consumer);
39 | }
40 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/core/TargetAssembler.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.core;
2 |
3 | import org.rcsb.strucmotif.domain.StructureSearchContext;
4 |
5 | /**
6 | * Where the magic happens. Lookup all word occurrences which need to be fulfilled and combine them in the most
7 | * efficient way.
8 | * Assembles the set of target structures to evaluate by focusing on the paths through targets. Basically, this is
9 | * subgraph isomorphism: the query is a graph, and we want to find all target structures which contain this query as a
10 | * subgraph.
11 | */
12 | public interface TargetAssembler {
13 | /**
14 | * Search: i.e. find all paths through all target structures which reasonably resemble the structure of the query
15 | * motif.
16 | * @param context the container to work on
17 | */
18 | void assemble(StructureSearchContext context);
19 | }
20 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/Pair.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain;
2 |
3 | /**
4 | * Defines a relation between 2 objects.
5 | * @param first 1st element
6 | * @param second 2nd element
7 | * @param the first type
8 | * @param the second type
9 | */
10 | public record Pair(F first, S second) {
11 | @Override
12 | public String toString() {
13 | return first + " - " + second;
14 | }
15 | }
16 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/align/AlignmentResult.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.align;
2 |
3 | /**
4 | * The result of an alignment.
5 | * @param transformation the transformation determined by the alignment
6 | * @param rmsd the alignment score
7 | */
8 | public record AlignmentResult(float[] transformation, float rmsd) {}
9 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/align/AtomPairingScheme.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.align;
2 |
3 | import org.rcsb.strucmotif.domain.structure.LabelAtomId;
4 |
5 | import java.util.function.Predicate;
6 |
7 | /**
8 | * Schemes on which atoms (by name) to use to align residues. Each entry is actually a {@link Predicate} which tests
9 | * atom names and returns true if fall into that particular scheme.
10 | */
11 | public enum AtomPairingScheme implements Predicate {
12 | /**
13 | * Use everything.
14 | */
15 | ALL(s -> true),
16 | /**
17 | * Use alpha carbons only.
18 | */
19 | ALPHA_CARBON(s -> s.equals(LabelAtomId.CA) ||
20 | s.equals(LabelAtomId.C4_PRIME)),
21 | /**
22 | * Use beta carbons only.
23 | */
24 | BETA_CARBON(s -> s.equals(LabelAtomId.CB) ||
25 | s.equals(LabelAtomId.C1_PRIME)),
26 | /**
27 | * Use backbone atoms only.
28 | */
29 | BACKBONE(s -> s.equals(LabelAtomId.N) || s.equals(LabelAtomId.CA) || s.equals(LabelAtomId.C) ||
30 | s.equals(LabelAtomId.O) || s.equals(LabelAtomId.P) || s.equals(LabelAtomId.OP1) ||
31 | s.equals(LabelAtomId.OP2) || s.equals(LabelAtomId.C2_PRIME) || s.equals(LabelAtomId.C3_PRIME) ||
32 | s.equals(LabelAtomId.O3_PRIME) || s.equals(LabelAtomId.C4_PRIME) || s.equals(LabelAtomId.O4_PRIME) ||
33 | s.equals(LabelAtomId.C5_PRIME) || s.equals(LabelAtomId.O5_PRIME)),
34 | /**
35 | * Use side-chain atoms only.
36 | */
37 | SIDE_CHAIN(BACKBONE.predicate.negate()),
38 | /**
39 | * Use pseudo-atoms defined by {@link org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor}.
40 | */
41 | PSEUDO_ATOMS(s -> s.equals(LabelAtomId.CA) || s.equals(LabelAtomId.CB) ||
42 | s.equals(LabelAtomId.C4_PRIME) || s.equals(LabelAtomId.C1_PRIME));
43 |
44 | private final Predicate predicate;
45 |
46 | AtomPairingScheme(Predicate predicate) {
47 | this.predicate = predicate;
48 | }
49 |
50 | @Override
51 | public boolean test(LabelAtomId s) {
52 | return predicate.test(s);
53 | }
54 | }
55 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/bucket/Bucket.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.bucket;
2 |
3 | import java.util.Set;
4 |
5 | /**
6 | * Represents a single file of the inverted index (e.g., AL-4-5-4). This file keeps track of all structures that contain
7 | * occurrences of the corresponding descriptor.
8 | */
9 | public interface Bucket {
10 | /**
11 | * All structures that contain occurrences of this descriptor.
12 | * @return a collection of structure indices
13 | */
14 | Set getStructureIndices();
15 |
16 | /**
17 | * True if there is another structure after the current one.
18 | * @return a boolean
19 | */
20 | boolean hasNextStructure();
21 |
22 | /**
23 | * True if there is another occurrence after the current one.
24 | * @return a boolean
25 | */
26 | boolean hasNextOccurrence();
27 |
28 | /**
29 | * Advance to the next structure, only safe if {@link #hasNextStructure()} is true.
30 | */
31 | void moveStructure();
32 |
33 | /**
34 | * Advance to the next structure, only safe if {@link #hasNextOccurrence()} is true.
35 | */
36 | void moveOccurrence();
37 |
38 | /**
39 | * The number of structures that contain this descriptor.
40 | * @return an int
41 | */
42 | int getStructureCount();
43 |
44 | /**
45 | * The total number of residue pairs registered in this bucket.
46 | * @return an int
47 | */
48 | int getResiduePairCount();
49 |
50 | /**
51 | * The current structure index.
52 | * @return a structure index
53 | */
54 | int getStructureIndex();
55 |
56 | /**
57 | * Convenience method that gives access to the current identifier represented by 2 ints.
58 | * @return the current residue indices
59 | */
60 | long getResiduePairIdentifier();
61 |
62 | /**
63 | * Move iterators back to start positions.
64 | */
65 | void reset();
66 |
67 | /**
68 | * Get the current occurrence start position associated with the current position pointer.
69 | * @return an int
70 | */
71 | int getStartPosition();
72 |
73 | /**
74 | * Get the current occurrence end position associated with the current position pointer.
75 | * @return an int
76 | */
77 | int getEndPosition();
78 | }
79 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/motif/AngleType.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.motif;
2 |
3 | import org.rcsb.strucmotif.math.Algebra;
4 |
5 | /**
6 | * Binned representation of the angle between residues.
7 | */
8 | public enum AngleType {
9 | /**
10 | * [0, 10) deg.
11 | */
12 | A0,
13 | /**
14 | * [10, 30) deg.
15 | */
16 | A20,
17 | /**
18 | * [30, 50) deg.
19 | */
20 | A40,
21 | /**
22 | * [50, 70) deg.
23 | */
24 | A60,
25 | /**
26 | * [70, 90) deg.
27 | */
28 | A80,
29 | /**
30 | * [90, 110) deg.
31 | */
32 | A100,
33 | /**
34 | * [110, 130) deg.
35 | */
36 | A120,
37 | /**
38 | * [130, 150) deg.
39 | */
40 | A140,
41 | /**
42 | * [150, 170) deg.
43 | */
44 | A160,
45 | /**
46 | * [170, 180]
47 | */
48 | A180;
49 |
50 | /**
51 | * Cached values of this enum. Don't manipulate this array or things will burn.
52 | */
53 | public static final AngleType[] values = values();
54 |
55 | /**
56 | * Width of an angle bin.
57 | */
58 | public static final int BIN_SIZE = 20;
59 |
60 | /**
61 | * Convert enum to angle value in degree (basically the lower bound of the interval).
62 | * @return lower bound of angles landing in this bin
63 | */
64 | public int getIntRepresentation() {
65 | return ordinal() * BIN_SIZE;
66 | }
67 |
68 | /**
69 | * Convert angle in degrees to enum value. Will cap results into interval of possible values.
70 | * @param angle raw value
71 | * @return the corresponding bin
72 | */
73 | public static AngleType ofAngle(float angle) {
74 | int i = Math.round(angle / BIN_SIZE);
75 | if (i < 0) {
76 | return AngleType.A0;
77 | } else if (i >= values.length) {
78 | return AngleType.A180;
79 | } else {
80 | return values[i];
81 | }
82 | }
83 |
84 | /**
85 | * Convert the ordinal to enum value. Somewhat trivial. Will cap results into interval of possible values.
86 | * @param ordinal the ordinal to get
87 | * @return the corresponding bin
88 | */
89 | public static AngleType ofIntRepresentation(int ordinal) {
90 | return values[Algebra.capToInterval(0, ordinal, values.length)];
91 | }
92 | }
93 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/motif/DistanceType.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.motif;
2 |
3 | import org.rcsb.strucmotif.math.Algebra;
4 |
5 | /**
6 | * Binned representation of the distance between residues.
7 | */
8 | public enum DistanceType {
9 | /**
10 | * [0, 0.5) A.
11 | */
12 | D0,
13 | /**
14 | * [0.5, 1.5) A.
15 | */
16 | D1,
17 | /**
18 | * [1.5, 2.5) A.
19 | */
20 | D2,
21 | /**
22 | * [2.5, 3.5) A.
23 | */
24 | D3,
25 | /**
26 | * [3.5, 4.5) A.
27 | */
28 | D4,
29 | /**
30 | * [4.5, 5.5) A.
31 | */
32 | D5,
33 | /**
34 | * [5.5, 6.5) A.
35 | */
36 | D6,
37 | /**
38 | * [6.5, 7.5) A.
39 | */
40 | D7,
41 | /**
42 | * [7.5, 8.5) A.
43 | */
44 | D8,
45 | /**
46 | * [8.5, 9.5) A.
47 | */
48 | D9,
49 | /**
50 | * [9.5, 10.5) A.
51 | */
52 | D10,
53 | /**
54 | * [10.5, 11.5) A.
55 | */
56 | D11,
57 | /**
58 | * [11.5, 12.5) A.
59 | */
60 | D12,
61 | /**
62 | * [12.5, 13.5) A.
63 | */
64 | D13,
65 | /**
66 | * [13.5, 14.5) A.
67 | */
68 | D14,
69 | /**
70 | * [14.5, 15.5) A.
71 | */
72 | D15,
73 | /**
74 | * [15.5, 16.5) A.
75 | */
76 | D16,
77 | /**
78 | * [16.5, 17.5) A.
79 | */
80 | D17,
81 | /**
82 | * [17.5, 18.5) A.
83 | */
84 | D18,
85 | /**
86 | * [18.5, 19.5) A.
87 | */
88 | D19,
89 | /**
90 | * [19.5, 20.5) A.
91 | */
92 | D20,
93 | /**
94 | * [20.5, 21.5) A.
95 | */
96 | D21,
97 | /**
98 | * [21.5, 22.5) A.
99 | */
100 | D22,
101 | /**
102 | * [22.5, 23.5) A.
103 | */
104 | D23,
105 | /**
106 | * [23.5, 24.5) A.
107 | */
108 | D24,
109 | /**
110 | * [24.5, 25.5) A.
111 | */
112 | D25,
113 | /**
114 | * [25.5, 26.5) A.
115 | */
116 | D26,
117 | /**
118 | * [26.5, 27.5) A.
119 | */
120 | D27,
121 | /**
122 | * [27.5, 28.5) A.
123 | */
124 | D28,
125 | /**
126 | * [28.5, 29.5) A.
127 | */
128 | D29,
129 | /**
130 | * [29.5, 30.5) A.
131 | */
132 | D30,
133 | /**
134 | * [30.5, 31.5) A.
135 | */
136 | D31; // this is the hard-limit for the distance between pairs
137 |
138 | /**
139 | * Cached values of this enum. Don't manipulate this array or things will burn.
140 | */
141 | public static final DistanceType[] values = values();
142 |
143 | /**
144 | * Width of a distance bin.
145 | */
146 | public static final int BIN_SIZE = 1;
147 |
148 | /**
149 | * Convert enum to distance value in Angstrom (basically the lower bound of the interval).
150 | * @return lower bound of distances landing in this bin
151 | */
152 | public int getIntRepresentation() {
153 | return ordinal() * BIN_SIZE;
154 | }
155 |
156 | /**
157 | * Convert distance in Angstrom to enum value. Will cap results into interval of possible values.
158 | * @param distance raw distance
159 | * @return the corresponding bin
160 | */
161 | public static DistanceType ofDistance(float distance) {
162 | int i = Math.round(distance / BIN_SIZE);
163 | if (i < 0) {
164 | return DistanceType.D0;
165 | } else if (i >= values.length) {
166 | return DistanceType.D31;
167 | } else {
168 | return values[i];
169 | }
170 | }
171 |
172 | /**
173 | * Convert the ordinal to enum value. Somewhat trivial. Will cap results into interval of possible values.
174 | * @param ordinal the ordinal to get
175 | * @return the corresponding bin
176 | */
177 | public static DistanceType ofIntRepresentation(int ordinal) {
178 | return values[Algebra.capToInterval(0, ordinal, values.length)];
179 | }
180 | }
181 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/motif/EnrichedMotifDefinition.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.motif;
2 |
3 | import org.rcsb.strucmotif.domain.structure.LabelAtomId;
4 | import org.rcsb.strucmotif.domain.structure.Structure;
5 |
6 | import java.util.List;
7 | import java.util.Map;
8 | import java.util.Objects;
9 |
10 | /**
11 | * Enriched motif definitions wrap a {@link MotifDefinition} and provide additionally access to the underlying
12 | * {@link Structure} as well as referenced residues.
13 | */
14 | public class EnrichedMotifDefinition extends MotifDefinition {
15 | private final Structure structure;
16 | private final List> residues;
17 |
18 | /**
19 | * Construct a enriched motif.
20 | * @param motifDefinition original definition
21 | * @param structure underlying structure
22 | * @param residues all relevant residues
23 | */
24 | public EnrichedMotifDefinition(MotifDefinition motifDefinition, Structure structure, List> residues) {
25 | super(motifDefinition.getMotifIdentifier(), motifDefinition.getStructureIdentifier(), motifDefinition.getTitle(), motifDefinition.getDescription(), motifDefinition.getLabelSelections(), motifDefinition.getPositionSpecificExchanges());
26 | this.structure = structure;
27 | this.residues = residues;
28 | }
29 |
30 | /**
31 | * Access to the structure object.
32 | * @return a {@link Structure}
33 | */
34 | public Structure getStructure() {
35 | return structure;
36 | }
37 |
38 | /**
39 | * All relevant residues.
40 | * @return a collection of maps from atom names to 3D vectors
41 | */
42 | public List> getResidues() {
43 | return residues;
44 | }
45 |
46 | @Override
47 | public boolean equals(Object o) {
48 | if (this == o) return true;
49 | if (o == null || getClass() != o.getClass()) return false;
50 | if (!super.equals(o)) return false;
51 | EnrichedMotifDefinition that = (EnrichedMotifDefinition) o;
52 | return Objects.equals(structure, that.structure) && Objects.equals(residues, that.residues);
53 | }
54 |
55 | @Override
56 | public int hashCode() {
57 | return Objects.hash(super.hashCode(), structure, residues);
58 | }
59 | }
60 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/motif/Overlap.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.motif;
2 |
3 | /**
4 | * Can be no overlap or both overlapping. Interesting case is when 1 pair overlaps. Can be LEFT_LEFT (left/first
5 | * identifier of first word paired to left/first of second word) and so on.
6 | */
7 | public enum Overlap {
8 | /**
9 | * No overlap.
10 | */
11 | NONE,
12 | /**
13 | * Left identifier of first word corresponds to left identifier of second word.
14 | */
15 | LEFT_LEFT,
16 | /**
17 | * Left identifier of first word corresponds to right identifier of second word.
18 | */
19 | LEFT_RIGHT,
20 | /**
21 | * Right identifier of first word corresponds to left identifier of second word.
22 | */
23 | RIGHT_LEFT,
24 | /**
25 | * Right identifier of first word corresponds to right identifier of second word.
26 | */
27 | RIGHT_RIGHT,
28 | /**
29 | * The degenerate case where both sides are referencing the same residues.
30 | */
31 | BOTH;
32 |
33 | /**
34 | * Determines the overlap between 2 residue pair identifiers.
35 | * @param r11 1st index of 1st identifier
36 | * @param r12 2nd index of 1st identifier
37 | * @param r21 1st index of 2nd identifier
38 | * @param r22 2nd index of 2nd identifier
39 | * @return a description of the observed overlap
40 | */
41 | public static Overlap ofResiduePairIdentifiers(int r11, int r12, int r21, int r22) {
42 | boolean equal1112 = r11 == r21;
43 | boolean equal1122 = r11 == r22;
44 | boolean equal1221 = r12 == r21;
45 | boolean equal1222 = r12 == r22;
46 | return of(equal1112, equal1122, equal1221, equal1222);
47 | }
48 |
49 | /**
50 | * Determines the overlap between 2 residue pair identifiers.
51 | * @param r1 1st identifier
52 | * @param r2 2nd identifier
53 | * @return a description of the observed overlap
54 | */
55 | public static Overlap ofResiduePairIdentifiers(long r1, long r2) {
56 | int r11 = ResiduePairIdentifier.getResidueIndex1(r1);
57 | int r12 = ResiduePairIdentifier.getResidueIndex2(r1);
58 | int r21 = ResiduePairIdentifier.getResidueIndex1(r2);
59 | int r22 = ResiduePairIdentifier.getResidueIndex2(r2);
60 | boolean equal1112 = r11 == r21;
61 | boolean equal1122 = r11 == r22;
62 | boolean equal1221 = r12 == r21;
63 | boolean equal1222 = r12 == r22;
64 | return of(equal1112, equal1122, equal1221, equal1222);
65 | }
66 |
67 | private static Overlap of(boolean equal1112, boolean equal1122, boolean equal1221, boolean equal1222) {
68 | if (!equal1112 && !equal1122 && !equal1221 && !equal1222) {
69 | return NONE;
70 | } else if ((equal1112 && equal1222) || (equal1122 && equal1221)) {
71 | return BOTH;
72 | } else if (equal1112) {
73 | return LEFT_LEFT;
74 | } else if (equal1222) {
75 | return RIGHT_RIGHT;
76 | } else if (equal1122) {
77 | return LEFT_RIGHT;
78 | } else {
79 | return RIGHT_LEFT;
80 | }
81 | }
82 | }
83 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/motif/ResiduePairIdentifier.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.motif;
2 |
3 | /**
4 | * A residue pair descriptor is a long that combines 2 residue indices. The upper 32 bit (A) are the 1st value, the
5 | * lower 32 bit (B) contain the 2nd value.
6 | *
7 | * AAAAAAAA AAAAAAAA AAAAAAAA AAAAAAAA BBBBBBBB BBBBBBBB BBBBBBBB BBBBBBBB
8 | */
9 | public class ResiduePairIdentifier {
10 | private ResiduePairIdentifier() {
11 | // deny
12 | }
13 |
14 | /**
15 | * Encode (residueIndex1, residueIndex2) as long.
16 | * @param residueIndex1 1st index
17 | * @param residueIndex2 2nd index
18 | * @return both represented as a single long
19 | */
20 | public static long encodeIdentifier(int residueIndex1, int residueIndex2) {
21 | return (long) residueIndex1 << 32 | residueIndex2;
22 | }
23 |
24 | /**
25 | * Extract the 1st index from a long identifier.
26 | * @param residuePairIdentifier long
27 | * @return 1st index as int
28 | */
29 | public static int getResidueIndex1(long residuePairIdentifier) {
30 | return (int) (residuePairIdentifier >>> 32);
31 | }
32 |
33 | /**
34 | * Extract the 2nd index from a long identifier.
35 | * @param residuePairIdentifier long
36 | * @return 2nd index as int
37 | */
38 | public static int getResidueIndex2(long residuePairIdentifier) {
39 | return (int) residuePairIdentifier;
40 | }
41 |
42 | /**
43 | * Pretty-print a long identifier.
44 | * @param residuePairIdentifier long
45 | * @return human-readable String
46 | */
47 | public static String toString(long residuePairIdentifier) {
48 | return getResidueIndex1(residuePairIdentifier) + "-" + getResidueIndex2(residuePairIdentifier);
49 | }
50 | }
51 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/query/ContextBuilder.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | import org.rcsb.strucmotif.config.MotifPruningStrategy;
4 | import org.rcsb.strucmotif.core.MotifPruner;
5 | import org.rcsb.strucmotif.domain.SearchContext;
6 | import org.rcsb.strucmotif.domain.align.AtomPairingScheme;
7 |
8 | /**
9 | * Step-wise builder of the search context.
10 | */
11 | public interface ContextBuilder {
12 | /**
13 | * Parameters are considered mandatory arguments (in the sense that some value has to be given - nonetheless,
14 | * default values will be used). But internally these values are strictly required. No input validation is performed
15 | * whatsoever.
16 | * @param type of the context to create
17 | */
18 | interface MandatoryBuilder> {
19 | /**
20 | * Specify the backbone distance tolerance (default: 1).
21 | * @param backboneDistanceTolerance an int
22 | * @return this builder
23 | */
24 | MandatoryBuilder backboneDistanceTolerance(int backboneDistanceTolerance);
25 |
26 | /**
27 | * Specify the side-chain distance tolerance (default: 1).
28 | * @param sideChainDistanceTolerance an int
29 | * @return this builder
30 | */
31 | MandatoryBuilder sideChainDistanceTolerance(int sideChainDistanceTolerance);
32 |
33 | /**
34 | * Specify the angle tolerance (default: 1).
35 | * @param angleTolerance an int
36 | * @return this builder
37 | */
38 | MandatoryBuilder angleTolerance(int angleTolerance);
39 |
40 | /**
41 | * Filter hits based on RMSD.
42 | * @param rmsdCutoff the RMSD cutoff above which hits are filtered
43 | * @return this builder
44 | */
45 | MandatoryBuilder rmsdCutoff(double rmsdCutoff);
46 |
47 | /**
48 | * Controls which atoms will be considered for alignment. Only relevant when scoring scheme is alignment-based.
49 | * @param atomPairingScheme how to pair atoms for alignment routine
50 | * @return this builder
51 | */
52 | MandatoryBuilder atomPairingScheme(AtomPairingScheme atomPairingScheme);
53 |
54 | /**
55 | * Specify the motif pruning strategy.
56 | * @param motifPruner the implementation to prune motifs
57 | * @return this builder
58 | */
59 | MandatoryBuilder motifPruningStrategy(MotifPruner motifPruner);
60 |
61 | /**
62 | * Specify the motif pruning strategy.
63 | * @param motifPruningStrategy the strategy to prune motifs
64 | * @return this builder
65 | */
66 | MandatoryBuilder motifPruningStrategy(MotifPruningStrategy motifPruningStrategy);
67 |
68 | /**
69 | * Timeout after this many milliseconds by throwing a {@link java.util.concurrent.TimeoutException}. Set to
70 | * Integer.MAX_VALUE to not enforce any timeout.
71 | * @param ms the timeout in ms
72 | * @return this builder
73 | */
74 | MandatoryBuilder timeout(int ms);
75 |
76 | /**
77 | * Create the parameter object and move on to the optional step.
78 | * @return the optional builder instance
79 | */
80 | OptionalBuilder buildParameters();
81 | }
82 |
83 | /**
84 | * Optional values.
85 | * @param type of the context to create
86 | */
87 | interface OptionalBuilder> {
88 | /**
89 | * Create the context.
90 | * @return a context
91 | */
92 | C buildContext();
93 | }
94 | }
95 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/query/MotifParameters.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | import org.rcsb.strucmotif.core.MotifPruner;
4 | import org.rcsb.strucmotif.domain.align.AtomPairingScheme;
5 |
6 | /**
7 | * Parameters of a 'detect-motifs' run.
8 | */
9 | public class MotifParameters implements Parameters {
10 | private final int backboneDistanceTolerance;
11 | private final int sideChainDistanceTolerance;
12 | private final int angleTolerance;
13 | private final float rmsdCutoff;
14 | private final AtomPairingScheme atomPairingScheme;
15 | private final MotifPruner motifPruner;
16 | private final int timeout;
17 |
18 | /**
19 | * Construct motif parameters.
20 | * @param backboneDistanceTolerance backbone tolerance
21 | * @param sideChainDistanceTolerance side-chain tolerance
22 | * @param angleTolerance angle tolerance
23 | * @param rmsdCutoff maximum RMSD
24 | * @param atomPairingScheme how to pair atoms
25 | * @param motifPruner how to prune motifs
26 | * @param timeout timeout in ms
27 | */
28 | public MotifParameters(int backboneDistanceTolerance, int sideChainDistanceTolerance, int angleTolerance, float rmsdCutoff, AtomPairingScheme atomPairingScheme, MotifPruner motifPruner, int timeout) {
29 | this.backboneDistanceTolerance = backboneDistanceTolerance;
30 | this.sideChainDistanceTolerance = sideChainDistanceTolerance;
31 | this.angleTolerance = angleTolerance;
32 | this.rmsdCutoff = rmsdCutoff;
33 | this.atomPairingScheme = atomPairingScheme;
34 | this.motifPruner = motifPruner;
35 | this.timeout = timeout;
36 | }
37 |
38 | /**
39 | * Employed backbone distance tolerance.
40 | * @return an int
41 | */
42 | public int getBackboneDistanceTolerance() {
43 | return backboneDistanceTolerance;
44 | }
45 |
46 | /**
47 | * Employed side-chain distance tolerance.
48 | * @return an int
49 | */
50 | public int getSideChainDistanceTolerance() {
51 | return sideChainDistanceTolerance;
52 | }
53 |
54 | /**
55 | * Employed angle tolerance.
56 | * @return an int
57 | */
58 | public int getAngleTolerance() {
59 | return angleTolerance;
60 | }
61 |
62 | /**
63 | * Maximum RMSD up to which hits will be accepted, can be 'infinite'.
64 | * @return a float
65 | */
66 | public float getRmsdCutoff() {
67 | return rmsdCutoff;
68 | }
69 |
70 | /**
71 | * If filtering by RMSD will happen.
72 | * @return true if there's a cutoff
73 | */
74 | public boolean hasRmsdCutoff() {
75 | return rmsdCutoff != Float.MAX_VALUE;
76 | }
77 |
78 | /**
79 | * Which atoms will get aligned.
80 | * @return an {@link AtomPairingScheme}
81 | */
82 | public AtomPairingScheme getAtomPairingScheme() {
83 | return atomPairingScheme;
84 | }
85 |
86 | /**
87 | * The associated motif pruning strategy.
88 | * @return a {@link MotifPruner}
89 | */
90 | public MotifPruner getMotifPruner() {
91 | return motifPruner;
92 | }
93 |
94 | @Override
95 | public int getTimeout() {
96 | return timeout;
97 | }
98 |
99 | @Override
100 | public boolean hasTimeout() {
101 | return timeout != Integer.MAX_VALUE;
102 | }
103 | }
104 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/query/MotifQuery.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | import org.rcsb.strucmotif.domain.motif.EnrichedMotifDefinition;
4 | import org.rcsb.strucmotif.domain.structure.Structure;
5 |
6 | import java.util.Set;
7 |
8 | /**
9 | * The immutable container for a structural motif query.
10 | */
11 | public class MotifQuery implements SearchQuery {
12 | private final MotifQueryStructure queryStructure;
13 | private final Set motifDefinitions;
14 | private final MotifParameters parameters;
15 |
16 | /**
17 | * Construct a motif search query.
18 | * @param structureIdentifier the referenced structure
19 | * @param structure structure data
20 | * @param motifDefinitions the motifs to consider
21 | * @param parameters query parameters
22 | */
23 | public MotifQuery(String structureIdentifier,
24 | Structure structure,
25 | Set motifDefinitions,
26 | MotifParameters parameters) {
27 | this.queryStructure = new MotifQueryStructure(structureIdentifier, structure);
28 | this.motifDefinitions = motifDefinitions;
29 | this.parameters = parameters;
30 | }
31 |
32 | /**
33 | * The structure used to define this query/motif.
34 | * @return a dedicated implementation wrapping a structure instance
35 | */
36 | @Override
37 | public MotifQueryStructure getQueryStructure() {
38 | return queryStructure;
39 | }
40 |
41 | /**
42 | * All associated motif definitions.
43 | * @return a collection of motifs
44 | */
45 | public Set getMotifDefinitions() {
46 | return motifDefinitions;
47 | }
48 |
49 | /**
50 | * All parameters defined for this search task.
51 | * @return a parameter instance
52 | */
53 | @Override
54 | public MotifParameters getParameters() {
55 | return parameters;
56 | }
57 | }
58 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/query/MotifQueryStructure.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | import org.rcsb.strucmotif.domain.structure.Structure;
4 |
5 | /**
6 | * A query structure when searching for motifs.
7 | */
8 | public class MotifQueryStructure implements QueryStructure {
9 | private final String structureIdentifier;
10 | private final Structure structure;
11 |
12 | /**
13 | * Construct a motif query structure.
14 | * @param structureIdentifier the identifier
15 | * @param structure the structure
16 | */
17 | public MotifQueryStructure(String structureIdentifier, Structure structure) {
18 | this.structureIdentifier = structureIdentifier;
19 | this.structure = structure;
20 | }
21 |
22 | /**
23 | * Get the identifier of this query structure.
24 | *
25 | * @return a String
26 | */
27 | @Override
28 | public String getStructureIdentifier() {
29 | return structureIdentifier;
30 | }
31 |
32 | /**
33 | * Delegate to wrapped structure.
34 | *
35 | * @return the structure instance
36 | */
37 | @Override
38 | public Structure getStructure() {
39 | return structure;
40 | }
41 | }
42 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/query/Parameters.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | /**
4 | * Parameters of a search run.
5 | */
6 | public interface Parameters {
7 | /**
8 | * Default tolerance value for backbone distances.
9 | */
10 | int DEFAULT_BACKBONE_DISTANCE_TOLERANCE = 1;
11 | /**
12 | * Default tolerance value for side-chain distances.
13 | */
14 | int DEFAULT_SIDE_CHAIN_DISTANCE_TOLERANCE = 1;
15 | /**
16 | * Default tolerance value for angles.
17 | */
18 | int DEFAULT_ANGLE_TOLERANCE = 1;
19 |
20 | /**
21 | * Timeout after this many milliseconds by throwing a {@link java.util.concurrent.TimeoutException}. No timeout is
22 | * enforced if set to Integer.MAX_VALUE.
23 | * @return the timeout specified for this query
24 | */
25 | int getTimeout();
26 |
27 | /**
28 | * Reports whether this query is configured to timeout.
29 | * @return true if this query will get interrupted after some time
30 | */
31 | boolean hasTimeout();
32 | }
33 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/query/PositionSpecificExchange.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | import org.rcsb.strucmotif.domain.structure.LabelSelection;
4 | import org.rcsb.strucmotif.domain.structure.ResidueType;
5 |
6 | import java.util.LinkedHashSet;
7 | import java.util.Set;
8 | import java.util.stream.Collectors;
9 | import java.util.stream.Stream;
10 |
11 | /**
12 | * Defines a position-specific exchange for a particular position in the query structure.
13 | */
14 | public class PositionSpecificExchange {
15 | private final LabelSelection labelSelection;
16 | private final Set residueTypes;
17 |
18 | /**
19 | * Constructs a new position-specific exchange.
20 | * @see PositionSpecificExchange (LabelSelection, Set)
21 | * @param labelSelection selector of the referenced position
22 | * @param residueTypes all allowed types (must include original type if still allowed)
23 | */
24 | public PositionSpecificExchange(LabelSelection labelSelection, ResidueType... residueTypes) {
25 | this(labelSelection, Stream.of(residueTypes).collect(Collectors.toCollection(LinkedHashSet::new)));
26 | }
27 |
28 | /**
29 | * Constructs a new position-specific exchange.
30 | * @param labelSelection selector of the referenced position
31 | * @param residueTypes all allowed types (must include original type if still allowed)
32 | */
33 | public PositionSpecificExchange(LabelSelection labelSelection, Set residueTypes) {
34 | this.labelSelection = labelSelection;
35 | this.residueTypes = residueTypes;
36 | }
37 |
38 | /**
39 | * The position this exchange references.
40 | * @return the {@link LabelSelection} of a residue
41 | */
42 | public LabelSelection getLabelSelection() {
43 | return labelSelection;
44 | }
45 |
46 | /**
47 | * The set of allowed component types at that position. Must explicitly include the original residue type if that
48 | * should still be allowed.
49 | * @return all types that can occur at this position
50 | */
51 | public Set getResidueTypes() {
52 | return residueTypes;
53 | }
54 | }
55 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/query/QueryStructure.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | import org.rcsb.strucmotif.domain.structure.Structure;
4 |
5 | /**
6 | * References the structure that is the basis of a query.
7 | */
8 | public interface QueryStructure {
9 | /**
10 | * The identifier of this structure.
11 | * @return a String
12 | */
13 | String getStructureIdentifier();
14 |
15 | /**
16 | * The structure data.
17 | * @return {@link Structure} instance
18 | */
19 | Structure getStructure();
20 | }
21 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/query/ResultsContentType.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | import java.util.function.Predicate;
4 |
5 | /**
6 | * Controls the set of allowed targets, effectively providing high-level control to find exclusively PDB structures, or
7 | * exclusively computed structure models.
8 | */
9 | public enum ResultsContentType implements Predicate {
10 | /**
11 | * Return only PDB-entries.
12 | */
13 | EXPERIMENTAL(s -> s.matches(Constants.PDB_REGEX)),
14 | /**
15 | * Return only computed structure models.
16 | */
17 | COMPUTATIONAL(s -> !s.matches(Constants.PDB_REGEX));
18 |
19 | private static class Constants {
20 | private static final String PDB_REGEX = "^[0-9][a-zA-Z0-9]{3}$";
21 | }
22 |
23 | private final Predicate condition;
24 |
25 | ResultsContentType(Predicate condition) {
26 | this.condition = condition;
27 | }
28 |
29 | @Override
30 | public boolean test(String s) {
31 | return condition.test(s);
32 | }
33 | }
34 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/query/SearchQuery.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | /**
4 | * Summarizes a query.
5 | * @param parameter type
6 | * @param query structure type
7 | */
8 | public interface SearchQuery
{
9 | /**
10 | * Access to the parameters used.
11 | * @return a {@link Parameters} instance
12 | */
13 | P getParameters();
14 |
15 | /**
16 | * Access to the underlying query structure.
17 | * @return a {@link QueryStructure} instance
18 | */
19 | S getQueryStructure();
20 | }
21 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/Hit.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | /**
4 | * One accepted hit.
5 | */
6 | public interface Hit {
7 |
8 | }
9 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/MotifHit.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | import org.rcsb.strucmotif.domain.structure.LabelSelection;
4 | import org.rcsb.strucmotif.domain.structure.ResidueType;
5 |
6 | import java.util.Arrays;
7 | import java.util.List;
8 |
9 | /**
10 | * The result of a structural motif search.
11 | * @param motifIdentifier the motif ID
12 | * @param labelSelections selections for each matched residue
13 | * @param residueTypes mapped residue types
14 | * @param rmsd the alignment score
15 | * @param transformation the transformation determined by the alignment
16 | */
17 | public record MotifHit(String motifIdentifier, List labelSelections, List residueTypes, float rmsd, float[] transformation) implements Hit {
18 | @Override
19 | public String toString() {
20 | return "MotifHit{" +
21 | "motifIdentifier='" + motifIdentifier + '\'' +
22 | ", labelSelections=" + labelSelections +
23 | ", residueTypes=" + residueTypes +
24 | ", rmsd=" + rmsd +
25 | ", transformation=" + Arrays.toString(transformation) +
26 | '}';
27 | }
28 | }
29 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/MotifSearchResult.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | import java.util.ArrayList;
4 | import java.util.List;
5 |
6 | /**
7 | * The results of a motif search run.
8 | */
9 | public class MotifSearchResult implements SearchResult {
10 | private final MotifTimings timings;
11 | private List hits;
12 |
13 | /**
14 | * Construct a result container.
15 | */
16 | public MotifSearchResult() {
17 | this.timings = new MotifTimings();
18 | this.hits = new ArrayList<>();
19 | }
20 |
21 | @Override
22 | public MotifTimings getTimings() {
23 | return timings;
24 | }
25 |
26 | /**
27 | * Update the collection of accepted hits.
28 | * @param hits a collection of hits
29 | */
30 | public void setHits(List hits) {
31 | this.hits = hits;
32 | }
33 |
34 | @Override
35 | public List getHits() {
36 | return hits;
37 | }
38 | }
39 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/MotifTimings.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | /**
4 | * Timings in the context of motif queries.
5 | */
6 | public class MotifTimings implements Timings {
7 | private final Timer query;
8 |
9 | /**
10 | * Constructs a new timer instance. Immediately starts the query timer.
11 | */
12 | public MotifTimings() {
13 | this.query = new Timer();
14 | queryStart();
15 | }
16 |
17 | @Override
18 | public void queryStart() {
19 | query.start();
20 | }
21 |
22 | @Override
23 | public void queryStop() {
24 | query.stop();
25 | }
26 |
27 | @Override
28 | public long getQueryTime() {
29 | return query.getMillisecondTime();
30 | }
31 | }
32 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/SearchResult.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | import java.util.List;
4 |
5 | /**
6 | * The results of a search run.
7 | * @param hit type
8 | */
9 | public interface SearchResult {
10 | /**
11 | * Associated timings.
12 | * @return captured timings
13 | */
14 | Timings getTimings();
15 |
16 | /**
17 | * All accepted hits.
18 | * @return a collection of hits
19 | */
20 | List getHits();
21 | }
22 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/StructureHit.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | import org.rcsb.strucmotif.domain.structure.LabelSelection;
4 | import org.rcsb.strucmotif.domain.structure.ResidueType;
5 |
6 | import java.util.Arrays;
7 | import java.util.List;
8 |
9 | /**
10 | * The result of a structural motif search.
11 | * @param structureIdentifier the entry ID
12 | * @param assemblyIdentifier the assembly ID
13 | * @param labelSelections selections for each matched residue
14 | * @param residueTypes mapped residue types
15 | * @param rmsd the alignment score
16 | * @param transformation the transformation determined by the alignment
17 | */
18 | public record StructureHit(String structureIdentifier, String assemblyIdentifier, List labelSelections, List residueTypes, float rmsd, float[] transformation) implements Hit {
19 | @Override
20 | public String toString() {
21 | return "StructureHit{" +
22 | "structureIdentifier='" + structureIdentifier + '\'' +
23 | ", assemblyIdentifier='" + assemblyIdentifier + '\'' +
24 | ", labelSelections=" + labelSelections +
25 | ", residueTypes=" + residueTypes +
26 | ", rmsd=" + rmsd +
27 | ", transformation=" + Arrays.toString(transformation) +
28 | '}';
29 | }
30 | }
31 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/StructureSearchResult.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | import java.util.ArrayList;
4 | import java.util.List;
5 | import java.util.Map;
6 |
7 | /**
8 | * The results of a structure search run.
9 | */
10 | public class StructureSearchResult implements SearchResult {
11 | private final StructureTimings timings;
12 |
13 | /**
14 | * Keep track of the generation we are currently in, i.e. how many words of the query have been consumed.
15 | */
16 | private int pathGeneration;
17 | private Map targetStructures;
18 |
19 | private List hits;
20 | private int numberOfPaths;
21 | private int numberOfTargetStructures;
22 |
23 | /**
24 | * Construct a result container.
25 | */
26 | public StructureSearchResult() {
27 | this.timings = new StructureTimings();
28 | this.pathGeneration = 0;
29 | this.hits = new ArrayList<>();
30 | }
31 |
32 | /**
33 | * Associated timings.
34 | * @return timings object
35 | */
36 | @Override
37 | public StructureTimings getTimings() {
38 | return timings;
39 | }
40 |
41 | /**
42 | * Access to all currently referenced target structures.
43 | * @return a map with structure identifiers as keys and target structure instances as values
44 | */
45 | public Map getTargetStructures() {
46 | return targetStructures;
47 | }
48 |
49 | /**
50 | * Update the currently referenced target structures.
51 | * @param targetStructures a map with structure indices as keys and target structure instances as values
52 | */
53 | public void setTargetStructures(Map targetStructures) {
54 | this.targetStructures = targetStructures;
55 | }
56 |
57 | /**
58 | * Update the collection of currently valid hits.
59 | * @param hits a collection of hits
60 | */
61 | public void setHits(List hits) {
62 | this.hits = hits;
63 | }
64 |
65 | /**
66 | * Access all (currently) valid hits.
67 | * @return a collection of hits
68 | */
69 | @Override
70 | public List getHits() {
71 | return hits;
72 | }
73 |
74 | /**
75 | * Update the number of valid paths.
76 | * @param numberOfPaths an int
77 | */
78 | public void setNumberOfPaths(int numberOfPaths) {
79 | this.numberOfPaths = numberOfPaths;
80 | }
81 |
82 | /**
83 | * The number of valid paths in all target structures.
84 | * @return an int
85 | */
86 | public int getNumberOfPaths() {
87 | return numberOfPaths;
88 | }
89 |
90 | /**
91 | * Update the number of referenced target structures.
92 | * @param numberOfTargetStructures an int
93 | */
94 | public void setNumberOfTargetStructures(int numberOfTargetStructures) {
95 | this.numberOfTargetStructures = numberOfTargetStructures;
96 | }
97 |
98 | /**
99 | * The number of referenced target structures.
100 | * @return an int
101 | */
102 | public int getNumberOfTargetStructures() {
103 | return numberOfTargetStructures;
104 | }
105 |
106 | /**
107 | * Called internally after a descriptor has been processed.
108 | * @return the new path generation
109 | */
110 | public int incrementAndGetPathGeneration() {
111 | pathGeneration++;
112 | return pathGeneration;
113 | }
114 | }
115 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/StructureTimings.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | /**
4 | * Timings in the context of structure queries.
5 | */
6 | public class StructureTimings implements Timings {
7 | private final Timer query;
8 | private final Timer paths;
9 | private final Timer scoreHits;
10 |
11 | /**
12 | * Constructs a new timer instance. Immediately starts the query timer.
13 | */
14 | public StructureTimings() {
15 | this.query = new Timer();
16 | this.paths = new Timer();
17 | this.scoreHits = new Timer();
18 | queryStart();
19 | }
20 |
21 | /**
22 | * Start the path assembly timer.
23 | */
24 | public void pathsStart() {
25 | paths.start();
26 | }
27 |
28 | /**
29 | * Stop the path assembly timer.
30 | */
31 | public void pathsStop() {
32 | paths.stop();
33 | }
34 |
35 | /**
36 | * Get the path assembly time in ms.
37 | * @return a long
38 | */
39 | public long getPathsTime() {
40 | return paths.getMillisecondTime();
41 | }
42 |
43 | /**
44 | * Start the hit scoring timer.
45 | */
46 | public void scoreHitsStart() {
47 | scoreHits.start();
48 | }
49 |
50 | /**
51 | * Stop the hit scoring timer.
52 | */
53 | public void scoreHitsStop() {
54 | this.scoreHits.stop();
55 | }
56 |
57 | /**
58 | * Get the hit scoring time in ms.
59 | * @return a long
60 | */
61 | public long getScoreHitsTime() {
62 | return scoreHits.getMillisecondTime();
63 | }
64 |
65 | @Override
66 | public void queryStart() {
67 | query.start();
68 | }
69 |
70 | @Override
71 | public void queryStop() {
72 | query.stop();
73 | }
74 |
75 | @Override
76 | public long getQueryTime() {
77 | return query.getMillisecondTime();
78 | }
79 | }
80 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/Timer.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | import java.util.concurrent.TimeUnit;
4 |
5 | /**
6 | * Tracks timings.
7 | */
8 | public class Timer {
9 | private long start;
10 | private long time;
11 | private boolean stopped;
12 |
13 | /**
14 | * Default constructor.
15 | */
16 | public Timer() {
17 | }
18 |
19 | /**
20 | * Start the time.
21 | */
22 | public void start() {
23 | if (start != 0) {
24 | throw new IllegalStateException("timer has been started before");
25 | }
26 | if (time != 0) {
27 | throw new IllegalStateException("timer has been stopped before");
28 | }
29 |
30 | this.start = System.nanoTime();
31 | }
32 |
33 | /**
34 | * Stop the time and 'freeze' the measurement for later retrieval/output.
35 | */
36 | public void stop() {
37 | if (start == 0) {
38 | throw new IllegalStateException("timer was never started");
39 | }
40 | if (time != 0) {
41 | throw new IllegalStateException("timer has been stopped before");
42 | }
43 |
44 | this.time = System.nanoTime() - start;
45 | this.stopped = true;
46 | }
47 |
48 | /**
49 | * Retrieve the measured time in milliseconds.
50 | * @return a long in ms
51 | */
52 | public long getMillisecondTime() {
53 | return getMeasuredTime(TimeUnit.MILLISECONDS);
54 | }
55 |
56 | /**
57 | * Retrieve the measured time.
58 | * @param timeUnit the {@link TimeUnit} in which to output
59 | * @return a long of the desired granularity
60 | */
61 | public long getMeasuredTime(TimeUnit timeUnit) {
62 | if (!stopped) throw new IllegalStateException("timer was never stopped");
63 | return timeUnit.convert(time, TimeUnit.NANOSECONDS);
64 | }
65 | }
66 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/result/Timings.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.result;
2 |
3 | /**
4 | * A helper class keeping track of internal timings. Useful for development and diagnosis. All but the query timer need
5 | * to be started at an appropriate time during the query. 'Overall' query timer is started upon creation of this class.
6 | * All timers need to be explicitly stopped. Timers return times in ms.
7 | */
8 | public interface Timings {
9 | /**
10 | * Start the query timer.
11 | */
12 | void queryStart();
13 |
14 | /**
15 | * Stop the query timer.
16 | */
17 | void queryStop();
18 |
19 | /**
20 | * Get the overall query timer in ms.
21 | * @return a long
22 | */
23 | long getQueryTime();
24 | }
25 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/structure/LabelSelection.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.structure;
2 |
3 | import java.util.Objects;
4 |
5 | /**
6 | * Identifies a residue unambiguously by label_asym_id, struct_oper_id, and label_seq_id. Basically, the 'natural' way
7 | * to reference residues.
8 | * @param labelAsymId the chain of interest
9 | * @param structOperId the operation of interest
10 | * @param labelSeqId the sequence position of interest
11 | */
12 | public record LabelSelection(String labelAsymId, String structOperId, int labelSeqId) {
13 | @Override
14 | public boolean equals(Object o) {
15 | if (this == o) return true;
16 | if (o == null || getClass() != o.getClass()) return false;
17 | LabelSelection that = (LabelSelection) o;
18 | return labelSeqId == that.labelSeqId &&
19 | Objects.equals(labelAsymId, that.labelAsymId) &&
20 | Objects.equals(structOperId, that.structOperId);
21 | }
22 |
23 | @Override
24 | public int hashCode() {
25 | return Objects.hash(labelAsymId, structOperId, labelSeqId);
26 | }
27 |
28 | @Override
29 | public String toString() {
30 | return labelAsymId + "_" + structOperId + "-" + labelSeqId;
31 | }
32 | }
33 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/structure/PolymerType.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.structure;
2 |
3 | import java.util.Arrays;
4 | import java.util.Collections;
5 | import java.util.Map;
6 | import java.util.Optional;
7 | import java.util.Set;
8 | import java.util.stream.Collectors;
9 |
10 | /**
11 | * Reports the polymer type for a component. Used to determine the correct constructor during model creation.
12 | */
13 | public enum PolymerType {
14 | /**
15 | * Amino acid chain.
16 | */
17 | AMINO_ACID(Set.of("d-peptide linking",
18 | "d-peptide nh3 amino terminus",
19 | "d-peptide cooh carboxy terminus",
20 | "d-gamma-peptide, c-delta linking",
21 | "d-beta-peptide, c-gamma linking",
22 | "l-peptide linking",
23 | "l-peptide nh3 amino terminus",
24 | "l-peptide cooh carboxy terminus",
25 | "l-gamma-peptide, c-delta linking",
26 | "l-beta-peptide, c-gamma linking",
27 | "peptide linking",
28 | "peptide-like")),
29 | /**
30 | * Nucleotide chain.
31 | */
32 | NUCLEOTIDE(Set.of("dna linking",
33 | "l-dna linking",
34 | "dna oh 5 prime terminus",
35 | "dna oh 3 prime terminus",
36 | "rna linking", "l-rna linking",
37 | "rna oh 5 prime terminus",
38 | "rna oh 3 prime terminus")),
39 | /**
40 | * Unknown but polymeric.
41 | */
42 | UNKNOWN_POLYMER(Collections.emptySet());
43 |
44 | /**
45 | * Cached values of this enum. Don't manipulate this array or things will burn.
46 | */
47 | public static final PolymerType[] values = values();
48 |
49 | private final Set typeNames;
50 |
51 | PolymerType(Set typeNames) {
52 | this.typeNames = typeNames;
53 | }
54 |
55 | /**
56 | * Access to CCD types that correspond to this polymer type.
57 | * @return all associated chem_comp.type values
58 | */
59 | public Set getTypeNames() {
60 | return typeNames;
61 | }
62 |
63 | private static final Map MAPPING = Arrays.stream(PolymerType.values)
64 | .flatMap(t -> t.getTypeNames().stream().map(n -> Map.entry(n, t)))
65 | .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue));
66 |
67 | /**
68 | * Map the type of polymeric component to the enum.
69 | * @param type value to resolve
70 | * @return the corresponding polymer type
71 | */
72 | public static Optional ofChemCompType(String type) {
73 | return Optional.ofNullable(MAPPING.get(type.toLowerCase()));
74 | }
75 | }
76 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/domain/structure/StructureInformation.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.structure;
2 |
3 | /**
4 | * Reports global properties of a structure.
5 | * @param structureIdentifier entry id
6 | * @param structureIndex globally unique identifier of this entry
7 | * @param majorRevision version info
8 | * @param minorRevision version info
9 | */
10 | public record StructureInformation(String structureIdentifier, int structureIndex, int majorRevision, int minorRevision) {}
11 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/Committable.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | /**
4 | * Allows writing data to FFindex-managed files without compromising production data. Call the providing function to
5 | * commit all data to the production files. This is rather slow and should only happen from time to time.
6 | */
7 | public interface Committable {
8 | /**
9 | * Process all temporary files and make them available in queries.
10 | */
11 | void commit();
12 | }
13 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/InvertedIndex.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.strucmotif.domain.bucket.ArrayBucket;
4 |
5 | import java.util.Collection;
6 | import java.util.Set;
7 | import java.util.stream.Stream;
8 |
9 | /**
10 | * The specification on how to insert and select residue pair occurrences. Update operate is not directly supported
11 | * (rather invalid/obsolete identifiers have to be removed manually and subsequently the new data can be inserted).
12 | * Insert operations are implemented by the update routine. It will place temporary files next to the index files and by
13 | * calling {@link #commit()}, these can be added to the index.
14 | */
15 | public interface InvertedIndex extends Committable {
16 | /**
17 | * Perform lookup for a particular bin.
18 | * @param residuePairDescriptor the bin for which occurrences should the lookup be performed
19 | * @return a {@link Stream} of all occurrences, grouped by their structure identifier
20 | */
21 | ArrayBucket select(int residuePairDescriptor);
22 |
23 | /**
24 | * Removes all information on a set of structures from the index.
25 | * @param structureIdentifiers what to remove
26 | */
27 | void delete(Collection structureIdentifiers);
28 |
29 | /**
30 | * Scans the entire index and returns all referenced descriptors.
31 | * @return a collection of all descriptors
32 | */
33 | Set reportKnownDescriptors();
34 |
35 | /**
36 | * Scans the entire index and returns all referenced structure indices.
37 | * @return a collection of all structure indices
38 | */
39 | Set reportKnownKeys();
40 | }
41 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/ResidueTypeResolver.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.strucmotif.domain.structure.ResidueType;
4 |
5 | /**
6 | * Maps from generic three-letter-codes to the {@link ResidueType} enum. Depending on the selected strategy, this will
7 | * completely ignore non-canonical components or map them to something known via their parent.
8 | */
9 | public interface ResidueTypeResolver {
10 | /**
11 | * Map a three-letter-code to a ResidueType.
12 | * @param threeLetterCode the input
13 | * @return a ResidueType, might be the unknown component
14 | */
15 | ResidueType selectResidueType(String threeLetterCode);
16 | }
17 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/SingleStructureDataProvider.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.cif.schema.mm.MmCifFile;
4 | import org.rcsb.strucmotif.domain.structure.Structure;
5 |
6 | import java.io.InputStream;
7 | import java.util.Collection;
8 | import java.util.Set;
9 |
10 | /**
11 | * An implementation of a {@link StructureDataProvider} that only deals with a single structure. Used in the
12 | * 'detect-motif' mode (see {@link org.rcsb.strucmotif.domain.query.MotifContextBuilder}).
13 | */
14 | public class SingleStructureDataProvider implements StructureDataProvider {
15 | private final Structure structure;
16 |
17 | /**
18 | * Create a data provider for this structure.
19 | * @param structure the content
20 | */
21 | public SingleStructureDataProvider(Structure structure) {
22 | this.structure = structure;
23 | }
24 |
25 | @Override
26 | public void initializeRenumberedStructureCache() {
27 | // no need to do anything
28 | }
29 |
30 | @Override
31 | public Structure readFromInputStream(InputStream inputStream) {
32 | return structure;
33 | }
34 |
35 | @Override
36 | public Structure readRenumbered(String structureIdentifier) {
37 | return structure;
38 | }
39 |
40 | @Override
41 | public Structure readOriginal(String structureIdentifier) {
42 | return structure;
43 | }
44 |
45 | @Override
46 | public Structure readSome(String structureIdentifier) {
47 | return structure;
48 | }
49 |
50 | @Override
51 | public void enterWriteMode() {
52 | immutable();
53 | }
54 |
55 | @Override
56 | public void writeRenumbered(String structureIdentifier, MmCifFile mmCifFile, int modelIdentifier) {
57 | immutable();
58 | }
59 |
60 | @Override
61 | public void deleteRenumbered(Collection structureIdentifiers) {
62 | immutable();
63 | }
64 |
65 | @Override
66 | public InputStream getOriginalInputStream(String structureIdentifier) {
67 | return null;
68 | }
69 |
70 | @Override
71 | public void commit() {
72 | immutable();
73 | }
74 |
75 | private void immutable() {
76 | throw new UnsupportedOperationException("This data provider is read-only");
77 | }
78 |
79 | @Override
80 | public Set reportKnownFiles() {
81 | throw new UnsupportedOperationException("This data provider contains a single not registered structure");
82 | }
83 | }
84 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/SingleStructureIndexProvider.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.strucmotif.domain.query.ResultsContentType;
4 | import org.rcsb.strucmotif.domain.structure.Structure;
5 |
6 | import java.util.Collection;
7 | import java.util.Set;
8 |
9 | /**
10 | * An implementation of a {@link StructureIndexProvider} that only deals with a single structure. Used in the
11 | * 'detect-motif' mode (see {@link org.rcsb.strucmotif.domain.query.MotifContextBuilder}).
12 | */
13 | public class SingleStructureIndexProvider implements StructureIndexProvider {
14 | private final int structureIndex;
15 | private final String structureIdentifier;
16 |
17 | /**
18 | * Create an index provider for this structure.
19 | * @param structure the content
20 | */
21 | public SingleStructureIndexProvider(Structure structure) {
22 | this.structureIndex = -1;
23 | this.structureIdentifier = structure.getStructureIdentifier();
24 | }
25 |
26 | @Override
27 | public String selectStructureIdentifier(int structureIndex) {
28 | return structureIdentifier;
29 | }
30 |
31 | @Override
32 | public int selectStructureIndex(String structureIdentifier) {
33 | return structureIndex;
34 | }
35 |
36 | @Override
37 | public int selectOrMintStructureIndex(String structureIdentifier) {
38 | throw new UnsupportedOperationException("This index provider is read-only");
39 | }
40 |
41 | @Override
42 | public int nextStructureIndex() {
43 | throw new UnsupportedOperationException("This index provider is read-only");
44 | }
45 |
46 | @Override
47 | public boolean containsKey(String structureIdentifier) {
48 | return this.structureIdentifier.equals(structureIdentifier);
49 | }
50 |
51 | @Override
52 | public boolean containsKey(int structureIndex) {
53 | return this.structureIndex == structureIndex;
54 | }
55 |
56 | @Override
57 | public Set selectByResultsContentType(Collection resultsContentType) {
58 | return Set.of(structureIndex);
59 | }
60 | }
61 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/SingleStructureInvertedIndex.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.strucmotif.domain.bucket.ArrayBucket;
4 | import org.rcsb.strucmotif.domain.motif.ResiduePairOccurrence;
5 | import org.rcsb.strucmotif.domain.structure.ResidueGraph;
6 |
7 | import java.util.Collection;
8 | import java.util.List;
9 | import java.util.Map;
10 | import java.util.Set;
11 | import java.util.stream.Collectors;
12 |
13 | /**
14 | * An implementation of a {@link InvertedIndex} that only deals with a single structure. Used in the
15 | * 'detect-motif' mode (see {@link org.rcsb.strucmotif.domain.query.MotifContextBuilder}).
16 | */
17 | public class SingleStructureInvertedIndex implements InvertedIndex {
18 | private final Map index;
19 |
20 | /**
21 | * Create an inverted index based on this graph.
22 | * @param residueGraph the content
23 | */
24 | public SingleStructureInvertedIndex(ResidueGraph residueGraph) {
25 | index = residueGraph.residuePairOccurrencesParallel()
26 | .collect(Collectors.groupingBy(ResiduePairOccurrence::getResiduePairDescriptor, Collectors.collectingAndThen(Collectors.toList(), this::toInvertedIndexBucket)));
27 | }
28 |
29 | private ArrayBucket toInvertedIndexBucket(List residuePairOccurrences) {
30 | int[] structureIndices = new int[] { 0 };
31 | int[] positionOffsets = new int[] { 0 };
32 | int[] positionData = new int[residuePairOccurrences.size() * 2];
33 |
34 | for (int i = 0; i < residuePairOccurrences.size(); i++) {
35 | ResiduePairOccurrence occurrence = residuePairOccurrences.get(i);
36 | positionData[2 * i] = occurrence.getResidueIndex1();
37 | positionData[2 * i + 1] = occurrence.getResidueIndex2();
38 | }
39 |
40 | return new ArrayBucket(structureIndices, positionOffsets, positionData);
41 | }
42 |
43 | @Override
44 | public void commit() {
45 | immutable();
46 | }
47 |
48 | @Override
49 | public ArrayBucket select(int residuePairDescriptor) {
50 | return index.getOrDefault(residuePairDescriptor, ArrayBucket.EMPTY_BUCKET);
51 | }
52 |
53 | @Override
54 | public void delete(Collection structureIdentifiers) {
55 | immutable();
56 | }
57 |
58 | @Override
59 | public Set reportKnownDescriptors() {
60 | return index.keySet();
61 | }
62 |
63 | @Override
64 | public Set reportKnownKeys() {
65 | throw new UnsupportedOperationException("This bin contains a single not registered structure");
66 | }
67 |
68 | private void immutable() {
69 | throw new UnsupportedOperationException("This index is read-only");
70 | }
71 | }
72 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/StateRepository.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.strucmotif.domain.structure.StructureInformation;
4 |
5 | import java.util.Set;
6 | import java.util.stream.Collectors;
7 |
8 | /**
9 | * The state of the application consists of two lists of structure identifiers:
10 | *
11 | * - known: entries that have been processed (might become invalid if e.g. alpha carbon trace)
12 | * - dirty: all identifiers that could cause a corrupted state (if update fails during inverted index writing) - useful to recover
13 | *
14 | */
15 | public interface StateRepository {
16 | /**
17 | * Returns all registered revisions.
18 | * @return a collection of ids and their corresponding revision
19 | */
20 | Set selectKnown();
21 |
22 | /**
23 | * Returns all referenced structure indices.
24 | * @return a collection of all structure indices
25 | */
26 | default Set reportKnownKeys() {
27 | return selectKnown()
28 | .stream()
29 | .map(StructureInformation::structureIndex)
30 | .collect(Collectors.toSet());
31 | }
32 |
33 | /**
34 | * The set of currently 'dirty' ids. Will be populated when update starts and emptied upon successful completion.
35 | * Problematic if not the empty set after an update.
36 | * @return a collection of ids
37 | */
38 | Set selectDirty();
39 |
40 | /**
41 | * Insert into 'known' collection.
42 | * @param additions a collection of ids
43 | */
44 | void insertKnown(Set additions);
45 |
46 | /**
47 | * Insert into 'dirty' collection.
48 | * @param additions a collection of ids
49 | */
50 | void insertDirty(Set additions);
51 |
52 | /**
53 | * Remove from 'known' collection.
54 | * @param removals a collection of ids
55 | */
56 | void deleteKnown(Set removals);
57 |
58 | /**
59 | * Remove from 'dirty' collection.
60 | * @param removals a collection of ids
61 | */
62 | void deleteDirty(Set removals);
63 | }
64 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/StructureDataProvider.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.cif.schema.mm.MmCifFile;
4 | import org.rcsb.strucmotif.domain.structure.Structure;
5 |
6 | import java.io.IOException;
7 | import java.io.InputStream;
8 | import java.util.Collection;
9 | import java.util.Set;
10 |
11 | /**
12 | * Access structure data.
13 | */
14 | public interface StructureDataProvider extends Committable {
15 | int DEFAULT_MODEL_IDENTIFIER = 1;
16 |
17 | /**
18 | * If `strucmotif.in-memory-strategy` is active: Initialize caching by reading all structures and keeping them in
19 | * memory for fast access.
20 | */
21 | void initializeRenumberedStructureCache();
22 |
23 | /**
24 | * Read everything from an input stream.
25 | * @param inputStream the source of data, assumed to be following the mmCIF schema
26 | * @return the corresponding {@link Structure}
27 | */
28 | Structure readFromInputStream(InputStream inputStream);
29 |
30 | /**
31 | * Read a renumbered structure entirely.
32 | * @param structureIdentifier the structure to read
33 | * @return the corresponding {@link Structure}
34 | */
35 | Structure readRenumbered(String structureIdentifier);
36 |
37 | /**
38 | * Read a selected range from an original structure.
39 | * @param structureIdentifier the structure to read
40 | * @return the corresponding {@link Structure}
41 | */
42 | Structure readOriginal(String structureIdentifier);
43 |
44 | /**
45 | * Read some structure entirely.
46 | * @param structureIdentifier the structure to read
47 | * @return the corresponding {@link Structure}
48 | */
49 | Structure readSome(String structureIdentifier);
50 |
51 | /**
52 | * Must be called before invoking {@link #writeRenumbered(String, MmCifFile, int)}.
53 | * @throws IOException if files can't be created
54 | */
55 | void enterWriteMode() throws IOException;
56 |
57 | /**
58 | * Write a renumbered structure. Make sure to call {@link #enterWriteMode()} if you need to write structure data.
59 | * @param structureIdentifier the structure identifier to write
60 | * @param mmCifFile the data source
61 | */
62 | default void writeRenumbered(String structureIdentifier, MmCifFile mmCifFile) {
63 | writeRenumbered(structureIdentifier, mmCifFile, DEFAULT_MODEL_IDENTIFIER);
64 | }
65 |
66 | /**
67 | * Write a renumbered structure. Make sure to call {@link #enterWriteMode()} if you need to write structure data.
68 | * @param structureIdentifier the structure identifier to write
69 | * @param mmCifFile the data source
70 | * @param modelIdentifier specific model to extract
71 | */
72 | void writeRenumbered(String structureIdentifier, MmCifFile mmCifFile, int modelIdentifier);
73 |
74 | /**
75 | * Drop information on a renumbered structure.
76 | * @param structureIdentifiers the collection of structure identifier to remove
77 | */
78 | void deleteRenumbered(Collection structureIdentifiers);
79 |
80 | /**
81 | * Acquire the input stream of an original structure.
82 | * @param structureIdentifier the structure identifier to read
83 | * @return the corresponding input stream
84 | */
85 | InputStream getOriginalInputStream(String structureIdentifier);
86 |
87 | /**
88 | * Report all known structure files.
89 | * @return a collection of filenames
90 | */
91 | Set reportKnownFiles();
92 | }
93 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/StructureIndexProvider.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.strucmotif.domain.query.ResultsContentType;
4 |
5 | import java.util.Collection;
6 | import java.util.Set;
7 |
8 | /**
9 | * Maps between structure indices (a compact int representation that is e.g. stored in the inverted index) and readable
10 | * Strings (that can be PDB-IDs or longer, namespaced identifiers used by computed structure models).
11 | */
12 | public interface StructureIndexProvider {
13 | /**
14 | * Maps between structure index and identifier.
15 | * @param structureIndex the int
16 | * @return the String
17 | */
18 | String selectStructureIdentifier(int structureIndex);
19 |
20 | /**
21 | * Maps between structure identifier and index.
22 | * @param structureIdentifier the String
23 | * @return the int
24 | */
25 | int selectStructureIndex(String structureIdentifier);
26 |
27 | /**
28 | * Get the structure index associated to this identifier. If none exists a new one will be created.
29 | * @param structureIdentifier the structure identifier
30 | * @return a unique int that maps to this identifier
31 | */
32 | int selectOrMintStructureIndex(String structureIdentifier);
33 |
34 | /**
35 | * Get the next available structureIndex. This may reuse a previously assigned index that is no longer referenced.
36 | * @return an int that is guaranteed to uniquely identify a structure in the inverted index
37 | */
38 | int nextStructureIndex();
39 |
40 | /**
41 | * Check if this structure identifier is known.
42 | * @param structureIdentifier the String
43 | * @return true if this key has a mapping
44 | */
45 | boolean containsKey(String structureIdentifier);
46 |
47 | /**
48 | * Check if this structure index is known.
49 | * @param structureIndex the int
50 | * @return true if this key has a mapping
51 | */
52 | boolean containsKey(int structureIndex);
53 |
54 | /**
55 | * Get all registered indices of a particular type.
56 | * @param resultsContentType search space identifier (PDB entries, computed structure models, everything)
57 | * @return a collection of all relevant structure indices
58 | */
59 | Set selectByResultsContentType(Collection resultsContentType);
60 | }
61 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/StructureReader.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.strucmotif.domain.structure.Structure;
4 |
5 | import java.io.InputStream;
6 |
7 | /**
8 | * Read structures from CIF files.
9 | */
10 | public interface StructureReader {
11 | /**
12 | * Neutral transform.
13 | */
14 | float[] IDENTITY_TRANSFORM = new float[] { 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1 };
15 |
16 | /**
17 | * Read from a InputStream and parse the corresponding Structure.
18 | * @param inputStream the source
19 | * @return the parsed Structure instance
20 | */
21 | Structure readFromInputStream(InputStream inputStream);
22 | }
23 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/StructureWriter.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.rcsb.cif.schema.mm.MmCifFile;
4 |
5 | /**
6 | * The contract to write optimized structure data that don't contain non-polymers, hydrogen, non-selected models etc.
7 | */
8 | public interface StructureWriter {
9 | /**
10 | * Converts a structure data to its binary representation.
11 | * @param source a MmCifFile to process
12 | * @return a byte[] with the file content or null if the structure would be empty
13 | */
14 | default byte[] write(MmCifFile source) {
15 | return write(source, StructureDataProvider.DEFAULT_MODEL_IDENTIFIER);
16 | }
17 |
18 | /**
19 | * Converts a structure data to its binary representation.
20 | * @param source a MmCifFile to process
21 | * @param modelIdentifier identifier of the model to extract
22 | * @return a byte[] with the file content or null if the structure would be empty
23 | */
24 | byte[] write(MmCifFile source, int modelIdentifier);
25 | }
26 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/codec/BucketCodec.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io.codec;
2 |
3 | import org.rcsb.strucmotif.domain.bucket.ArrayBucket;
4 |
5 | import java.io.IOException;
6 | import java.nio.ByteBuffer;
7 |
8 | /**
9 | * Persistence of inverted index buckets.
10 | */
11 | public interface BucketCodec {
12 | /**
13 | * Deserialize a bucket from an InputStream.
14 | * @param byteBuffer data source
15 | * @return the decoded bucket
16 | */
17 | ArrayBucket decode(ByteBuffer byteBuffer);
18 |
19 | /**
20 | * Serialize a bucket as binary stream.
21 | * @param bucket data source
22 | * @return the encoded data
23 | * @throws IOException writing failed
24 | */
25 | ByteBuffer encode(ArrayBucket bucket) throws IOException;
26 | }
27 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/io/codec/JsonCodec.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io.codec;
2 |
3 | import com.google.gson.Gson;
4 | import com.google.gson.GsonBuilder;
5 | import com.google.gson.reflect.TypeToken;
6 | import org.rcsb.strucmotif.domain.bucket.ArrayBucket;
7 |
8 | import java.io.ByteArrayInputStream;
9 | import java.io.InputStreamReader;
10 | import java.lang.reflect.Type;
11 | import java.nio.ByteBuffer;
12 | import java.nio.charset.StandardCharsets;
13 | import java.util.Map;
14 |
15 | /**
16 | * Text-based implementation of a codec serializer. Useful for debugging.
17 | */
18 | public class JsonCodec implements BucketCodec {
19 | /**
20 | * Tag of the structure index array.
21 | */
22 | public static final String STRUCTURE_INDICES = "structure_indices";
23 | /**
24 | * Tag of the position offset array.
25 | */
26 | public static final String POSITION_OFFSETS = "position_offsets";
27 | /**
28 | * Tag of the identifier data array.
29 | */
30 | public static final String IDENTIFIER_DATA = "identifier_data";
31 | private final Type mapType;
32 | private final Gson gson;
33 |
34 | /**
35 | * Default constructor.
36 | */
37 | public JsonCodec() {
38 | this.gson = new GsonBuilder().setPrettyPrinting().create();
39 | this.mapType = new TypeToken>() {}.getType();
40 | }
41 |
42 | @Override
43 | public ArrayBucket decode(ByteBuffer byteBuffer) {
44 | Map map = gson.fromJson(new InputStreamReader(new ByteArrayInputStream(toByteArray(byteBuffer))), mapType);
45 | return new ArrayBucket(map.get(STRUCTURE_INDICES), map.get(POSITION_OFFSETS), map.get(IDENTIFIER_DATA));
46 | }
47 |
48 | private byte[] toByteArray(ByteBuffer byteBuffer) {
49 | byteBuffer.rewind();
50 | byte[] out = new byte[byteBuffer.remaining()];
51 | byteBuffer.get(out);
52 | return out;
53 | }
54 |
55 | @Override
56 | public ByteBuffer encode(ArrayBucket arrayBucket) {
57 | Map map = Map.of(STRUCTURE_INDICES, arrayBucket.getStructureIndexArray(), POSITION_OFFSETS, arrayBucket.getPositionOffsetArray(), IDENTIFIER_DATA, arrayBucket.getIdentifierDataArray());
58 | byte[] bytes = gson.toJson(map).getBytes(StandardCharsets.UTF_8);
59 | return ByteBuffer.wrap(bytes);
60 | }
61 | }
62 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/java/org/rcsb/strucmotif/math/Partition.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.math;
2 |
3 | import java.util.AbstractList;
4 | import java.util.ArrayList;
5 | import java.util.Collection;
6 | import java.util.Collections;
7 | import java.util.List;
8 | import java.util.Objects;
9 |
10 | /**
11 | * Partitions a collection into (roughly) equal-sized chunks. Will shuffle the original collection.
12 | *
13 | * code from: https://e.printstacktrace.blog/divide-a-list-to-lists-of-n-size-in-Java-8/
14 | * @param type of the original collection
15 | */
16 | public class Partition extends AbstractList> {
17 | private final List list;
18 | private final int chunkSize;
19 |
20 | /**
21 | * Split a collection into partitions up to a defined size.
22 | * @param list collection to partition
23 | * @param chunkSize how many elements in one batch
24 | */
25 | public Partition(Collection list, int chunkSize) {
26 | this.list = new ArrayList<>(list);
27 | // shuffle to prevent troublemakers such as ribosome and virus capsids occurring in the same chunk
28 | Collections.shuffle(this.list);
29 | this.chunkSize = chunkSize;
30 | }
31 |
32 | @Override
33 | public List get(int index) {
34 | int start = index * chunkSize;
35 | int end = Math.min(start + chunkSize, list.size());
36 |
37 | if (start > end) {
38 | throw new IndexOutOfBoundsException("Index " + index + " is out of the list range <0," + (size() - 1) + ">");
39 | }
40 |
41 | return new ArrayList<>(list.subList(start, end));
42 | }
43 |
44 | @Override
45 | public int size() {
46 | return (int) Math.ceil((double) list.size() / (double) chunkSize);
47 | }
48 |
49 | @Override
50 | public boolean equals(Object o) {
51 | if (this == o) return true;
52 | if (o == null || getClass() != o.getClass()) return false;
53 | if (!super.equals(o)) return false;
54 | Partition partition = (Partition) o;
55 | return chunkSize == partition.chunkSize && Objects.equals(list, partition.list);
56 | }
57 |
58 | @Override
59 | public int hashCode() {
60 | return Objects.hash(super.hashCode(), list, chunkSize);
61 | }
62 | }
63 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/resources/META-INF/spring.factories:
--------------------------------------------------------------------------------
1 | org.springframework.boot.diagnostics.FailureAnalyzer=\
2 | org.rcsb.strucmotif.NoSuchFileFailureAnalyzer
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/resources/application.properties:
--------------------------------------------------------------------------------
1 | spring.main.banner-mode=off
2 | spring.autoconfigure.exclude=org.springframework.boot.autoconfigure.mongo.MongoAutoConfiguration,org.springframework.boot.autoconfigure.data.mongo.MongoDataAutoConfiguration
--------------------------------------------------------------------------------
/strucmotif-search-core/src/main/resources/motifs.json:
--------------------------------------------------------------------------------
1 | [
2 | {
3 | "motifIdentifier": "CK",
4 | "structureIdentifier": "6zwf",
5 | "title": "NOS bridge",
6 | "description": "A covalent crosslink between a cysteine and a lysine residue with a NOS bridge that serves as an allosteric redox switch in the transaldolase enzyme of Neisseria gonorrhoeae, the pathogen that causes gonorrhoea.",
7 | "labelSelections": [{
8 | "labelAsymId": "A",
9 | "structOperId": "1",
10 | "labelSeqId": 9
11 | }, {
12 | "labelAsymId": "A",
13 | "structOperId": "1",
14 | "labelSeqId": 39
15 | }],
16 | "positionSpecificExchanges": []
17 | }
18 | ]
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/java/org/rcsb/strucmotif/Demo.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif;
2 |
3 | import org.rcsb.strucmotif.domain.motif.EnrichedMotifDefinition;
4 | import org.rcsb.strucmotif.domain.structure.LabelSelection;
5 |
6 | import java.util.List;
7 | import java.util.Set;
8 |
9 | public class Demo {
10 | public static void main(String[] args) {
11 | // use a single motif definition to search for all structure that contain this motif
12 | Strucmotif.searchForStructures()
13 | // several ways can be used to define the query motif - e.g., specify a PDB entry id
14 | .defineByPdbIdAndSelection("4cha",
15 | // and a collection of sequence positions to extract residues to use as motif
16 | List.of(new LabelSelection("B", "1", 42), // HIS
17 | new LabelSelection("B", "1", 87), // ASP
18 | new LabelSelection("C", "1", 47))) // SER
19 | .rmsdCutoff(1.0)
20 | .buildParameters()
21 | .buildContext()
22 | .run()
23 | .getHits()
24 | .stream()
25 | .map(hit -> hit.structureIdentifier() + "_" +
26 | hit.assemblyIdentifier() + " @ " +
27 | hit.labelSelections() + " - RMSD: " +
28 | hit.rmsd())
29 | .forEach(System.out::println);
30 |
31 | // use a single structure to detect all motifs that occur therein
32 | Set motifs = Strucmotif.getMotifDefinitionRegistry().getEnrichedMotifDefinitions();
33 | Strucmotif.detectMotifs()
34 | .defineByPdbIdAndAssemblyId("2mnr", "1")
35 | .withMotifs(motifs)
36 | .rmsdCutoff(1.0)
37 | .buildParameters()
38 | .buildContext()
39 | .run()
40 | .getHits()
41 | .stream()
42 | .map(hit -> hit.motifIdentifier() + " @ " +
43 | hit.labelSelections() + " - RMSD: " +
44 | hit.rmsd())
45 | .forEach(System.out::println);
46 | }
47 | }
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/java/org/rcsb/strucmotif/Helpers.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif;
2 |
3 | import java.io.File;
4 | import java.io.InputStream;
5 | import java.nio.file.Path;
6 | import java.nio.file.Paths;
7 | import java.util.Objects;
8 |
9 | public class Helpers {
10 | public static final float DELTA = 0.001f;
11 | public static final float RELAXED_DELTA = 0.1f;
12 |
13 | public static short[] convertCoordsToShort(double[] array) {
14 | short[] out = new short[array.length];
15 | for (int i = 0; i < out.length; i++) {
16 | out[i] = (short) Math.round(array[i] * 10);
17 | }
18 | return out;
19 | }
20 |
21 | public static InputStream getOriginalBcif(String pdbId) {
22 | return getResource("orig/" + pdbId.toLowerCase() + ".bcif");
23 | }
24 |
25 | public static InputStream getRenumberedBcif(String pdbId) {
26 | return getResource("renum/" + pdbId + ".bcif");
27 | }
28 |
29 | public static InputStream getResource(String location) {
30 | InputStream resourceAsStream = Thread.currentThread().getContextClassLoader().getResourceAsStream(location);
31 | return Objects.requireNonNull(resourceAsStream, "failed to locate test resource: " + location);
32 | }
33 |
34 | public static byte[] convertEnumToByte(Enum... array) {
35 | byte[] out = new byte[array.length];
36 | for (int i = 0; i < out.length; i++) {
37 | out[i] = (byte) array[i].ordinal();
38 | }
39 | return out;
40 | }
41 |
42 | public static Path getResourceAsPath(String path) {
43 | return Paths.get(new File("src/test/resources/").getAbsolutePath()).resolve(path);
44 | }
45 | }
46 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/java/org/rcsb/strucmotif/UpdateTestData.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif;
2 |
3 | import org.rcsb.cif.CifIO;
4 | import org.rcsb.cif.schema.StandardSchemata;
5 | import org.rcsb.cif.schema.mm.MmCifFile;
6 | import org.rcsb.strucmotif.config.StrucmotifConfig;
7 | import org.rcsb.strucmotif.io.DefaultResidueTypeResolver;
8 | import org.rcsb.strucmotif.io.DefaultStructureWriter;
9 | import org.rcsb.strucmotif.io.StructureWriter;
10 |
11 | import java.io.FileOutputStream;
12 | import java.io.IOException;
13 | import java.io.UncheckedIOException;
14 | import java.net.URL;
15 | import java.nio.channels.Channels;
16 | import java.nio.channels.FileChannel;
17 | import java.nio.channels.ReadableByteChannel;
18 | import java.nio.file.Files;
19 | import java.nio.file.Path;
20 | import java.nio.file.Paths;
21 | import java.util.stream.Stream;
22 |
23 | public class UpdateTestData {
24 | private static final Path updateRoot;
25 | private static final StrucmotifConfig strucmotifConfig;
26 | private static final StructureWriter structureWriter;
27 |
28 | static {
29 | Path root = Paths.get(".").toAbsolutePath();
30 | System.out.println("Project path: " + root);
31 | updateRoot = root.resolve("strucmotif-search-core/src/test/resources/");
32 | System.out.println("Update root: " + updateRoot);
33 | strucmotifConfig = new StrucmotifConfig();
34 | strucmotifConfig.setRootPath(updateRoot.toString());
35 | structureWriter = new DefaultStructureWriter(new DefaultResidueTypeResolver(strucmotifConfig), strucmotifConfig);
36 | }
37 |
38 | public static void main(String[] args) throws IOException {
39 | updateOriginalBcif(updateRoot.resolve("orig"));
40 | updateRenumberedBcif(updateRoot.resolve("renum"));
41 | }
42 |
43 | private static void updateOriginalBcif(Path path) throws IOException {
44 | try (Stream paths = Files.list(path)) {
45 | paths.forEach(p -> {
46 | String fileName = p.getFileName().toString();
47 | System.out.println("Updating original: " + fileName);
48 | download("https://models.rcsb.org/" + fileName, p);
49 | });
50 | }
51 | }
52 |
53 | private static void updateRenumberedBcif(Path path) throws IOException {
54 | try (Stream paths = Files.list(path)) {
55 | paths.forEach(p -> {
56 | String fileName = p.getFileName().toString();
57 | System.out.println("Updating renumbered: " + fileName);
58 |
59 | try {
60 | MmCifFile cif = CifIO.readFromURL(new URL("https://models.rcsb.org/" + fileName)).as(StandardSchemata.MMCIF);
61 | byte[] bytes = structureWriter.write(cif, 1);
62 | Files.write(p, bytes);
63 | } catch (IOException e) {
64 | throw new UncheckedIOException(e);
65 | }
66 | });
67 | }
68 | }
69 |
70 | private static void download(String sourceUrl, Path dest) {
71 | try (ReadableByteChannel readableByteChannel = Channels.newChannel(new URL(sourceUrl).openStream());
72 | FileOutputStream outputStream = new FileOutputStream(dest.toFile());
73 | FileChannel outputChannel = outputStream.getChannel()) {
74 | outputChannel.transferFrom(readableByteChannel, 0, Long.MAX_VALUE);
75 | } catch (IOException e) {
76 | throw new UncheckedIOException(e);
77 | }
78 | }
79 | }
80 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/java/org/rcsb/strucmotif/core/MotifDefinitionRegistryTest.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.core;
2 |
3 | import org.junit.jupiter.api.BeforeEach;
4 | import org.junit.jupiter.api.Test;
5 | import org.rcsb.strucmotif.domain.motif.MotifDefinition;
6 |
7 | import java.util.Collection;
8 | import java.util.Set;
9 |
10 | import static org.junit.jupiter.api.Assertions.*;
11 |
12 | class MotifDefinitionRegistryTest {
13 | private DefaultMotifDefinitionRegistry registry;
14 |
15 | @BeforeEach
16 | public void init() {
17 | this.registry = new DefaultMotifDefinitionRegistry(null);
18 | }
19 |
20 | @Test
21 | void afterRegistryInitialized_thenHardCodedAndDynamicMotifsAvailable() {
22 | Set motifDefinitions = registry.getMotifDefinitions();
23 | assertTrue(motifDefinitions.contains(MotifDefinition.CHCH));
24 | assertTrue(motifDefinitions.contains(MotifDefinition.CHH));
25 | assertTrue(motifDefinitions.contains(MotifDefinition.GGGG));
26 | assertTrue(motifDefinitions.contains(MotifDefinition.HDS));
27 | assertTrue(motifDefinitions.contains(MotifDefinition.KDDDE));
28 | assertTrue(motifDefinitions.contains(MotifDefinition.KDEEH));
29 | assertTrue(motifDefinitions.contains(MotifDefinition.KDEEH_EXCHANGES));
30 | assertTrue(motifDefinitions.stream().anyMatch(m -> m.getTitle().startsWith("NOS")), "NOS parsed from JSON missing");
31 | assertTrue(motifDefinitions.size() > 7);
32 |
33 | assertTrue(motifDefinitions.stream()
34 | .map(MotifDefinition::getLabelSelections)
35 | .flatMap(Collection::stream)
36 | .allMatch(l -> l.labelAsymId() != null && l.structOperId() != null && l.labelSeqId() != 0), "Not all label-selections were parsed properly");
37 | }
38 |
39 | @Test
40 | void whenRegistryCleared_thenIsEmpty() {
41 | registry.getMotifDefinitions().clear();
42 | assertTrue(registry.getMotifDefinitions().isEmpty());
43 | }
44 | }
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/java/org/rcsb/strucmotif/domain/motif/ResiduePairOccurrenceTest.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.motif;
2 |
3 | import org.junit.jupiter.api.Test;
4 | import org.rcsb.strucmotif.domain.structure.ResidueType;
5 |
6 | import java.util.List;
7 | import java.util.Map;
8 | import java.util.Set;
9 |
10 | import static org.junit.jupiter.api.Assertions.*;
11 |
12 | class ResiduePairOccurrenceTest {
13 | @Test
14 | void whenStreamingDescriptorsWithExchanges_thenAllPresent() {
15 | // DD-5-4-4 -> 10-55
16 | ResiduePairOccurrence occurrence = new ResiduePairOccurrence(42949673015L, 8522308);
17 | Map> exchanges = Map.of(10, Set.of(ResidueType.GLUTAMIC_ACID, ResidueType.ASPARTIC_ACID));
18 |
19 | List out = occurrence.residuePairDescriptorsByTolerance(1, 1, 1, exchanges)
20 | .boxed()
21 | .toList();
22 |
23 | assertEquals(out.stream().distinct().count(), out.size(), "There are duplicates");
24 | assertEquals(2, out.stream().map(ResiduePairDescriptor::getResidueType2).distinct().count(), "Didn't observe exchange");
25 | }
26 | }
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/java/org/rcsb/strucmotif/domain/query/ResultsContentTypeTest.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.query;
2 |
3 | import org.junit.jupiter.api.Test;
4 |
5 | import java.util.Set;
6 |
7 | import static org.junit.jupiter.api.Assertions.*;
8 |
9 | class ResultsContentTypeTest {
10 | private static final Set TEST_CASES = Set.of("1acj", "1MUW", "1eXr", "AF-Q8W3K0-F1", "ma-bak-cepc-0001");
11 |
12 | @Test
13 | void whenHandlingPdbIds_thenArchiveEntriesRetained() {
14 | assertEquals(3, TEST_CASES.stream()
15 | .filter(ResultsContentType.EXPERIMENTAL)
16 | .count());
17 | }
18 |
19 | @Test
20 | void whenHandlingModelIds_thenArchiveEntriesIgnored() {
21 | assertEquals(2, TEST_CASES.stream()
22 | .filter(ResultsContentType.COMPUTATIONAL)
23 | .count());
24 | }
25 |
26 | @Test
27 | void whenAllSearchSpace_thenNoOperation() {
28 | assertEquals(TEST_CASES.size(), TEST_CASES.stream()
29 | .filter(ResultsContentType.EXPERIMENTAL.or(ResultsContentType.COMPUTATIONAL))
30 | .count());
31 | }
32 | }
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/java/org/rcsb/strucmotif/domain/structure/OffsetArrayIndexOfTest.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.domain.structure;
2 |
3 | import org.junit.jupiter.api.Test;
4 |
5 | import static org.junit.jupiter.api.Assertions.*;
6 |
7 | class OffsetArrayIndexOfTest {
8 | private static final int[] TEST_DATA = new int[] { 0, 25, 50, 60, 70, 80, 90, 100, 200, 250, 400 };
9 |
10 | @Test
11 | void whenElementAtStart_thenFirstIndexReturned() {
12 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, 0);
13 | assertEquals(0, i);
14 | }
15 |
16 | @Test
17 | void whenElementPastStart_thenFirstIndexReturned() {
18 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, 1);
19 | assertEquals(0, i);
20 | }
21 |
22 | @Test
23 | void whenElementBeforeOffset_thenFirstIndexReturned() {
24 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, 24);
25 | assertEquals(0, i);
26 | }
27 |
28 | @Test
29 | void whenElementAtOffset_thenSecondIndexReturned() {
30 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, 25);
31 | assertEquals(1, i);
32 | }
33 |
34 | @Test
35 | void whenElementBeforePenultimateOffset_thenAntepenultimateIndexReturned() {
36 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, 249);
37 | assertEquals(8, i);
38 | }
39 |
40 | @Test
41 | void whenElementAtPenultimateOffset_thenPenultimateIndexReturned() {
42 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, 250);
43 | assertEquals(9, i);
44 | }
45 |
46 | @Test
47 | void whenElementBeforeLastOffset_thenPenultimateIndexReturned() {
48 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, 399);
49 | assertEquals(9, i);
50 | }
51 |
52 | @Test
53 | void whenElementAtLastOffset_thenLastIndexReturned() {
54 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, 400);
55 | assertEquals(10, i);
56 | }
57 |
58 | @Test
59 | void whenElementAfterLastOffset_thenLastIndexReturned() {
60 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, 401);
61 | assertEquals(10, i);
62 | }
63 |
64 | @Test
65 | void whenNegativeInput_thenMinus1Returned() {
66 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, -1);
67 | assertEquals(-1, i);
68 | }
69 |
70 | @Test
71 | void whenAboveHighestValue_thenLastIndexReturned() {
72 | int i = DefaultStructure.offsetArrayIndexOf(TEST_DATA, Integer.MAX_VALUE);
73 | assertEquals(TEST_DATA.length - 1, i);
74 | }
75 | }
76 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/java/org/rcsb/strucmotif/io/DefaultInvertedIndexTest.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.io;
2 |
3 | import org.junit.jupiter.api.BeforeEach;
4 | import org.junit.jupiter.api.Test;
5 | import org.rcsb.ffindex.FileBundleIO;
6 | import org.rcsb.ffindex.ReadableFileBundle;
7 | import org.rcsb.strucmotif.Helpers;
8 | import org.rcsb.strucmotif.config.StrucmotifConfig;
9 | import org.rcsb.strucmotif.domain.bucket.ArrayBucket;
10 | import org.rcsb.strucmotif.domain.motif.AngleType;
11 | import org.rcsb.strucmotif.domain.motif.DistanceType;
12 | import org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor;
13 | import org.rcsb.strucmotif.domain.structure.ResidueType;
14 | import org.rcsb.strucmotif.io.codec.ColferCodec;
15 |
16 | import java.io.IOException;
17 | import java.io.UncheckedIOException;
18 |
19 | import static org.junit.jupiter.api.Assertions.assertArrayEquals;
20 | import static org.junit.jupiter.api.Assertions.assertEquals;
21 |
22 | class DefaultInvertedIndexTest {
23 | private InvertedIndex invertedIndex;
24 |
25 | @BeforeEach
26 | public void init() throws IOException {
27 | StrucmotifConfig strucmotifConfig = new StrucmotifConfig();
28 | ReadableFileBundle fileBundle = FileBundleIO.openBundle(Helpers.getResourceAsPath("index.data"), Helpers.getResourceAsPath("index.ffindex")).inReadOnlyMode();
29 | ColferCodec bucketCodec = new ColferCodec();
30 | invertedIndex = new DefaultInvertedIndex(strucmotifConfig) {
31 | @Override
32 | public ArrayBucket select(int residuePairDescriptor) {
33 | String filename = residuePairDescriptor + ".colf";
34 | if (!fileBundle.containsFile(filename)) {
35 | return ArrayBucket.EMPTY_BUCKET;
36 | }
37 |
38 | try {
39 | return bucketCodec.decode(fileBundle.readFile(filename));
40 | } catch (IOException e) {
41 | throw new UncheckedIOException(e);
42 | }
43 | }
44 | };
45 | }
46 |
47 | private static final int BIN_WITH_ASSEMBLY = ResiduePairDescriptor.encodeDescriptor(ResidueType.ASPARTIC_ACID,
48 | ResidueType.LYSINE,
49 | DistanceType.D6,
50 | DistanceType.D7,
51 | AngleType.A80);
52 | @Test
53 | void whenAccessingSpecificBin_thenObserveAssemblies() {
54 | ArrayBucket bucket = invertedIndex.select(BIN_WITH_ASSEMBLY);
55 | int structures = 0;
56 | int occurrences = 0;
57 | while (bucket.hasNextStructure()) {
58 | bucket.moveStructure();
59 | structures++;
60 | while (bucket.hasNextOccurrence()) {
61 | bucket.moveOccurrence();
62 | occurrences++;
63 | }
64 | }
65 | assertEquals(13, structures);
66 | assertEquals(241, occurrences);
67 | }
68 |
69 | @Test
70 | void whenSelectingByFlippedDescriptor_thenContentMatchesOriginal() {
71 | ArrayBucket original = invertedIndex.select(BIN_WITH_ASSEMBLY);
72 | ArrayBucket flipped = invertedIndex.select(BIN_WITH_ASSEMBLY & ~(1 << 28));
73 | assertArrayEquals(original.getStructureIndexArray(), flipped.getStructureIndexArray());
74 | assertArrayEquals(original.getPositionOffsetArray(), flipped.getPositionOffsetArray());
75 | assertArrayEquals(original.getIdentifierDataArray(), flipped.getIdentifierDataArray());
76 | }
77 | }
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/index.data:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/index.data
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/known.list:
--------------------------------------------------------------------------------
1 | 3CXO,21,1,1
2 | 4X2P,53,1,4
3 | 4H19,73,1,0
4 | 3FXG,10,1,3
5 | 3EKG,70,1,3
6 | 2QGY,84,1,5
7 | 4M6U,23,1,3
8 | 4KEM,39,1,0
9 | 2PP0,19,1,1
10 | 3UXK,31,1,1
11 | 5OLC,59,1,0
12 | 2OO6,41,1,5
13 | 3SN0,54,1,3
14 | 3VCC,27,1,0
15 | 4H83,32,1,1
16 | 3CYJ,36,1,4
17 | 1ZDM,9,1,2
18 | 6VIM,72,1,2
19 | 3N4F,30,1,4
20 | 1MDR,35,1,3
21 | 4JN7,11,1,0
22 | 4FP1,1,1,4
23 | 2OG9,89,1,3
24 | 4IP5,76,1,0
25 | 2DW7,61,1,2
26 | 2PP3,22,1,2
27 | 3T8Q,58,1,1
28 | 3P3B,8,1,3
29 | 4HPN,13,1,1
30 | 2HZG,24,1,5
31 | 2P3Z,34,1,6
32 | 2NQL,15,1,4
33 | 3NO1,86,1,2
34 | 2GGE,3,1,5
35 | 4GGB,14,1,2
36 | 3CK5,56,1,2
37 | 2MNR,87,1,6
38 | 4H1Z,40,1,0
39 | 1DTN,17,1,3
40 | 2OVL,48,1,3
41 | 3TJ4,69,1,2
42 | 2HXU,92,2,1
43 | 3OZY,51,1,0
44 | 2HXT,29,1,2
45 | 4HNC,16,1,4
46 | 1MRA,65,1,3
47 | 2HNE,75,1,4
48 | 3TTE,2,1,1
49 | 2QQ6,63,1,2
50 | 3MSY,55,1,2
51 | 3V5F,68,1,0
52 | 3T9P,20,1,0
53 | 3H12,62,1,5
54 | 4IP4,88,1,0
55 | 1YEY,6,1,3
56 | 3SN4,47,1,2
57 | 2GSH,95,1,5
58 | 2P0I,64,1,5
59 | 3OP2,33,1,3
60 | 2PPG,91,1,5
61 | 2I5Q,37,1,5
62 | 6TNE,83,2,0
63 | 3TCS,77,1,0
64 | 3TOY,82,1,1
65 | 3SN1,18,1,2
66 | 3V5C,43,1,0
67 | 5XD8,52,1,0
68 | 3SJN,71,1,3
69 | 3D46,0,1,3
70 | 3CB3,94,1,2
71 | 2OZ3,25,1,5
72 | 4DN1,45,1,1
73 | 3OPS,42,1,3
74 | 5XD7,81,1,0
75 | 4A35,60,1,2
76 | 1MNS,50,1,2
77 | 4DWD,5,1,3
78 | 4JN8,80,1,0
79 | 3UGV,12,1,1
80 | 3UXL,28,1,1
81 | 3BOX,90,1,3
82 | 2PP1,93,1,1
83 | 3BJS,38,1,4
84 | 3U4F,4,1,0
85 | 3N4E,7,1,4
86 | 3RRA,79,1,1
87 | 3D47,66,1,3
88 | 2DW6,26,1,3
89 | 1MDL,74,1,4
90 | 3RR1,85,1,1
91 | 2GDQ,46,1,5
92 | 1TZZ,49,1,3
93 | 3OZM,44,1,0
94 | 3QPE,57,2,0
95 | 3GO2,67,1,4
96 | 2POZ,78,1,3
97 |
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1acj.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1acj.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1c3c.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1c3c.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1ec6.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1ec6.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1eta.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1eta.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1exr.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1exr.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1ezc.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1ezc.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1g2f.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1g2f.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1kp0.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1kp0.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1lap.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1lap.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1m4x.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1m4x.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1nmr.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1nmr.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1qd6.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1qd6.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1w27.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1w27.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/1zdm.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/1zdm.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/200l.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/200l.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/2bfu.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/2bfu.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/2bwx.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/2bwx.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/2mnr.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/2mnr.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/3djy.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/3djy.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/3ibk.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/3ibk.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/3pei.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/3pei.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/3uud.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/3uud.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/4cha.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/4cha.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/4oog.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/4oog.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/6lxk.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/6lxk.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/6tne.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/6tne.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/6zwf.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/6zwf.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/7a3x.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/7a3x.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/7els.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/7els.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/orig/AF_AFA0A0R0FWM3F1.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/orig/AF_AFA0A0R0FWM3F1.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1DTN.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1DTN.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1MDL.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1MDL.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1MDR.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1MDR.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1MNS.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1MNS.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1MRA.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1MRA.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1TZZ.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1TZZ.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1YEY.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1YEY.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1ZDM.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1ZDM.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1acj.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1acj.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1dsd.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1dsd.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1eta.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1eta.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1exr.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1exr.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/1m4x.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/1m4x.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/200l.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/200l.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2DW6.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2DW6.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2DW7.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2DW7.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2GDQ.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2GDQ.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2GGE.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2GGE.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2GSH.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2GSH.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2HNE.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2HNE.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2HXT.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2HXT.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2HXU.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2HXU.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2HZG.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2HZG.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2I5Q.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2I5Q.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2MNR.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2MNR.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2NQL.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2NQL.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2OG9.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2OG9.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2OO6.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2OO6.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2OVL.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2OVL.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2OZ3.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2OZ3.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2P0I.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2P0I.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2P3Z.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2P3Z.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2POZ.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2POZ.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2PP0.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2PP0.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2PP1.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2PP1.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2PP3.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2PP3.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2PPG.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2PPG.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2QGY.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2QGY.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2QQ6.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2QQ6.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2bfu.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2bfu.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/2bwx.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/2bwx.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3BJS.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3BJS.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3BOX.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3BOX.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3CB3.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3CB3.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3CK5.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3CK5.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3CXO.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3CXO.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3CYJ.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3CYJ.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3D46.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3D46.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3D47.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3D47.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3EKG.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3EKG.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3FXG.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3FXG.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3GO2.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3GO2.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3H12.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3H12.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3MSY.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3MSY.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3N4E.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3N4E.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3N4F.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3N4F.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3NO1.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3NO1.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3OP2.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3OP2.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3OPS.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3OPS.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3OZM.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3OZM.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3OZY.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3OZY.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3P3B.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3P3B.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3QPE.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3QPE.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3RR1.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3RR1.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3RRA.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3RRA.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3SJN.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3SJN.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3SN0.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3SN0.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3SN1.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3SN1.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3SN4.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3SN4.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3T8Q.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3T8Q.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3T9P.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3T9P.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3TCS.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3TCS.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3TJ4.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3TJ4.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3TOY.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3TOY.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3TTE.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3TTE.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3U4F.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3U4F.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3UGV.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3UGV.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3UXK.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3UXK.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3UXL.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3UXL.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3V5C.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3V5C.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3V5F.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3V5F.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3VCC.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3VCC.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3uud.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3uud.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3vk6.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3vk6.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/3vvk.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/3vvk.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4A35.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4A35.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4DN1.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4DN1.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4DWD.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4DWD.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4FP1.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4FP1.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4GGB.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4GGB.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4H19.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4H19.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4H1Z.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4H1Z.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4H83.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4H83.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4HNC.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4HNC.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4HPN.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4HPN.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4IP4.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4IP4.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4IP5.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4IP5.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4JN7.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4JN7.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4JN8.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4JN8.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4KEM.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4KEM.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4M6U.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4M6U.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4X2P.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4X2P.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4cha.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4cha.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/4ob8.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/4ob8.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/5OLC.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/5OLC.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/5XD7.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/5XD7.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/5XD8.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/5XD8.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/5ire.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/5ire.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/6TNE.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/6TNE.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/6VIM.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/6VIM.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renum/6j6q.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renum/6j6q.bcif
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renumbered.data:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-core/src/test/resources/renumbered.data
--------------------------------------------------------------------------------
/strucmotif-search-core/src/test/resources/renumbered.ffindex:
--------------------------------------------------------------------------------
1 | 1ZDM.bcif.gz 0 6097
2 | 4JN7.bcif.gz 6097 10102
3 | 3N4E.bcif.gz 16199 15029
4 | 3P3B.bcif.gz 31228 15498
5 | 4FP1.bcif.gz 46726 14823
6 | 4DWD.bcif.gz 61549 15153
7 | 3TTE.bcif.gz 76702 14670
8 | 3U4F.bcif.gz 91372 27400
9 | 1YEY.bcif.gz 118772 31499
10 | 4HPN.bcif.gz 150271 9589
11 | 2GGE.bcif.gz 159860 53335
12 | 4GGB.bcif.gz 213195 8993
13 | 3D46.bcif.gz 222188 56334
14 | 3UGV.bcif.gz 278522 50431
15 | 3FXG.bcif.gz 328953 55748
16 | 2NQL.bcif.gz 384701 16232
17 | 1DTN.bcif.gz 400933 9029
18 | 4HNC.bcif.gz 409962 14842
19 | 3SN1.bcif.gz 424804 10062
20 | 2PP0.bcif.gz 434866 23148
21 | 3T9P.bcif.gz 458014 15058
22 | 3CXO.bcif.gz 473072 16613
23 | 2HXT.bcif.gz 489685 10565
24 | 4M6U.bcif.gz 500250 14878
25 | 2HZG.bcif.gz 515128 15555
26 | 3VCC.bcif.gz 530683 16069
27 | 2PP3.bcif.gz 546752 23155
28 | 2DW6.bcif.gz 569907 28238
29 | 3UXL.bcif.gz 598145 26337
30 | 3N4F.bcif.gz 624482 28323
31 | 3UXK.bcif.gz 652805 25680
32 | 1MDR.bcif.gz 678485 9037
33 | 3OP2.bcif.gz 687522 15343
34 | 2P3Z.bcif.gz 702865 16822
35 | 4H83.bcif.gz 719687 38778
36 | 2I5Q.bcif.gz 758465 16101
37 | 2OZ3.bcif.gz 774566 54879
38 | 3CYJ.bcif.gz 829445 25714
39 | 3BJS.bcif.gz 855159 15389
40 | 4KEM.bcif.gz 870548 15840
41 | 2OO6.bcif.gz 886388 10017
42 | 4DN1.bcif.gz 896405 15937
43 | 2GDQ.bcif.gz 912342 15925
44 | 3SN4.bcif.gz 928267 10036
45 | 3OPS.bcif.gz 938303 28508
46 | 3V5C.bcif.gz 966811 28128
47 | 1TZZ.bcif.gz 994939 15381
48 | 1MNS.bcif.gz 1010320 9036
49 | 2OVL.bcif.gz 1019356 26092
50 | 4X2P.bcif.gz 1045448 9068
51 | 4H1Z.bcif.gz 1054516 52171
52 | 3SN0.bcif.gz 1106687 10172
53 | 5XD8.bcif.gz 1116859 15078
54 | 3OZY.bcif.gz 1131937 15893
55 | 3OZM.bcif.gz 1147830 53157
56 | 4A35.bcif.gz 1200987 10985
57 | 3T8Q.bcif.gz 1211972 15299
58 | 3CK5.bcif.gz 1227271 26097
59 | 3QPE.bcif.gz 1253368 28106
60 | 3H12.bcif.gz 1281474 16294
61 | 3MSY.bcif.gz 1297768 37637
62 | 2QQ6.bcif.gz 1335405 16058
63 | 1MRA.bcif.gz 1351463 9031
64 | 5OLC.bcif.gz 1360494 49238
65 | 3GO2.bcif.gz 1409732 9884
66 | 3V5F.bcif.gz 1419616 9523
67 | 3TJ4.bcif.gz 1429139 15301
68 | 3SJN.bcif.gz 1444440 15653
69 | 3EKG.bcif.gz 1460093 16443
70 | 1MDL.bcif.gz 1476536 8992
71 | 2P0I.bcif.gz 1485528 54422
72 | 4IP5.bcif.gz 1539950 17284
73 | 3D47.bcif.gz 1557234 56385
74 | 3TCS.bcif.gz 1613619 15455
75 | 2HNE.bcif.gz 1629074 31442
76 | 5XD7.bcif.gz 1660516 9087
77 | 6TNE.bcif.gz 1669603 3444
78 | 3RRA.bcif.gz 1673047 15698
79 | 4JN8.bcif.gz 1688745 9979
80 | 6VIM.bcif.gz 1698724 118853
81 | 2QGY.bcif.gz 1817577 15888
82 | 2MNR.bcif.gz 1833465 9026
83 | 3RR1.bcif.gz 1842491 15633
84 | 2DW7.bcif.gz 1858124 102426
85 | 3TOY.bcif.gz 1960550 26189
86 | 4IP4.bcif.gz 1986739 17284
87 | 2OG9.bcif.gz 2004023 14692
88 | 2POZ.bcif.gz 2018715 51584
89 | 3BOX.bcif.gz 2070299 16626
90 | 2HXU.bcif.gz 2086925 10566
91 | 3NO1.bcif.gz 2097491 37798
92 | 2PPG.bcif.gz 2135289 27877
93 | 2PP1.bcif.gz 2163166 40061
94 | 4H19.bcif.gz 2203227 99555
95 | 3CB3.bcif.gz 2302782 26672
96 | 2GSH.bcif.gz 2329454 13929
97 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/main/java/org/rcsb/strucmotif/update/Context.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update;
2 |
3 | import org.rcsb.strucmotif.config.StrucmotifConfig;
4 | import org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor;
5 | import org.rcsb.strucmotif.domain.structure.StructureInformation;
6 | import org.slf4j.Logger;
7 | import org.slf4j.LoggerFactory;
8 |
9 | import java.io.BufferedOutputStream;
10 | import java.io.Closeable;
11 | import java.io.FileOutputStream;
12 | import java.io.Flushable;
13 | import java.io.IOException;
14 | import java.io.OutputStream;
15 | import java.nio.file.Files;
16 | import java.nio.file.Path;
17 | import java.nio.file.Paths;
18 | import java.util.*;
19 | import java.util.concurrent.CopyOnWriteArrayList;
20 | import java.util.concurrent.atomic.AtomicInteger;
21 |
22 | /**
23 | * Captures global state of the update process.
24 | */
25 | public class Context implements Closeable, Flushable {
26 | private static final Logger logger = LoggerFactory.getLogger(Context.class);
27 | private static final int BUFFER_SIZE = 65536;
28 | private final String rootPath;
29 | final List updateItems;
30 | final Set processed;
31 | int partitionSize;
32 | String partitionContext;
33 | private final Map outputStreams;
34 | private final List outputPaths;
35 | AtomicInteger structureCounter;
36 |
37 | /**
38 | * Construct a new update context.
39 | * @param strucmotifConfig global config
40 | * @param updateItems update list
41 | */
42 | public Context(StrucmotifConfig strucmotifConfig, List updateItems) {
43 | this.rootPath = strucmotifConfig.getRootPath();
44 | this.updateItems = updateItems;
45 | this.processed = Collections.synchronizedSet(new HashSet<>());
46 | this.outputStreams = Collections.synchronizedMap(new HashMap<>());
47 | this.outputPaths = new CopyOnWriteArrayList<>();
48 | }
49 |
50 | private String getPrefix(int descriptor) {
51 | return ResiduePairDescriptor.getResidueType1(descriptor).getInternalCode() + ResiduePairDescriptor.getResidueType2(descriptor).getInternalCode();
52 | }
53 |
54 | /**
55 | * Get an output stream that a thread can use to dump data.
56 | * @param descriptor the descriptor to write
57 | * @return a new or previously created output stream that is specific to this thread
58 | * @throws IOException IO operation failed
59 | */
60 | public OutputStream getOutputStream(int descriptor) throws IOException {
61 | String key = Thread.currentThread().getId() + "-" + getPrefix(descriptor);
62 | OutputStream ref = outputStreams.get(key);
63 | if (ref != null) {
64 | return ref;
65 | }
66 |
67 | Path path = Paths.get(rootPath).resolve(StrucmotifConfig.INDEX + "." + key + StrucmotifConfig.TMP_EXT);
68 | logger.debug("Creating thread-specific index dump at {}", path);
69 | ref = new BufferedOutputStream(new FileOutputStream(path.toFile()), BUFFER_SIZE);
70 | outputStreams.put(key, ref);
71 | outputPaths.add(path);
72 | return ref;
73 | }
74 |
75 | @Override
76 | public void flush() throws IOException {
77 | for (OutputStream stream : outputStreams.values()) {
78 | stream.flush();
79 | }
80 | }
81 |
82 | @Override
83 | public void close() throws IOException {
84 | logger.info("Closing thread-specific index dumps");
85 | for (OutputStream stream : outputStreams.values()) {
86 | stream.close();
87 | }
88 | outputStreams.clear();
89 | for (Path path : outputPaths) {
90 | Files.deleteIfExists(path);
91 | }
92 | outputPaths.clear();
93 | }
94 | }
95 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/main/java/org/rcsb/strucmotif/update/Operation.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update;
2 |
3 | import java.util.Arrays;
4 | import java.util.NoSuchElementException;
5 |
6 | /**
7 | * The possible operations during a strucmotif update ('ADD' structures, 'REMOVE' structures, 'RECOVER').
8 | */
9 | public enum Operation {
10 | /**
11 | * Add structures.
12 | */
13 | ADD,
14 | /**
15 | * Remove structures.
16 | */
17 | REMOVE,
18 | /**
19 | * Try to recover - this is used when the JVM dies while manipulating the inverted index.
20 | */
21 | RECOVER;
22 |
23 | /**
24 | * Map from string to Operation enum.
25 | * @param s the name
26 | * @return the corresponding enum entry
27 | */
28 | public static Operation resolve(String s) {
29 | String uc = s.toUpperCase();
30 | return Arrays.stream(Operation.values())
31 | .filter(e -> e.name().equals(uc))
32 | .findFirst()
33 | .orElseThrow(() -> new NoSuchElementException("Unrecognized Operation: " + s + " - options are: " + Arrays.toString(Operation.values())));
34 | }
35 | }
36 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/main/java/org/rcsb/strucmotif/update/UpdateItem.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update;
2 |
3 | import org.rcsb.strucmotif.io.StructureDataProvider;
4 |
5 | import java.net.URL;
6 |
7 | /**
8 | * One piece of the update. Usually just references a PDB entry.
9 | * Can also point to external resources or local files via a URL. In that case, you must make sure to provide a unique
10 | * structureIdentifier.
11 | */
12 | public class UpdateItem {
13 | private final String structureIdentifier;
14 | private final URL url;
15 | private final int modelIdentifier;
16 |
17 | /**
18 | * Update by PDB-ID.
19 | * @param structureIdentifier a PDB entry ID
20 | */
21 | public UpdateItem(String structureIdentifier) {
22 | this(structureIdentifier, null, StructureDataProvider.DEFAULT_MODEL_IDENTIFIER);
23 | }
24 |
25 | /**
26 | * Update a specific model of a PDB-ID.
27 | * @param structureIdentifier a PDB entry ID
28 | */
29 | public UpdateItem(String structureIdentifier, int modelIdentifier) {
30 | this(structureIdentifier, null, modelIdentifier);
31 | }
32 |
33 | /**
34 | * Update by identifier and external URL.
35 | * @param structureIdentifier the unique ID this item will have
36 | * @param url data source pointing to non-PDB structures, either by URL to some external resource or to a local file
37 | */
38 | public UpdateItem(String structureIdentifier, URL url) {
39 | this(structureIdentifier, url, StructureDataProvider.DEFAULT_MODEL_IDENTIFIER);
40 | }
41 |
42 | /**
43 | * Update by identifier and external URL, while being model-aware.
44 | * @param structureIdentifier the unique ID this item will have
45 | * @param url data source pointing to non-PDB structures, either by URL to some external resource or to a local file
46 | * @param modelIdentifier int value of the model to index
47 | */
48 | public UpdateItem(String structureIdentifier, URL url, int modelIdentifier) {
49 | this.structureIdentifier = structureIdentifier;
50 | this.url = url;
51 | this.modelIdentifier = modelIdentifier;
52 | }
53 |
54 | /**
55 | * Get the key with which this item will be registered.
56 | * @return a String, usually a PDB-ID or some compact identifier
57 | */
58 | public String getStructureIdentifier() {
59 | return structureIdentifier;
60 | }
61 |
62 | /**
63 | * Get the resource URL to load.
64 | * @return the URL to load, or null if referencing a PDB entry
65 | */
66 | public URL getUrl() {
67 | return url;
68 | }
69 |
70 | /**
71 | * Which model to index?
72 | * @return an int (usually, 1)
73 | */
74 | public int getModelIdentifier() {
75 | return modelIdentifier;
76 | }
77 | }
78 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/main/java/org/rcsb/strucmotif/update/extractor/AlphaFoldKeyExtractor.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update.extractor;
2 |
3 | /**
4 | * Handles files from the AlphaFoldDB.
5 | */
6 | public class AlphaFoldKeyExtractor implements KeyExtractor {
7 | private static final String NAMESPACE = "AF-";
8 |
9 | /**
10 | * Default constructor.
11 | */
12 | public AlphaFoldKeyExtractor() {
13 | }
14 |
15 | @Override
16 | public String getNameSpace() {
17 | return NAMESPACE;
18 | }
19 |
20 | @Override
21 | public String getKey(String resource) {
22 | // https://alphafold.ebi.ac.uk/files/AF-Q76EI6-F1-model_v1.cif -> AF-Q76EI6-F1
23 | String name = resource.contains("/") ? resource.substring(resource.lastIndexOf("/") + 1) : resource;
24 | return name.replaceAll("(?i)-model_v\\d+\\.b?cif(?:\\.gz)?", "").toUpperCase();
25 | }
26 | }
27 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/main/java/org/rcsb/strucmotif/update/extractor/GenericKeyExtractor.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update.extractor;
2 |
3 | /**
4 | * Fallback strategy of extracting keys: use file name.
5 | */
6 | public class GenericKeyExtractor implements KeyExtractor {
7 | private static final String NAMESPACE = "";
8 |
9 | /**
10 | * Default constructor.
11 | */
12 | public GenericKeyExtractor() {
13 | }
14 |
15 | @Override
16 | public String getNameSpace() {
17 | return NAMESPACE;
18 | }
19 |
20 | @Override
21 | public String getKey(String resource) {
22 | // /path/to/1abc.cif -> 1ABC
23 | String name = resource.contains("/") ? resource.substring(resource.lastIndexOf("/") + 1) : resource;
24 | return name.replaceAll("(?i)\\.b?cif(?:\\.gz)?", "").toUpperCase();
25 | }
26 | }
27 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/main/java/org/rcsb/strucmotif/update/extractor/KeyExtractor.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update.extractor;
2 |
3 | import java.nio.file.Path;
4 |
5 | /**
6 | * Converts {@link Path} instances to a (hopefully) unique key.
7 | */
8 | public interface KeyExtractor {
9 | /**
10 | * The expected namespace prefix used by this data-source.
11 | * @return a String which can be empty
12 | */
13 | String getNameSpace();
14 |
15 | /**
16 | * Extract the key of this path or URL. The input will be processed in a case-insensitive manner, the output will be
17 | * upper-case.
18 | * @param resource the path/URL to process
19 | * @return a key
20 | */
21 | String getKey(String resource);
22 | }
23 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/main/java/org/rcsb/strucmotif/update/extractor/KeyExtractorFactory.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update.extractor;
2 |
3 | import java.util.List;
4 |
5 | /**
6 | * Finds an appropriate key extractor.
7 | */
8 | public class KeyExtractorFactory {
9 | private final List nonGeneric;
10 | private final GenericKeyExtractor generic;
11 | private static final KeyExtractorFactory INSTANCE = new KeyExtractorFactory();
12 |
13 | private KeyExtractorFactory() {
14 | nonGeneric = List.of(new AlphaFoldKeyExtractor(), new ModelArchiveKeyExtractor());
15 | generic = new GenericKeyExtractor();
16 | }
17 |
18 | /**
19 | * Determine the key extractor for this resource.
20 | * @param resource the resource
21 | * @return a {@link KeyExtractor} that supports this namespace, the generic implementation if none matches
22 | */
23 | public static KeyExtractor getKeyExtractor(String resource) {
24 | String name = resource.contains("/") ? resource.substring(resource.lastIndexOf("/") + 1) : resource;
25 | String upperCase = name.toUpperCase();
26 | for (KeyExtractor keyExtractor : INSTANCE.nonGeneric) {
27 | if (upperCase.startsWith(keyExtractor.getNameSpace())) {
28 | return keyExtractor;
29 | }
30 | }
31 | return INSTANCE.generic;
32 | }
33 |
34 | /**
35 | * Short-cut to extract keys.
36 | * @param resource the resource
37 | * @return the extracted key
38 | */
39 | public static String getKey(String resource) {
40 | return getKeyExtractor(resource).getKey(resource);
41 | }
42 | }
43 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/main/java/org/rcsb/strucmotif/update/extractor/ModelArchiveKeyExtractor.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update.extractor;
2 |
3 | /**
4 | * Handles files from the ModelArchive.
5 | */
6 | public class ModelArchiveKeyExtractor implements KeyExtractor {
7 | private static final String NAMESPACE = "MA-";
8 |
9 | /**
10 | * Default constructor.
11 | */
12 | public ModelArchiveKeyExtractor() {
13 | }
14 |
15 | @Override
16 | public String getNameSpace() {
17 | return NAMESPACE;
18 | }
19 |
20 | @Override
21 | public String getKey(String resource) {
22 | // /path/to/ma-9z55z.cif -> MA-9Z55Z
23 | String name = resource.contains("/") ? resource.substring(resource.lastIndexOf("/") + 1) : resource;
24 | return name.replaceAll("(?i)\\.b?cif(?:\\.gz)?", "").toUpperCase();
25 | }
26 | }
27 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/test/java/org/rcsb/strucmotif/update/Demo.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update;
2 |
3 | class Demo {
4 | public static void main(String[] args) {
5 | // perform a full load of all structures in RCSB PDB with default configuration
6 | // use 'full_csm' to also fetch all computed structure models integrated into RCSB.org (~200k experimentally-determined structures, ~1M CSMs)
7 | StrucmotifUpdate.main(new String[] { "ADD", "full" });
8 |
9 | // load some arbitrary (external) structure data like AlphaFold models
10 | StrucmotifUpdate.main(new String[] {
11 | "ADD",
12 | "AF-Q76EI6-F1,https://alphafold.ebi.ac.uk/files/AF-Q76EI6-F1-model_v4.cif",
13 | "ma-bak-cepc-0886,https://www.modelarchive.org/api/projects/ma-bak-cepc-0886?type=basic__model_file_name",
14 | });
15 | }
16 | }
--------------------------------------------------------------------------------
/strucmotif-search-update/src/test/java/org/rcsb/strucmotif/update/TestCases.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update;
2 |
3 | import java.io.InputStream;
4 | import java.util.Arrays;
5 | import java.util.NoSuchElementException;
6 |
7 | /**
8 | * Some small structures and their expected properties when processed by the update routine.
9 | */
10 | enum TestCases {
11 | PDB_2RLL("2RLL.cif.gz"),
12 | PDB_3ULN("3uln.cif.gz"),
13 | PDB_3UM4("3UM4.cif"),
14 | PDB_4TUT("4TUT.bcif.gz"),
15 | PDB_5XES("5xes.bcif"),
16 | PDB_6FCE("6fce.cif"),
17 | AF_A0A0R0FWM3("af_afa0a0r0fwm3f1.bcif"), // helix, fragmented
18 | AF_Q8SY76("af_afq8sy76f1.bcif"); // helix
19 |
20 | private final String filename;
21 | private final String key;
22 |
23 | TestCases(String name) {
24 | this.filename = name;
25 | this.key = filename.split("\\.")[0].replace("-model_v1", "");
26 | }
27 |
28 | public String getFilename() {
29 | return filename;
30 | }
31 |
32 | public String getKey() {
33 | return key;
34 | }
35 |
36 | public InputStream getInputStream() {
37 | return Thread.currentThread().getContextClassLoader().getResourceAsStream(this.filename);
38 | }
39 |
40 | public static InputStream getInputStream(String key) {
41 | return Arrays.stream(TestCases.values())
42 | .filter(t -> t.getKey().equalsIgnoreCase(key))
43 | .findFirst()
44 | .map(TestCases::getInputStream)
45 | .orElseThrow(() -> new NoSuchElementException("Couldn't find resource for case '" + key + "'"));
46 | }
47 |
48 | public String getExpression() {
49 | if (filename.equalsIgnoreCase(key)) {
50 | return key;
51 | } else {
52 | return key + ",https://rcsb.org"; // any URL works here
53 | }
54 | }
55 | }
56 |
--------------------------------------------------------------------------------
/strucmotif-search-update/src/test/java/org/rcsb/strucmotif/update/extractor/KeyExtractorFactoryTest.java:
--------------------------------------------------------------------------------
1 | package org.rcsb.strucmotif.update.extractor;
2 |
3 | import org.junit.jupiter.api.Test;
4 |
5 | import static org.junit.jupiter.api.Assertions.*;
6 |
7 | class KeyExtractorFactoryTest {
8 | @Test
9 | public void whenRequestingExtractor_thenCorrectOnesReturned() {
10 | KeyExtractor extractor1 = KeyExtractorFactory.getKeyExtractor("AF-Q76EI6-F1-model_v1.cif");
11 | assertInstanceOf(AlphaFoldKeyExtractor.class, extractor1);
12 |
13 | KeyExtractor extractor2 = KeyExtractorFactory.getKeyExtractor("/path/to/ma-9z55z.cif");
14 | assertInstanceOf(ModelArchiveKeyExtractor.class, extractor2);
15 |
16 | KeyExtractor extractor3 = KeyExtractorFactory.getKeyExtractor("/1acj.cif");
17 | assertInstanceOf(GenericKeyExtractor.class, extractor3);
18 |
19 | KeyExtractor extractor4 = KeyExtractorFactory.getKeyExtractor("/");
20 | assertInstanceOf(GenericKeyExtractor.class, extractor4);
21 |
22 | KeyExtractor extractor5 = KeyExtractorFactory.getKeyExtractor("");
23 | assertInstanceOf(GenericKeyExtractor.class, extractor5);
24 | }
25 |
26 | @Test
27 | public void whenExtractingKeys_thenCorrectOnesReturned() {
28 | String key1 = KeyExtractorFactory.getKey("AF-Q76EI6-F1-model_v1.cif");
29 | assertEquals("AF-Q76EI6-F1", key1);
30 |
31 | String key2 = KeyExtractorFactory.getKey("/path/to/ma-9z55z.cif");
32 | assertEquals("MA-9Z55Z", key2);
33 |
34 | String key3 = KeyExtractorFactory.getKey("/1acj.cif");
35 | assertEquals("1ACJ", key3);
36 | }
37 | }
--------------------------------------------------------------------------------
/strucmotif-search-update/src/test/resources/2RLL.cif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-update/src/test/resources/2RLL.cif.gz
--------------------------------------------------------------------------------
/strucmotif-search-update/src/test/resources/3uln.cif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-update/src/test/resources/3uln.cif.gz
--------------------------------------------------------------------------------
/strucmotif-search-update/src/test/resources/4TUT.bcif.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-update/src/test/resources/4TUT.bcif.gz
--------------------------------------------------------------------------------
/strucmotif-search-update/src/test/resources/5xes.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-update/src/test/resources/5xes.bcif
--------------------------------------------------------------------------------
/strucmotif-search-update/src/test/resources/af_afa0a0r0fwm3f1.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-update/src/test/resources/af_afa0a0r0fwm3f1.bcif
--------------------------------------------------------------------------------
/strucmotif-search-update/src/test/resources/af_afq8sy76f1.bcif:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/rcsb/strucmotif-search/7662e218d891706e03ce0cf02e4583df40b69766/strucmotif-search-update/src/test/resources/af_afq8sy76f1.bcif
--------------------------------------------------------------------------------