si...
  function autocorrelation_derivative (line 173) | def autocorrelation_derivative(mol, prop_vec, orig, d, oct=True):
  function deltametric (line 227) | def deltametric(mol, prop_vec, orig, d, oct=True, use_dist=False, size_n...
  function deltametric_derivative (line 287) | def deltametric_derivative(mol, prop_vec, orig, d, oct=True):
  function construct_property_vector (line 338) | def construct_property_vector(mol, prop, oct=True, modifier=False, custo...
  function full_autocorrelation (line 482) | def full_autocorrelation(mol, prop, d, oct=True, modifier=False, use_dis...
  function full_autocorrelation_derivative (line 529) | def full_autocorrelation_derivative(mol, prop, d, oct=True, modifier=Fal...
  function generate_full_complex_autocorrelations (line 565) | def generate_full_complex_autocorrelations(mol,
  function generate_full_complex_autocorrelation_derivatives (line 666) | def generate_full_complex_autocorrelation_derivatives(mol, depth=4, oct=...
  function atom_only_autocorrelation (line 722) | def atom_only_autocorrelation(mol, prop, d, atomIdx, oct=True, use_dist=...
  function atom_only_autocorrelation_derivative (line 771) | def atom_only_autocorrelation_derivative(mol, prop, d, atomIdx, oct=True):
  function metal_only_autocorrelation (line 808) | def metal_only_autocorrelation(
  function metal_only_autocorrelation_derivative (line 871) | def metal_only_autocorrelation_derivative(
  function atom_only_deltametric (line 916) | def atom_only_deltametric(mol, prop, d, atomIdx, oct=True, modifier=False,
  function atom_only_deltametric_derivative (line 966) | def atom_only_deltametric_derivative(mol, prop, d, atomIdx, oct=True, mo...
  function metal_only_deltametric (line 1006) | def metal_only_deltametric(
  function metal_only_deltametric_derivative (line 1065) | def metal_only_deltametric_derivative(
  function generate_metal_autocorrelations (line 1109) | def generate_metal_autocorrelations(mol, depth=4, oct=True, flag_name=Fa...
  function generate_metal_autocorrelation_derivatives (line 1203) | def generate_metal_autocorrelation_derivatives(mol, depth=4, oct=True, f...
  function generate_metal_deltametrics (line 1262) | def generate_metal_deltametrics(mol, depth=4, oct=True, flag_name=False,
  function generate_metal_deltametric_derivatives (line 1371) | def generate_metal_deltametric_derivatives(mol, depth=4, oct=True, flag_...
  function generate_atomonly_autocorrelations (line 1430) | def generate_atomonly_autocorrelations(mol, atomIdx, depth=4, oct=True, ...
  function generate_atomonly_autocorrelation_derivatives (line 1512) | def generate_atomonly_autocorrelation_derivatives(mol, atomIdx, depth=4,...
  function generate_atomonly_deltametrics (line 1541) | def generate_atomonly_deltametrics(mol, atomIdx, depth=4, oct=True, Gval...
  function generate_atomonly_deltametric_derivatives (line 1637) | def generate_atomonly_deltametric_derivatives(mol, atomIdx, depth=4, oct...
  function get_metal_index (line 1666) | def get_metal_index(mol, transition_metals_only=True):
  function ratiometric (line 1688) | def ratiometric(mol, prop_vec_num, prop_vec_den, orig, d, oct=True):
  function summetric (line 1725) | def summetric(mol, prop_vec, orig, d, oct=True):
  function autocorrelation_catoms (line 1762) | def autocorrelation_catoms(mol, prop_vec, orig, d, oct=True, catoms=None):
  function deltametric_catoms (line 1787) | def deltametric_catoms(mol, prop_vec, orig, d, oct=True, catoms=None):
  function multiatom_only_autocorrelation (line 1811) | def multiatom_only_autocorrelation(mol, prop, d, oct=True,
  function atom_only_ratiometric (line 1827) | def atom_only_ratiometric(mol, prop_num, prop_den, d, atomIdx, oct=True):
  function atom_only_summetric (line 1842) | def atom_only_summetric(mol, prop, d, atomIdx, oct=True):
  function multiatom_only_deltametric (line 1856) | def multiatom_only_deltametric(mol, prop, d, oct=True,
  function metal_only_layer_density (line 1872) | def metal_only_layer_density(mol, prop, d, oct=True):
  function layer_density_in_3D (line 1884) | def layer_density_in_3D(mol, prop_vec, orig, d, oct=True):
  function find_ligand_autocorrelations_oct (line 1914) | def find_ligand_autocorrelations_oct(mol, prop, loud, depth, name=False,
  function find_ligand_autocorrelation_derivatives_oct (line 1978) | def find_ligand_autocorrelation_derivatives_oct(mol, prop, loud, depth, ...
  function find_ligand_autocorrs_and_deltametrics_oct_dimers (line 2050) | def find_ligand_autocorrs_and_deltametrics_oct_dimers(mol, prop, depth, ...
  function find_ligand_deltametrics_oct (line 2119) | def find_ligand_deltametrics_oct(mol, prop, loud, depth, name=False, oct...
  function find_ligand_deltametric_derivatives_oct (line 2162) | def find_ligand_deltametric_derivatives_oct(mol, prop, loud, depth, name...
  function generate_all_ligand_autocorrelations (line 2208) | def generate_all_ligand_autocorrelations(mol, loud, depth=4, name=False,...
  function generate_all_ligand_autocorrelation_derivatives (line 2262) | def generate_all_ligand_autocorrelation_derivatives(mol, loud, depth=4, ...
  function generate_all_ligand_autocorrs_and_deltametrics_dimers (line 2324) | def generate_all_ligand_autocorrs_and_deltametrics_dimers(mol, loud, dep...
  function generate_all_ligand_deltametrics (line 2385) | def generate_all_ligand_deltametrics(mol, loud, depth=4, name=False, fla...
  function generate_all_ligand_deltametric_derivatives (line 2420) | def generate_all_ligand_deltametric_derivatives(mol, loud, depth=4, name...
  function generate_multiatom_autocorrelations (line 2462) | def generate_multiatom_autocorrelations(mol, depth=4, oct=True, flag_nam...
  function generate_metal_ox_eff_autocorrelations (line 2482) | def generate_metal_ox_eff_autocorrelations(oxmodifier, mol, depth=4, oct...
  function generate_metal_ox_eff_deltametrics (line 2499) | def generate_metal_ox_eff_deltametrics(oxmodifier, mol, depth=4, oct=Tru...
  function generate_multiatom_deltametrics (line 2516) | def generate_multiatom_deltametrics(mol, depth=4, oct=True, flag_name=Fa...
  function generate_full_complex_coulomb_autocorrelations (line 2536) | def generate_full_complex_coulomb_autocorrelations(mol,
  function generate_metal_ox_autocorrelations (line 2562) | def generate_metal_ox_autocorrelations(oxmodifier, mol, depth=4,
  function generate_metal_ox_autocorrelation_derivatives (line 2583) | def generate_metal_ox_autocorrelation_derivatives(oxmodifier, mol, depth...
  function generate_metal_ox_deltametrics (line 2599) | def generate_metal_ox_deltametrics(oxmodifier, mol, depth=4, oct=True,
  function generate_metal_ox_deltametric_derivatives (line 2627) | def generate_metal_ox_deltametric_derivatives(oxmodifier, mol, depth=4, ...

FILE: molSimplify/Informatics/coulomb_analyze.py
  function create_columb_matrix (line 10) | def create_columb_matrix(mol):
  function create_coulomb_matrix (line 14) | def create_coulomb_matrix(mol):
  function pad_mol (line 49) | def pad_mol(mol, target_atoms):

FILE: molSimplify/Informatics/decoration_manager.py
  function decorate_molecule (line 32) | def decorate_molecule(mol: mol3D, dec_list, dec_idxs,

FILE: molSimplify/Informatics/geo_analyze.py
  function getOctBondDistances (line 13) | def getOctBondDistances(mol):
  function getLigFormulae (line 35) | def getLigFormulae(mol):
  function maximum_ML_dist (line 51) | def maximum_ML_dist(mol):
  function maximum_any_dist (line 61) | def maximum_any_dist(mol):
  function minimum_ML_dist (line 71) | def minimum_ML_dist(mol):
  function mean_ML_dist (line 81) | def mean_ML_dist(mol):

FILE: molSimplify/Informatics/geometrics.py
  function get_percentile_csd_geometrics (line 8) | def get_percentile_csd_geometrics(geometrics_csd, geodict, geotype, maxd...
  function get_percentile_from_mol2 (line 33) | def get_percentile_from_mol2(mol2string,

FILE: molSimplify/Informatics/graph_analyze.py
  function obtain_truncation (line 15) | def obtain_truncation(mol, con_atoms, hops):
  function obtain_truncation_metal (line 57) | def obtain_truncation_metal(mol, hops, transition_metals_only=True):
  function create_graph (line 106) | def create_graph(mol):
  function get_lig_EN (line 121) | def get_lig_EN(mol, connection_atoms):
  function remove_diagonals (line 137) | def remove_diagonals(matrix):
  function kier (line 144) | def kier(mol):
  function get_truncated_kier (line 162) | def get_truncated_kier(ligand, connection_atoms):

FILE: molSimplify/Informatics/graph_racs.py
  function racs_property_vector (line 9) | def racs_property_vector(mol: Mol2D, node: int) -> np.ndarray:
  function atom_centered_AC (line 40) | def atom_centered_AC(
  function multi_centered_AC (line 80) | def multi_centered_AC(
  function octahedral_racs (line 117) | def octahedral_racs(
  function octahedral_racs_names (line 248) | def octahedral_racs_names(depth=3, properties=None) -> List[str]:
  function ligand_racs (line 271) | def ligand_racs(
  function ligand_racs_names (line 315) | def ligand_racs_names(depth: int = 3, properties=None, full_scope: bool ...

FILE: molSimplify/Informatics/jupyter_vis.py
  function type_convert (line 15) | def type_convert(structures):
  function view_structures (line 81) | def view_structures(structures, w=400, h=400, columns=2,

FILE: molSimplify/Informatics/lacRACAssemble.py
  function get_descriptor_vector (line 40) | def get_descriptor_vector(this_complex,
  function get_descriptor_derivatives (line 251) | def get_descriptor_derivatives(this_complex, custom_ligand_dict=False, o...
  function generate_all_ligand_misc (line 381) | def generate_all_ligand_misc(mol, loud=False, custom_ligand_dict=False, ...
  function generate_all_ligand_autocorrelations_lac (line 487) | def generate_all_ligand_autocorrelations_lac(mol, loud=False, depth=4, f...
  function generate_all_ligand_autocorrelation_derivatives_lac (line 675) | def generate_all_ligand_autocorrelation_derivatives_lac(mol, loud=False,...
  function generate_all_ligand_deltametrics_lac (line 802) | def generate_all_ligand_deltametrics_lac(mol, loud=False, depth=4, flag_...
  function generate_all_ligand_deltametric_derivatives_lac (line 941) | def generate_all_ligand_deltametric_derivatives_lac(mol, loud=False, dep...

FILE: molSimplify/Informatics/misc_descriptors.py
  function generate_all_ligand_misc (line 8) | def generate_all_ligand_misc(mol, loud, custom_ligand_dict=False, force_...
  function generate_all_ligand_misc_dimers (line 125) | def generate_all_ligand_misc_dimers(mol, loud, custom_ligand_dict=False):

FILE: molSimplify/Informatics/organic_fingerprints.py
  function get_morgan (line 18) | def get_morgan(mol, morgan_radius=4):
  function get_substructure_smiles (line 34) | def get_substructure_smiles(mol, atomID, radius):

FILE: molSimplify/Informatics/partialcharges.py
  function fpriority (line 6) | def fpriority(mol):
  function fsym (line 185) | def fsym(mol):
  function fvalency (line 196) | def fvalency(mol):
  function fcharge (line 207) | def fcharge(mol, charge, bond=False):
  function scharge_ave (line 219) | def scharge_ave(mol, charge, bond=False):
  function all_prop (line 252) | def all_prop(mol, charge, bond=False):
  function f_prop (line 273) | def f_prop(mol, charge, bond=False):
  function features (line 291) | def features(mol, charge, bond=False):
  function ffeatures (line 319) | def ffeatures(mol, charge, bond=False):

FILE: molSimplify/Ligands/alphabetizer.py
  function main (line 4) | def main():

FILE: molSimplify/Scripts/addtodb.py
  function initialize_custom_database (line 23) | def initialize_custom_database(globs):
  function addtoldb (line 44) | def addtoldb(smimol, sminame, smident, smicat, smigrps, smictg, ffopt, o...
  function addtocdb (line 138) | def addtocdb(smimol, sminame, smicat):
  function addtobdb (line 196) | def addtobdb(smimol, sminame):
  function removefromDB (line 256) | def removefromDB(sminame, ropt):

FILE: molSimplify/Scripts/align.py
  function moments_of_inertia (line 3) | def moments_of_inertia(coords, masses):
  function principal_axes (line 36) | def principal_axes(coords, masses):
  function rot_mat_from_angle_axis (line 62) | def rot_mat_from_angle_axis(angle, axis):
  function rotate_onto_principal_axes (line 90) | def rotate_onto_principal_axes(mol):
  function project_onto_principal_axes (line 166) | def project_onto_principal_axes(mol):

FILE: molSimplify/Scripts/cellbuilder.py
  function d_fix (line 53) | def d_fix(unit_cell, cell_vector):
  function cut_cell_to_index (line 80) | def cut_cell_to_index(unit_cell, cell_vector, miller_index):
  function concave_hull (line 138) | def concave_hull(points, alpha):
  function unit_to_super (line 151) | def unit_to_super(unit_cell, cell_vector, duplication_vector):
  function multialign_objective_function (line 182) | def multialign_objective_function(payload, surface_coord_list, cand_list...
  function tracked_merge (line 202) | def tracked_merge(payload, super_cell):
  function force_field_relax_with_slab (line 219) | def force_field_relax_with_slab(super_cell, payload, cand_list, its):
  function surface_center (line 248) | def surface_center(super_cell):
  function choose_nearest_neighbour (line 265) | def choose_nearest_neighbour(target_site, avail_sites_dict, occupied_sit...
  function choose_best_site (line 318) | def choose_best_site(avail_sites_dict, occupied_sites_dict, centroid, su...
  function align_payload_to_multi_site (line 380) | def align_payload_to_multi_site(payload, surface_coord_list, cand_list, ...
  function combine_multi_aligned_payload_with_cell (line 464) | def combine_multi_aligned_payload_with_cell(super_cell, super_cell_vecto...
  function molecule_placement_supervisor (line 740) | def molecule_placement_supervisor(super_cell, super_cell_vector, target_...
  function centered_align_coord (line 932) | def centered_align_coord(super_cell_vector):
  function staggered2_align_coord (line 941) | def staggered2_align_coord(super_cell):
  function axes_angle_align (line 971) | def axes_angle_align(payload, cand_ind, align_ind, align_target, angle):
  function slab_module_supervisor (line 1020) | def slab_module_supervisor(args, rootdir):

FILE: molSimplify/Scripts/cellbuilder_tools.py
  function cell_ffopt (line 33) | def cell_ffopt(ff, mol, frozenats):
  function import_from_cif (line 85) | def import_from_cif(fst, return_extra_cif_info=False):
  function center_of_sym (line 169) | def center_of_sym(list_of_points):
  function zero_z_csm (line 179) | def zero_z_csm(super_cell):
  function xgcd (line 189) | def xgcd(b, n):
  function distance_zw (line 202) | def distance_zw(r1, r2):
  function mdistance (line 211) | def mdistance(r1, r2):
  function get_basis_coefficients (line 220) | def get_basis_coefficients(point, basis):
  function evaluate_basis_coefficients (line 230) | def evaluate_basis_coefficients(coefficients, basis):
  function change_basis (line 242) | def change_basis(mol, old_basis, new_basis):
  function normalize_vector (line 255) | def normalize_vector(v):
  function threshold_basis (line 265) | def threshold_basis(basis, threshold):
  function threshold_vector (line 271) | def threshold_vector(v, threshold):
  function find_all_surface_atoms (line 280) | def find_all_surface_atoms(super_cell, tol=1e-2, type_of_atom=False):
  function distance_2d_torus (line 313) | def distance_2d_torus(R1, R2, dim):
  function distance_2d_torus_next_only (line 335) | def distance_2d_torus_next_only(R1, R2, dim):
  function periodic_2d_distance (line 355) | def periodic_2d_distance(R1, R2, cell_vector):
  function periodic_mindist (line 379) | def periodic_mindist(mol, surf, dim):
  function periodic_selfdist (line 396) | def periodic_selfdist(mol, dim):
  function closest_torus_point (line 414) | def closest_torus_point(mol, dim):
  function check_top_layer_correct (line 427) | def check_top_layer_correct(super_cell, atom_type):
  function shave_surface_layer (line 460) | def shave_surface_layer(super_cell, TOL=1e-1):
  function shave_under_layer (line 478) | def shave_under_layer(super_cell):
  function shave__type (line 497) | def shave__type(super_cell, dim, mode):
  function zero_z (line 530) | def zero_z(super_cell):
  function zero_x (line 542) | def zero_x(super_cell):
  function zero_y (line 554) | def zero_y(super_cell):
  function point_in_box (line 568) | def point_in_box(point, box):
  function apply_plane_to_point (line 579) | def apply_plane_to_point(point, n):
  function fractionate_points_by_plane (line 585) | def fractionate_points_by_plane(super_cell, n, tol=1E-8):
  function points_below_plane (line 604) | def points_below_plane(point, n, refd):
  function freeze_bottom_n_layers (line 616) | def freeze_bottom_n_layers(super_cell, n):
  function freeze_under_layer (line 629) | def freeze_under_layer(super_cell):
  function find_extents (line 650) | def find_extents(super_cell):
  function find_extents_cv (line 671) | def find_extents_cv(super_cell_vector):

FILE: molSimplify/Scripts/chains.py
  function mdistance (line 22) | def mdistance(r1, r2):
  function find_extents (line 30) | def find_extents(mol):
  function interatomic_dist (line 51) | def interatomic_dist(mol, ind1, ind2):
  function find_term_heavy (line 61) | def find_term_heavy(mol, reference_point):
  function trim_H (line 75) | def trim_H(mol, reference_point):
  function zero_dim (line 84) | def zero_dim(mol, dim):
  function zero_z (line 95) | def zero_z(mol):
  function zero_x (line 107) | def zero_x(mol):
  function zero_y (line 119) | def zero_y(mol):
  function zero_1st (line 131) | def zero_1st(mol):
  function remove_closest_h (line 139) | def remove_closest_h(mol, other_mol):
  function grow_linear_step (line 156) | def grow_linear_step(chain, new_unit, dim, interv, conatom, freezehead):
  function chain_builder_supervisor (line 195) | def chain_builder_supervisor(args, rundir):

FILE: molSimplify/Scripts/convert_2to3.py
  function run_bash (line 5) | def run_bash(filein):
  function main (line 13) | def main():

FILE: molSimplify/Scripts/dbinteract.py
  function float_from_str (line 30) | def float_from_str(txt):
  function setupdb (line 43) | def setupdb(dbselect):
  function obfilters (line 67) | def obfilters():
  function checkscr (line 107) | def checkscr(args):
  function getsimilar (line 157) | def getsimilar(smi, nmols, dbselect, finger, squery, args):
  function stripsalts (line 203) | def stripsalts(fname):
  function getels (line 242) | def getels(smistr):
  function checkels (line 269) | def checkels(fname, allowedels):
  function dissim (line 299) | def dissim(outf, n):
  function matchsmarts (line 377) | def matchsmarts(smarts, outf, catoms, args):
  function dbsearch (line 421) | def dbsearch(rundir, args, globs):

FILE: molSimplify/Scripts/distgeom.py
  function CosRule (line 37) | def CosRule(AB: float, BC: float, theta: float) -> float:
  function inverseCosRule (line 60) | def inverseCosRule(A, B, C) -> float:
  function GetBoundsMatrices (line 85) | def GetBoundsMatrices(mol, natoms, catoms=[], shape=[], A=[]):
  function Triangle (line 175) | def Triangle(LB, UB, natoms):
  function Metrize (line 214) | def Metrize(LB, UB, natoms, Full=False, seed=False):
  function GetCMDists (line 266) | def GetCMDists(D, natoms):
  function GetMetricMatrix (line 301) | def GetMetricMatrix(D, D0, natoms):
  function Get3Eigs (line 327) | def Get3Eigs(G, natoms):
  function DistErr (line 354) | def DistErr(x, *args):
  function DistErrGrad (line 385) | def DistErrGrad(x, *args):
  function SaveConf (line 422) | def SaveConf(X, mol, ffclean=True, catoms=[]):
  function findshape (line 491) | def findshape(args, master_ligand) -> Dict:
  function GetConf (line 546) | def GetConf(mol, args, catoms=[]):

FILE: molSimplify/Scripts/enhanced_structgen.py
  function _metal_indices_from_elements (line 33) | def _metal_indices_from_elements(elements):
  function _nearest_metal_axes (line 45) | def _nearest_metal_axes(donor_indices, sample_coords, complex_coords, co...
  function load_in_ligand (line 85) | def load_in_ligand(inp):
  function _get_catoms (line 92) | def _get_catoms(userligand, emsg, usercatoms):
  function _check_list_lengths (line 121) | def _check_list_lengths(userligand_list, usercatoms_list, occupancy_list...
  function _create_ligand_tuple (line 128) | def _create_ligand_tuple(userligand, usercatoms=None, occupancy=1, isome...
  function create_ligand_list (line 133) | def create_ligand_list(userligand_list, usercatoms_list=None, occupancy_...
  function generate_complex (line 155) | def generate_complex(
  function run_sterics_check (line 480) | def run_sterics_check(core3D, per_atom_ff_force, optimized_coords):
  function visualize_molecule (line 514) | def visualize_molecule(coords, bond_dict=None, steric_pairs=None, severi...
  function _maybe_none (line 588) | def _maybe_none(x: str):
  function _parse_usercatoms (line 591) | def _parse_usercatoms(s: str):
  function enhanced_init_ANN (line 741) | def enhanced_init_ANN(metal, ox, spin, ligands, occs, dents,
  function enforce_metal_ligand_distances_and_optimize (line 800) | def enforce_metal_ligand_distances_and_optimize(

FILE: molSimplify/Scripts/enhanced_structgen_functionality.py
  function apply_aromatic_flags_from_bodict (line 35) | def apply_aromatic_flags_from_bodict(core3D):
  function sync_obmol_from_bodict (line 50) | def sync_obmol_from_bodict(core3D):
  function add_ligand_to_complex (line 58) | def add_ligand_to_complex(
  function kabsch_align_with_reflection_option (line 118) | def kabsch_align_with_reflection_option(P, Q, allow_reflection=False):
  function rmsd (line 158) | def rmsd(P, Q):
  function find_best_alignment_with_subsets (line 171) | def find_best_alignment_with_subsets(ligand_coords, backbone_coords, all...
  function transform_ligand (line 223) | def transform_ligand(ligand_all_coords, Rm, t):
  function get_all_coords (line 238) | def get_all_coords(mol):
  function zero_small_values (line 254) | def zero_small_values(coords, threshold=1e-6):
  function add_ligand_to_metals (line 270) | def add_ligand_to_metals(ligand_donor_coords, ligand_all_coords, metals,...
  function nudge_ligand_coords (line 322) | def nudge_ligand_coords(
  function select_best_subset_by_kabsch (line 365) | def select_best_subset_by_kabsch(ligand_coords, donor_indices, backbone_...
  function initialize_core (line 404) | def initialize_core(metals="Fe", coords=None, geometry=None):
  function initialize_metal_coordinates (line 438) | def initialize_metal_coordinates(
  function generate_backbone_sites (line 521) | def generate_backbone_sites(
  function create_metals_structure (line 550) | def create_metals_structure(metal_elements, metal_coords, metal_backbone...
  function get_valid_isomer_subsets (line 581) | def get_valid_isomer_subsets(metal_info, isomer=None, denticity=1):
  function get_ligand_coordinates (line 621) | def get_ligand_coordinates(lig3D, donor_indices):
  function set_new_coords (line 642) | def set_new_coords(mol, coords):
  function set_metal_ligand_bond_lengths (line 662) | def set_metal_ligand_bond_lengths(ligand_coords, donor_indices, metal_co...
  function get_all_bonded_atoms_bonded_to_metal (line 690) | def get_all_bonded_atoms_bonded_to_metal(mol, include_metal=True, transi...
  function get_all_coords_and_elements (line 718) | def get_all_coords_and_elements(mol):
  function iterative_dual_clash_resolution (line 752) | def iterative_dual_clash_resolution(
  function try_optimize_body_hybrid (line 1017) | def try_optimize_body_hybrid(
  function get_next_structure (line 1191) | def get_next_structure(metals_structures, denticity):
  function map_donors_to_sites (line 1201) | def map_donors_to_sites(donor_indices, best_perm_idx, chosen_subset):
  function _metal_indices_from_elements (line 1241) | def _metal_indices_from_elements(elements):
  function outward_orientation_penalty (line 1251) | def outward_orientation_penalty(
  function _hard_outward_flip_no_elements (line 1329) | def _hard_outward_flip_no_elements(coords, donor_indices, complex_coords...
  function is_iterable_but_not_str (line 1400) | def is_iterable_but_not_str(x):
  function _virtual_point_for_group (line 1405) | def _virtual_point_for_group(group_idx_list, coords):
  function _plane_normal_for_group (line 1420) | def _plane_normal_for_group(group_idx_list, coords):
  function parse_donor_spec_make_virtuals (line 1442) | def parse_donor_spec_make_virtuals(donor_indices, ligand_all_coords):
  function nearest_metal_vector (line 1463) | def nearest_metal_vector(point, complex_coords, complex_elements):
  function align_group_normal_to_axis (line 1477) | def align_group_normal_to_axis(coords_all, group_idx_list, desired_axis):
  function map_donors_to_sites_haptic_aware (line 1503) | def map_donors_to_sites_haptic_aware(donor_groups, best_perm_group_ids, ...
  function _simple_voxel_score_factory (line 1524) | def _simple_voxel_score_factory(VoxelGridClass, complex_coords, complex_...
  function _nearest_metal_axes (line 1541) | def _nearest_metal_axes(donor_indices, sample_coords, complex_coords, co...
  function _simple_outward_cos_report (line 1566) | def _simple_outward_cos_report(sample_coords, donor_indices, k_neighbors...
  function clash_aware_kabsch (line 1577) | def clash_aware_kabsch(
  function _site_equivalence_classes (line 1882) | def _site_equivalence_classes(backbone_coords, tol=1e-4):
  function _dedupe_subsets_by_site_classes (line 1924) | def _dedupe_subsets_by_site_classes(valid_subsets, class_of):
  function _ensure_dir (line 1967) | def _ensure_dir(path):
  function _scatter_voxels (line 1972) | def _scatter_voxels(ax, coords, label, alpha=0.35, s=6):
  function _scatter_atoms (line 1984) | def _scatter_atoms(ax, coords, label, s=25, alpha=0.9):
  function _plot_voxel_dots (line 1994) | def _plot_voxel_dots(ax, coords, label, marker="s", s=10, alpha=0.8, col...
  function _unique_path (line 2005) | def _unique_path(dirpath, filename):
  function _set_equal_3d (line 2022) | def _set_equal_3d(ax, points=None, padding=0.0, orthographic=True):
  function _plot_voxel_cubes (line 2056) | def _plot_voxel_cubes(
  function save_voxel_frame (line 2100) | def save_voxel_frame(
  function make_gif_from_frames (line 2277) | def make_gif_from_frames(frame_paths, gif_path, fps=8):
  function visualize_initial_metal_voxels (line 2298) | def visualize_initial_metal_voxels(
  function visualize_final_complex_voxels (line 2327) | def visualize_final_complex_voxels(
  function detect_ring_piercing (line 2376) | def detect_ring_piercing(
  function estimate_minimum_shift_distance (line 2575) | def estimate_minimum_shift_distance(ring_coords, bond_coords, buffer=5):
  function correct_ring_piercings (line 2592) | def correct_ring_piercings(
  function build_kdtree (line 2768) | def build_kdtree(coords):
  function _build_bond_graph (line 2773) | def _build_bond_graph(bo_dict):
  function _donors_by_metal (line 2783) | def _donors_by_metal(elements, bond_pairs):
  function _shares_metal (line 2800) | def _shares_metal(u, v, donors_by_m):
  function _pca_frame (line 2808) | def _pca_frame(P):
  function _pca_align (line 2844) | def _pca_align(P, Q):
  function _cheap_group_rmsd (line 2855) | def _cheap_group_rmsd(donor_virtuals, site_coords):
  function prefilter_subsets_by_donor_reps (line 2878) | def prefilter_subsets_by_donor_reps(
  function check_sterics (line 2914) | def check_sterics(tree, coords, elements, vdw_radii, bo_dict=None, scale...
  function _ring_sets_from_graph (line 2962) | def _ring_sets_from_graph(G):
  function _same_ring (line 2967) | def _same_ring(i, j, ring_sets):
  function _normalize_bonds_auto (line 2971) | def _normalize_bonds_auto(bo_dict, N):
  function _build_graph_from_bonds (line 3005) | def _build_graph_from_bonds(N, bo_dict0):
  function _normalize_bonds_zero_based (line 3015) | def _normalize_bonds_zero_based(bo_dict):
  function check_sterics_with_ff_embedding (line 3033) | def check_sterics_with_ff_embedding(
  function check_badjob (line 3167) | def check_badjob(core3D):
  function apply_rotation_about_vector (line 3186) | def apply_rotation_about_vector(coords, donor_coords, axis, angle_deg):
  function generate_rotated_conformations (line 3199) | def generate_rotated_conformations(coords, donor_coords, axis, angles):
  function get_voxel_coords_by_group (line 3211) | def get_voxel_coords_by_group(voxel_grid):
  function add_haptic_multibonds_to_metal (line 3236) | def add_haptic_multibonds_to_metal(
  function map_ligand_local_to_core_indices_by_range (line 3303) | def map_ligand_local_to_core_indices_by_range(core_before_count, core_af...
  function map_ligand_local_to_core_indices_geometric (line 3314) | def map_ligand_local_to_core_indices_geometric(core3D, ligand_coords, to...
  function to_global_groups (line 3360) | def to_global_groups(donor_groups_local, local2global):
  function add_haptic_multibonds_to_metal_for_core (line 3367) | def add_haptic_multibonds_to_metal_for_core(
  function reapply_all_haptics_and_sync (line 3434) | def reapply_all_haptics_and_sync(core3D, bond_order=1, prefer_nearest_me...

FILE: molSimplify/Scripts/findcorrelations.py
  function analysis_supervisor (line 15) | def analysis_supervisor(args, rootdir):
  function accquire_file (line 42) | def accquire_file(path):
  function correlation_supervisor (line 103) | def correlation_supervisor(path, rootdir, simple=False, lig_only=False, ...

FILE: molSimplify/Scripts/generator.py
  function startgen_pythonic (line 30) | def startgen_pythonic(input_dict={'-core': 'fe', '-lig': 'cl,cl,cl,cl,cl...
  function startgen (line 67) | def startgen(argv, flag, inputfile_str=None, write_files=True):

FILE: molSimplify/Scripts/geometry.py
  function norm (line 14) | def norm(u):
  function normalize (line 32) | def normalize(u):
  function distance (line 55) | def distance(r1, r2):
  function vecdiff (line 74) | def vecdiff(r1, r2):
  function midpt (line 94) | def midpt(r1, r2):
  function checkcolinear (line 116) | def checkcolinear(r1, r2, r3):
  function checkplanar (line 140) | def checkplanar(r1, r2, r3, r4):
  function vecangle (line 168) | def vecangle(r1, r2):
  function getPointu (line 192) | def getPointu(Rr, dist, u):
  function rotation_params (line 219) | def rotation_params(r0, r1, r2):
  function dihedral (line 264) | def dihedral(mol, idx1, idx2, idx3, idx4):
  function kabsch (line 312) | def kabsch(mol0, mol1):
  function ReflectPlane (line 370) | def ReflectPlane(u, r, Rp):
  function PointRotateAxis (line 416) | def PointRotateAxis(u, rp, r, theta):
  function PointRotateMat (line 468) | def PointRotateMat(r, R):
  function PointTranslateSph (line 491) | def PointTranslateSph(Rp, p0, D) -> List[float]:
  function PointTranslateSphgivenphi (line 527) | def PointTranslateSphgivenphi(Rp, p0, D):
  function PointTranslateSphgivenr (line 563) | def PointTranslateSphgivenr(Rp, p0, D, pref, r):
  function PointTranslatetoPSph (line 608) | def PointTranslatetoPSph(Rp, p0, D):
  function PointRotateSph (line 644) | def PointRotateSph(Rp, p0, D):
  function reflect_through_plane (line 678) | def reflect_through_plane(mol, u, Rp):
  function rotate_around_axis (line 707) | def rotate_around_axis(mol, Rp, u, theta):
  function rotate_mat (line 739) | def rotate_mat(mol, R):
  function setPdistance (line 763) | def setPdistance(mol, Rr, Rp, bond):
  function setPdistanceu (line 803) | def setPdistanceu(mol, Rr, Rp, bond, u):
  function setcmdistance (line 837) | def setcmdistance(mol, Rp, bond):
  function protate (line 870) | def protate(mol, Rr, D):
  function protateref (line 903) | def protateref(mol, Rr, Rref, D):
  function cmrotate (line 937) | def cmrotate(mol, D):
  function rotateRef (line 967) | def rotateRef(mol, Ref, D):
  function aligntoaxis (line 998) | def aligntoaxis(mol, Rr, Rp, u):
  function aligntoaxis2 (line 1029) | def aligntoaxis2(mol, Rr, Rp, u, d):
  function alignPtoaxis (line 1060) | def alignPtoaxis(Rr, Rp, u, d):
  function pmrotate (line 1087) | def pmrotate(mol, Rp, D):
  function connectivity_match (line 1118) | def connectivity_match(inds1, inds2, mol1, mol2):
  function best_fit_plane (line 1154) | def best_fit_plane(coordinates):
  function move_point (line 1180) | def move_point(initial_point, vector, distance):
  function align_axis (line 1208) | def align_axis(mol,Rp,u1,u2):

FILE: molSimplify/Scripts/inparse.py
  function checkinput (line 26) | def checkinput(args, calctype="base"):
  function checkTrue (line 370) | def checkTrue(arg):
  function is_number (line 384) | def is_number(s):
  function cleaninput (line 402) | def cleaninput(args):
  function parseCLI (line 529) | def parseCLI(args):
  function parseinputfile (line 553) | def parseinputfile(args, inputfile_str=None):
  function parseall (line 1102) | def parseall(parser):
  function parseinputs_basic (line 1134) | def parseinputs_basic(*p):
  function parseinputs_advanced (line 1186) | def parseinputs_advanced(*p):
  function parseinputs_slabgen (line 1250) | def parseinputs_slabgen(*p):
  function parseinputs_autocorr (line 1324) | def parseinputs_autocorr(*p):
  function parseinputs_chainb (line 1351) | def parseinputs_chainb(*p):
  function parseinputs_db (line 1369) | def parseinputs_db(*p):
  function parseinputs_inputgen (line 1439) | def parseinputs_inputgen(*p):
  function parseinputs_postproc (line 1521) | def parseinputs_postproc(*p):
  function parseinputs_random (line 1559) | def parseinputs_random(*p):
  function parseinputs_binding (line 1583) | def parseinputs_binding(*p):
  function parseinputs_tsgen (line 1627) | def parseinputs_tsgen(*p):
  function parseinputs_customcore (line 1653) | def parseinputs_customcore(*p):
  function parseinputs_naming (line 1671) | def parseinputs_naming(*p):
  function parseinputs_ligdict (line 1692) | def parseinputs_ligdict(*p):
  function deserialize_json (line 1714) | def deserialize_json(filein):
  function args_parser_retrain (line 1720) | def args_parser_retrain():

FILE: molSimplify/Scripts/io.py
  function resolve_existing_directory (line 33) | def resolve_existing_directory(
  function printgeoms (line 86) | def printgeoms():
  function getgeoms (line 112) | def getgeoms():
  function _raise_custom_data_dir_missing (line 163) | def _raise_custom_data_dir_missing(fname: str, from_err: Optional[Except...
  function readdict (line 189) | def readdict(fname):
  function readdict_sub (line 214) | def readdict_sub(fname):
  function getligs (line 239) | def getligs() -> str:
  function getlicores (line 247) | def getlicores(flip: bool = True) -> Dict[str, Any]:
  function getsimpleligs (line 263) | def getsimpleligs() -> str:
  function getslicores (line 270) | def getslicores() -> Dict[str, Any]:
  function getligroups (line 283) | def getligroups(licores: dict) -> str:
  function checkTMsmiles (line 294) | def checkTMsmiles(smi: str) -> str:
  function getbinds (line 303) | def getbinds() -> str:
  function getbcores (line 310) | def getbcores() -> dict:
  function getcores (line 321) | def getcores():
  function getmcores (line 333) | def getmcores():
  function getsubstrates (line 344) | def getsubstrates():
  function getsubcores (line 356) | def getsubcores():
  function loaddata (line 369) | def loaddata(path: str) -> dict:
  function loaddata_ts (line 391) | def loaddata_ts(path: str) -> dict:
  function loadcdxml (line 413) | def loadcdxml(cdxml: str) -> Tuple[str, str]:
  function loadcoord (line 492) | def loadcoord(coord: str) -> List[List[float]]:
  function core_load (line 510) | def core_load(usercore: str, mcores: Optional[dict] = None) -> Tuple[Uni...
  function substr_load (line 588) | def substr_load(usersubstrate: str,
  function lig_load (line 698) | def lig_load(userligand: str, licores: Optional[dict] = None) -> Tuple[A...
  function lig_load_safe (line 873) | def lig_load_safe(userligand: str, licores: Optional[dict] = None) -> Tu...
  function bind_load (line 1065) | def bind_load(userbind: str, bindcores: dict) -> Tuple[Union[mol3D, None...
  function getinputargs (line 1130) | def getinputargs(args, fname: str):
  function plugin_defs (line 1158) | def plugin_defs() -> str:
  function name_complex (line 1173) | def name_complex(rootdir: str, core, geometry, ligs, ligoc, sernum: int,
  function name_ts_complex (line 1244) | def name_ts_complex(rootdir, core, geometry, ligs, ligoc, substrate, sub...
  function copy_to_custom_path (line 1305) | def copy_to_custom_path():
  function _coerce_scalar (line 1341) | def _coerce_scalar(tok: str) -> Any:
  function _normalize_list (line 1347) | def _normalize_list(obj: Any) -> Any:
  function parse_bracketed_list (line 1359) | def parse_bracketed_list(obj: Union[List[Any], str]) -> List[Any]:

FILE: molSimplify/Scripts/isomers.py
  function generateisomers (line 23) | def generateisomers(args):
  function expandrepresentation (line 48) | def expandrepresentation(args):
  function findpermutations (line 73) | def findpermutations(lst, master=None):
  function checkunique (line 104) | def checkunique(args, permutations):
  function collapserepresentation (line 138) | def collapserepresentation(args, permutations):
  function generatestereo (line 183) | def generatestereo(collapsed_representation):
  function checkallowedbidentates (line 235) | def checkallowedbidentates(simple_geometry, geometry):
  function checkdenticity (line 284) | def checkdenticity(ligand):
  function getadjacency (line 295) | def getadjacency(geo):
  function searchlist (line 320) | def searchlist(lst, key):
  function checkincluded (line 333) | def checkincluded(geometry, unique_representations):
  function checksymmetric (line 366) | def checksymmetric(lig):

FILE: molSimplify/Scripts/jobgen.py
  function sgejobgen (line 13) | def sgejobgen(args, jobdirs):
  function slurmjobgen (line 158) | def slurmjobgen(args, jobdirs):

FILE: molSimplify/Scripts/krr_prep.py
  function feature_prep (line 45) | def feature_prep(mol, idx):
  function normalize (line 206) | def normalize(data, mean, std):
  function krr_model_training (line 223) | def krr_model_training(csvf, colnum_label, colnum_desc, alpha=1, gamma=1...
  function krr_model_training_loo (line 352) | def krr_model_training_loo(csvf, colnum_label, colnum_desc, feature_name...
  function gbr_model_training (line 506) | def gbr_model_training(csvf, colnum_i_label, colnum_j_label, colnum_desc):
  function ML_model_predict (line 615) | def ML_model_predict(core3D, spin, train_dict, stat_dict, impt_dict, regr):
  function krr_model_predict (line 673) | def krr_model_predict(core3D, spin, mligcatom):
  function invoke_KRR_from_mol3d_dQ (line 826) | def invoke_KRR_from_mol3d_dQ(mol, charge):
  function invoke_KRR_from_mol3d_RACs (line 906) | def invoke_KRR_from_mol3d_RACs(mol, charge):
  function get_descriptor_vector_for_atidx (line 950) | def get_descriptor_vector_for_atidx(mol, atidx, depth=4, oct=False):
  function generate_revised_atomonly_autocorrelations (line 970) | def generate_revised_atomonly_autocorrelations(mol, atomIdx, loud, depth...
  function generate_atomonly_ratiometrics (line 994) | def generate_atomonly_ratiometrics(mol, atomIdx, loud, depth=4, oct=True):
  function generate_atomonly_summetrics (line 1022) | def generate_atomonly_summetrics(mol, atomIdx, loud, depth=4, oct=True):
  function generate_revised_atomonly_deltametrics (line 1046) | def generate_revised_atomonly_deltametrics(mol, atomIdx, loud, depth=4, ...
  function get_revised_descriptor_vector_for_atidx (line 1076) | def get_revised_descriptor_vector_for_atidx(mol, atidx, depth=4, oct=Fal...
  function default_plot (line 1113) | def default_plot(x, y, name=False):

FILE: molSimplify/Scripts/namegen.py
  function name_complex (line 16) | def name_complex(core, ligs, ligoc, args) -> str:

FILE: molSimplify/Scripts/nn_prep.py
  function get_bond_order (line 20) | def get_bond_order(OBMol, connection_atoms, mol) -> int:
  function check_ligands (line 47) | def check_ligands(ligs, batlist, dents, tcats):
  function check_metal (line 136) | def check_metal(metal: str, oxidation_state: str) -> Tuple[bool, str]:
  function get_con_at_type (line 149) | def get_con_at_type(mol, connection_atoms: List[Union[int, str]]) -> Tup...
  function ANN_preproc (line 179) | def ANN_preproc(args, ligs: List[str], occs: List[int], dents: List[int],
  function ax_lig_corrector (line 477) | def ax_lig_corrector(excitation, con_atom_type):
  function eq_lig_corrector (line 489) | def eq_lig_corrector(excitation, con_atom_type):
  function metal_corrector (line 500) | def metal_corrector(excitation, metal):
  function spin_classify (line 511) | def spin_classify(metal, spin, ox):
  function get_splitting (line 531) | def get_splitting(excitation):
  function get_slope (line 536) | def get_slope(slope_excitation):
  function get_ls_dist (line 541) | def get_ls_dist(excitation):
  function get_hs_dist (line 546) | def get_hs_dist(excitation):

FILE: molSimplify/Scripts/nx_helpers.py
  function mol3D_to_networkx (line 10) | def mol3D_to_networkx(mol,get_symbols:bool=True,get_bond_order:bool=True...

FILE: molSimplify/Scripts/oct_check_mols.py
  function create_mol_with_xyz (line 36) | def create_mol_with_xyz(_file_in):
  function readfromtxt (line 42) | def readfromtxt(mol, txt):
  function find_nearest_ind (line 66) | def find_nearest_ind(array, value):
  function comp_two_angle_array_ (line 73) | def comp_two_angle_array_(input_angle, target_angle, catoms_map, picked):
  function comp_two_angle_array (line 97) | def comp_two_angle_array(input_angle, target_angle, catoms_map, picked_i...
  function comp_angle_pick_one_best (line 144) | def comp_angle_pick_one_best(input_arr, target_angle, catoms_map, picked):
  function loop_target_angle_arr (line 172) | def loop_target_angle_arr(input_arr, target_arr, catoms_map):
  function sort_sec_ele (line 187) | def sort_sec_ele(ele):
  function get_num_coord_metal (line 199) | def get_num_coord_metal(file_in, debug=False):
  function ligand_comp_org (line 218) | def ligand_comp_org(file_in, file_init_geo, catoms_arr, flag_deleteH=Tru...
  function match_lig_list (line 288) | def match_lig_list(file_in, file_init_geo, catoms_arr,
  function find_the_other_ind (line 354) | def find_the_other_ind(arr, ind):
  function is_linear_ligand (line 363) | def is_linear_ligand(mol, ind):
  function get_linear_angle (line 384) | def get_linear_angle(mol, ind):
  function check_angle_linear (line 397) | def check_angle_linear(file_in, catoms_arr):
  function oct_comp (line 431) | def oct_comp(file_in, angle_ref=oct_angle_ref, catoms_arr=None,
  function dict_check_processing (line 506) | def dict_check_processing(dict_info, dict_check, std_not_use,
  function Oct_inspection (line 537) | def Oct_inspection(file_in, file_init_geo=None, catoms_arr=None, dict_ch...
  function IsOct (line 599) | def IsOct(file_in, file_init_geo=None, dict_check=dict_oct_check_st,
  function IsStructure (line 649) | def IsStructure(file_in, file_init_geo=None, dict_check=dict_oneempty_ch...
  function loop_structure (line 695) | def loop_structure(_path, path_init_geo):
  function find_file_with_unique_num (line 727) | def find_file_with_unique_num(_path, unique_num):
  function gen_file_with_name (line 738) | def gen_file_with_name(path_init_geo, name_opt):

FILE: molSimplify/Scripts/periodic_QE.py
  function write_periodic_mol3d_to_qe (line 14) | def write_periodic_mol3d_to_qe(mol, cell_vector, path):

FILE: molSimplify/Scripts/postmold.py
  class AtomClass (line 18) | class AtomClass:
  function getrange (line 36) | def getrange(idx, atoms):
  function parse (line 48) | def parse(folder, molf):
  function parsed (line 231) | def parsed(orbf):
  function getresd (line 268) | def getresd(dirf):
  function moldpost (line 294) | def moldpost(molf, folder, flog):

FILE: molSimplify/Scripts/postmwfn.py
  function distance (line 25) | def distance(R1, R2):
  function find_between (line 39) | def find_between(s, first, last):
  function radial (line 58) | def radial(v):
  function calc (line 70) | def calc(den, dV):
  function spreadcalc (line 87) | def spreadcalc(den, ELF, totel, dV):
  function calcHELP (line 130) | def calcHELP(den, ELF, dV):
  function parsecube (line 147) | def parsecube(cubef):
  function wfncalc (line 231) | def wfncalc(denf, elff):
  function cubespin (line 244) | def cubespin(cubefTOT, cubefSPIN):
  function readden (line 279) | def readden(inputf):
  function getcubes (line 341) | def getcubes(molf, folder, flog):
  function getwfnprops (line 402) | def getwfnprops(molf, folder, flog):
  function getcharges (line 459) | def getcharges(molf, folder, flog):
  function deloc (line 553) | def deloc(molf, folder, flog):

FILE: molSimplify/Scripts/postparse.py
  function find_between (line 19) | def find_between(s, first, last):
  function nbo_parser_unrestricted (line 38) | def nbo_parser_unrestricted(s):
  function nbo_parser_restricted (line 123) | def nbo_parser_restricted(s):
  function spinnbo (line 174) | def spinnbo(s, metal):
  function spinnlmo (line 212) | def spinnlmo(s, metal):
  function nbopost (line 234) | def nbopost(resfiles, folder, flog):
  function terapost (line 278) | def terapost(resfiles, folder, flog):
  function gampost (line 371) | def gampost(resfiles, folder, flog):

FILE: molSimplify/Scripts/postproc.py
  function checkmultiwfn (line 30) | def checkmultiwfn(mdir):
  function postproc (line 42) | def postproc(rundir, args, globs):

FILE: molSimplify/Scripts/qcgen.py
  function multitcgen (line 16) | def multitcgen(args, strfiles):
  function tcgen (line 57) | def tcgen(args, strfiles, method):
  function xyz2gxyz (line 260) | def xyz2gxyz(filename):
  function multigamgen (line 282) | def multigamgen(args, strfiles):
  function gamgen (line 314) | def gamgen(args, strfiles, method):
  function multiqgen (line 497) | def multiqgen(args, strfiles):
  function qgen (line 529) | def qgen(args, strfiles, method):
  function mlpgen (line 657) | def mlpgen(args, strfiles, rootdir):
  function multiogen (line 744) | def multiogen(args, strfiles):
  function ogen (line 781) | def ogen(args, strfiles, method):
  function ogenwrt (line 972) | def ogenwrt(output, jobparams, xyzf):
  function molcgen (line 1030) | def molcgen(args, strfiles, method):
  function molcwrt (line 1191) | def molcwrt(output, jobparams, xyzf, xyzind):
  function multimolcgen (line 1242) | def multimolcgen(args, strfiles):
  function molcbasis (line 1278) | def molcbasis(strfiles, basistyp):
  function molcras2s (line 1358) | def molcras2s(strfiles):
  function molcnactels (line 1390) | def molcnactels(strfiles, oxnum):
  function molcfrozens (line 1425) | def molcfrozens(strfiles):

FILE: molSimplify/Scripts/rmsd.py
  function rmsd (line 7) | def rmsd(V, W):
  function kabsch_rmsd (line 30) | def kabsch_rmsd(P, Q, translate=False):
  function kabsch_rotate (line 55) | def kabsch_rotate(P, Q):
  function kabsch (line 77) | def kabsch(P, Q):
  function quaternion_rmsd (line 121) | def quaternion_rmsd(P, Q) -> float:
  function quaternion_transform (line 142) | def quaternion_transform(r):
  function makeW (line 158) | def makeW(r1, r2, r3, r4=0):
  function makeQ (line 186) | def makeQ(r1, r2, r3, r4=0):
  function quaternion_rotate (line 214) | def quaternion_rotate(X, Y):
  function centroid (line 241) | def centroid(X):
  function hungarian (line 260) | def hungarian(A, B):
  function reorder_hungarian (line 288) | def reorder_hungarian(p_atoms, q_atoms, p_coord, q_coord):
  function reorder_distance (line 329) | def reorder_distance(p_atoms, q_atoms, p_coord, q_coord):
  function rmsd_reorder_rotate (line 375) | def rmsd_reorder_rotate(p_atoms, q_atoms, p_coord, q_coord,
  function reorder_rotate (line 449) | def reorder_rotate(p_atoms, q_atoms, p_coord, q_coord,
  function rigorous_rmsd (line 531) | def rigorous_rmsd(mol_p, mol_q, rotation: str = "kabsch",
  function align_rmsd_project (line 560) | def align_rmsd_project(mol_p, mol_q, rotation: str = "kabsch",
  function align_rmsd_rotate (line 648) | def align_rmsd_rotate(mol_p, mol_q, rotation: str = "kabsch",
  function test_case (line 755) | def test_case():

FILE: molSimplify/Scripts/rungen.py
  function constrgen (line 55) | def constrgen(rundir: str, args: Namespace) -> Tuple[Union[Namespace, bo...
  function getconstsample (line 160) | def getconstsample(no_rgen, args, licores, coord):
  function multigenruns (line 209) | def multigenruns(rundir, args, write_files=True):
  function checkmultilig (line 312) | def checkmultilig(ligs: List[str]) -> Tuple[List[List[str]], List[List[s...
  function draw_supervisor (line 361) | def draw_supervisor(args: Namespace, rundir: str):
  function rungen (line 396) | def rungen(rundir, args: Namespace, chspfname=None, write_files: bool = ...

FILE: molSimplify/Scripts/structgen.py
  function getbackbcombsall (line 67) | def getbackbcombsall(nums):
  function getnupdateb (line 90) | def getnupdateb(backbatoms: List[List[int]], denticity: int) -> Tuple[Li...
  function init_ANN (line 129) | def init_ANN(args, ligands: List[str], occs: List[int], dents: List[int],
  function init_template (line 225) | def init_template(args: Namespace, cpoints_required: int) -> Tuple[mol3D...
  function init_ligand (line 404) | def init_ligand(args: Namespace, lig: mol3D, tcats,
  function modifybackbonep (line 510) | def modifybackbonep(backb, pangles):
  function distortbackbone (line 535) | def distortbackbone(backb, distort):
  function smartreorderligs (line 559) | def smartreorderligs(ligs: List[str], dentl: List[int],
  function ffopt (line 605) | def ffopt(ff: str, mol: mol3D, connected: List[int], constopt: int,
  function openbabel_ffopt (line 662) | def openbabel_ffopt(ff: str, mol: mol3D, connected: List[int], constopt:...
  function xtb_opt (line 843) | def xtb_opt(ff: str, mol: mol3D, connected: List[int], constopt: int,
  function getconnection (line 971) | def getconnection(core: mol3D, cidx: int, BL: float) -> List[float]:
  function findsmarts (line 1008) | def findsmarts(lig3D: mol3D, smarts: List[str], catom: int) -> bool:
  function align_lig_centersym (line 1044) | def align_lig_centersym(corerefcoords, lig3D, atom0, core3D, EnableAutoL...
  function align_linear_pi_lig (line 1104) | def align_linear_pi_lig(corerefcoords, lig3D, atom0, ligpiatoms):
  function rotation_objective_func (line 1166) | def rotation_objective_func(rotations, lig3D, atom0, ligpiatoms, metal_l...
  function align_pi_ring_lig (line 1213) | def align_pi_ring_lig(corerefcoords, lig3D, atom0, ligpiatoms, u):
  function check_rotate_linear_lig (line 1259) | def check_rotate_linear_lig(corerefcoords, lig3D, atom0):
  function check_rotate_symm_lig (line 1294) | def check_rotate_symm_lig(corerefcoords, lig3D, atom0, core3D):
  function rotate_MLaxis_minimize_steric (line 1336) | def rotate_MLaxis_minimize_steric(corerefcoords, lig3D, atom0, core3D):
  function rotate_catom_fix_Hs (line 1380) | def rotate_catom_fix_Hs(lig3D, catoms, n, mcoords, core3D):
  function rotate_catoms_fix_Hs (line 1497) | def rotate_catoms_fix_Hs(lig3D: mol3D, catoms: List[int], mcoords, core3...
  function get_MLdist (line 1525) | def get_MLdist(metal: atom3D, oxstate: str, spin: str, lig3D: mol3D,
  function get_MLdist_database (line 1598) | def get_MLdist_database(metal: atom3D, oxstate: str, spin: str, lig3D: m...
  function get_batoms (line 1663) | def get_batoms(batslist, ligsused):
  function align_dent2_catom2_coarse (line 1686) | def align_dent2_catom2_coarse(args, lig3D, core3D, catoms, r1, r0, m3D, ...
  function align_dent2_catom2_refined (line 1800) | def align_dent2_catom2_refined(args, lig3D, catoms, bondl, r1, r0, core3...
  function align_dent1_lig (line 1903) | def align_dent1_lig(args, cpoint, core3D, coreref, ligand, lig3D, catoms,
  function align_dent2_lig (line 1991) | def align_dent2_lig(args, cpoint, batoms, m3D, core3D, coreref, ligand, ...
  function align_dent3_lig (line 2082) | def align_dent3_lig(args, cpoint, batoms, m3D, core3D, coreref, ligand, ...
  function mcomplex (line 2228) | def mcomplex(args: Namespace, ligs: List[str], ligoc: List[int], smart_g...
  function generate_report (line 2774) | def generate_report(args: Namespace, ligands: List[str], ligoc: List[int]
  function structgen (line 2892) | def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: ...

FILE: molSimplify/Scripts/tf_nn_prep.py
  function spin_classify (line 32) | def spin_classify(metal: str, spin: Union[int, str], ox: int) -> Tuple[b...
  function invoke_ANNs_from_mol3d (line 54) | def invoke_ANNs_from_mol3d(mol: mol3D, oxidation_state: int,
  function tf_check_ligands (line 99) | def tf_check_ligands(ligs: List[str], batslist: List[List[int]],
  function check_metal (line 273) | def check_metal(metal: str, oxidation_state: str) -> Tuple[bool, str]:
  function tf_ANN_preproc (line 286) | def tf_ANN_preproc(metal: str, oxstate, spin, ligs: List[str], occs: Lis...
  function evaluate_tmc_anns (line 527) | def evaluate_tmc_anns(this_complex: mol3D, metal: str, ox: int, spin: int,
  function _flat_floats (line 752) | def _flat_floats(x):
  function evaluate_catalytic_anns (line 760) | def evaluate_catalytic_anns(this_complex: mol3D, metal: str, ox: int, sp...

FILE: molSimplify/Scripts/tsgen.py
  function getconnections (line 50) | def getconnections(core, catom, Midx, BL, ABXang):
  function substplacecheap (line 72) | def substplacecheap(core, connPts, catom):
  function substplaceff_mode3 (line 101) | def substplaceff_mode3(core, substr, substreact, compreact, cpoint, args...
  function substplaceff_mode1 (line 146) | def substplaceff_mode1(core, substr, substreact, compreact, cpoint, liga...
  function tsgen (line 180) | def tsgen(mode, args, rootdir, core, substr, compreact, substreact, globs):

FILE: molSimplify/Scripts/uq_calibration.py
  function nlm (line 7) | def nlm(func, p0,
  function linear_variance_model (line 33) | def linear_variance_model(dist, theta):
  function zero_linear_variance_model (line 43) | def zero_linear_variance_model(dist, theta):
  function maximum_likelihood_loss (line 53) | def maximum_likelihood_loss(theta, dists, epsilons, varfun=linear_varian...

FILE: molSimplify/__main__.py
  function run_legacy (line 102) | def run_legacy(args):
  function run_build_complex (line 130) | def run_build_complex(args):
  function main (line 483) | def main(args=None):

FILE: molSimplify/ml/kernels.py
  class Masking (line 5) | class Masking(Kernel):
    method __init__ (line 6) | def __init__(self, mask, kernel):
    method theta (line 11) | def theta(self):
    method theta (line 15) | def theta(self, theta):
    method bounds (line 19) | def bounds(self):
    method __call__ (line 22) | def __call__(self, X, Y=None, eval_gradient=False):
    method diag (line 29) | def diag(self, X):
    method __repr__ (line 32) | def __repr__(self):
    method is_stationary (line 35) | def is_stationary(self):
  class PermutationalKernel (line 40) | class PermutationalKernel(Kernel):
    method __init__ (line 41) | def __init__(self, shape, permutations, kernel):
    method theta (line 47) | def theta(self):
    method theta (line 51) | def theta(self, theta):
    method bounds (line 55) | def bounds(self):
    method __call__ (line 58) | def __call__(self, X, Y=None, eval_gradient=False):
    method diag (line 97) | def diag(self, X):
    method __repr__ (line 101) | def __repr__(self):
    method is_stationary (line 104) | def is_stationary(self):

FILE: molSimplify/ml/layers.py
  class PermutationLayer (line 12) | class PermutationLayer(tf.keras.layers.Layer):
    method __init__ (line 14) | def __init__(self, permutations: List[Tuple[int]]):
    method call (line 18) | def call(self, inputs):
    method get_config (line 38) | def get_config(self):

FILE: molSimplify/python_krr/sklearn_models.py
  function load_sklearn_model (line 10) | def load_sklearn_model(predictor):
  function sklearn_supervisor (line 17) | def sklearn_supervisor(predictor, descriptors, descriptor_names, debug=F...

FILE: molSimplify/python_nn/ANN.py
  function simple_network_builder (line 19) | def simple_network_builder(layers: List[int], partial_path: str):
  function simple_network_builder_pybrain (line 47) | def simple_network_builder_pybrain(layers: List[int], partial_path: str):
  function csv_loader (line 92) | def csv_loader(path: str) -> List[float]:
  function matrix_loader (line 103) | def matrix_loader(path, rownames=False):
  function simple_splitting_ann (line 119) | def simple_splitting_ann(excitation):
  function simple_slope_ann (line 128) | def simple_slope_ann(slope_excitation):
  function simple_ls_ann (line 136) | def simple_ls_ann(excitation):
  function simple_hs_ann (line 144) | def simple_hs_ann(excitation):
  function excitation_standardizer (line 152) | def excitation_standardizer(excitation, tag):
  function find_eu_dist (line 169) | def find_eu_dist(excitation):

FILE: molSimplify/python_nn/clf_analysis_tool.py
  function get_acc (line 10) | def get_acc(pred_std, pred_err, stds):
  function dist_neighbor (line 30) | def dist_neighbor(fmat1, fmat2, labels, l=5, dist_ref=1):  # noqa: E741
  function array_stack (line 57) | def array_stack(array, _idx):
  function dist_penalty (line 67) | def dist_penalty(d):
  function get_entropy (line 71) | def get_entropy(dists, neighbor_targets) -> np.ndarray:
  function get_layer_outputs (line 99) | def get_layer_outputs(model, layer_index, input,
  function lse_trust (line 111) | def lse_trust(lse):

FILE: molSimplify/python_nn/dictionary_toolbox.py
  function write_dictionary (line 2) | def write_dictionary(dictionary, path):
  function read_dictionary (line 13) | def read_dictionary(path):

FILE: molSimplify/python_nn/ensemble_test.py
  function reset_weights (line 29) | def reset_weights(model):
  function array_stack (line 37) | def array_stack(array, _idx):
  function mc_dropout_logp (line 47) | def mc_dropout_logp(tau, err):
  function ensemble_maker_inner (line 56) | def ensemble_maker_inner(train_mat, labels, model_gen_function, info_dict,
  function ensemble_maker (line 85) | def ensemble_maker(predictor, num=10):
  function ensemble_uq (line 103) | def ensemble_uq(predictor, descriptors=False, descriptor_names=False, su...
  function mc_dropout_uq (line 154) | def mc_dropout_uq(predictor, descriptors=False, descriptor_names=False, ...
  function latent_space_uq (line 200) | def latent_space_uq(predictor, layer_index=-2, descriptors=False, descri...

FILE: molSimplify/python_nn/tf_ANN.py
  function get_layer_outputs2 (line 56) | def get_layer_outputs2(model, layer_index, input_array, training_flag=Fa...
  function _prepare_inputs_for_model (line 80) | def _prepare_inputs_for_model(model, X):
  function _install_sklearn_compat_shims (line 87) | def _install_sklearn_compat_shims():
  function perform_ANN_prediction (line 143) | def perform_ANN_prediction(RAC_dataframe: pd.DataFrame, predictor_name: ...
  function get_error_params (line 208) | def get_error_params(latent_distances, errors):
  function matrix_loader (line 222) | def matrix_loader(path: str, rownames: bool = False) -> Union[Tuple[List...
  function get_key (line 238) | def get_key(predictor: str, suffix: Optional[str] = None) -> str:
  function data_rescale (line 268) | def data_rescale(scaled_dat, train_mean, train_var, debug=False) -> np.n...
  function data_normalize (line 276) | def data_normalize(data, train_mean, train_var, debug=False) -> np.ndarray:
  function load_normalization_data (line 302) | def load_normalization_data(name: str):
  function get_data_mean_std (line 333) | def get_data_mean_std(predictor: str):
  function load_ANN_variables (line 378) | def load_ANN_variables(predictor: str, suffix: str = 'vars') -> List[str]:
  function load_training_data (line 388) | def load_training_data(predictor: str) -> List[List[str]]:
  function load_latent_training_data (line 410) | def load_latent_training_data(predictor):
  function load_test_data (line 433) | def load_test_data(predictor):
  function load_training_labels (line 453) | def load_training_labels(predictor: str) -> List[List[str]]:
  function load_test_labels (line 475) | def load_test_labels(predictor: str) -> List[List[str]]:
  function load_train_info (line 497) | def load_train_info(predictor: str, suffix: str = 'info') -> dict:
  function load_keras_ann (line 505) | def load_keras_ann(predictor: str, suffix: str = 'model', compile: bool ...
  function _try_load_sklearn_classifier (line 558) | def _try_load_sklearn_classifier(predictor: str):
  function _fix_shape_for_model (line 604) | def _fix_shape_for_model(model, X: np.ndarray) -> np.ndarray:
  function load_keras_ann2 (line 632) | def load_keras_ann2(predictor: str, suffix: str = "model", compile: bool...
  function tf_ANN_excitation_prepare (line 779) | def tf_ANN_excitation_prepare(predictor: str, descriptors: List[float], ...
  function ANN_supervisor (line 802) | def ANN_supervisor(predictor: str,
  function find_true_min_eu_dist (line 847) | def find_true_min_eu_dist(predictor: str,
  function find_ANN_10_NN_normalized_latent_dist (line 895) | def find_ANN_10_NN_normalized_latent_dist(predictor, latent_space_vector...
  function find_ANN_latent_dist (line 938) | def find_ANN_latent_dist(predictor, latent_space_vector, debug=False):
  function find_clf_lse (line 997) | def find_clf_lse(predictor: str,
  function save_model (line 1058) | def save_model(model: tf.keras.Model, predictor: str,
  function initialize_model_weights (line 1078) | def initialize_model_weights(model: tf.keras.Model) -> tf.keras.Model:

FILE: molSimplify/utils/Graph_Hash.py
  function get_hash (line 4) | def get_hash(mol):

FILE: molSimplify/utils/Importing_Functions.py
  function readfrommol2 (line 7) | def readfrommol2(mol, filename, readstring=False, trunc_sym="X"):

FILE: molSimplify/utils/LigandBreakdown.py
  function ligand_breakdown (line 6) | def ligand_breakdown(mol,dummy_bool=False):
  function mol3D_to_networkx (line 36) | def mol3D_to_networkx(mol,get_symbols:bool=True,get_bond_order:bool=True...
  function bridging_ligand_helper (line 60) | def bridging_ligand_helper(mol,set_of_nodes,metal_indices):

FILE: molSimplify/utils/decorators.py
  function deprecated (line 5) | def deprecated(message):

FILE: molSimplify/utils/metaclasses.py
  class Singleton (line 4) | class Singleton(type):
    method __call__ (line 9) | def __call__(cls, *args, **kwargs):

FILE: molSimplify/utils/nx_helpers.py
  function graph_from_mol2_string (line 3) | def graph_from_mol2_string(m2_string, positions=False):

FILE: molSimplify/utils/openbabel_helpers.py
  function count_aromatic (line 5) | def count_aromatic(obmol):
  function constrained_forcefield_optimization_bu (line 13) | def constrained_forcefield_optimization_bu(
  function constrained_forcefield_optimization (line 179) | def constrained_forcefield_optimization(
  function bond_order_from_str_bu (line 434) | def bond_order_from_str_bu(bo_str):
  function bond_order_from_str (line 455) | def bond_order_from_str(bo):
  function replace_bonds_bu (line 471) | def replace_bonds_bu(obmol, bo_dict):
  function _is_aromatic_token (line 507) | def _is_aromatic_token(bo):
  function _numeric_bond_order (line 517) | def _numeric_bond_order(bo):
  function replace_bonds (line 533) | def replace_bonds(obmol, bo_dict):
  function get_all_bonds (line 557) | def get_all_bonds(obmol):
  function get_all_atoms (line 572) | def get_all_atoms(obmol):
  function get_bond_dict (line 593) | def get_bond_dict(obmol):

FILE: molSimplify/utils/tensorflow.py
  function tensorflow_silence (line 5) | def tensorflow_silence():

FILE: molSimplify/utils/timer.py
  class DebugTimer (line 4) | class DebugTimer:
    method __init__ (line 6) | def __init__(self, name: str, print: bool = True):
    method __enter__ (line 10) | def __enter__(self):
    method __exit__ (line 13) | def __exit__(self, exc_type, exc_value, exc_tb):

FILE: tests/examples/test_example_1.py
  function test_example_1 (line 4) | def test_example_1(tmp_path, resource_path_root):
  function test_example_1_No_FF (line 19) | def test_example_1_No_FF(tmp_path, resource_path_root):

FILE: tests/examples/test_example_3.py
  function test_example_3_No_FF (line 4) | def test_example_3_No_FF(tmp_path, resource_path_root):

FILE: tests/examples/test_example_5.py
  function test_example_5 (line 4) | def test_example_5(tmp_path, resource_path_root):
  function test_example_5_No_FF (line 25) | def test_example_5_No_FF(tmp_path, resource_path_root):

FILE: tests/examples/test_example_7.py
  function test_example_7 (line 4) | def test_example_7(tmp_path, resource_path_root):

FILE: tests/examples/test_example_8.py
  function test_example_8 (line 4) | def test_example_8(tmp_path, resource_path_root):

FILE: tests/examples/test_example_tbp.py
  function test_example_tbp (line 4) | def test_example_tbp(tmp_path, resource_path_root):

FILE: tests/helperFuncs.py
  function is_number (line 19) | def is_number(s: str) -> bool:
  function get_parent_folder (line 41) | def get_parent_folder(test_name):
  function get_in_files_subfolder (line 79) | def get_in_files_subfolder(name: str) -> str:
  function get_ref_subfolder (line 99) | def get_ref_subfolder(parent_folder: str, name: str) -> str:
  function working_directory (line 113) | def working_directory(path: Path):
  function fuzzy_equal (line 122) | def fuzzy_equal(x1, x2, thresh: float) -> bool:
  function fuzzy_compare_xyz (line 126) | def fuzzy_compare_xyz(xyz1, xyz2, thresh: float) -> bool:
  function getAllLigands (line 157) | def getAllLigands(xyz, transition_metals_only=True):
  function getMetalLigBondLength (line 214) | def getMetalLigBondLength(mymol3d: mol3D, transition_metals_only=True) -...
  function compareNumAtoms (line 242) | def compareNumAtoms(xyz1, xyz2) -> bool:
  function compareMLBL (line 270) | def compareMLBL(xyz1, xyz2, thresh: float, transition_metals_only=True) ...
  function compareLG (line 319) | def compareLG(xyz1, xyz2, thresh: float, transition_metals_only=True) ->...
  function compareOG (line 361) | def compareOG(xyz1, xyz2, thresh: float) -> bool:
  function compareGeo (line 386) | def compareGeo(xyz1, xyz2, threshMLBL, threshLG, threshOG, slab=False, t...
  function comparedict (line 441) | def comparedict(ref, gen, thresh):
  function jobname (line 477) | def jobname(infile: str) -> str:
  function jobdir (line 483) | def jobdir(infile):
  function parse4test (line 490) | def parse4test(infile, tmp_path: Path, extra_args: Dict[str, str] = {},
  function parse4testNoFF (line 548) | def parse4testNoFF(infile, tmp_path: Path) -> str:
  function report_to_dict (line 575) | def report_to_dict(lines):
  function compare_report_new (line 602) | def compare_report_new(report1, report2):
  function compare_qc_input (line 674) | def compare_qc_input(inp, inp_ref):
  function runtest (line 713) | def runtest(tmp_path, resource_path_root, name, threshMLBL, threshLG, th...
  function runtest_multispin (line 823) | def runtest_multispin(
  function runtest_slab (line 925) | def runtest_slab(tmp_path, resource_path_root, name, threshOG, extra_fil...
  function runtest_molecule_on_slab (line 976) | def runtest_molecule_on_slab(tmp_path, resource_path_root, name, threshO...
  function runtestgeo (line 1040) | def runtestgeo(tmp_path, resource_path_root, name, thresh, deleteH=True,...
  function runtestNoFF (line 1094) | def runtestNoFF(tmp_path, resource_path_root, name, threshMLBL, threshLG...
  function runtest_reportonly (line 1181) | def runtest_reportonly(tmp_path, resource_path_root, name, seed=31415):

FILE: tests/informatics/test_MOF_descriptors.py
  function ref_names (line 10) | def ref_names():
  function helper_RAC_check (line 39) | def helper_RAC_check(resource_path_root, tmp_path, name, ref_names, Gval...
  function test_get_MOF_descriptors_ODAC (line 79) | def test_get_MOF_descriptors_ODAC(resource_path_root, tmp_path, name, re...
  function test_get_MOF_descriptors_JACS (line 98) | def test_get_MOF_descriptors_JACS(resource_path_root, tmp_path, name, re...
  function test_get_MOF_descriptors_ligand_containing (line 116) | def test_get_MOF_descriptors_ligand_containing(resource_path_root, tmp_p...
  function test_get_MOF_descriptors_non_trivial (line 133) | def test_get_MOF_descriptors_non_trivial(resource_path_root, tmp_path, n...

FILE: tests/informatics/test_MOF_functional_group_add.py
  function test_fg_addition (line 23) | def test_fg_addition(resource_path_root, tmp_path, num_func, func_group):

FILE: tests/informatics/test_MOF_functional_group_add_v2.py
  function test_fg_addition (line 35) | def test_fg_addition(resource_path_root, tmp_path, num_func, func_group):

FILE: tests/informatics/test_MOF_linker_rotation.py
  function test_linker_rotation (line 17) | def test_linker_rotation(resource_path_root, tmp_path, cif_name, rotatio...

FILE: tests/informatics/test_PBC_functions.py
  function test_mkcell (line 36) | def test_mkcell(cpar, reference_cell):
  function test_cell_to_cellpar (line 50) | def test_cell_to_cellpar(cell, reference_cpar):
  function test_fractional2cart (line 64) | def test_fractional2cart(fcoords, cell, reference_cart_coord):
  function test_frac_coord (line 78) | def test_frac_coord(coord, cell, reference_fcoords):
  function test_compute_image_flag (line 98) | def test_compute_image_flag(cell, fcoord1, fcoord2, reference_shift):
  function test_writeXYZandGraph (line 102) | def test_writeXYZandGraph(resource_path_root, tmp_path):
  function test_readcif (line 140) | def test_readcif(resource_path_root, name):
  function test_compute_distance_matrix (line 164) | def test_compute_distance_matrix(resource_path_root, name):
  function test_compute_adj_matrix (line 183) | def test_compute_adj_matrix(resource_path_root, name):
  function test_solvent_removal (line 199) | def test_solvent_removal(resource_path_root, tmp_path, name):
  function test_overlap_removal (line 221) | def test_overlap_removal(resource_path_root, tmp_path, name, case):
  function test_findPaths (line 248) | def test_findPaths(resource_path_root, anchor_idx, path_bf, correct_answ...
  function quick_load (line 262) | def quick_load(file_list):
  function test_get_closed_subgraph (line 269) | def test_get_closed_subgraph(resource_path_root):
  function test_XYZ_connected (line 291) | def test_XYZ_connected():
  function test_write_cif (line 333) | def test_write_cif(resource_path_root, tmp_path):

FILE: tests/informatics/test_active_learning.py
  function test_get_pareto_indices (line 11) | def test_get_pareto_indices():
  function test_get_2D_PI_and_centroid (line 42) | def test_get_2D_PI_and_centroid(method, ref_PI, atol=1e-6):
  function test_get_2D_EI (line 70) | def test_get_2D_EI(method, ref_EI, atol=1e-6):
  function test_get_2D_EHVI (line 106) | def test_get_2D_EHVI(pred_mean, pred_std, pareto_points, r, ref_EHVI, at...

FILE: tests/informatics/test_coulomb_analyze.py
  function test_create_coulomb_matrix (line 6) | def test_create_coulomb_matrix(resource_path_root):

FILE: tests/informatics/test_graph_racs.py
  function furan (line 17) | def furan():
  function test_atom_centered_AC (line 38) | def test_atom_centered_AC(furan):
  function test_atom_centered_AC_diff (line 50) | def test_atom_centered_AC_diff(furan):
  function test_multi_centered_AC (line 62) | def test_multi_centered_AC(furan):
  function test_octahedral_racs (line 90) | def test_octahedral_racs(
  function test_ligand_racs (line 136) | def test_ligand_racs(

FILE: tests/ml/test_kernels.py
  function test_masking (line 6) | def test_masking():
  function test_permutational_kernel (line 23) | def test_permutational_kernel():
  function test_permutational_kernel_gradient (line 48) | def test_permutational_kernel_gradient():

FILE: tests/ml/test_layers.py
  function test_permutation_layer (line 6) | def test_permutation_layer():
  function test_permutational_nn (line 27) | def test_permutational_nn():

FILE: tests/test_atom3D.py
  function test_repr (line 12) | def test_repr(sym, coords):
  function test_symbol (line 28) | def test_symbol(sym):
  function test_coords (line 40) | def test_coords(coords):
  function test_defaults (line 45) | def test_defaults():
  function test_distance (line 58) | def test_distance(coords1, coords2, correct_answer):
  function test_distancev (line 71) | def test_distancev(coords1, coords2, correct_answer):
  function test_setcoords (line 86) | def test_setcoords(coords):
  function test_mutate (line 99) | def test_mutate(sym, mass, atno, rad):
  function test_ismetal (line 134) | def test_ismetal(sym, transition_metals_only, correct_answer):
  function test_translate (line 147) | def test_translate(xyz, dxyz, new_xyz):

FILE: tests/test_autocorrelation.py
  function load_complex1 (line 27) | def load_complex1(resource_path_root):
  function load_complex2 (line 36) | def load_complex2(resource_path_root):
  function load_complex3 (line 45) | def load_complex3(resource_path_root):
  function get_ref (line 53) | def get_ref(ref_path, np_array=True):
  function get_atomIdx_str (line 70) | def get_atomIdx_str(atomIdx):
  function test_construct_property_vector (line 93) | def test_construct_property_vector(resource_path_root, load_complex1, pr...
  function test_autocorrelation (line 110) | def test_autocorrelation(resource_path_root, load_complex1, orig, d, oct...
  function test_deltametric (line 131) | def test_deltametric(resource_path_root, load_complex1, orig, d, oct_fla...
  function test_full_autocorrelation (line 152) | def test_full_autocorrelation(resource_path_root, load_complex1, prop, d...
  function test_atom_only_autocorrelation (line 171) | def test_atom_only_autocorrelation(resource_path_root, load_complex1, at...
  function test_atom_only_deltametric (line 195) | def test_atom_only_deltametric(resource_path_root, load_complex1, atomId...
  function test_metal_only_autocorrelation_1 (line 217) | def test_metal_only_autocorrelation_1(resource_path_root, load_complex1,...
  function test_metal_only_autocorrelation_2 (line 234) | def test_metal_only_autocorrelation_2(resource_path_root, load_complex2,...
  function test_metal_only_autocorrelation_3 (line 251) | def test_metal_only_autocorrelation_3(resource_path_root, load_complex3,...
  function test_metal_only_autocorrelation_4 (line 260) | def test_metal_only_autocorrelation_4(load_complex3):
  function test_metal_only_deltametric_1 (line 277) | def test_metal_only_deltametric_1(resource_path_root, load_complex1, pro...
  function test_metal_only_deltametric_2 (line 294) | def test_metal_only_deltametric_2(resource_path_root, load_complex2, pro...
  function test_metal_only_deltametric_3 (line 311) | def test_metal_only_deltametric_3(resource_path_root, load_complex3, pro...
  function test_metal_only_deltametric_4 (line 320) | def test_metal_only_deltametric_4(load_complex3):
  function test_generate_atomonly_autocorrelations (line 339) | def test_generate_atomonly_autocorrelations(resource_path_root, load_com...
  function test_generate_atomonly_deltametrics (line 363) | def test_generate_atomonly_deltametrics(resource_path_root, load_complex...
  function test_generate_metal_autocorrelations_1 (line 387) | def test_generate_metal_autocorrelations_1(resource_path_root, load_comp...
  function test_generate_metal_autocorrelations_2 (line 411) | def test_generate_metal_autocorrelations_2(resource_path_root, load_comp...
  function test_generate_metal_autocorrelations_3 (line 435) | def test_generate_metal_autocorrelations_3(resource_path_root, load_comp...
  function test_generate_metal_autocorrelations_4 (line 448) | def test_generate_metal_autocorrelations_4(load_complex3):
  function test_generate_metal_deltametrics_1 (line 467) | def test_generate_metal_deltametrics_1(resource_path_root, load_complex1...
  function test_generate_metal_deltametrics_2 (line 491) | def test_generate_metal_deltametrics_2(resource_path_root, load_complex2...
  function test_generate_metal_deltametrics_3 (line 515) | def test_generate_metal_deltametrics_3(resource_path_root, load_complex3...
  function test_generate_metal_deltametrics_4 (line 528) | def test_generate_metal_deltametrics_4(load_complex3):
  function test_generate_full_complex_autocorrelations (line 547) | def test_generate_full_complex_autocorrelations(resource_path_root, load...
  function test_get_descriptor_vector (line 571) | def test_get_descriptor_vector(resource_path_root, load_complex1, depth,...

FILE: tests/test_basic_imports.py
  function test_molsimplify_imported (line 8) | def test_molsimplify_imported():
  function test_tf_import (line 15) | def test_tf_import():
  function test_openbabel_import (line 26) | def test_openbabel_import():

FILE: tests/test_cli.py
  function test_help_no_error (line 9) | def test_help_no_error():
  function test_main_does_not_import_pydentate_with_explicit_usercatoms (line 20) | def test_main_does_not_import_pydentate_with_explicit_usercatoms(monkeyp...

FILE: tests/test_decoration.py
  function test_molecule_dec (line 7) | def test_molecule_dec(tmp_path, resource_path_root):

FILE: tests/test_distgeom.py
  function test_CosRule (line 8) | def test_CosRule(atol=1e-6):
  function test_GetCMDists (line 29) | def test_GetCMDists():
  function test_Metrize (line 49) | def test_Metrize():
  function test_findshape (line 83) | def test_findshape():

FILE: tests/test_ff_xtb.py
  function test_xtb_before (line 12) | def test_xtb_before(tmp_path, resource_path_root):
  function test_xtb_ANC_fail (line 29) | def test_xtb_ANC_fail(tmp_path, resource_path_root):
  function test_xtb_high_spin (line 46) | def test_xtb_high_spin(tmp_path, resource_path_root):
  function test_xtb_final_opt (line 63) | def test_xtb_final_opt(tmp_path, resource_path_root):
  function test_gfnff (line 80) | def test_gfnff(tmp_path, resource_path_root):

FILE: tests/test_geocheck_oct.py
  function test_geocheck_oct (line 22) | def test_geocheck_oct(tmp_path, resource_path_root, testName):

FILE: tests/test_geocheck_one_empty.py
  function test_example_1 (line 4) | def test_example_1(tmp_path, resource_path_root):
  function test_example_2 (line 11) | def test_example_2(tmp_path, resource_path_root):

FILE: tests/test_geometry.py
  function test_norm (line 12) | def test_norm():
  function test_normalize (line 18) | def test_normalize():
  function test_checkplanar (line 25) | def test_checkplanar():
  function test_dihedral (line 37) | def test_dihedral():
  function test_reflect_through_plane (line 48) | def test_reflect_through_plane():

FILE: tests/test_inparse.py
  function test_parseinputfile_empty (line 9) | def test_parseinputfile_empty():
  function test_parseinputs_basic (line 23) | def test_parseinputs_basic(monkeypatch):
  function test_parseinputs_advanced (line 36) | def test_parseinputs_advanced(monkeypatch):
  function test_checkinput (line 50) | def test_checkinput(monkeypatch):
  function test_parseinputfile_inputfile_kwarg (line 63) | def test_parseinputfile_inputfile_kwarg(resource_path_root):

FILE: tests/test_io.py
  function test_lig_load (line 11) | def test_lig_load(resource_path_root):
  function test_core_load (line 29) | def test_core_load():
  function test_printgeoms (line 45) | def test_printgeoms(capsys):
  function test_readdict_sub (line 66) | def test_readdict_sub():
  function test_getsubstrates (line 75) | def test_getsubstrates():

FILE: tests/test_jobgen.py
  function test_sgejobgen_default (line 5) | def test_sgejobgen_default(tmp_path):
  function test_sgejobgen (line 27) | def test_sgejobgen(tmp_path):
  function test_sgejobgen_jobmanager (line 52) | def test_sgejobgen_jobmanager(tmp_path):
  function test_slurmjobgen_default (line 83) | def test_slurmjobgen_default(tmp_path):
  function test_slurmjobgen (line 103) | def test_slurmjobgen(tmp_path):
  function test_slurmjobgen_jobmanager (line 125) | def test_slurmjobgen_jobmanager(tmp_path):

FILE: tests/test_joption_pythonic.py
  function test_joption_pythonic (line 4) | def test_joption_pythonic(tmp_path, resource_path_root):
  function test_pythonic_metalloid_structure (line 29) | def test_pythonic_metalloid_structure(tmp_path, resource_path_root):

FILE: tests/test_lig_load.py
  function test_ligand_loading (line 12) | def test_ligand_loading(tmp_path, resource_path_root, lig_name):

FILE: tests/test_ligand_assign.py
  function test_six_monodentate (line 5) | def test_six_monodentate(resource_path_root):
  function test_triple_bidentate (line 34) | def test_triple_bidentate(resource_path_root):

FILE: tests/test_ligand_assign_consistent.py
  function test_six_monodentate (line 5) | def test_six_monodentate(resource_path_root):
  function test_triple_bidentate (line 35) | def test_triple_bidentate(resource_path_root):

FILE: tests/test_ligand_class.py
  function test_ligand_class (line 4) | def test_ligand_class(resource_path_root):

FILE: tests/test_ligands.py
  function test_ligands_dict (line 15) | def test_ligands_dict(lig_name):
  function test_no_repeats (line 55) | def test_no_repeats():
  function test_unused_geometries (line 83) | def test_unused_geometries(file_name):

FILE: tests/test_mol2D.py
  function water_Mol2D (line 6) | def water_Mol2D():
  function furan_Mol2D (line 15) | def furan_Mol2D():
  function acac_Mol2D (line 36) | def acac_Mol2D():
  function test_Mol2D_repr (line 70) | def test_Mol2D_repr(mol, ref):
  function test_Mol2D_constructors (line 82) | def test_Mol2D_constructors(resource_path_root, name, smiles, mol_ref):
  function test_Mol2D_graph_hash (line 120) | def test_Mol2D_graph_hash(resource_path_root, filename, node_hash_ref, e...
  function test_find_metal (line 133) | def test_find_metal(resource_path_root):

FILE: tests/test_mol3D.py
  function quick_load (line 9) | def quick_load(file_list):
  function test_addAtom (line 17) | def test_addAtom():
  function test_getAtoms (line 29) | def test_getAtoms():
  function test_get_pair_distance (line 47) | def test_get_pair_distance():
  function test_getAtomwithinds (line 71) | def test_getAtomwithinds(idxs):
  function test_copymol3D (line 99) | def test_copymol3D(make_graph, make_obmol):
  function test_initialize (line 129) | def test_initialize():
  function test_adding_and_deleting_atoms (line 148) | def test_adding_and_deleting_atoms():
  function test_finding_and_counting_methods (line 171) | def test_finding_and_counting_methods():
  function test_make_formula (line 207) | def test_make_formula():
  function test_add_bond (line 236) | def test_add_bond():
  function test_readfromxyz (line 273) | def test_readfromxyz(resource_path_root):
  function test_centersym (line 332) | def test_centersym(resource_path_root, name, correct_answer):
  function test_centermass (line 347) | def test_centermass(resource_path_root, name, correct_answer):
  function test_distance (line 362) | def test_distance(resource_path_root, name1, name2, correct_answer):
  function test_mindist (line 379) | def test_mindist(resource_path_root, name1, name2, correct_answer):
  function test_alignmol (line 409) | def test_alignmol(resource_path_root, name1, name2, idx1, idx2, correct_...
  function test_get_geometry_type (line 442) | def test_get_geometry_type(resource_path_root, name, geometry_str):
  function test_get_geometry_type_catoms_arr (line 452) | def test_get_geometry_type_catoms_arr(resource_path_root):
  function test_get_geometry_type_hapticity (line 480) | def test_get_geometry_type_hapticity(resource_path_root, name, geometry_...
  function test_is_sandwich_compound (line 502) | def test_is_sandwich_compound(resource_path_root, name, con_atoms):
  function test_is_edge_compound (line 526) | def test_is_edge_compound(resource_path_root, name, con_atoms):
  function test_mol3D_from_smiles_macrocycles (line 539) | def test_mol3D_from_smiles_macrocycles():
  function test_mol3D_from_smiles_benzene (line 589) | def test_mol3D_from_smiles_benzene():
  function test_dev_from_ideal_geometry (line 640) | def test_dev_from_ideal_geometry(resource_path_root, geo_type, key):
  function test_geo_geometry_type_distance (line 675) | def test_geo_geometry_type_distance(resource_path_root, geo_type, ref):
  function test_get_graph_hash (line 691) | def test_get_graph_hash(resource_path_root, geo):
  function test_getAtom (line 716) | def test_getAtom(resource_path_root, name, idx, sym, coords):
  function test_findMetal (line 740) | def test_findMetal(resource_path_root, name, transition_metals_only, cor...
  function test_createMolecularGraph (line 758) | def test_createMolecularGraph(resource_path_root, name, oct_flag):
  function test_getBondedAtoms (line 787) | def test_getBondedAtoms(resource_path_root, name, idx, get_graph, correc...
  function test_getBondedAtomsSmart (line 810) | def test_getBondedAtomsSmart(resource_path_root, name, idx, oct_flag, co...
  function test_getBondedAtomsH (line 827) | def test_getBondedAtomsH(resource_path_root, name, idx, correct_answer):
  function test_getBondedAtomsnotH (line 843) | def test_getBondedAtomsnotH(resource_path_root, name, idx, correct_answer):
  function test_getBondedAtomsOct (line 859) | def test_getBondedAtomsOct(resource_path_root, name, idx, correct_answer):
  function test_assign_graph_from_net (line 876) | def test_assign_graph_from_net(resource_path_root, name, return_graph):
  function test_convert2OBMol (line 909) | def test_convert2OBMol(resource_path_root, name, force_clean_flag):
  function test_convert2OBMol2 (line 940) | def test_convert2OBMol2(resource_path_root, name):
  function test_get_smiles (line 982) | def test_get_smiles(resource_path_root, name, canonicalize, use_mol2, co...
  function test_populateBOMatrix (line 998) | def test_populateBOMatrix(resource_path_root, name, bonddict):
  function test_deleteatom (line 1037) | def test_deleteatom(resource_path_root, name, idx, bo_dict_flag, graph_f...
  function test_deleteatoms (line 1087) | def test_deleteatoms(resource_path_root, name, idxs, bo_dict_flag, graph...
  function test_readfrommol2 (line 1132) | def test_readfrommol2(resource_path_root, name, readstring):
  function test_readfrommol (line 1187) | def test_readfrommol(resource_path_root, name):
  function test_getAtomCoords (line 1227) | def test_getAtomCoords(resource_path_root, name, idx, correct_answer):
  function test_writemol2 (line 1244) | def test_writemol2(resource_path_root, tmp_path, writestring, ignoreX):
  function test_writexyz (line 1292) | def test_writexyz(resource_path_root, tmp_path, writestring, withgraph, ...
  function test_writemol (line 1331) | def test_writemol(resource_path_root, tmp_path):
  function test_translate (line 1350) | def test_translate(resource_path_root):
  function test_num_rings (line 1366) | def test_num_rings(resource_path_root):
  function test_findsubMol (line 1376) | def test_findsubMol(resource_path_root):
  function test_BCM (line 1394) | def test_BCM():
  function test_get_mol_graph_det (line 1422) | def test_get_mol_graph_det(resource_path_root, name, ref_det):
  function test_get_octetrule_charge (line 1440) | def test_get_octetrule_charge(resource_path_root, name, ref_charge):

FILE: tests/test_molcas_caspt2.py
  function test_molcas_caspt2 (line 4) | def test_molcas_caspt2(tmp_path, resource_path_root):

FILE: tests/test_molcas_casscf.py
  function test_molcas_casscf (line 4) | def test_molcas_casscf(tmp_path, resource_path_root):

FILE: tests/test_old_ANNs.py
  function test_old_ANN (line 6) | def test_old_ANN(tmp_path, resource_path_root):
  function test_simple_network_builder (line 20) | def test_simple_network_builder():

FILE: tests/test_orca_ccsdt.py
  function test_orca_ccsdt (line 4) | def test_orca_ccsdt(tmp_path, resource_path_root):

FILE: tests/test_orca_dft.py
  function test_orca_dft (line 4) | def test_orca_dft(tmp_path, resource_path_root):

FILE: tests/test_qcgen.py
  function test_qcgen_defaults (line 12) | def test_qcgen_defaults(resource_path_root, gen_function, default_name, ...

FILE: tests/test_racs.py
  function test_Mn_water2_ammonia_furan2_ammonia (line 15) | def test_Mn_water2_ammonia_furan2_ammonia(resource_path_root, xyz_path, ...
  function test_six_pyridine_vs_three_bipy (line 30) | def test_six_pyridine_vs_three_bipy(resource_path_root):
  function test_create_OHE (line 54) | def test_create_OHE():

FILE: tests/test_rmsd.py
  function test_rigorous_rmsd (line 16) | def test_rigorous_rmsd(resource_path_root, path1, path2, ref_hungarian, ...
  function test_methane_rotation (line 34) | def test_methane_rotation(atol=1e-3):
  function test_tbpd_rotation (line 60) | def test_tbpd_rotation(atol=1e-3):
  function test_quaternion_rotate (line 95) | def test_quaternion_rotate(atol=1e-3):

FILE: tests/test_structgen_functions.py
  function test_smartreorderligs (line 16) | def test_smartreorderligs():
  function test_get_MLdist_database (line 48) | def test_get_MLdist_database():
  function test_get_MLdist (line 79) | def test_get_MLdist():
  function test_init_template (line 128) | def test_init_template(geometry, coordination):
  function test_init_ANN (line 145) | def test_init_ANN():
  function test_getnupdateb (line 189) | def test_getnupdateb():

FILE: tests/test_tetrahedral.py
  function test_example_1 (line 4) | def test_example_1(tmp_path, resource_path_root):
  function test_example_2 (line 18) | def test_example_2(tmp_path, resource_path_root):

FILE: tests/testresources/refs/racs/generate_references.py
  function get_ligand (line 10) | def get_ligand(lig_str):
  function generate_ligand_dict (line 17) | def generate_ligand_dict(eq_ligands, ax_ligands):
  function assemble_mol (line 34) | def assemble_mol(metal_str, eq_ligands, ax_ligands):
  function features_from_mol (line 45) | def features_from_mol(mol, ligand_dict):
  function generate_features (line 51) | def generate_features(metal_str, eq_ligands, ax_ligands):
  function main (line 57) | def main():

FILE: tests/tutorials/test_tutorial_10.py
  function test_tutorial_10_acetate_homoleptic (line 9) | def test_tutorial_10_acetate_homoleptic(tmp_path, resource_path_root):
  function test_tutorial_10_ligadd_smiles (line 25) | def test_tutorial_10_ligadd_smiles(tmp_path, resource_path_root):
  function test_tutorial_10_ligadd_mol (line 73) | def test_tutorial_10_ligadd_mol(tmp_path, resource_path_root):

FILE: tests/tutorials/test_tutorial_11.py
  function test_tutorial_11_isoct (line 9) | def test_tutorial_11_isoct(resource_path_root):

FILE: tests/tutorials/test_tutorial_2.py
  function test_tutorial_2 (line 4) | def test_tutorial_2(tmp_path, resource_path_root):

FILE: tests/tutorials/test_tutorial_3.py
  function test_tutorial_3 (line 4) | def test_tutorial_3(tmp_path, resource_path_root):

FILE: tests/tutorials/test_tutorial_4.py
  function run_db_search (line 7) | def run_db_search(tmp_path, resource_path_root, name):
  function test_tutorial_4_query (line 20) | def test_tutorial_4_query(tmp_path, resource_path_root):
  function test_tutorial_4_dissim (line 32) | def test_tutorial_4_dissim(tmp_path, resource_path_root):
  function test_tutorial_4_human (line 48) | def test_tutorial_4_human(tmp_path, resource_path_root):

FILE: tests/tutorials/test_tutorial_5.py
  function test_tutorial_5 (line 4) | def test_tutorial_5(tmp_path, resource_path_root):

FILE: tests/tutorials/test_tutorial_6.py
  function test_tutorial_6_1co (line 12) | def test_tutorial_6_1co(tmp_path, resource_path_root):
  function test_tutorial_6_stag_3co (line 21) | def test_tutorial_6_stag_3co(tmp_path, resource_path_root):
  function test_tutorial_6_mno4 (line 31) | def test_tutorial_6_mno4(tmp_path, resource_path_root):
  function test_tutorial_6_fepo (line 43) | def test_tutorial_6_fepo(tmp_path, resource_path_root):
  function test_tutorial_6_loaded_fepo (line 54) | def test_tutorial_6_loaded_fepo(tmp_path, resource_path_root):

FILE: tests/tutorials/test_tutorial_7.py
  function test_tutorial_7 (line 4) | def test_tutorial_7(tmp_path, resource_path_root):
  function test_tutorial_7_decoration (line 23) | def test_tutorial_7_decoration(tmp_path, resource_path_root):
  function test_tutorial_7_decoration_multi (line 40) | def test_tutorial_7_decoration_multi(tmp_path, resource_path_root):
  function test_tutorial_7_decoration_4lig (line 59) | def test_tutorial_7_decoration_4lig(tmp_path, resource_path_root):

FILE: tests/tutorials/test_tutorial_8.py
  function test_tutorial_8_part_one (line 4) | def test_tutorial_8_part_one(tmp_path, resource_path_root):
  function test_tutorial_8_part_two (line 18) | def test_tutorial_8_part_two(tmp_path, resource_path_root):

FILE: tests/tutorials/test_tutorial_9_part_one.py
  function _normalize_svg_for_compare (line 7) | def _normalize_svg_for_compare(svg_str: str) -> str:
  function test_tutorial_9_drawmode (line 25) | def test_tutorial_9_drawmode(tmp_path, resource_path_root):
  function test_tutorial_9_part_one (line 44) | def test_tutorial_9_part_one(tmp_path, resource_path_root):

FILE: tests/tutorials/test_tutorial_9_part_two.py
  function test_tutorial_9_part_two (line 4) | def test_tutorial_9_part_two(tmp_path, resource_path_root):

FILE: workflows/NandyJACSAu2022/bridge_functionalizer.py
  function read_synthesized_macrocycles (line 30) | def read_synthesized_macrocycles(input_file):
  function split_at_idx (line 49) | def split_at_idx(smiles, idx):
  function compatibility (line 64) | def compatibility(func, bridge):
  function count_atoms (line 77) | def count_atoms(smiles):
  function main (line 81) | def main(temp_list):

FILE: workflows/NandyJACSAu2022/frag_functionalizer.py
  function read_synthesized_macrocycles (line 30) | def read_synthesized_macrocycles(input_file):
  function count_atoms (line 48) | def count_atoms(smiles):
  function split_at_idx (line 52) | def split_at_idx(smiles, idx):
  function main (line 67) | def main(temp_list):

FILE: workflows/NandyJACSAu2022/fragment_classes.py
  class fragment (line 7) | class fragment:
    method __init__ (line 13) | def __init__(self, name, options, start_macrocycle=False, ring_closure...
    method give_compatible_fragments (line 40) | def give_compatible_fragments(self, bridge, next_fragment):
    method adjust_ring_closure_index (line 78) | def adjust_ring_closure_index(self, new_index, smiles_tuple=False):
    method start_macrocycle_ring (line 110) | def start_macrocycle_ring(self, smiles, start_position=0, macro_ind=9):
    method check_allowed (line 147) | def check_allowed(self, left, center, right):
    method split_smiles_at_lc_adjacent (line 157) | def split_smiles_at_lc_adjacent(self, smiles_tuple):
  class bridge (line 215) | class bridge:
    method __init__ (line 220) | def __init__(self, name, bonding, func=()):
    method get_possible_motifs (line 235) | def get_possible_motifs(self):
    method return_name (line 241) | def return_name(self):
  class tetradentate (line 251) | class tetradentate:
    method __init__ (line 252) | def __init__(self, fragment1, fragment2, fragment3, fragment4, bridge1...
    method cyclic_equiv (line 272) | def cyclic_equiv(self, u, v):
    method check_allowed (line 288) | def check_allowed(self, left, center, right):
    method split_smiles_at_lc_adjacent (line 298) | def split_smiles_at_lc_adjacent(self, smiles_tuple):
    method sp3_hybridization_checker (line 355) | def sp3_hybridization_checker(self, left, prev_center, right, bridge):
    method non_planar (line 386) | def non_planar(self, left, center, right, frag):
    method get_charge (line 406) | def get_charge(self, smiles):
    method get_atoms (line 411) | def get_atoms(self, smiles):
    method get_formula (line 414) | def get_formula(self, smiles):
    method count_atoms (line 423) | def count_atoms(self, smiles):
    method stitch (line 426) | def stitch(self):

FILE: workflows/NandyJACSAu2022/macrocycle_synthesis.py
  function cyclic_equiv (line 8) | def cyclic_equiv(u, v):
  function main (line 62) | def main():