Package org.biojava.nbio.structure.io
Class FileConvert
- java.lang.Object
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- org.biojava.nbio.structure.io.FileConvert
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public class FileConvert extends Object
Methods to convert a structure object into different file formats.- Since:
- 1.4
- Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static DecimalFormat
d2
static DecimalFormat
d3
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Constructor Summary
Constructors Constructor Description FileConvert(Structure struc)
Constructs a FileConvert object.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
doPrintConnections()
Returns if the Connections should be added default is true;static String
getAtomSiteHeader()
void
setPrintConnections(boolean printConnections)
enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.void
toDASStructure(XMLWriter xw)
Convert a protein Structure to a DAS Structure XML response .String
toMMCIF()
static String
toMMCIF(Chain chain, boolean writeHeader)
static String
toMMCIF(Chain chain, String authId, String asymId, boolean writeHeader)
String
toPDB()
Convert a structure into a PDB file.static String
toPDB(Atom a)
Prints the content of an Atom object as a PDB formatted line.static String
toPDB(Atom a, String chainId)
static void
toPDB(Atom a, StringBuffer str)
static void
toPDB(Atom a, StringBuffer str, String chainID)
Print ATOM record in the following syntaxstatic String
toPDB(Chain chain)
Convert a Chain object to PDB representationstatic String
toPDB(Group g)
Convert a Group object to PDB representation
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Field Detail
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d3
public static DecimalFormat d3
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d2
public static DecimalFormat d2
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Constructor Detail
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FileConvert
public FileConvert(Structure struc)
Constructs a FileConvert object.- Parameters:
struc
- a Structure object
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Method Detail
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doPrintConnections
public boolean doPrintConnections()
Returns if the Connections should be added default is true;- Returns:
- if the printConnections flag is set
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setPrintConnections
public void setPrintConnections(boolean printConnections)
enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.- Parameters:
printConnections
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toPDB
public String toPDB()
Convert a structure into a PDB file.- Returns:
- a String representing a PDB file.
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toPDB
public static String toPDB(Atom a)
Prints the content of an Atom object as a PDB formatted line.- Parameters:
a
-- Returns:
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toPDB
public static String toPDB(Chain chain)
Convert a Chain object to PDB representation- Parameters:
chain
-- Returns:
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toPDB
public static String toPDB(Group g)
Convert a Group object to PDB representation- Parameters:
g
-- Returns:
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toPDB
public static void toPDB(Atom a, StringBuffer str, String chainID)
Print ATOM record in the following syntaxATOM 1 N ASP A 15 110.964 24.941 59.191 1.00 83.44 N COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator. 18 - 20 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Code for insertion of residues. 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms. 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms. 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms. 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. 73 - 76 LString(4) segID Segment identifier, left-justified. 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom.
- Parameters:
a
-str
-chainID
- the chain ID that the Atom will have in the output string
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toPDB
public static void toPDB(Atom a, StringBuffer str)
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toDASStructure
public void toDASStructure(XMLWriter xw) throws IOException
Convert a protein Structure to a DAS Structure XML response . Since 5.0, bond (CONECT records) information is not supported anymore.- Parameters:
xw
- a XMLWriter object- Throws:
IOException
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toMMCIF
public static String toMMCIF(Chain chain, String authId, String asymId, boolean writeHeader)
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getAtomSiteHeader
public static String getAtomSiteHeader()
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