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KotmolPdbParser Integration

Overview

The PDB parser library (com.kotmol.kotmolpdbparser:kotmolpdbparser) has been moved from a Maven Central dependency into the repo as a local Gradle module at pdbparser/.

This gives full control over the source, enables in-repo debugging, and eliminates the external Maven dependency.

Module Location

pdbparser/
├── build.gradle.kts                           # Pure Kotlin/JVM module, JUnit 5
└── src/
    ├── main/java/com/kotmol/pdbParser/        # 8 core source files
    │   ├── AtomInformationTable.kt            # Periodic table (118 elements, VdW radii, colors)
    │   ├── BondInfo.kt                        # ~80KB hardcoded bond database from EBI
    │   ├── ChainRenderingDescriptor.kt        # Chain rendering metadata (RIBBON, ALPHA_HELIX, etc.)
    │   ├── Molecule.kt                        # Output container (atoms, bonds, helices, sheets)
    │   ├── ParserPdbFile.kt                   # Main parser (Builder pattern)
    │   ├── PdbAtom.kt                         # Atom data + KotmolVector3
    │   ├── PdbBetaSheet.kt                    # SHEET record data
    │   └── PdbHelix.kt                        # HELIX record data
    └── test/java/com/kotmol/pdbParser/        # 23 unit test files

Usage

The package name com.kotmol.pdbParser is unchanged — existing imports in mollib/ work without modification.

val mol = Molecule()
ParserPdbFile.Builder(mol)
    .loadPdbFromStream(pdbByteStream)
    .parse()
// Access mol.atomNumberToAtomInfoHash, mol.bondList, mol.helixList, etc.

Build Commands

# Run pdbparser unit tests only
./gradlew.bat :pdbparser:test

# Build mollib (depends on pdbparser)
./gradlew.bat :mollib:build

# Full build
./gradlew.bat build

Updating the Parser Source

The upstream source is at C:\a\j\kotlinIdea\KotmolPdbParser. To pull in changes, copy the updated .kt files from:

KotmolPdbParser/kotmolpdbparser/src/main/java/com/kotmol/pdbParser/

into:

pdbparser/src/main/java/com/kotmol/pdbParser/

Then run :pdbparser:test to confirm nothing broke.

Modules That Depend on pdbparser

Module Dependency
mollib project(":pdbparser")
motmbrowser project(":pdbparser")
standalone project(":pdbparser")
captureimages project(":pdbparser")

Original Source

The parser was originally published to Maven Central as: com.kotmol.kotmolpdbparser:kotmolpdbparser:1.0.5

Source repo: C:\a\j\kotlinIdea\KotmolPdbParser (local) / GitHub: kotmol/KotmolPdbParser