public interface StructureIOFile extends StructureIO
Modifier and Type | Method and Description |
---|---|
void |
addExtension(java.lang.String ext)
add a known File extension.
|
void |
clearExtensions()
clear all file extensions
|
FileParsingParameters |
getFileParsingParameters()
Get the parameters that should be used for file parsing
|
java.lang.String |
getPath()
get the directory path to the files
|
Structure |
getStructure(java.io.File file)
read file from File and returns
a Structure object.
|
Structure |
getStructure(java.lang.String filename)
open filename and returns
a Structure object.
|
Structure |
getStructureById(java.lang.String pdbId)
Get a Structure based on its PDB id.
|
boolean |
isAutoFetch()
Fetch files automatically from FTP server.
|
boolean |
isPdbDirectorySplit()
The PDB files are organized hierarchically (as on the PDB - FTP server.
|
void |
setAutoFetch(boolean autoFetch)
Tell the parser to fetch missing PDB files from the FTP server automatically.
|
void |
setFileParsingParameters(FileParsingParameters params)
Set the parameters that should be used for file parsing
|
void |
setPath(java.lang.String path)
Set path to file / connection string to db.
|
void |
setPdbDirectorySplit(boolean isSplit)
The PDB files are organized hierarchically (as on the PDB - FTP server.
|
void setPath(java.lang.String path)
path
- a String specifying the path valuejava.lang.String getPath()
void addExtension(java.lang.String ext)
ext
- a String ...void clearExtensions()
Structure getStructure(java.lang.String filename) throws java.io.IOException
filename
- a Stringjava.io.IOException
- ...Structure getStructure(java.io.File file) throws java.io.IOException
file
- file containing a PDB or mmcif filejava.io.IOException
- ...boolean isAutoFetch()
void setAutoFetch(boolean autoFetch)
autoFetch
- flag.void setPdbDirectorySplit(boolean isSplit)
isSplit
- boolean isPdbDirectorySplit()
Structure getStructureById(java.lang.String pdbId) throws java.io.IOException
getStructureById
in interface StructureIO
pdbId
- a String specifying the id value (PDB code)java.io.IOException
- ...void setFileParsingParameters(FileParsingParameters params)
params
- FileParsingParametersFileParsingParameters getFileParsingParameters()