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snurr-group / mofid

A system for rapid identification and analysis of metal-organic frameworks
https://snurr-group.github.io/mofid/
GNU General Public License v2.0
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Inconsistent output between local mofid and webmofid #31

Open kbsezginel opened 1 year ago

kbsezginel commented 1 year ago

I getting different results using MOFid locally vs. the web interface. When I use the web MOFid I am getting the following result:

MOFid:
[Co].[O-]C(=O)c1ccncc1 MOFid-v1.dia.cat0;CEYPUT02
MOFkey:
Co.TWBYWOBDOCUKOW.MOFkey-v1.dia

However when I run locally I get:

{'mofid': '[Co].[O-]C(=O)c1ccncc1 MOFid-v1.ERROR.cat0;CEYPUT02',
 'mofkey': 'Co.TWBYWOBDOCUKOW.MOFkey-v1.ERROR',
 'smiles_nodes': ['[Co]'],
 'smiles_linkers': ['[O-]C(=O)c1ccncc1'],
 'smiles': '[Co].[O-]C(=O)c1ccncc1',
 'topology': 'ERROR',
 'cat': '0',
 'cifname': 'CEYPUT02'}

Any ideas why this might be happening? I didn't see any parameters I can change to get different results but I might be wrong. Can they be using different versions? I compiled mofid from the source today by following the instructions. Please let me know if I can provide more information. The cif file is below. Thanks!

data_image0
_chemical_formula_structural       CoO4N2C3HCHCHCHC3HCHCHCHCoO2NC3HCHCHCHO2NC3HCHCHCH
_chemical_formula_sum              "Co2 O8 N4 C24 H16"
_cell_length_a       6.3043
_cell_length_b       12.6051
_cell_length_c       10.4868
_cell_angle_alpha    90
_cell_angle_beta     91.365
_cell_angle_gamma    90

_space_group_name_H-M_alt    "P 1"
_space_group_IT_number       1

loop_
  _space_group_symop_operation_xyz
  'x, y, z'

loop_
  _atom_site_type_symbol
  _atom_site_label
  _atom_site_symmetry_multiplicity
  _atom_site_fract_x
  _atom_site_fract_y
  _atom_site_fract_z
  _atom_site_occupancy
  Co  Co1       1.0  0.48890  0.24615  0.83518  1.0000
  O   O1        1.0  0.92040  0.64330  0.49570  1.0000
  O   O2        1.0  0.22590  0.65280  0.40080  1.0000
  O   O3        1.0  0.76020  0.86520  0.37980  1.0000
  O   O4        1.0  0.07220  0.88580  0.47240  1.0000
  N   N1        1.0  0.34430  0.35560  0.71280  1.0000
  N   N2        1.0  0.63270  0.15620  0.69500  1.0000
  C   C1        1.0  0.10460  0.61330  0.48440  1.0000
  C   C2        1.0  0.19160  0.52320  0.56560  1.0000
  C   C3        1.0  0.38970  0.48180  0.54590  1.0000
  H   H1        1.0  0.47504  0.50969  0.48302  1.0000
  C   C4        1.0  0.46100  0.39760  0.62090  1.0000
  H   H2        1.0  0.59477  0.36946  0.60669  1.0000
  C   C5        1.0  0.15170  0.39670  0.73290  1.0000
  H   H3        1.0  0.07023  0.36800  0.79720  1.0000
  C   C6        1.0  0.06940  0.48030  0.66150  1.0000
  H   H4        1.0  0.93517  0.50706  0.67735  1.0000
  C   C7        1.0  0.88360  0.91240  0.45810  1.0000
  C   C8        1.0  0.79740  0.00190  0.53640  1.0000
  C   C9        1.0  0.91870  0.04480  0.63680  1.0000
  H   H5        1.0  0.05699  0.02171  0.65248  1.0000
  C   C10       1.0  0.83080  0.12170  0.71240  1.0000
  H   H6        1.0  0.91324  0.15081  0.77824  1.0000
  C   C11       1.0  0.51850  0.11760  0.59540  1.0000
  H   H7        1.0  0.38285  0.14426  0.57955  1.0000
  C   C12       1.0  0.59410  0.04030  0.51620  1.0000
  H   H8        1.0  0.50934  0.01401  0.44958  1.0000
  Co  Co2       1.0  0.98890  0.75385  0.33518  1.0000
  O   O5        1.0  0.42040  0.35670  0.99570  1.0000
  O   O6        1.0  0.72590  0.34720  0.90080  1.0000
  N   N3        1.0  0.84430  0.64440  0.21280  1.0000
  C   C13       1.0  0.60460  0.38670  0.98440  1.0000
  C   C14       1.0  0.69160  0.47680  0.06560  1.0000
  C   C15       1.0  0.88970  0.51820  0.04590  1.0000
  H   H9        1.0  0.97504  0.49030  0.98303  1.0000
  C   C16       1.0  0.96100  0.60240  0.12090  1.0000
  H   H10       1.0  0.09477  0.63054  0.10669  1.0000
  C   C17       1.0  0.65170  0.60330  0.23290  1.0000
  H   H11       1.0  0.57023  0.63200  0.29720  1.0000
  C   C18       1.0  0.56940  0.51970  0.16150  1.0000
  H   H12       1.0  0.43517  0.49294  0.17735  1.0000
  O   O7        1.0  0.26020  0.13480  0.87980  1.0000
  O   O8        1.0  0.57220  0.11420  0.97240  1.0000
  N   N4        1.0  0.13270  0.84380  0.19500  1.0000
  C   C19       1.0  0.38360  0.08760  0.95810  1.0000
  C   C20       1.0  0.29740  0.99810  0.03640  1.0000
  C   C21       1.0  0.41870  0.95520  0.13680  1.0000
  H   H13       1.0  0.55699  0.97829  0.15248  1.0000
  C   C22       1.0  0.33080  0.87830  0.21240  1.0000
  H   H14       1.0  0.41324  0.84919  0.27824  1.0000
  C   C23       1.0  0.01850  0.88240  0.09540  1.0000
  H   H15       1.0  0.88285  0.85574  0.07955  1.0000
  C   C24       1.0  0.09410  0.95970  0.01620  1.0000
  H   H16       1.0  0.00934  0.98599  0.94958  1.0000
bbucior commented 1 year ago

Thanks for the cif and great writeup! I'm having trouble reproducing the ERROR topology and successfully getting dia for both.

My best guess is that it's something to do with the systre/java dependency. For more diagnostics, could you try running the rerun_systre.py tool, something like:

python Python/run_mofid.py ~/Downloads/example.cif
python Python/rerun_systre.py