Added functionality to OutputPDBFile so that projections can be written out

regtest/.gitignore

regtest/dimred/rt-mds/analysis.0.embed.reference

regtest/dimred/rt-mds/embed.reference

regtest/dimred/rt-mds/plumed.dat

src/analysis/AnalysisBase.h

src/analysis/AnalysisWithDataCollection.cpp

src/analysis/AnalysisWithDataCollection.h

src/analysis/EuclideanDissimilarityMatrix.cpp

src/analysis/LandmarkSelectionBase.h

src/analysis/OutputColvarFile.cpp

src/analysis/OutputPDBFile.cpp

src/analysis/ReadDissimilarityMatrix.cpp

src/dimred/DimensionalityReductionBase.cpp

src/dimred/DimensionalityReductionBase.h

src/dimred/ProjectNonLandmarkPoints.cpp

src/reference/ReferenceArguments.cpp

src/reference/ReferenceArguments.h

src/reference/ReferenceConfiguration.cpp

src/reference/ReferenceConfiguration.h