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Fix to MutatePDB so patches are not discarded after mutations are made. #308

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Merged
mjschnie merged 1 commit into from
May 6, 2026
Merged

Fix to MutatePDB so patches are not discarded after mutations are made. #308

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11 changes: 11 additions & 0 deletions modules/algorithms/src/main/java/ffx/algorithms/commands/MutatePDB.java
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Original file line number Diff line number Diff line change
Expand Up @@ -205,6 +205,17 @@ public MutatePDB run() {
CompositeConfiguration properties = Keyword.loadProperties(structureFile);
ForceFieldFilter forceFieldFilter = new ForceFieldFilter(properties);
ForceField forceField = forceFieldFilter.parse();
String[] patches = properties.getStringArray("patch");
if (patches != null) {
for (String patch : patches) {
logger.info(" Attempting to read force field patch from " + patch + ".");
CompositeConfiguration patchConfiguration = new CompositeConfiguration();
patchConfiguration.addProperty("parameters", patch);
forceFieldFilter = new ForceFieldFilter(patchConfiguration);
ForceField patchForceField = forceFieldFilter.parse();
forceField.append(patchForceField);
}
}
molecularAssembly.setForceField(forceField);

PDBFilter pdbFilter = new PDBFilter(structureFile, molecularAssembly, forceField, properties);
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