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java.lang.Objectbelka.SelectExpression
public class SelectExpression
Object of this class represents an expression stating set of atoms. Object represents only part of the expression not including boolean logic. The boolean logic is implement by linking with next object and by knowing boolean operation 'and' or 'or' applied to sum values returned by current and next expressions.
For example expression:
val28 and *.CA
will be represented inside of the program by two objects of this class linked by boolean operation 'and'
obj1--and-->obj2
Constructor Summary | |
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SelectExpression(boolean notExpr)
Object constructor |
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SelectExpression(SelectExpression subExpression,
boolean notExpr)
Object constructor |
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SelectExpression(String molName,
String chainIds,
String assemblyName,
String assemblyNum,
String atomName,
boolean notExpr)
Object constructor |
Method Summary | |
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boolean |
assemblyMaySatisfy(Assembly assembly)
Returns true if any atom in assembly may satisfy the expression, false otherwise. |
boolean |
atomMaySatisfy(Atom atom)
Returns true if the atom may satisfy the expression, false otherwise. |
boolean |
chainMaySatisfy(Chain chain)
Returns true if any atom in chain may satisfy the expression, false otherwise. |
boolean |
isAndBoolean()
Returns true if boolean operation with next expression is 'and', false otherwise. |
boolean |
isOrBoolean()
Returns true if boolean operation with next expression is 'or', false otherwise. |
boolean |
moleculeMaySatisfy(Molecule mol)
Returns true if any atom in molecule may satisfy the expression, false otherwise. |
SelectExpression |
next()
Returns next expression. |
int |
numChainsSpecified()
The function returns the number of chains specified in selection. |
boolean |
satisfy(Molecule mol,
Chain chain,
Assembly assembly,
Atom atom)
Checks if specified atom from specified assembly from specified chain from specified molecule satisfies the selection. |
void |
setAssemblyAttribute(int assemblyAtt)
Sets assembly attribute. |
void |
setAtomAttribute(int atomAtt)
Sets atom attribute. |
boolean |
setNextAnd(SelectExpression expr)
Sets next expression and boolean operation 'and' with it. |
boolean |
setNextOr(SelectExpression expr)
Sets next expression and boolean operation 'or' with it. |
boolean |
specifiesChain(Chain chain)
Checks if given chain is explicitly specified in selection. |
boolean |
specifiesChainAs(Chain chain,
int index)
Checks if given chain is explicitly specified in selection in specific order. |
boolean |
specifiesMolecule(Molecule mol)
Checks if given molecule is explicitly specified in selection. |
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 SelectExpression(boolean notExpr)
notExpr
- flag for indicating that expression must be reversed.public SelectExpression(String molName, String chainIds, String assemblyName, String assemblyNum, String atomName, boolean notExpr)
molName
- molecule name. Ignored in selection if null.chainIds
- chain identifie. Ignored in selection if null or length
is not one.assemblyName
- assembly name. Ignored in selection if null.assemblyNum
- assembly number. Ignored in selection if not number.atomName
- atom name. Ignored in selection if null.notExpr
- flag for indicating that expression must be reversed.public SelectExpression(SelectExpression subExpression, boolean notExpr)
subExpression
- sub-expression, i.e. (...) or 1-20.notExpr
- flag to indicate that expression must be reversed.Method Detail |
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public void setAssemblyAttribute(int assemblyAtt)
assemblyAtt
- assembly attribute.public void setAtomAttribute(int atomAtt)
atomAtt
- atom attribute.public boolean isOrBoolean()
public boolean isAndBoolean()
public SelectExpression next()
public boolean setNextOr(SelectExpression expr)
expr
- expression to set.
public boolean setNextAnd(SelectExpression expr)
expr
- expression to set.
public boolean moleculeMaySatisfy(Molecule mol)
mol
- molecule to check.
public boolean chainMaySatisfy(Chain chain)
chain
- chain to check.
public boolean assemblyMaySatisfy(Assembly assembly)
assembly
- assembly to check.
public boolean atomMaySatisfy(Atom atom)
atom
- atom to check.
public boolean satisfy(Molecule mol, Chain chain, Assembly assembly, Atom atom)
mol
- molecule to check.chain
- chain to check.assembly
- assembly to check.atom
- atom to check.
public boolean specifiesMolecule(Molecule mol)
mol
- molecule to check.
public int numChainsSpecified()
public boolean specifiesChain(Chain chain)
chain
- chain to check.
public boolean specifiesChainAs(Chain chain, int index)
chain
- chain to check.index
- chain index in selection.
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