-
Notifications
You must be signed in to change notification settings - Fork 4
/
schema.xsd
11463 lines (11455 loc) · 604 KB
/
schema.xsd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<?xml version="1.0" encoding="utf-8"?>
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://www.xml-cml.org/schema"
elementFormDefault="qualified"
xmlns="http://www.xml-cml.org/schema"
xmlns:h="http://www.w3.org/1999/xhtml"
id="cmlschema">
<xsd:simpleType id="st.actionOrderType" name="actionOrderType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Describes whether child elements are sequential or parallel.</h:div>
<h:div class="description">There is no default.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="sequential"/>
<xsd:enumeration value="parallel"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="angleUnitsType" id="st.angleUnitsType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An enumeration of allowed angle units.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="degrees"/>
<xsd:enumeration value="radians"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="atomIDType" id="st.atomIDType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An identifier for an atom.</h:div>
<h:div class="description">
<h:p>
Of the form prefix:suffix where prefix and suffix
are purely alphanumeric (with _ and -) and prefix
is optional. This is similar to XML IDs (and we promote
this as good practice for atomIDs. Other punctuation and
whitespace is forbidden, so IDs from (say) PDB files are
not satisfactory.
</h:p>
<h:p>
The prefix is intended to form a pseudo-namespace so that
atom IDs in different molecules may have identical suffixes.
It is also useful if the prefix is the ID for the molecule
(though this clearly has its limitation). Atom IDs should not
be typed as XML IDs since they may not validate.
</h:p>
</h:div>
<h:div class="example" href="atomIDType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="[A-Za-z_][A-Za-z0-9_\-]*(:[A-Za-z0-9_\-]+)?"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="atomRefArrayType" id="st.atomRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of atomRefs.</h:div>
<h:div class="description">
The atomRefs
cannot be schema- or schematron-validated. Instances of this type will
be used in array-style representation of bonds and atomParitys.
It can also be used for arrays of atomIDTypes such as in complex stereochemistry,
geometrical definitions, atom groupings, etc.
</h:div>
<h:div class="example" href="atomRefArrayType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="atomIDType"/>
</xsd:simpleType>
<xsd:simpleType name="atomRefs2Type" id="st.atomRefs2Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to two distinct existing atoms in order.</h:div>
<h:div class="example" href="atomRefs21.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="atomIDType"/>
</xsd:simpleType>
<xsd:length value="2"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="atomRefs3Type" id="st.atomRefs3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to three distinct existing atoms in order.</h:div>
<h:div class="example" href="atomRefs31.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="atomIDType"/>
</xsd:simpleType>
<xsd:length value="3"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="atomRefs4Type" id="st.atomRefs4Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to four distinct existing atoms in order.</h:div>
<h:div class="example" href="atomRefs41.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="atomIDType"/>
</xsd:simpleType>
<xsd:length value="4"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="atomRefType" id="st.atomRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to an existing atom.</h:div>
<h:div class="example" href="atomRefType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="atomIDType"/>
</xsd:simpleType>
<xsd:simpleType name="bondRefArrayType" id="st.bondRefArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of references to bonds.</h:div>
<h:div class="description">
The references cannot (yet)
cannot be schema- or schematron-validated. Instances of this type will
be used in array-style representation of electron counts, etc.
It can also be used for arrays of bondIDTypes such as in complex stereochemistry,
geometrical definitions, bond groupings, etc.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="bondRefType"/>
</xsd:simpleType>
<xsd:simpleType name="bondRefType" id="st.bondRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to an existing bond.</h:div>
<h:div class="general">A reference to a bond may be made by atoms (e.g. for multicentre or pi-bonds),
electrons (for annotating reactions or describing electronic properties) or possibly other bonds (no
examples yet). The semantics are relatively flexible.
</h:div>
<h:div class="example" href="bond1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="[A-Za-z0-9_\-]+(:[A-Za-z0-9_\-]+)?"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="box3Type" id="st.box3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A box in 3-space.</h:div>
<h:div class="description">
Defined by 6 real numbers
(x1 y1 z1 x2 y2 z2). By default these are Cartesian coordinates (with units
specified elsewhere - responsibility of schema creator.) If there is a means
of specifying oblique axes (e.g. crystallographic cell) the box may be a
parallelipiped. The components are grouped in threes ans separated by a semicolon
to avoid problems of guessing the convention.
</h:div>
<h:div class="example" href="box31.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:double"/>
</xsd:simpleType>
<xsd:length value="6"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="cellParameterType" id="st.cellParameterType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">enumerated type of cellParameter</h:div>
<h:div class="description"/>
<h:div class="example" href="cellParameterType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="length"/>
<xsd:enumeration value="angle"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="chiralityType" id="st.chiralityType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The chirality of a system or molecule.</h:div>
<h:div class="description">This is being actively investigated by a IUPAC committee (2002) so the
convention is likely to change. No formal default.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="enantiomer"/>
<xsd:enumeration value="racemate"/>
<xsd:enumeration value="unknown"/>
<xsd:enumeration value="other"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="complexType" id="st.complexType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A pair of floats representing a complex number.</h:div>
<h:div class="example" href="complex1.xml"/>
<h:div class="example" href="complex.bad.xml">
<h:p>This example is schema-invalid as it has three floats</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:double"/>
</xsd:simpleType>
<xsd:length value="2"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="coordinate2Type" id="st.coordinate2Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An x/y coordinate pair.</h:div>
<h:div class="description">
An x/y coordinate pair consisting of
two real numbers, separated by whitespace or a comma.
In arrays and matrices, it may be useful to set a separate delimiter
</h:div>
<h:div class="example" href="coordinate2Type1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:double"/>
</xsd:simpleType>
<xsd:length value="2"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="coordinate3Type" id="st.coordinate3Type">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An x/y/z coordinate triple.</h:div>
<h:div class="description">
An x/y/z coordinate triple consisting of three real
numbers, separated by whitespace or commas. In arrays and matrices, it may be
useful to set a separate delimiter.
</h:div>
<h:div class="example" href="coordinate3Type1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction>
<xsd:simpleType>
<xsd:list itemType="xsd:double"/>
</xsd:simpleType>
<xsd:length value="3"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="coordinateComponentArrayType" id="st.coordinateComponentArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of coordinateComponents for a single coordinate.</h:div>
<h:div class="description">
An array of coordinateComponents for a single coordinate
where these all refer to an X-coordinate (NOT x,y,z).Instances of this type will be
used in array-style representation of 2-D or 3-D coordinates. Currently no machine
validation. Currently not used in STMML, but re-used by CML (see example).
</h:div>
<h:div class="example" href="coordinateComponentArrayType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="xsd:double"/>
</xsd:simpleType>
<xsd:simpleType name="countArrayType" id="st.countArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of counts.</h:div>
<h:div class="description">Normally, but not always, integers. can be used with a number of elements
</h:div>
<h:div class="curation">
2005-11-01: PMR the combination of dataType and list does not work
with JUMBO5.0 - so for the meantime we have removed the restriction
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="countType"/>
<!--<xsd:list itemType="xsd:double"/>-->
</xsd:simpleType>
<xsd:simpleType name="countType" id="st.countType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A count multiplier for an object.</h:div>
<h:div class="description">
Many elements represent objects which can occur an arbitrary number of times in a scientific
context. Examples are<h:tt>action</h:tt>,
<h:tt>object</h:tt>
or<h:tt>molecule</h:tt>s.
</h:div>
<h:div class="curation">2005-10-16. Changed to positiveNumerType.</h:div>
<h:div class="example" href="countType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="positiveNumberType"/>
</xsd:simpleType>
<xsd:simpleType name="dataTypeType" id="st.dataTypeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">an enumerated type for all dataTypes in STM.</h:div>
<h:div class="description">
<h:p>
<h:tt>dataTypeType</h:tt>
represents an enumeration of allowed dataTypes
(at present identical with those in XML-Schemas (Part2- datatypes).
This means that implementers should be able to use standard XMLSchema-based
tools for validation without major implementation problems.
</h:p>
<h:p>
It will often be used an an attribute on
<h:a href="el.scalar">scalar</h:a>,
<h:a href="el.array">array</h:a>
or
<h:a href="el.matrix">matrix</h:a>
elements.
</h:p>
</h:div>
<h:div class="description">Note: the attribute xsi:type might be used to enforce the type-checking but I
haven't worked this through yet.
</h:div>
<h:div class="example" href="dataTypeType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="xsd:string"/>
<xsd:enumeration value="xsd:boolean"/>
<xsd:enumeration value="xsd:float"/>
<xsd:enumeration value="xsd:double"/>
<xsd:enumeration value="xsd:decimal"/>
<xsd:enumeration value="xsd:duration"/>
<xsd:enumeration value="xsd:dateTime"/>
<xsd:enumeration value="xsd:time"/>
<xsd:enumeration value="xsd:date"/>
<xsd:enumeration value="xsd:gYearMonth"/>
<xsd:enumeration value="xsd:gYear"/>
<xsd:enumeration value="xsd:gMonthDay"/>
<xsd:enumeration value="xsd:gDay"/>
<xsd:enumeration value="xsd:gMonth"/>
<xsd:enumeration value="xsd:hexBinary"/>
<xsd:enumeration value="xsd:base64Binary"/>
<xsd:enumeration value="xsd:anyURI"/>
<xsd:enumeration value="xsd:QName"/>
<xsd:enumeration value="xsd:NOTATION"/>
<xsd:enumeration value="xsd:normalizedString"/>
<xsd:enumeration value="xsd:token"/>
<xsd:enumeration value="xsd:language"/>
<xsd:enumeration value="xsd:IDREFS"/>
<xsd:enumeration value="xsd:ENTITIES"/>
<xsd:enumeration value="xsd:NMTOKEN"/>
<xsd:enumeration value="xsd:NMTOKENS"/>
<xsd:enumeration value="xsd:Name"/>
<xsd:enumeration value="xsd:NCName"/>
<xsd:enumeration value="xsd:ID"/>
<xsd:enumeration value="xsd:IDREF"/>
<xsd:enumeration value="xsd:ENTITY"/>
<xsd:enumeration value="xsd:integer"/>
<xsd:enumeration value="xsd:nonPositiveInteger"/>
<xsd:enumeration value="xsd:negativeInteger"/>
<xsd:enumeration value="xsd:long"/>
<xsd:enumeration value="xsd:int"/>
<xsd:enumeration value="xsd:short"/>
<xsd:enumeration value="xsd:byte"/>
<xsd:enumeration value="xsd:nonNegativeInteger"/>
<xsd:enumeration value="xsd:unsignedLong"/>
<xsd:enumeration value="xsd:unsignedInt"/>
<xsd:enumeration value="xsd:unsignedShort"/>
<xsd:enumeration value="xsd:unsignedByte"/>
<xsd:enumeration value="xsd:positiveInteger"/>
<xsd:enumeration value="dataTypeType"/>
<xsd:enumeration value="namespaceRefType"/>
<xsd:enumeration value="unitsType"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="namespaceRefType"/>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType name="delimiterType" id="st.delimiterType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A single non-whitespace character to separate components in arrays.</h:div>
<h:div class="description">
<h:p>
Some STMML elements (such as<h:a href="el.array">array</h:a>) have
content representing concatenated values. The default separator is
whitespace (which can be normalised) and this should be used whenever
possible. However in some cases the values are empty, or contain whitespace or other
problematic punctuation, and a delimiter is required.
</h:p>
<h:p>
Note that the content string MUST start and end with the delimiter so
there is no ambiguity as to what the components are. Only printable
characters from the ASCII character set should be used, and character
entities should be avoided.
</h:p>
<h:p>
When delimiters are used to separate precise whitespace this should always
consist of spaces and not the other allowed whitespace characters
(newline, tabs, etc.). If the latter are important it is probably best to redesign
the application.
</h:p>
<h:p>At present there is a controlled pattern of characters selected so as not to collide with
common usage in XML doc
</h:p>
</h:div>
<h:div class="example" href="delimiterType1.xml">
<h:em>The values in the array are</h:em>
"A", "B12", "" (empty string) and "D and E"
<h:em>note the spaces</h:em>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="[!%\^\*@~;#,|/]"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="dictionaryPrefixType" id="st.dictionaryPrefixType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A dictionaryPrefix</h:div>
<h:div class="description">
<h:p>
used to identify a dictionary, units, convention or other metadata.
</h:p>
</h:div>
<h:div class="curation">2005-12-12: PMR. Added for use with dictionary</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="description">
<h:p>The dictionary prefix must conform to XSD.</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:pattern value="[A-Za-z][A-Za-z0-9_\.\-]*"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="dimensionType" id="st.dimensionType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Allowed values for dimension Types in quantities.</h:div>
<h:div class="description">
<h:p>
These are the 7 types prescribed by the SI system, together
with the "dimensionless" type. We intend to be somewhat uncoventional
and explore enhanced values of "dimensionless", such as "angle".
This may be heretical, but we find the present system impossible to implement
in many cases.
</h:p>
<h:p>Used for constructing entries in a dictionary of units</h:p>
</h:div>
<h:div class="example" href="dimensionType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="mass"/>
<xsd:enumeration value="length"/>
<xsd:enumeration value="time"/>
<xsd:enumeration value="current"/>
<xsd:enumeration value="amount"/>
<xsd:enumeration value="luminosity"/>
<xsd:enumeration value="temperature"/>
<xsd:enumeration value="dimensionless"/>
<xsd:enumeration value="angle">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An angl.</h:div>
<h:div class="description">(formally dimensionless, but useful to have units).</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="eigenOrientationType" id="st.eigenOrientationType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Orientation of the eigenvector matrix.</h:div>
<h:div class="description">
<h:p>
Specifies whether the rows or columns of the (square) matrix
correspond to the eigenvectors. For example, in molecular orbitals
the vectors are normally represented as columns, and each column
would correspond to a different eigenvalue
</h:p>
</h:div>
<h:div class="curation">2006-01-13: PMR. Created.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="columnVectors">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The columns are the eigenvectors.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="rowVectors">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The columns are the eigenvectors.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="other">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A value not in the controlled vocabulary - use dictRef to add further information.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="elementTypeArrayType" id="st.elementTypeArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An array of elementTypes.</h:div>
<h:div class="description">Instances of this type will be used in array-style representation of atoms.
</h:div>
<h:div class="example" href="elementTypeArrayType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="elementTypeType"/>
</xsd:simpleType>
<xsd:simpleType name="elementTypeType" id="st.elementTypeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Allowed elementType values.</h:div>
<h:div class="description">
<h:p>
The periodic table (up to
element number 118. In addition the following strings are allowed:
<h:ul>
<h:li>
<h:tt>Du</h:tt>. ("dummy") This does not correspond to a "real" atom and can
support a point in space or within a chemical graph.
</h:li>
<h:li>
<h:tt>R</h:tt>. ("R-group") This indicates that an atom or group of atoms could be
attached at this point.
</h:li>
</h:ul>
</h:p>
</h:div>
<h:div class="example" href="elementTypeType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:union>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="Ac"/>
<xsd:enumeration value="Al"/>
<xsd:enumeration value="Ag"/>
<xsd:enumeration value="Am"/>
<xsd:enumeration value="Ar"/>
<xsd:enumeration value="As"/>
<xsd:enumeration value="At"/>
<xsd:enumeration value="Au"/>
<xsd:enumeration value="B"/>
<xsd:enumeration value="Ba"/>
<xsd:enumeration value="Bh"/>
<xsd:enumeration value="Bi"/>
<xsd:enumeration value="Be"/>
<xsd:enumeration value="Bk"/>
<xsd:enumeration value="Br"/>
<xsd:enumeration value="C"/>
<xsd:enumeration value="Ca"/>
<xsd:enumeration value="Cd"/>
<xsd:enumeration value="Ce"/>
<xsd:enumeration value="Cf"/>
<xsd:enumeration value="Cl"/>
<xsd:enumeration value="Cm"/>
<xsd:enumeration value="Co"/>
<xsd:enumeration value="Cr"/>
<xsd:enumeration value="Cs"/>
<xsd:enumeration value="Cu"/>
<xsd:enumeration value="Db"/>
<xsd:enumeration value="Ds"/>
<xsd:enumeration value="Dy"/>
<xsd:enumeration value="Er"/>
<xsd:enumeration value="Es"/>
<xsd:enumeration value="Eu"/>
<xsd:enumeration value="F"/>
<xsd:enumeration value="Fe"/>
<xsd:enumeration value="Fl"/>
<xsd:enumeration value="Fm"/>
<xsd:enumeration value="Fr"/>
<xsd:enumeration value="Ga"/>
<xsd:enumeration value="Gd"/>
<xsd:enumeration value="Ge"/>
<xsd:enumeration value="H">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Any isotope of hydrogen.</h:div>
<h:div class="description">
<h:p>
There are no special element symbols for D and T which should use the
<h:tt>isotope</h:tt>
attribute.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="He"/>
<xsd:enumeration value="Hf"/>
<xsd:enumeration value="Hg"/>
<xsd:enumeration value="Ho"/>
<xsd:enumeration value="Hs"/>
<xsd:enumeration value="I"/>
<xsd:enumeration value="In"/>
<xsd:enumeration value="Ir"/>
<xsd:enumeration value="K"/>
<xsd:enumeration value="Kr"/>
<xsd:enumeration value="La"/>
<xsd:enumeration value="Li"/>
<xsd:enumeration value="Lr"/>
<xsd:enumeration value="Lu"/>
<xsd:enumeration value="Lv"/>
<xsd:enumeration value="Md"/>
<xsd:enumeration value="Mg"/>
<xsd:enumeration value="Mn"/>
<xsd:enumeration value="Mo"/>
<xsd:enumeration value="Mt"/>
<xsd:enumeration value="N"/>
<xsd:enumeration value="Na"/>
<xsd:enumeration value="Nb"/>
<xsd:enumeration value="Nd"/>
<xsd:enumeration value="Ne"/>
<xsd:enumeration value="Ni"/>
<xsd:enumeration value="No"/>
<xsd:enumeration value="Np"/>
<xsd:enumeration value="O"/>
<xsd:enumeration value="Os"/>
<xsd:enumeration value="P"/>
<xsd:enumeration value="Pa"/>
<xsd:enumeration value="Pb"/>
<xsd:enumeration value="Pd"/>
<xsd:enumeration value="Pm"/>
<xsd:enumeration value="Po"/>
<xsd:enumeration value="Pr"/>
<xsd:enumeration value="Pt"/>
<xsd:enumeration value="Pu"/>
<xsd:enumeration value="Ra"/>
<xsd:enumeration value="Rb"/>
<xsd:enumeration value="Re"/>
<xsd:enumeration value="Rf"/>
<xsd:enumeration value="Rg"/>
<xsd:enumeration value="Rh"/>
<xsd:enumeration value="Rn"/>
<xsd:enumeration value="Ru"/>
<xsd:enumeration value="S"/>
<xsd:enumeration value="Sb"/>
<xsd:enumeration value="Sc"/>
<xsd:enumeration value="Se"/>
<xsd:enumeration value="Sg"/>
<xsd:enumeration value="Si"/>
<xsd:enumeration value="Sm"/>
<xsd:enumeration value="Sn"/>
<xsd:enumeration value="Sr"/>
<xsd:enumeration value="Ta"/>
<xsd:enumeration value="Tb"/>
<xsd:enumeration value="Tc"/>
<xsd:enumeration value="Te"/>
<xsd:enumeration value="Th"/>
<xsd:enumeration value="Ti"/>
<xsd:enumeration value="Tl"/>
<xsd:enumeration value="Tm"/>
<xsd:enumeration value="U"/>
<xsd:enumeration value="Uun"/>
<xsd:enumeration value="Uuu"/>
<xsd:enumeration value="Uub"/>
<xsd:enumeration value="Uut"/>
<xsd:enumeration value="Uuq"/>
<xsd:enumeration value="Uup"/>
<xsd:enumeration value="Uuh"/>
<xsd:enumeration value="Uus"/>
<xsd:enumeration value="Uuo"/>
<xsd:enumeration value="V"/>
<xsd:enumeration value="W"/>
<xsd:enumeration value="Xe"/>
<xsd:enumeration value="Y"/>
<xsd:enumeration value="Yb"/>
<xsd:enumeration value="Zn"/>
<xsd:enumeration value="Zr"/>
<xsd:enumeration value="Du">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A point or object with no chemical semantics.</h:div>
<h:div class="description">
<h:p>Examples can be centroids, bond-midpoints, orienting "atoms" in small
z-matrices.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="R">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A point at which an atom or group might be attached.</h:div>
<h:div class="description">
<h:p>
Examples are abbreviated organic functional groups, Markush representations,
polymers, unknown atoms, etc. Semantics may be determined by the
<h:tt>role</h:tt>
attribute on the atom.
</h:p>
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:pattern value="[A-Za-z]+:[A-Za-z][A-Za-z0-9\-]+"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType name="errorBasisType" id="st.errorBasisType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The basis of an error value.</h:div>
<h:div class="description">
Errors in values can be of several types and this simpleType
provides a small controlled vocabulary.
</h:div>
<h:div class="example" href="scalar1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="observedRange"/>
<xsd:enumeration value="observedStandardDeviation"/>
<xsd:enumeration value="observedStandardError"/>
<xsd:enumeration value="estimatedStandardDeviation"/>
<xsd:enumeration value="estimatedStandardError"/>
<xsd:enumeration value="other">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A value not in the controlled vocabulary - use dictRef to add further information.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="errorValueArrayType" id="st.errorValueArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of error estimate values.</h:div>
<h:div class="description">An observed or calculated estimate of the error in the value of a numeric
quantity. It should be ignored for dataTypes such as URL, date or string. The statistical basis of
the errorValueType is not defined - it could be a range, an estimated standard deviation, an
observed standard error, etc. This information can be added through _errorBasisType_.
</h:div>
<h:div class="example" href="scalar1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="errorValueType"/>
</xsd:simpleType>
<xsd:simpleType name="errorValueType" id="st.errorValueType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">An estimate of the error in the value of a quantity.</h:div>
<h:div class="description">An observed or calculated estimate of the error in the value of a numeric
quantity. It should be ignored for dataTypes such as URL, date or string. The statistical basis of
the errorValueType is not defined - it could be a range, an estimated standard deviation, an
observed standard error, etc. This information can be added through _errorBasisType_.
</h:div>
<h:div class="example" href="scalar1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:double"/>
</xsd:simpleType>
<xsd:simpleType name="floatArrayType" id="st.floatArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">OBSOLETE An array of floats.</h:div>
<h:div class="description">
An array of floats or other real numbers.
Not used in STM Schema, but re-used by CML and other languages.
</h:div>
<h:div class="example" href="floatArrayType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="xsd:double"/>
</xsd:simpleType>
<xsd:simpleType name="formalChargeArrayType" id="st.formalChargeArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of formalCharges.</h:div>
<h:div class="description">Used for electron-bookeeping. This has no relation to its calculated
(fractional) charge or oxidation state.
</h:div>
<h:div class="example" href="formalChargeType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="formalChargeType"/>
</xsd:simpleType>
<xsd:simpleType name="formalChargeType" id="st.formalChargeType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The formal charge on an object.</h:div>
<h:div class="description">Used for electron-bookeeping. This has no relation to its calculated
(fractional) charge or oxidation state.
</h:div>
<h:div class="example" href="formalChargeType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:integer"/>
</xsd:simpleType>
<xsd:simpleType id="st.formatType" name="formatType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Format of a spectrum.</h:div>
<h:div class="description">The data structure of the spectrum. (Not the format of the data). This
describes how the data structure is to be interpreted.
</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="1D">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">one dimensional spectrum.</h:div>
<h:div class="description">
Data are represented by two _array_s, one representing the independent variable
(e.g. wavelength, mass number) and the other the measured dependent variable
(absorption, intensity, etc.). This can normally be plotted directly with the
independent variable as the x-axis. The order of the points is not necessarily
significant and may be increasing or decreasing.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="2Dsymm">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Two dimensional spectrum.</h:div>
<h:div class="description">
Data are represented by a single symmetric _matrix_ with both axes identical (i.e.
the same independent variable). A typical example is a "2D 1HNMR spectrum". The
dependent variable is represented by the matrix elements. This can normally be
plotted as a square symmentric about a diagonal.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="2Dasymm">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Two dimensional spectrum with different axe.</h:div>
<h:div class="description">Data are represented by non-square _matrix_ with independent
axes. A typical example is a "2D 1H 13C NMR spectrum". The dependent variable is
represented by the matrix elements. .
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="other">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A value not in the controlled vocabulary - use dictRef to add further information.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="formulaType" id="st.formulaType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A concise representation for a molecular formula.</h:div>
<h:div class="description">
This MUST adhere to a whitespaced syntax so that it is trivially
machine-parsable. Each element is followed by its count (which may be decimal),
and the string is optionally ended by a formal charge (of form d or -d, i.e. no '+')
NO brackets or other nesting is allowed.
</h:div>
<h:div class="example" href="formulaType1.xml"/>
<h:div class="curation">2005-08-30: allowed decimal points</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="\s*([A-Z][a-z]?\s+(([0-9]+(\.[0-9]*)?)|(\.[0-9]*))?\s*)+(\s+[\-]?[0-9]+)?\s*"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType id="st.ftType" name="ftType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Domain of an FT spectrum.</h:div>
<h:div class="description">Indicates whether a spectrum is raw FID or has been transforme.</h:div>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="raw">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Data are raw, so will normally require transforming.</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="transformed">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Data have been transformed. This value indicates that an FT
experiment and transformation have been performe.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="none">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">This was not known to be an FT experiment. (It may have been, but
the author or abstracter omitted to mention it).
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
<xsd:enumeration value="other">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A value not in the controlled vocabulary - use dictRef to add further information.
</h:div>
</xsd:documentation>
</xsd:annotation>
</xsd:enumeration>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="headType" id="st.headType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The head linker in a polymeric repeat unit</h:div>
<h:div class="description">
<h:p>
A polymeric chain may be described by liniing the head of one repeat
unit to the tail or head of another. The head attribute indicates the atom
id (normally on an atom of elementType="R") which acts as the head
</h:p>
</h:div>
<h:div class="curation">2006-05-20: PMR added</h:div>
<h:div class="example" href="headType1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:string">
<xsd:pattern value="[A-z][A-z0-9_]*"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="hydrogenCountArrayType" id="st.hydrogenCountArrayType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">Array of hydrogenCounts.</h:div>
<h:div class="description">The total number of hydrogen atoms bonded to an atom or contained in a
molecule, whether explicitly included as atoms or not. It is an error to have hydrogen count less
than the explicit hydrogen count. There is no default value and no assumptions about hydrogen Count
can be made if it is not given. If hydrogenCount is given on every atom, then the values can be
summed to give the total hydrogenCount for the (sub)molecule. Because of this hydrogenCount should
not be used where hydrogen atoms bridge 2 or more atoms.
</h:div>
<h:div class="example" href="atom1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:list itemType="hydrogenCountType"/>
</xsd:simpleType>
<xsd:simpleType name="hydrogenCountType" id="st.hydrogenCountType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The total number of hydrogen atoms bonded to an object.</h:div>
<h:div class="description">The total number of hydrogen atoms bonded to an atom or contained in a
molecule, whether explicitly included as atoms or not. It is an error to have hydrogen count less
than the explicit hydrogen count. There is no default value and no assumptions about hydrogen Count
can be made if it is not given. If hydrogenCount is given on every atom, then the values can be
summed to give the total hydrogenCount for the (sub)molecule. Because of this hydrogenCount should
not be used where hydrogen atoms bridge 2 or more atoms.
</h:div>
<h:div class="example" href="atom1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:restriction base="xsd:nonNegativeInteger"/>
</xsd:simpleType>
<xsd:simpleType name="idArrayType" id="st.idArrayType">