pdbHomoFilter: Modeled PDB files filtration

In hongzhonglu/Yeastspot3D: Mutation mapping analysis with protein 3D structure for yeast

Description

Remove modeled PDB file of low quality

Usage

pdbHomoFilter(
  pdb_homo,
  qmean0 = -4,
  identity0 = 25,
  similarity0 = 0.31,
  resolution0 = 3.4
)

Arguments

pdb_homo	A dataframe contains paramters for each homology pdb file
qmean0	A paramter to evaluate the pdb quality defined in Swiss model database
identity0	Seq-identity, identity between target protein sequence and the residues sequence of templated PDB files
similarity0	Seq_similarity, similarity between target protein sequence and the residues sequence of templated PDB files
resolution0	Resolution of the template pdb file

Value

A dataframe contain the modeled PDB files of high quality

Examples

s1 = data.frame(qmean=c(-6,1,2),Seq_identity=c(10,30,40),Seq_similarity=c(0.15,20,45), Resolution=c(6,2,3), stringsAsFactors = FALSE)
pdbHomoFilter(pdb_homo=s1)

hongzhonglu/Yeastspot3D documentation built on March 28, 2020, 6:06 p.m.