Import a pdb file either by fetching the Protein Data Bank or from the file system and return the alpha-Carbon atoms coordinates.
a single element character vector containing the path to the file in the file
system and the name of the PDB file to be read, or the four letter PDB identifier for
online file access (fetched from the PDB). For the latter, the
logical (default FALSE). If TRUE, gaps are joined together with a straight line.
numeric (in Angstrom), distances between consecutive alpha-Carbon atoms
any other parameter for the
If the selected PDB entry contains more than one polypeptide chain, all the available
chains are loaded or downloaded. The PDB atom field is then filtered individually to retain the coordinates of the
protein C-alpha trace. If
join.gaps is FALSE, additional chains (one for each split) will be produced and
labeled according to the following: if C is a chain and C is split in j subchains due to gaps,
the resulting subchains will be labeled with C_1, …, C_j.
Notice that any other model or any three-dimensional structure can be
directly loaded in R as an N x 3 matrix, where the columns represents the x, y, z coordinates.
To this purpose, please see the help pages of
A list of length equal to the number of polypeptide chain (if gaps are not present or not considered) or greater (if gaps are present), where each element contains an N x 3 matrix with the x, y, z coordinates of the chain (or subchain) model.
This function makes use of the
read.pdb function in the
See references for additional details and credits.
Federico Comoglio, [email protected]
Grant, Rodrigues, ElSawy, McCammon, Caves (2006) Bio3D: An R package for the comparative analysis of protein structures., Bioinformatics 22, 2695-2696
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## Not run: ## Loading from the file system fn <- system.file("extdata", "1AJC_chainA.pdb", package="Rknots") protein <- loadProtein(fn) ## Fetching the PDB protein<- loadProtein('2K0A') #more than one chain (notice the split) protein <- loadProtein('1GZ0') str(protein) #A protein with two subunits. The first one is split in two subchains. protein <- loadProtein('1AJC', join.gaps = FALSE, cutoff = 7) str(protein) ## End(Not run)
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