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java.lang.Objectorg.biojava.bio.structure.io.FileConvert
public class FileConvert
Methods to convert a structure object into different file formats.
Constructor Summary | |
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FileConvert(Structure struc)
Constructs a FileConvert object. |
Method Summary | |
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boolean |
doPrintConnections()
returns if the Connections should be added default is true; |
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 |
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 void |
toPDB(Atom a,
StringBuffer str)
print ATOM record in the following syntax |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public FileConvert(Structure struc)
struc
- a Structure objectMethod Detail |
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public boolean doPrintConnections()
public void setPrintConnections(boolean printConnections)
printConnections
- public String toPDB()
public static String toPDB(Atom a)
a
-
public static void toPDB(Atom a, StringBuffer str)
ATOM 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.
public void toDASStructure(XMLWriter xw) throws IOException
xw
- a XMLWriter object
IOException
- ...
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