public class PdbReader_3D
extends java.lang.Object
Modifier and Type | Class and Description |
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class |
PdbReader_3D.PdbAttributes
A kind of sheet that stores some strings.
|
Modifier and Type | Field and Description |
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int |
numberOfIntervals |
Constructor and Description |
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PdbReader_3D() |
Modifier and Type | Method and Description |
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static javax.vecmath.Matrix3f |
autorotateUpwards(Lipid_3D lip)
Tries to autorotate the passed lipid, so that its head faces upwards
|
javax.vecmath.Point3f[] |
calculateLevelExtremes(javax.vecmath.Point3f[] levelpoints)
Calculates all extremepoints in XZ directions from the passed list of
points.
|
boolean |
checkForModels(java.io.File file)
Tests (and only tests!) if the passed file contains multiple models
|
PdbReader_3D.PdbAttributes |
readAttributes(java.io.File file)
Reads in some attributes of the passed Pdb File.
|
PdbReader_3D.PdbAttributes |
readAttributes(java.lang.String[] pdbFile)
Reads in some attributes of the passed pdb file contents (must be the
lines from an Pdb File in Strings).
|
java.lang.String[] |
readFile(java.io.File file)
Just reads the passed pdb File
|
Lipid_3D |
readLipid(java.io.File file,
int modelnumber,
java.util.Vector<java.lang.String> alteredAtoms)
Constructs a Lipid_3D according to the file
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java.lang.String[][] |
readModel(java.lang.String[] strings,
int modelnumber)
Reads all ATOM/HETATM/TER lines for the specified model
|
Protein_3D |
readProtein(java.io.File file,
int modelnumber,
java.util.Vector<java.lang.String> alteredAtoms)
Constructs a Protein_3D according to the file
|
java.lang.String[] |
readSection(java.io.File file,
java.lang.String tag)
Reads (only!) the lines of a section in a pdb file that uses the passed
tag as recordname
|
float[] |
redoMesh(java.util.Vector<javax.vecmath.Point3f> finals,
javax.vecmath.Point3f tocheckwith) |
void |
shapeIt(Molecule_3D mol) |
public Protein_3D readProtein(java.io.File file, int modelnumber, java.util.Vector<java.lang.String> alteredAtoms) throws java.lang.Exception
file
- the
- number of the pdb model that should be taken into account.
Pass "0" for deafult model or if there isnt any!java.lang.Exception
- - if something went wrongpublic Lipid_3D readLipid(java.io.File file, int modelnumber, java.util.Vector<java.lang.String> alteredAtoms) throws java.lang.Exception
file
- the
- number of the pdb model that should be taken into account.
Pass "0" for deafult model or if there isnt any!java.lang.Exception
- - if something went wrongpublic java.lang.String[] readFile(java.io.File file) throws java.io.IOException
file
- java.io.IOException
public PdbReader_3D.PdbAttributes readAttributes(java.io.File file) throws java.io.IOException
java.lang.Exception
java.io.IOException
java.io.IOException
public PdbReader_3D.PdbAttributes readAttributes(java.lang.String[] pdbFile) throws java.io.IOException
Lines
- as Stringsjava.io.IOException
public void shapeIt(Molecule_3D mol)
public java.lang.String[][] readModel(java.lang.String[] strings, int modelnumber)
all
- the lines of the pdb file
first array=normal atoms, second array=opm atoms, third array
TER Entriesmodelnumber
- java.io.IOException
public boolean checkForModels(java.io.File file) throws java.io.IOException
file
- java.io.IOException
public static javax.vecmath.Matrix3f autorotateUpwards(Lipid_3D lip)
lip
- public java.lang.String[] readSection(java.io.File file, java.lang.String tag) throws java.io.IOException
file
- the
- tag (usually 6 letters) of the sectionjava.io.IOException
public javax.vecmath.Point3f[] calculateLevelExtremes(javax.vecmath.Point3f[] levelpoints)
levelpoints
- public float[] redoMesh(java.util.Vector<javax.vecmath.Point3f> finals, javax.vecmath.Point3f tocheckwith)