Unusual custom "ligand" crashed structgen

[dbkchu]

Database properties:

• graph_hash_with_X: "6f9e80dd920e81ad17b36aef03a2b9be"
• _id: "5fad66f535c34d073da34cd1"

mol2 file: ligMN0772.mol2.txt

Code used to add to ligands.dict:

basedir = 'ligands_monodentate_neutral'

cursor = db.ligands.find({'graph_hash_with_X':lig_hash})
entry = next(cursor)
while 'csd-consistent-charge' not in entry:
    entry = next(cursor)

# load ligand into mol3D
lig3D = mol3D()
lig3D.readfrommol2(entry['rep_mol2string'],readstring=True)

# find X 
xidx = lig3D.find_atom('X')[0]

# get connecting atom info
catoms = lig3D.getBondedAtoms(xidx)
catoms = [idx if idx > xidx else idx + 1 for idx in catoms ]
ligname = f"ligMN0772"

# write mol2
mol2_name = os.path.join(basedir, f"{ligname}.mol2")
if not os.path.exists(mol2_name):
    lig3D.writemol2(mol2_name, ignoreX=True)

# add to database
addtoldb(smimol=mol2_name, sminame=ligname, smident=1, smicat=str(catoms).strip('[]'), smigrps="custom", smictg="custom", ffopt='N', smichg=0)

Line in ligands.dict after adding:
ligMN0772:ligMN0772.mol2,ligMN0772,9,build custom custom,N,0

Code run before traceback:

base_molS = {
    "-core": "Fe",
    "-oxstate": "II",
    "-geometry": "oct",
    "-coord": "6",
    "-ligocc": "1,1,1,1,1,1",
    "-ligloc": "true",
    "-skipANN": "true",
    "-keepHs": "yes",
    "-rundir": "homoleptic",
    "-spin": "1"
}

lig_list = ["ligMN0772"]*6

Error Traceback:

ZeroDivisionError                         Traceback (most recent call last)
Cell In[6], line 5
      3 molS_commands = {"-lig":f"{','.join(lig_list)}"}
      4 molS_commands.update(base_molS)
----> 5 startgen_pythonic(molS_commands, write=True)

File ~/src/molSimplify/molSimplify/Scripts/generator.py:64, in startgen_pythonic(input_dict, argv, flag, gui, write)
     62 inputfile_str = '\n'.join([k + ' ' + v for k, v in list(input_dict.items())])
     63 if write:
---> 64     startgen(argv, flag, gui, inputfile_str, write_files=write)
     65 else:
     66     strfiles, emsg, this_diag = startgen(argv, flag, gui, inputfile_str, write_files=write)

File ~/src/molSimplify/molSimplify/Scripts/generator.py:255, in startgen(argv, flag, gui, inputfile_str, write_files)
    253 for cc in corests:
    254     args.core = cc
--> 255     emsg = multigenruns(rundir, args, write_files=write_files)
    256     if emsg:
    257         print(emsg)

File ~/src/molSimplify/molSimplify/Scripts/rungen.py:308, in multigenruns(rundir, args, write_files)
    306     if args.spin:
    307         args.spin = args.spin[0]
--> 308     emsg = rungen(rundir, args, write_files=write_files)
    309 return emsg

File ~/src/molSimplify/molSimplify/Scripts/rungen.py:614, in rungen(rundir, args, chspfname, write_files)
    611     strfiles = tstrfiles
    612 else:
    613     # generate xyz files
--> 614     strfiles, emsg, this_diag = structgen(
    615         args, rootdir, ligands, ligocc, mcount, write_files=write_files)
    616 # generate QC input files
    617 if args.qccode and (not emsg) and write_files:

File ~/src/molSimplify/molSimplify/Scripts/structgen.py:2969, in structgen(args, rootdir, ligands, ligoc, sernum, write_files)
   2967         return strfiles, emsg, this_diag
   2968 else:
-> 2969     core3D, complex3D, emsg, this_diag, subcatoms_ext, mligcatoms_ext = mcomplex(
   2970         args, ligands, ligoc)
   2971     if args.debug:
   2972         print(('subcatoms_ext are ' + str(subcatoms_ext)))

File ~/src/molSimplify/molSimplify/Scripts/structgen.py:2549, in mcomplex(args, ligs, ligoc)
   2547     print(('backbone atoms: ' + str(batoms)))
   2548 if (denticity == 1):
-> 2549     lig3D, MLoptbds = align_dent1_lig(
   2550         args, cpoint, core3D, coreref, ligand, lig3D, catoms,
   2551         rempi, ligpiatoms, MLb, ANN_flag, ANN_bondl[ligsused],
   2552         this_diag, MLbonds, MLoptbds, i)
   2553     if args.debug:
   2554         print(('adding monodentate at distance: ' + str(
   2555             ANN_bondl[totlig]) + '/'+str(MLb) + '/'+' at catoms ' + str(catoms)))

File ~/src/molSimplify/molSimplify/Scripts/structgen.py:2010, in align_dent1_lig(args, cpoint, core3D, coreref, ligand, lig3D, catoms, rempi, ligpiatoms, MLb, ANN_flag, ANN_bondl, this_diag, MLbonds, MLoptbds, i, EnableAutoLinearBend)
   2007         lig3D = align_pi_ring_lig(corerefcoords, lig3D, atom0, ligpiatoms, u)
   2008 elif lig3D.natoms > 1:
   2009     # align ligand center of symmetry
-> 2010     lig3D = align_lig_centersym(
   2011         corerefcoords, lig3D, atom0, core3D, EnableAutoLinearBend)
   2012     if lig3D.natoms > 2:
   2013         # check for linear molecule and align
   2014         lig3D = check_rotate_linear_lig(corerefcoords, lig3D, atom0)

File ~/src/molSimplify/molSimplify/Scripts/structgen.py:1088, in align_lig_centersym(corerefcoords, lig3D, atom0, core3D, EnableAutoLinearBend)
   1086 for at in lig3D.getBondedAtoms(atom0):
   1087     auxmol.addAtom(lig3D.getAtom(at))
-> 1088 r2 = auxmol.centersym()
   1089 theta, u = rotation_params(r0, r1, r2)
   1090 # rotate around axis and get both images

File ~/src/molSimplify/molSimplify/Classes/mol3D.py:583, in mol3D.centersym(self)
    581     center_of_symmetry[2] += xyz[2]
    582 # normalize
--> 583 center_of_symmetry[0] /= self.natoms
    584 center_of_symmetry[1] /= self.natoms
    585 center_of_symmetry[2] /= self.natoms

ZeroDivisionError: float division by zero

[dbkchu]

"Ligand" visualized: