Rd \usage section for S3 methods

[Barry Grant]

Rd doc files need to be changed for the following S3 functions

S3 methods shown with full name in documentation object 'plot.bio3d': ‘plot.bio3d’

S3 methods shown with full name in documentation object 'plot.blast': ‘plot.blast’

S3 methods shown with full name in documentation object 'plot.core': ‘plot.core’

S3 methods shown with full name in documentation object 'plot.dccm': ‘plot.dccm’

S3 methods shown with full name in documentation object 'plot.dmat': ‘plot.dmat’

S3 methods shown with full name in documentation object 'plot.pca': ‘plot.pca’ ‘plot.pca.scree’ ‘plot.pca.score’

S3 methods shown with full name in documentation object 'plot.pca.loadings': ‘plot.pca.loadings’

S3 methods shown with full name in documentation object 'print.core': ‘print.core’

S3 methods shown with full name in documentation object 'read.pdb': ‘print.pdb’

S3 methods shown with full name in documentation object 'seq.pdb': ‘seq.pdb’

S3 methods shown with full name in documentation object 'split.pdb': ‘split.pdb’

The \usage entries for S3 methods should use the \method markup and not their full name.

[Xinqiu Yao]

This issue is resolved by slightly modifying the Rd files. There are still warning report for seq.pdb and split.pdb, which is taken care in another issue.