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first check of just removing redundant spaces #175

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7d32dea
first check of just removing redundant spaces
jpielesiak May 11, 2026
2b59baf
main to spaces-in-ct (#178)
jpielesiak Jul 3, 2026
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84 changes: 23 additions & 61 deletions devenv.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,11 @@
"devenv": {
"locked": {
"dir": "src/modules",
"lastModified": 1761922975,
"lastModified": 1781800860,
"narHash": "sha256-LrEo0eC5ckMvjpBRCuk5q5/vjItKlxnb4n/clHNRZlk=",
"owner": "cachix",
"repo": "devenv",
"rev": "c9f0b47815a4895fadac87812de8a4de27e0ace1",
"rev": "d59d872d80876d9eeb3e214d3b088bc4a14a9c4f",
"type": "github"
},
"original": {
Expand All @@ -16,88 +17,49 @@
"type": "github"
}
},
"flake-compat": {
"flake": false,
"locked": {
"lastModified": 1761588595,
"owner": "edolstra",
"repo": "flake-compat",
"rev": "f387cd2afec9419c8ee37694406ca490c3f34ee5",
"type": "github"
},
"original": {
"owner": "edolstra",
"repo": "flake-compat",
"type": "github"
}
},
"git-hooks": {
"nixpkgs": {
"inputs": {
"flake-compat": "flake-compat",
"gitignore": "gitignore",
"nixpkgs": [
"nixpkgs"
]
"nixpkgs-src": "nixpkgs-src"
},
"locked": {
"lastModified": 1760663237,
"lastModified": 1781620901,
"narHash": "sha256-UF6scQlG+6lRkZBUpn/3KNavhOo5G8kDWhjVHcno8uc=",
"owner": "cachix",
"repo": "git-hooks.nix",
"rev": "ca5b894d3e3e151ffc1db040b6ce4dcc75d31c37",
"repo": "devenv-nixpkgs",
"rev": "2df109b343d3c68efd752e32a444a1d9b9f89afa",
"type": "github"
},
"original": {
"owner": "cachix",
"repo": "git-hooks.nix",
"type": "github"
}
},
"gitignore": {
"inputs": {
"nixpkgs": [
"git-hooks",
"nixpkgs"
]
},
"locked": {
"lastModified": 1709087332,
"owner": "hercules-ci",
"repo": "gitignore.nix",
"rev": "637db329424fd7e46cf4185293b9cc8c88c95394",
"type": "github"
},
"original": {
"owner": "hercules-ci",
"repo": "gitignore.nix",
"ref": "rolling",
"repo": "devenv-nixpkgs",
"type": "github"
}
},
"nixpkgs": {
"nixpkgs-src": {
"flake": false,
"locked": {
"lastModified": 1761313199,
"owner": "cachix",
"repo": "devenv-nixpkgs",
"rev": "d1c30452ebecfc55185ae6d1c983c09da0c274ff",
"lastModified": 1781454065,
"narHash": "sha256-d2xfDjnfRuf/xYGdu9VVRHiav/2w5hDL/5cw2TuVAXw=",
"owner": "NixOS",
"repo": "nixpkgs",
"rev": "9eac87a12312b8f60dd52e1c6e1a265f6fc7f5fc",
"type": "github"
},
"original": {
"owner": "cachix",
"ref": "rolling",
"repo": "devenv-nixpkgs",
"owner": "NixOS",
"ref": "nixpkgs-unstable",
"repo": "nixpkgs",
"type": "github"
}
},
"root": {
"inputs": {
"devenv": "devenv",
"git-hooks": "git-hooks",
"nixpkgs": "nixpkgs",
"pre-commit-hooks": [
"git-hooks"
]
"nixpkgs": "nixpkgs"
}
}
},
"root": "root",
"version": 7
}
}
2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@
<dependency>
<groupId>org.immutables</groupId>
<artifactId>value</artifactId>
<version>2.12.1</version>
<version>2.12.2</version>
<scope>provided</scope>
</dependency>

Expand Down
79 changes: 65 additions & 14 deletions src/main/java/pl/poznan/put/rnapdbee/engine/shared/basepair/boundary/BasePairAnalyzer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import java.util.stream.Stream;
Expand Down Expand Up @@ -41,6 +42,7 @@
import pl.poznan.put.rnapdbee.engine.shared.multiplet.MultipletSet;
import pl.poznan.put.structure.AnalyzedBasePair;
import pl.poznan.put.structure.ImmutableAnalyzedBasePair;
import pl.poznan.put.structure.ImmutableBasePair;

// TODO: WebFlux would be really efficient with the 3D->multi 2D analysis as we there perform multiple calls to the
// adapters, it could be done in parallel and then joined up after each call is performed. We would save a tone of
Expand Down Expand Up @@ -124,7 +126,12 @@ protected BasePairAnalysis performPostAnalysisOnResponseFromAdapter(
.filter(pair -> pair.isCanonical(structureModel))
.map(pair -> BasePairDTO.ofBasePairDTOWithNameFromMap(pair,
pairIdentifiersWithTheirShortNames))
.map(basePair -> ImmutableAnalyzedBasePair.of(basePair.toBasePair(structureModel))
.map(basePair -> {
ImmutableBasePair bp = basePair.toBasePair(structureModel);
if (bp == null) {
return null;
}
return ImmutableAnalyzedBasePair.of(bp)
.withInteractionType(InteractionType.BASE_BASE)
.withSaenger(basePair.getSaengerType() != null
? SaengerType.mapToBioCommonsForm(
Expand All @@ -136,13 +143,20 @@ protected BasePairAnalysis performPostAnalysisOnResponseFromAdapter(
: LeontisWesthof.UNKNOWN)
.withBph(BPh.UNKNOWN)
.withBr(BR.UNKNOWN)
.withStackingTopology(StackingTopology.UNKNOWN))
.withStackingTopology(StackingTopology.UNKNOWN);
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
List<AnalyzedBasePair> nonCanonical = responseFromAdapter.getBasePairs().stream()
.filter(pair -> !pair.isCanonical(structureModel))
.map(pair -> BasePairDTO.ofBasePairDTOWithNameFromMap(pair,
pairIdentifiersWithTheirShortNames))
.map(basePair -> ImmutableAnalyzedBasePair.of(basePair.toBasePair(structureModel))
.map(basePair -> {
ImmutableBasePair bp = basePair.toBasePair(structureModel);
if (bp == null) {
return null;
}
return ImmutableAnalyzedBasePair.of(bp)
.withInteractionType(InteractionType.BASE_BASE)
.withSaenger(basePair.getSaengerType() != null
? SaengerType.mapToBioCommonsForm(
Expand All @@ -154,56 +168,91 @@ protected BasePairAnalysis performPostAnalysisOnResponseFromAdapter(
: LeontisWesthof.UNKNOWN)
.withBph(BPh.UNKNOWN)
.withBr(BR.UNKNOWN)
.withStackingTopology(StackingTopology.UNKNOWN))
.withStackingTopology(StackingTopology.UNKNOWN);
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
List<AnalyzedBasePair> stackings = responseFromAdapter.getStackings().stream()
.map(pair -> BasePairDTO.ofBasePairDTOWithNameFromMap(pair,
pairIdentifiersWithTheirShortNames))
.map(basePair -> ImmutableAnalyzedBasePair.of(basePair.toBasePair(structureModel))
.map(basePair -> {
ImmutableBasePair bp = basePair.toBasePair(structureModel);
if (bp == null) {
return null;
}
return ImmutableAnalyzedBasePair.of(bp)
.withInteractionType(InteractionType.STACKING)
.withSaenger(Saenger.UNKNOWN)
.withLeontisWesthof(LeontisWesthof.UNKNOWN)
.withBph(BPh.UNKNOWN)
.withBr(BR.UNKNOWN)
.withStackingTopology(mapToBioCommonsForm(basePair.getTopology())))
.withStackingTopology(mapToBioCommonsForm(basePair.getTopology()));
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
List<AnalyzedBasePair> basePhosphate = responseFromAdapter.getBasePhosphateInteractions().stream()
.map(pair -> BasePairDTO.ofBasePairDTOWithNameFromMap(pair,
pairIdentifiersWithTheirShortNames))
.map(basePair -> ImmutableAnalyzedBasePair.of(basePair.toBasePair(structureModel))
.map(basePair -> {
ImmutableBasePair bp = basePair.toBasePair(structureModel);
if (bp == null) {
return null;
}
return ImmutableAnalyzedBasePair.of(bp)
.withInteractionType(InteractionType.BASE_PHOSPHATE)
.withSaenger(Saenger.UNKNOWN)
.withLeontisWesthof(LeontisWesthof.UNKNOWN)
.withBph(BasePhosphateType.mapToBioCommonsForm(basePair.getBph()))
.withBr(BR.UNKNOWN)
.withStackingTopology(StackingTopology.UNKNOWN))
.withStackingTopology(StackingTopology.UNKNOWN);
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
List<AnalyzedBasePair> baseRibose = responseFromAdapter.getBaseRiboseInteractions().stream()
.map(pair -> BasePairDTO.ofBasePairDTOWithNameFromMap(pair,
pairIdentifiersWithTheirShortNames))
.map(basePair -> ImmutableAnalyzedBasePair.of(basePair.toBasePair(structureModel))
.map(basePair -> {
ImmutableBasePair bp = basePair.toBasePair(structureModel);
if (bp == null) {
return null;
}
return ImmutableAnalyzedBasePair.of(bp)
.withInteractionType(InteractionType.BASE_RIBOSE)
.withSaenger(Saenger.UNKNOWN)
.withLeontisWesthof(LeontisWesthof.UNKNOWN)
.withBph(BPh.UNKNOWN)
.withBr(BaseRiboseType.mapToBioCommonsForm(basePair.getBr()))
.withStackingTopology(StackingTopology.UNKNOWN))
.withStackingTopology(StackingTopology.UNKNOWN);
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
List<AnalyzedBasePair> otherInteractions = responseFromAdapter.getOther().stream()
.map(pair -> BasePairDTO.ofBasePairDTOWithNameFromMap(pair,
pairIdentifiersWithTheirShortNames))
.map(basePair -> ImmutableAnalyzedBasePair.of(basePair.toBasePair(structureModel))
.map(basePair -> {
ImmutableBasePair bp = basePair.toBasePair(structureModel);
if (bp == null) {
return null;
}
return ImmutableAnalyzedBasePair.of(bp)
.withInteractionType(InteractionType.OTHER)
.withSaenger(Saenger.UNKNOWN)
.withLeontisWesthof(LeontisWesthof.UNKNOWN)
.withBph(BPh.UNKNOWN)
.withBr(BR.UNKNOWN)
.withStackingTopology(StackingTopology.UNKNOWN))
.withStackingTopology(StackingTopology.UNKNOWN);
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
List<AnalyzedBasePair> interStrand = responseFromAdapter.getBasePairs().stream()
.map(pair -> BasePairDTO.ofBasePairDTOWithNameFromMap(pair,
pairIdentifiersWithTheirShortNames))
.map(basePair -> ImmutableAnalyzedBasePair.of(basePair.toBasePair(structureModel))
.map(basePair -> {
ImmutableBasePair bp = basePair.toBasePair(structureModel);
if (bp == null) {
return null;
}
return ImmutableAnalyzedBasePair.of(bp)
.withInteractionType(InteractionType.BASE_BASE)
.withSaenger(basePair.getSaengerType() != null
? SaengerType.mapToBioCommonsForm(
Expand All @@ -215,7 +264,9 @@ protected BasePairAnalysis performPostAnalysisOnResponseFromAdapter(
: LeontisWesthof.UNKNOWN)
.withBph(BPh.UNKNOWN)
.withBr(BR.UNKNOWN)
.withStackingTopology(StackingTopology.UNKNOWN))
.withStackingTopology(StackingTopology.UNKNOWN);
})
.filter(Objects::nonNull)
.filter(basePair -> !basePair.basePair()
.left()
.chainIdentifier()
Expand Down
16 changes: 13 additions & 3 deletions src/main/java/pl/poznan/put/rnapdbee/engine/shared/basepair/domain/BasePairDTO.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
package pl.poznan.put.rnapdbee.engine.shared.basepair.domain;

import com.fasterxml.jackson.annotation.JsonProperty;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import pl.poznan.put.pdb.PdbNamedResidueIdentifier;
import pl.poznan.put.pdb.analysis.PdbModel;
import pl.poznan.put.rnapdbee.engine.shared.basepair.boundary.ChainNumberKey;
Expand All @@ -19,6 +21,7 @@
*/
public class BasePairDTO {

private static final Logger LOGGER = LoggerFactory.getLogger(BasePairDTO.class);
private static final Set<String> CANONICAL_ONE_LETTER_NAME_SORTED_PAIRS = new HashSet<>(Arrays.asList("AU", "GU", "CG"));

@JsonProperty("nt1")
Expand Down Expand Up @@ -122,6 +125,9 @@ public static BasePairDTO ofBasePairDTOWithNameFromMap(BasePairDTO basePairDTO,
public ImmutableBasePair toBasePair(PdbModel pdbModel) {
PdbNamedResidueIdentifier left = mapResidueToPdbNamedResidueIdentifier(nt1, pdbModel);
PdbNamedResidueIdentifier right = mapResidueToPdbNamedResidueIdentifier(nt2, pdbModel);
if (left == null || right == null) {
return null;
}
return ImmutableBasePair.of(left, right);
}

Expand All @@ -130,14 +136,15 @@ private PdbNamedResidueIdentifier mapResidueToPdbNamedResidueIdentifier(Residue
return pdbModel.findResidue(residue).namedResidueIdentifier();
}

throw new IllegalStateException(String.format(
"Residue not found in model: chain='%s', number=%d, icode=%s, name='%s'. "
LOGGER.warn(
"Residue not found in model: chain='{}', number={}, icode={}, name='{}'. "
+ "This may indicate a mismatch between adapter response and parsed structure "
+ "(e.g., chain identifier normalization issue).",
residue.chainIdentifier(),
residue.residueNumber(),
residue.insertionCode().orElse("(none)"),
residue.getAuth().getName()));
residue.getAuth().getName());
return null;
}

public boolean isCanonical(PdbModel pdbModel) {
Expand All @@ -147,6 +154,9 @@ public boolean isCanonical(PdbModel pdbModel) {
if (leontisWesthofType == LeontisWesthofType.CWW) {
PdbNamedResidueIdentifier left = mapResidueToPdbNamedResidueIdentifier(nt1, pdbModel);
PdbNamedResidueIdentifier right = mapResidueToPdbNamedResidueIdentifier(nt2, pdbModel);
if (left == null || right == null) {
return false;
}
String sequence = Stream.of(left.oneLetterName(), right.oneLetterName())
.map(c -> Character.toString(c))
.map(String::toUpperCase)
Expand Down
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