Add tests for rigorous_rmsd()

tests/inputs/rmsd/BUWGOQ.xyz

@@ -0,0 +1,46 @@
+44
+5fad73dd2b6428eefef6b38f
+Cu      11.744500       3.786200        3.439900
+Cl      13.835200       4.761600        2.599900
+N       12.257100       3.715000        5.341500
+C       12.347500       5.084500        5.949800
+H       12.113200       5.052800        6.889700
+H       13.250100       5.431200        5.867900
+N       12.204600       1.853300        2.990300
+C       13.471300       2.944000        5.672200
+H       13.596100       2.948500        6.634200
+H       14.240700       3.378100        5.272100
+N       10.514900       4.030900        1.918400
+C       13.411800       1.516700        5.194000
+H       12.600800       1.107900        5.533400
+H       14.164600       1.031100        5.565200
+C       13.435600       1.374600        3.694000
+H       14.197900       1.867700        3.350900
+H       13.570000       0.438700        3.476200
+C       11.060700       0.982700        3.379800
+H       11.310500       0.061800        3.278600
+H       10.306800       1.174300        2.816800
+H       10.827700       1.151700        4.295600
+C       12.492500       1.693100        1.533700
+H       12.710200       0.762700        1.366000
+H       13.278600       2.218900        1.317800
+C       11.378300       2.096800        0.601500
+H       10.576700       1.605400        0.842500
+H       11.619700       1.840500        -0.301700
+C       11.061900       3.578300        0.617900
+H       11.870600       4.077500        0.423200
+H       10.418600       3.773000        -0.081900
+C       10.003600       5.440200        1.784400
+H       10.500600       5.912000        1.099000
+H       9.065300        5.434200        1.537600
+C       10.183100       6.100600        3.093500
+C       11.010800       5.462100        3.983200
+C       11.397300       5.946500        5.209500
+C       10.895500       7.194800        5.571000
+H       11.128500       7.570200        6.389400
+C       10.047600       7.877700        4.714000
+H       9.712200        8.705200        4.972300
+C       9.693200        7.360600        3.491600
+H       9.129500        7.841500        2.927700
+H       9.775200        3.477600        2.130400
+H       11.487700       3.135400        5.649000

tests/inputs/rmsd/BUWGOQ_final.xyz

@@ -0,0 +1,46 @@
+44
+-1.4066843014153758e+03 frame 35   xyz file generated by TeraChem
+    Cu     0.2158254167    0.0005950532    0.0851857734
+    Cl     0.3566297180   -0.0033428331   -2.4276433566
+     N    -0.0690154824    1.9813591615    0.4428477162
+     C    -1.4487927726    2.4159274563    0.0491684329
+     H    -1.7493953003    3.2833308898    0.6450959947
+     H    -1.4013273376    2.7237382155   -1.0001996566
+     N     2.2441589139    0.0007428913    0.5003923820
+     C     0.9640604153    2.8496217766   -0.1720495401
+     H     0.7011484912    3.8918565636    0.0475271682
+     H     0.8989314900    2.6958614809   -1.2522693640
+     N    -0.0695676791   -1.9811740382    0.4418830336
+     C     2.3672997560    2.5523077443    0.3312183498
+     H     2.4225041186    2.6944199208    1.4160066042
+     H     3.0314954557    3.3061838451   -0.1050327097
+     C     2.9171812408    1.1957284952   -0.0938754794
+     H     2.8308348444    1.0931125787   -1.1784138085
+     H     3.9813135590    1.1405661305    0.1718375293
+     C     2.3990388643    0.0031916786    1.9790215885
+     H     1.9271498285   -0.8779245543    2.4124234185
+     H     1.9283429303    0.8861766283    2.4098101602
+     H     3.4644433583    0.0029201380    2.2426223559
+     C     2.9171916591   -1.1964978587   -0.0892598428
+     H     3.9813060835   -1.1401270009    0.1762612623
+     H     2.8309858104   -1.0977246661   -1.1741684084
+     C     2.3674916655   -2.5515331235    0.3407524212
+     H     2.4200259692   -2.6886897006    1.4262877702
+     H     3.0336340701   -3.3066780187   -0.0903005364
+     C     0.9658106438   -2.8521900193   -0.1646858375
+     H     0.9039463536   -2.7053289172   -1.2460465574
+     H     0.7026830676   -3.8931467346    0.0608029288
+     C    -1.4468071901   -2.4135808440    0.0384893806
+     H    -1.3937495659   -2.7089847231   -1.0142144341
+     H    -1.7494131136   -3.2881344644    0.6228468002
+     C    -2.3375176111   -1.2289763819    0.1925325901
+     C    -1.7018807279    0.0004473810    0.1484626222
+     C    -2.3381522665    1.2293710568    0.1962218177
+     C    -3.7325513878    1.2187933130    0.3208427123
+     H    -4.2772805780    2.1574366869    0.3709330992
+     C    -4.4135014818   -0.0007369744    0.3830240789
+     H    -5.4940043043   -0.0011810988    0.4894195124
+     C    -3.7317832619   -1.2198077418    0.3175571948
+     H    -4.2759182530   -2.1589378140    0.3647816342
+     H    -0.0107524978   -2.0502524535    1.4609379433
+     H    -0.0030622640    2.0530119310    1.4612390346

tests/inputs/rmsd/BUWGOQ_final_reordered.xyz

@@ -0,0 +1,46 @@
+44
+-1.4066843014153758e+03 frame 35   xyz file generated by TeraChem
+    Cu     0.2158254167    0.0005950532    0.0851857734
+    Cl     0.3566297180   -0.0033428331   -2.4276433566
+     N    -0.0690154824    1.9813591615    0.4428477162
+     C    -1.4487927726    2.4159274563    0.0491684329
+     H    -1.3937495659   -2.7089847231   -1.0142144341
+     H    -4.2759182530   -2.1589378140    0.3647816342
+     N     2.2441589139    0.0007428913    0.5003923820
+     C     0.9640604153    2.8496217766   -0.1720495401
+     H     0.7011484912    3.8918565636    0.0475271682
+     H     0.8989314900    2.6958614809   -1.2522693640
+     N    -0.0695676791   -1.9811740382    0.4418830336
+     C    -4.4135014818   -0.0007369744    0.3830240789
+     H     2.4225041186    2.6944199208    1.4160066042
+     H     3.0314954557    3.3061838451   -0.1050327097
+     C     2.9171812408    1.1957284952   -0.0938754794
+     H     2.8308348444    1.0931125787   -1.1784138085
+     H     3.9813135590    1.1405661305    0.1718375293
+     C     2.3990388643    0.0031916786    1.9790215885
+     H     1.9271498285   -0.8779245543    2.4124234185
+     H     1.9283429303    0.8861766283    2.4098101602
+     H     3.4644433583    0.0029201380    2.2426223559
+     C     2.9171916591   -1.1964978587   -0.0892598428
+     H     3.9813060835   -1.1401270009    0.1762612623
+     H     2.8309858104   -1.0977246661   -1.1741684084
+     C     2.3674916655   -2.5515331235    0.3407524212
+     H    -4.2772805780    2.1574366869    0.3709330992
+     H     2.4200259692   -2.6886897006    1.4262877702
+     C     0.9658106438   -2.8521900193   -0.1646858375
+     H     0.9039463536   -2.7053289172   -1.2460465574
+     H     0.7026830676   -3.8931467346    0.0608029288
+     C    -1.4468071901   -2.4135808440    0.0384893806
+     H    -1.4013273376    2.7237382155   -1.0001996566
+     H    -1.7494131136   -3.2881344644    0.6228468002
+     C    -2.3375176111   -1.2289763819    0.1925325901
+     C    -1.7018807279    0.0004473810    0.1484626222
+     C    -2.3381522665    1.2293710568    0.1962218177
+     C    -3.7325513878    1.2187933130    0.3208427123
+     H     3.0336340701   -3.3066780187   -0.0903005364
+     C     2.3672997560    2.5523077443    0.3312183498
+     H    -5.4940043043   -0.0011810988    0.4894195124
+     C    -3.7317832619   -1.2198077418    0.3175571948
+     H    -0.0107524978   -2.0502524535    1.4609379433
+     H    -0.0030622640    2.0530119310    1.4612390346
+     H    -1.7493953003    3.2833308898    0.6450959947

tests/inputs/rmsd/BUWGOQ_noH.xyz

@@ -0,0 +1,22 @@
+20
+
+Cu      11.744500       3.786200        3.439900
+Cl      13.835200       4.761600        2.599900
+N       12.257100       3.715000        5.341500
+C       12.347500       5.084500        5.949800
+N       12.204600       1.853300        2.990300
+C       13.471300       2.944000        5.672200
+N       10.514900       4.030900        1.918400
+C       13.411800       1.516700        5.194000
+C       13.435600       1.374600        3.694000
+C       11.060700       0.982700        3.379800
+C       12.492500       1.693100        1.533700
+C       11.378300       2.096800        0.601500
+C       11.061900       3.578300        0.617900
+C       10.003600       5.440200        1.784400
+C       10.183100       6.100600        3.093500
+C       11.010800       5.462100        3.983200
+C       11.397300       5.946500        5.209500
+C       10.895500       7.194800        5.571000
+C       10.047600       7.877700        4.714000
+C       9.693200        7.360600        3.491600

tests/inputs/rmsd/BUWGOQ_noH_final.xyz

@@ -0,0 +1,22 @@
+20
+
+    Cu     0.2158254167    0.0005950532    0.0851857734
+    Cl     0.3566297180   -0.0033428331   -2.4276433566
+     N    -0.0690154824    1.9813591615    0.4428477162
+     C    -1.4487927726    2.4159274563    0.0491684329
+     N     2.2441589139    0.0007428913    0.5003923820
+     C     0.9640604153    2.8496217766   -0.1720495401
+     N    -0.0695676791   -1.9811740382    0.4418830336
+     C     2.3672997560    2.5523077443    0.3312183498
+     C     2.9171812408    1.1957284952   -0.0938754794
+     C     2.3990388643    0.0031916786    1.9790215885
+     C     2.9171916591   -1.1964978587   -0.0892598428
+     C     2.3674916655   -2.5515331235    0.3407524212
+     C     0.9658106438   -2.8521900193   -0.1646858375
+     C    -1.4468071901   -2.4135808440    0.0384893806
+     C    -2.3375176111   -1.2289763819    0.1925325901
+     C    -1.7018807279    0.0004473810    0.1484626222
+     C    -2.3381522665    1.2293710568    0.1962218177
+     C    -3.7325513878    1.2187933130    0.3208427123
+     C    -4.4135014818   -0.0007369744    0.3830240789
+     C    -3.7317832619   -1.2198077418    0.3175571948

tests/inputs/rmsd/example_1.xyz

@@ -0,0 +1,88 @@
+86
+10/18/2018 23:07, XYZ structure generated by mol3D Class, molSimplify
+Co 	0.000000	0.000000	0.000000
+N 	-0.000952	2.067750	-0.001425
+N 	2.067766	-0.000950	0.001425
+N 	-2.067764	0.000952	0.001425
+N 	0.000950	-2.067751	-0.001425
+C 	-1.169301	2.841644	-0.016059
+C 	-0.653312	4.209510	0.004172
+C 	0.685140	4.228047	-0.000525
+C 	1.064743	2.789017	0.007601
+H 	-1.262515	5.102310	0.016581
+H 	1.341744	5.080824	-0.003000
+C 	2.515400	2.424104	0.010956
+C 	-2.473887	2.494047	-0.031852
+C 	4.238750	0.668051	-0.002624
+C 	4.240901	-0.662142	-0.043374
+C 	2.865249	-1.120152	-0.029335
+C 	2.860480	1.115955	0.004315
+H 	5.123920	1.280372	0.009955
+H 	5.123774	-1.277306	-0.074733
+C 	2.533300	-2.439131	-0.027572
+C 	-2.838763	-1.110143	0.010953
+C 	-4.179044	-0.742830	0.017696
+C 	-4.216049	0.629382	-0.036023
+C 	-2.902117	1.046419	-0.026935
+H 	-5.038596	-1.400331	0.041565
+H 	-5.108596	1.240275	-0.065690
+C 	0.755456	-4.271578	0.032003
+C 	-0.574406	-4.276022	0.010552
+C 	-1.089023	-2.925718	0.008900
+C 	1.067790	-2.829968	-0.002817
+H 	1.424943	-5.107532	0.056699
+H 	-1.180939	-5.169721	0.008969
+C 	-2.393468	-2.569366	0.009123
+C 	3.545275	3.492143	0.004788
+C 	4.275503	3.768788	-1.160229
+C 	5.246250	4.772243	-1.164412
+C 	5.481799	5.519316	-0.011071
+C 	4.758758	5.254879	1.151709
+C 	3.802191	4.237367	1.164299
+H 	4.114810	3.171953	-2.056962
+H 	5.830894	4.955717	-2.062278
+H 	6.244957	6.293588	-0.012985
+H 	4.955433	5.826784	2.054718
+H 	3.269326	4.015519	2.086004
+C 	-3.500107	3.576892	-0.019074
+C 	-4.267211	3.801398	1.135316
+C 	-5.267961	4.774693	1.138938
+C 	-5.498798	5.541269	-0.001698
+C 	-4.737863	5.330598	-1.150668
+C 	-3.749478	4.344667	-1.165875
+H 	-4.113992	3.203258	2.032063
+H 	-5.877154	4.928309	2.027157
+H 	-4.926037	5.926425	-2.041165
+H 	-3.186519	4.178327	-2.082448
+C 	-3.431182	-3.643846	0.001781
+C 	-3.725850	-4.363552	1.167674
+C 	-4.751649	-5.310878	1.169914
+C 	-5.503863	-5.530759	0.015978
+C 	-5.226343	-4.812354	-1.146042
+C 	-4.188633	-3.878504	-1.157105
+H 	-3.157330	-4.182509	2.077877
+H 	-4.968009	-5.872009	2.075170
+H 	-6.308321	-6.262033	0.023103
+H 	-5.820060	-4.975206	-2.041988
+H 	-3.985808	-3.315398	-2.066450
+C 	3.575891	-3.497857	-0.022088
+C 	4.337768	-3.743380	1.129965
+C 	5.308142	-4.747422	1.136921
+C 	5.509975	-5.528805	-0.000139
+C 	4.751397	-5.299939	-1.148023
+C 	3.797149	-4.280590	-1.163571
+H 	4.183410	-3.130725	2.016191
+H 	5.908200	-4.912205	2.027429
+H 	4.904992	-5.908983	-2.034262
+H 	3.213627	-4.097709	-2.063127
+H 	6.263684	-6.311140	0.005599
+H 	-6.281503	6.296906	0.000581
+C 	0.471652	-0.537234	4.244156
+C 	0.734536	-0.809834	2.920676
+N 	0.000000	0.000000	2.069739
+C 	-0.707789	0.741259	2.904623
+N 	-0.439044	0.472648	4.213528
+H 	-0.856890	0.933197	5.008495
+H 	0.845073	-0.960338	5.163838
+H 	1.415035	-1.547181	2.520716
+H 	-1.433587	1.485795	2.625365

tests/inputs/rmsd/example_1_noff.xyz

@@ -0,0 +1,88 @@
+86
+10/18/2018 23:08, XYZ structure generated by mol3D Class, molSimplify
+Co 	0.000000	0.000000	0.000000
+N 	-0.000952	2.067750	-0.001425
+N 	2.067766	-0.000950	0.001425
+N 	-2.067764	0.000952	0.001425
+N 	0.000950	-2.067751	-0.001425
+C 	-1.151505	2.907978	-0.013935
+C 	-0.705739	4.299764	-0.002482
+C 	0.657261	4.253279	0.015963
+C 	1.043916	2.834054	0.022608
+H 	-1.298321	5.204068	-0.004894
+H 	1.302123	5.121101	0.022866
+C 	2.476955	2.384874	0.000655
+C 	-2.449914	2.511026	-0.000467
+C 	4.210881	0.682455	-0.014152
+C 	4.211760	-0.681088	-0.008162
+C 	2.884951	-1.087278	0.004287
+C 	2.885123	1.086249	-0.011327
+H 	5.098849	1.300339	-0.014828
+H 	5.101445	-1.295930	-0.016568
+C 	2.479379	-2.387107	-0.006198
+C 	-2.884809	-1.081421	-0.020975
+C 	-4.209337	-0.682464	-0.020427
+C 	-4.209948	0.682076	-0.008816
+C 	-2.885808	1.082827	0.010121
+H 	-5.091016	-1.308512	-0.025067
+H 	-5.092494	1.306504	-0.015087
+C 	0.655001	-4.254318	0.011070
+C 	-0.707363	-4.298556	0.028914
+C 	-1.151049	-2.906414	0.021514
+C 	1.044749	-2.836472	-0.015679
+H 	1.296883	-5.124643	0.016491
+H 	-1.303387	-5.201158	0.043445
+C 	-2.448455	-2.508549	0.001785
+C 	3.512066	3.459953	-0.001934
+C 	4.333547	3.653958	-1.126901
+C 	5.299237	4.665991	-1.130891
+C 	5.464518	5.480493	-0.007764
+C 	4.657681	5.291507	1.117557
+C 	3.678101	4.291992	1.119270
+H 	4.214043	3.031164	-2.004770
+H 	5.920813	4.817680	-2.004120
+H 	6.218054	6.257992	-0.009555
+H 	4.792148	5.919384	1.988974
+H 	3.062871	4.153034	1.999354
+C 	-3.514730	3.552732	-0.001264
+C 	-4.370635	3.692705	1.104393
+C 	-5.363534	4.677461	1.106092
+C 	-5.521460	5.515140	-0.001553
+C 	-4.681106	5.375575	-1.109329
+C 	-3.675215	4.404839	-1.107598
+H 	-4.255391	3.051805	1.970055
+H 	-6.010811	4.791297	1.966013
+H 	-4.808771	6.019768	-1.969633
+H 	-3.032251	4.303679	-1.973349
+C 	-3.513208	-3.548703	0.006634
+C 	-3.702704	-4.368471	1.132039
+C 	-4.709961	-5.338033	1.135050
+C 	-5.522121	-5.508221	0.010217
+C 	-5.334334	-4.701965	-1.116142
+C 	-4.339906	-3.718515	-1.116629
+H 	-3.081481	-4.242975	2.010309
+H 	-4.860872	-5.957846	2.009341
+H 	-6.296306	-6.264279	0.011723
+H 	-5.959711	-4.839637	-1.988923
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