Crystal reader can't deal with files where there are numbers in the first column of _atom loop

[Surluson]

PorousMaterials fails to read the following cif file. From a quick glance, it looks like the reader assumes atom labels are in the first column in the _atom loop.

Some cif files only contain the atom_site_label tag (in addition to the coordinates) so it's not as easy as only looking at one specific column.

Thoughts how to deal with this?

data_C132H126N12O18_2018-02-15_11:45:50
#******************************************
#
# CIF file created by Zeo++
# Zeo++ is an open source package to
# analyze microporous materials
#
#*******************************************

_cell_length_a      30.8683   
_cell_length_b      30.8684   
_cell_length_c      35.0319   
_cell_angle_alpha       90   
_cell_angle_beta        90   
_cell_angle_gamma       120   

_symmetry_space_group_name_H-M      'P1'
_symmetry_Int_Tables_number     1   
_symmetry_cell_setting      Monoclinic

loop_
_symmetry_equiv_pos_as_xyz
'+x,+y,+z'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
1   C   0.502983    0.988842    0.009974
2   C   0.501284    0.956851    0.039354
3   C   0.465216    0.905491    0.039245
4   C   0.429763    0.886817    0.009378
5   C   0.430024    0.918239    0.97983
6   C   0.467501    0.969506    0.980015
7   H   0.527016    0.971118    0.060998
8   H   0.403333    0.849619    0.009162
9   C   0.541625    0.039467    0.010572
10  C   0.540608    0.074255    0.036399
11  C   0.580923    0.124471    0.037492
12  C   0.621053    0.138657    0.011623
13  C   0.622595    0.104336    0.985773
14  C   0.582884    0.054506    0.986044
15  H   0.649788    0.174972    0.011506
16  H   0.583779    0.02903 0.967769
17  O   0.467179    0.001084    0.952894
18  O   0.498429    0.059384    0.057606
19  H   0.493664    0.007029    0.934514
20  H   0.501097    0.041448    0.079872
21  C   0.664327    0.119912    0.958184
22  H   0.681599    0.096708    0.962089
23  H   0.693343    0.158636    0.963884
24  C   0.583509    0.164241    0.063369
25  H   0.57979 0.191077    0.045295
26  H   0.620658    0.183867    0.076563
27  C   0.465103    0.872576    0.070308
28  H   0.460975    0.88733 0.097619
29  H   0.433034    0.834776    0.067247
30  C   0.391628    0.897243    0.949104
31  H   0.373876    0.92014 0.946218
32  H   0.361987    0.859607    0.957005
33  C   0.054578    0.5082  0.67664
34  C   0.086569    0.538492    0.706022
35  C   0.13793 0.553784    0.705911
36  C   0.156603    0.537003    0.676044
37  C   0.125179    0.505843    0.646496
38  C   0.073915    0.492055    0.646682
39  H   0.072303    0.549957    0.727665
40  H   0.193801    0.547773    0.67583
41  C   0.003954    0.496218    0.67724
42  C   0.969166    0.460412    0.703065
43  C   0.918951    0.45051 0.704158
44  C   0.904762    0.476452    0.67829
45  C   0.939087    0.512318    0.65244
46  C   0.988917    0.522437    0.652711
47  H   0.868449    0.468877    0.678173
48  H   0.014389    0.548805    0.634436
49  O   0.042336    0.460154    0.619561
50  O   0.984036    0.433105    0.724274
51  H   0.036392    0.480694    0.601181
52  H   0.001972    0.453709    0.74654
53  C   0.923511    0.538473    0.62485
54  H   0.946712    0.578948    0.628755
55  H   0.884787    0.528766    0.630551
56  C   0.87918 0.413328    0.730035
57  H   0.852342    0.38277 0.711963
58  H   0.859552    0.430849    0.743228
59  C   0.170845    0.586587    0.736977
60  H   0.156089    0.567703    0.764286
61  H   0.208645    0.592317    0.733914
62  C   0.146177    0.488445    0.61577
63  H   0.123279    0.447795    0.612884
64  H   0.183812    0.496439    0.623672
65  C   0.535221    0.540437    0.343307
66  C   0.504928    0.542136    0.372686
67  C   0.489636    0.578204    0.372578
68  C   0.506416    0.613658    0.34271
69  C   0.537578    0.613396    0.313163
70  C   0.551367    0.575922    0.313349
71  H   0.493463    0.516403    0.394332
72  H   0.495647    0.640087    0.342496

[SimonEnsemble]

@Surluson is this the symmetry reader branch or master?

[Surluson]

This fails on both branches

[SimonEnsemble]

@ahyork in case you have an opinion.

how about making a PR on top of the symmetry branch: if only _atom_site_type_symbol or atom_site_label exists, then use that one. if both exist, choose a default as we do now? @Surluson can you look up the difference between these two labels and how they are used? my understanding is that we should default to atom_site_label since the _atom_site_type_symbol will always be an element but sometimes in molecular simulations we want to distinguish between atoms of the same element, like C_aromatic vs. C_double_bonded.

[eahenle]

Resolved as of #145