Skip to content

Commit

Permalink
Debugging ACEYOW YETBUV
Browse files Browse the repository at this point in the history
  • Loading branch information
@choglass
choglass committed Apr 25, 2024
1 parent f4d3f99 commit d1229bd
Show file tree
Hide file tree
Showing 15 changed files with 4,610 additions and 6 deletions.
16 changes: 10 additions & 6 deletions cell2mol/classes.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1291,7 +1291,7 @@ def get_reference_molecules(self, ref_labels: list, ref_fracs: list, cov_factor:
return self.refmoleclist

#######################################################
def get_moleclist(self, blocklist=None, debug: int=0):
def get_moleclist(self, debug: int=0):
if debug > 0: print(f"Entered CELL.MOLECLIST with debug={debug}")
if not hasattr(self,"labels") or not hasattr(self,"coord"):
if debug > 0: print(f"CELL.MOLECLIST. Labels or coordinates not found. Returning None")
Expand All @@ -1302,10 +1302,13 @@ def get_moleclist(self, blocklist=None, debug: int=0):
if debug > 0: print(f"CELL.MOLECLIST passed initial checks")
cov_factor = 1.3

if blocklist is None: blocklist = split_species(self.labels, self.coord, cov_factor=cov_factor, debug=debug)
if blocklist is None: return None
if debug > 0: print(f"CELL.MOLECLIST: found {len(blocklist)} blocks")
if debug > 0: print(f"CELL.MOLECLIST: {blocklist=}")
blocklist = split_species(self.labels, self.coord, cov_factor=cov_factor, debug=debug)

if blocklist is None:
return None
else :
if debug > 0: print(f"CELL.MOLECLIST: found {len(blocklist)} blocks")
if debug > 0: print(f"CELL.MOLECLIST: {blocklist=}")

self.moleclist = []
for b in blocklist:
Expand Down Expand Up @@ -1370,7 +1373,8 @@ def reconstruct(self, cov_factor: float=None, metal_factor: float=None, debug: i
if metal_factor is None: metal_factor = self.refmoleclist[0].metal_factor

## Get the fragments, which is the moleclist of a fragmented cell
fragments = self.get_moleclist(debug=debug).copy()
fragments = self.get_moleclist(debug=debug)

if fragments is None:
self.error_get_fragments = True
return # Stopping. self.error_get_fragments must be False to reconstruct the cell
Expand Down
195 changes: 195 additions & 0 deletions cell2mol/test/ACEYOW/ACEYOW.cif
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,195 @@

#######################################################################
#
# Cambridge Crystallographic Data Centre
# CCDC
#
#######################################################################
#
# If this CIF has been generated from an entry in the Cambridge
# Structural Database, then it will include bibliographic, chemical,
# crystal, experimental, refinement or atomic coordinate data resulting
# from the CCDC's data processing and validation procedures.
#
#######################################################################

data_CSD_CIF_ACEYOW
_audit_creation_date 2002-02-27
_audit_creation_method CSD-ConQuest-V1
_database_code_CSD ACEYOW
_database_code_depnum_ccdc_archive 'CCDC 175987'
_chemical_formula_sum 'C12 H18 F12 Fe1 N6 Sb2'
_chemical_formula_moiety
;
C12 H18 Fe1 N6 2+,2(F6 Sb1 1-)
;
_journal_coeditor_code "IUCr YA6066"
_journal_coden_Cambridge 1370
_journal_volume 57
_journal_year 2001
_journal_page_first m545
_journal_name_full 'Acta Crystallogr.,Sect.E:Struct.Rep.Online '
loop_
_publ_author_name
"W.W.Brennessel"
"N.R.Brooks"
"M.P.Mehn"
"L.Que Junior"
"V.G.Young Junior"
_chemical_name_systematic
;
hexakis(Acetonitrile)-iron(ii) hexafluoroantimonate
;
_cell_volume 1933.086
_exptl_crystal_colour 'colorless'
_exptl_crystal_density_diffrn 1.994
_exptl_special_details
;
isostructural with the Ni complex

;
_exptl_crystal_description 'hexagonal prism'
_exptl_crystal_preparation 'diethyl ether/acetonitrile'
_diffrn_ambient_temperature 173
#These two values have been output from a single CSD field.
_refine_ls_R_factor_gt 0.024
_refine_ls_wR_factor_gt 0.024
_symmetry_cell_setting rhombohedral
_symmetry_space_group_name_H-M 'R -3'
_symmetry_Int_Tables_number 148
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 -y,x-y,z
3 -x+y,-x,z
4 2/3+x,1/3+y,1/3+z
5 2/3-y,1/3+x-y,1/3+z
6 2/3-x+y,1/3-x,1/3+z
7 1/3+x,2/3+y,2/3+z
8 1/3-y,2/3+x-y,2/3+z
9 1/3-x+y,2/3-x,2/3+z
10 -x,-y,-z
11 y,-x+y,-z
12 x-y,x,-z
13 -2/3-x,-1/3-y,-1/3-z
14 -2/3+y,-1/3-x+y,-1/3-z
15 -2/3+x-y,-1/3+x,-1/3-z
16 -1/3-x,-2/3-y,-2/3-z
17 -1/3+y,-2/3-x+y,-2/3-z
18 -1/3+x-y,-2/3+x,-2/3-z
_cell_length_a 11.3398(6)
_cell_length_b 11.3398(6)
_cell_length_c 17.3584(11)
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 120
_cell_formula_units_Z 3
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
H 0.23
F 0.64
Fe 1.34
N 0.68
Sb 1.46
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Fe1 Fe 0.66670 0.33330 0.33330
N1 N 0.6659(2) 0.4906(2) 0.40253(12)
C1 C 0.6658(2) 0.5774(2) 0.43437(14)
C2 C 0.6651(3) 0.6881(3) 0.4763(2)
H1 H 0.67230 0.67600 0.53160
H2 H 0.58000 0.68780 0.46570
H3 H 0.74250 0.77510 0.45970
Sb1 Sb 0.66670 0.33330 0.661838(14)
F1 F 0.6682(3) 0.1981(3) 0.7195(2)
F2 F 0.5350(3) 0.1968(3) 0.60083(19)
N1A N 0.5094(2) 0.1753(2) 0.40253(12)
C1A C 0.4226(2) 0.0884(2) 0.43437(14)
C2A C 0.3119(3) -0.0230(3) 0.4763(2)
H1A H 0.32400 -0.00370 0.53160
H2A H 0.31220 -0.10780 0.46570
H3A H 0.22490 -0.03260 0.45970
N1B N 0.8247(2) 0.3341(2) 0.40253(12)
C1B C 0.9116(2) 0.3342(2) 0.43437(14)
C2B C 1.0230(3) 0.3349(3) 0.4763(2)
H1B H 1.00370 0.32770 0.53160
H2B H 1.10780 0.42000 0.46570
H3B H 1.03260 0.25750 0.45970
N1L N 0.667433(200) 0.176067(200) 0.264137(120)
C1L C 0.667533(200) 0.089267(200) 0.232297(140)
C2L C 0.668233(300) -0.021433(300) 0.190367(200)
H1L H 0.66103 -0.00933 0.13507
H2L H 0.75333 -0.02113 0.20097
H3L H 0.59083 -0.10843 0.20697
N1M N 0.823933(200) 0.491367(200) 0.264137(120)
C1M C 0.910733(200) 0.578267(200) 0.232297(140)
C2M C 1.021433(300) 0.689667(300) 0.190367(200)
H1M H 1.00933 0.67037 0.13507
H2M H 1.02113 0.77447 0.20097
H3M H 1.10843 0.69927 0.20697
N1N N 0.508633(200) 0.332567(200) 0.264137(120)
C1N C 0.421733(200) 0.332467(200) 0.232297(140)
C2N C 0.310333(300) 0.331767(300) 0.190367(200)
H1N H 0.32963 0.33897 0.13507
H2N H 0.22553 0.24667 0.20097
H3N H 0.30073 0.40917 0.20697
F1A F 0.8019(3) 0.4701(3) 0.7195(2)
F1B F 0.5299(3) 0.3318(3) 0.7195(2)
F2A F 0.8032(3) 0.3382(3) 0.60083(19)
F2B F 0.6618(3) 0.4650(3) 0.60083(19)
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_1
_geom_bond_site_symmetry_2
Fe1 N1 2.155 1_555 1_555
N1 C1 1.129 1_555 1_555
C1 C2 1.455 1_555 1_555
C2 H1 0.979 1_555 1_555
H2 C2 0.981 1_555 1_555
H3 C2 0.980 1_555 1_555
Sb1 F1 1.838 1_555 1_555
F2 Sb1 1.854 1_555 1_555
N1A Fe1 2.154 1_555 1_555
C1A N1A 1.129 1_555 1_555
C2A C1A 1.455 1_555 1_555
H1A C2A 0.979 1_555 1_555
H2A C2A 0.981 1_555 1_555
H3A C2A 0.980 1_555 1_555
N1B Fe1 2.154 1_555 1_555
C1B N1B 1.129 1_555 1_555
C2B C1B 1.455 1_555 1_555
H1B C2B 0.979 1_555 1_555
H2B C2B 0.981 1_555 1_555
H3B C2B 0.980 1_555 1_555
N1L Fe1 2.153 1_555 1_555
C1L N1L 1.129 1_555 1_555
C2L C1L 1.455 1_555 1_555
H1L C2L 0.979 1_555 1_555
H2L C2L 0.981 1_555 1_555
H3L C2L 0.980 1_555 1_555
N1M Fe1 2.153 1_555 1_555
C1M N1M 1.129 1_555 1_555
C2M C1M 1.455 1_555 1_555
H1M C2M 0.979 1_555 1_555
H2M C2M 0.981 1_555 1_555
H3M C2M 0.980 1_555 1_555
N1N Fe1 2.154 1_555 1_555
C1N N1N 1.129 1_555 1_555
C2N C1N 1.455 1_555 1_555
H1N C2N 0.979 1_555 1_555
H2N C2N 0.981 1_555 1_555
H3N C2N 0.980 1_555 1_555
F1A Sb1 1.839 1_555 1_555
F1B Sb1 1.839 1_555 1_555
F2A Sb1 1.853 1_555 1_555
F2B Sb1 1.854 1_555 1_555
#END
133 changes: 133 additions & 0 deletions cell2mol/test/ACEYOW/ACEYOW.info
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,133 @@
CIF2CELL 2.0.0
2024-04-23 15:31
Output for None (hexakis(Acetonitrile)-iron(ii) hexafluoroantimonate)
CIF file exported from Cambridge Structural Database.
Database reference code: ACEYOW.
BIBLIOGRAPHIC INFORMATION
W.W.Brennessel et al., Acta Crystallogr.,Sect.E:Struct.Rep.Online 57, m545- (2001)
INPUT CELL INFORMATION
Symmetry information:
Trigonal crystal system.
Space group number : 148
Hall symbol : -R 3
Hermann-Mauguin symbol : R-3

Lattice parameters:
a b c
11.3398000 11.3398000 17.3584000
alpha beta gamma
90.0000000 90.0000000 120.0000000
Representative sites :
Atom x y z
Fe 0.6667000 0.3333000 0.3333000
N 0.6659000 0.4906000 0.4025300
C 0.6658000 0.5774000 0.4343700
C 0.6651000 0.6881000 0.4763000
H 0.6723000 0.6760000 0.5316000
H 0.5800000 0.6878000 0.4657000
H 0.7425000 0.7751000 0.4597000
Sb 0.6667000 0.3333000 0.6618380
F 0.6682000 0.1981000 0.7195000
F 0.5350000 0.1968000 0.6008300
N 0.5094000 0.1753000 0.4025300
C 0.4226000 0.0884000 0.4343700
C 0.3119000 -0.0230000 0.4763000
H 0.3240000 -0.0037000 0.5316000
H 0.3122000 -0.1078000 0.4657000
H 0.2249000 -0.0326000 0.4597000
N 0.8247000 0.3341000 0.4025300
C 0.9116000 0.3342000 0.4343700
C 1.0230000 0.3349000 0.4763000
H 1.0037000 0.3277000 0.5316000
H 1.1078000 0.4200000 0.4657000
H 1.0326000 0.2575000 0.4597000
N 0.6674330 0.1760670 0.2641370
C 0.6675330 0.0892670 0.2322970
C 0.6682330 -0.0214330 0.1903670
H 0.6610300 -0.0093300 0.1350700
H 0.7533300 -0.0211300 0.2009700
H 0.5908300 -0.1084300 0.2069700
N 0.8239330 0.4913670 0.2641370
C 0.9107330 0.5782670 0.2322970
C 1.0214330 0.6896670 0.1903670
H 1.0093300 0.6703700 0.1350700
H 1.0211300 0.7744700 0.2009700
H 1.1084300 0.6992700 0.2069700
N 0.5086330 0.3325670 0.2641370
C 0.4217330 0.3324670 0.2322970
C 0.3103330 0.3317670 0.1903670
H 0.3296300 0.3389700 0.1350700
H 0.2255300 0.2466700 0.2009700
H 0.3007300 0.4091700 0.2069700
F 0.8019000 0.4701000 0.7195000
F 0.5299000 0.3318000 0.7195000
F 0.8032000 0.3382000 0.6008300
F 0.6618000 0.4650000 0.6008300

OUTPUT CELL INFORMATION
Symmetry information:
Trigonal crystal system.
Space group number : 148
Hall symbol : -R 3
Hermann-Mauguin symbol : R-3

Bravais lattice vectors :
6.5470366 0.0000000 5.7861333
-3.2735183 5.6699000 5.7861333
-3.2735183 -5.6699000 5.7861333
All sites, (cartesian coordinates):
Atom x y z
Fe 0.0000000 0.0000000 0.0000000
N -3.2810474 -3.8821805 6.9872768
N 3.2810474 3.8821805 10.3711232
N -5.0025907 0.9003801 10.3711232
N -1.7215433 4.7825606 6.9872768
N 1.7215433 -4.7825606 10.3711232
N 5.0025907 -0.9003801 6.9872768
C -3.2820294 -2.8973189 7.5399682
C 3.2820294 2.8973189 9.8184318
C -4.1501665 1.3936614 9.8184318
C -0.8681371 4.2909803 7.5399682
C 0.8681371 -4.2909803 9.8184318
C 4.1501665 -1.3936614 7.5399682
C -3.2889038 -1.6380341 8.2678059
C 3.2889038 1.6380341 9.0905941
C -3.0630311 2.0292572 9.0905941
C 0.2258728 3.6672913 8.2678059
C -0.2258728 -3.6672913 9.0905941
C 3.0630311 -2.0292572 8.2678059
H -3.2181958 -1.8160690 9.2277254
H 3.2181958 1.8160690 8.1306746
H -3.1818598 1.8790049 8.1306746
H 0.0363361 3.6950738 9.2277254
H -0.0363361 -3.6950738 8.1306746
H 3.1818598 -1.8790049 9.2277254
H -4.1246330 -1.1589276 8.0838069
H 4.1246330 1.1589276 9.2745931
H -3.0659772 2.9925732 9.2745931
H 1.0586558 4.1515008 8.0838069
H -1.0586558 -4.1515008 9.2745931
H 3.0659772 -2.9925732 8.0838069
H -2.5287929 -1.0903218 7.9796565
H 2.5287929 1.0903218 9.3787435
H -2.2086428 1.6448380 9.3787435
H 0.3201501 2.7351598 7.9796565
H -0.3201501 -2.7351598 9.3787435
H 2.2086428 -1.6448380 7.9796565
Sb 0.0000000 0.0000000 5.7023154
Sb 0.0000000 0.0000000 11.6560846
F 0.0150582 -1.5422128 6.7032355
F -0.0150582 1.5422128 10.6551645
F -1.3280664 -0.7841472 10.6551645
F -1.3431246 0.7580656 6.7032355
F 1.3431246 -0.7580656 10.6551645
F 1.3280664 0.7841472 6.7032355
F -1.2930397 -0.8017239 4.6433141
F 1.2930397 0.8017239 12.7150859
F -1.3408331 0.7189433 12.7150859
F -0.0477934 1.5206672 4.6433141
F 0.0477934 -1.5206672 12.7150859
F 1.3408331 -0.7189433 4.6433141

Unit cell volume : 644.3619079 A^3
Unit cell density : 1.2006330 u/A^3 = 13.4541390 g/cm^3
Binary file added cell2mol/test/ACEYOW/Cell_ACEYOW.cell
View file
Binary file not shown.
Binary file added cell2mol/test/ACEYOW/Ref_Cell_ACEYOW.cell
View file
Binary file not shown.
Loading

0 comments on commit d1229bd

Please sign in to comment.