public class SmilesMolSupplier extends MolSupplier
swigCMemOwn
Modifier | Constructor and Description |
---|---|
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SmilesMolSupplier() |
protected |
SmilesMolSupplier(long cPtr,
boolean cMemoryOwn) |
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SmilesMolSupplier(java.lang.String fileName) |
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SmilesMolSupplier(java.lang.String fileName,
java.lang.String delimiter) |
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SmilesMolSupplier(java.lang.String fileName,
java.lang.String delimiter,
int smilesColumn) |
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SmilesMolSupplier(java.lang.String fileName,
java.lang.String delimiter,
int smilesColumn,
int nameColumn) |
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SmilesMolSupplier(java.lang.String fileName,
java.lang.String delimiter,
int smilesColumn,
int nameColumn,
boolean titleLine) |
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SmilesMolSupplier(java.lang.String fileName,
java.lang.String delimiter,
int smilesColumn,
int nameColumn,
boolean titleLine,
boolean sanitize) |
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SmilesMolSupplier(SWIGTYPE_p_std__istream inStream) |
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SmilesMolSupplier(SWIGTYPE_p_std__istream inStream,
boolean takeOwnership) |
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SmilesMolSupplier(SWIGTYPE_p_std__istream inStream,
boolean takeOwnership,
java.lang.String delimiter) |
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SmilesMolSupplier(SWIGTYPE_p_std__istream inStream,
boolean takeOwnership,
java.lang.String delimiter,
int smilesColumn) |
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SmilesMolSupplier(SWIGTYPE_p_std__istream inStream,
boolean takeOwnership,
java.lang.String delimiter,
int smilesColumn,
int nameColumn) |
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SmilesMolSupplier(SWIGTYPE_p_std__istream inStream,
boolean takeOwnership,
java.lang.String delimiter,
int smilesColumn,
int nameColumn,
boolean titleLine) |
|
SmilesMolSupplier(SWIGTYPE_p_std__istream inStream,
boolean takeOwnership,
java.lang.String delimiter,
int smilesColumn,
int nameColumn,
boolean titleLine,
boolean sanitize) |
Modifier and Type | Method and Description |
---|---|
boolean |
atEnd() |
void |
delete() |
protected void |
finalize() |
protected static long |
getCPtr(SmilesMolSupplier obj) |
java.lang.String |
getItemText(long idx) |
void |
init() |
long |
length() |
void |
moveTo(long idx) |
ROMol |
next() |
void |
reset() |
void |
setData(java.lang.String text) |
void |
setData(java.lang.String text,
java.lang.String delimiter) |
void |
setData(java.lang.String text,
java.lang.String delimiter,
int smilesColumn) |
void |
setData(java.lang.String text,
java.lang.String delimiter,
int smilesColumn,
int nameColumn) |
void |
setData(java.lang.String text,
java.lang.String delimiter,
int smilesColumn,
int nameColumn,
boolean titleLine) |
void |
setData(java.lang.String text,
java.lang.String delimiter,
int smilesColumn,
int nameColumn,
boolean titleLine,
boolean sanitize) |
getCPtr
protected SmilesMolSupplier(long cPtr, boolean cMemoryOwn)
public SmilesMolSupplier(java.lang.String fileName, java.lang.String delimiter, int smilesColumn, int nameColumn, boolean titleLine, boolean sanitize)
fileName
- - the name of smiles table file
delimiter - delimiting characters between records on a each line NOTE that this is not a string, the tokenizer looks for the individual characters in delimiter, not the full string itself. So the default delimiter: ' ', means ' ' or ' '.
smilesColumn - column number for the SMILES string (defaults to the first column)
nameColumn - column number for the molecule name (defaults to the second column) If set to -1 we assume that no name is available for the molecule and the name is defaulted to the smiles string
titleLine - if true, the first line is assumed to list the names of properties in order seperated by 'delimiter'. It is also assume that the 'SMILES' column and the 'name' column are not specified here if false - no title line is assumed and the properties are recorded as the 'columnX' where 'X' is the cloumn number
sanitize - if true sanitize the molecule before returning itpublic SmilesMolSupplier(java.lang.String fileName, java.lang.String delimiter, int smilesColumn, int nameColumn, boolean titleLine)
fileName
- - the name of smiles table file
delimiter - delimiting characters between records on a each line NOTE that this is not a string, the tokenizer looks for the individual characters in delimiter, not the full string itself. So the default delimiter: ' ', means ' ' or ' '.
smilesColumn - column number for the SMILES string (defaults to the first column)
nameColumn - column number for the molecule name (defaults to the second column) If set to -1 we assume that no name is available for the molecule and the name is defaulted to the smiles string
titleLine - if true, the first line is assumed to list the names of properties in order seperated by 'delimiter'. It is also assume that the 'SMILES' column and the 'name' column are not specified here if false - no title line is assumed and the properties are recorded as the 'columnX' where 'X' is the cloumn number
sanitize - if true sanitize the molecule before returning itpublic SmilesMolSupplier(java.lang.String fileName, java.lang.String delimiter, int smilesColumn, int nameColumn)
fileName
- - the name of smiles table file
delimiter - delimiting characters between records on a each line NOTE that this is not a string, the tokenizer looks for the individual characters in delimiter, not the full string itself. So the default delimiter: ' ', means ' ' or ' '.
smilesColumn - column number for the SMILES string (defaults to the first column)
nameColumn - column number for the molecule name (defaults to the second column) If set to -1 we assume that no name is available for the molecule and the name is defaulted to the smiles string
titleLine - if true, the first line is assumed to list the names of properties in order seperated by 'delimiter'. It is also assume that the 'SMILES' column and the 'name' column are not specified here if false - no title line is assumed and the properties are recorded as the 'columnX' where 'X' is the cloumn number
sanitize - if true sanitize the molecule before returning itpublic SmilesMolSupplier(java.lang.String fileName, java.lang.String delimiter, int smilesColumn)
fileName
- - the name of smiles table file
delimiter - delimiting characters between records on a each line NOTE that this is not a string, the tokenizer looks for the individual characters in delimiter, not the full string itself. So the default delimiter: ' ', means ' ' or ' '.
smilesColumn - column number for the SMILES string (defaults to the first column)
nameColumn - column number for the molecule name (defaults to the second column) If set to -1 we assume that no name is available for the molecule and the name is defaulted to the smiles string
titleLine - if true, the first line is assumed to list the names of properties in order seperated by 'delimiter'. It is also assume that the 'SMILES' column and the 'name' column are not specified here if false - no title line is assumed and the properties are recorded as the 'columnX' where 'X' is the cloumn number
sanitize - if true sanitize the molecule before returning itpublic SmilesMolSupplier(java.lang.String fileName, java.lang.String delimiter)
fileName
- - the name of smiles table file
delimiter - delimiting characters between records on a each line NOTE that this is not a string, the tokenizer looks for the individual characters in delimiter, not the full string itself. So the default delimiter: ' ', means ' ' or ' '.
smilesColumn - column number for the SMILES string (defaults to the first column)
nameColumn - column number for the molecule name (defaults to the second column) If set to -1 we assume that no name is available for the molecule and the name is defaulted to the smiles string
titleLine - if true, the first line is assumed to list the names of properties in order seperated by 'delimiter'. It is also assume that the 'SMILES' column and the 'name' column are not specified here if false - no title line is assumed and the properties are recorded as the 'columnX' where 'X' is the cloumn number
sanitize - if true sanitize the molecule before returning itpublic SmilesMolSupplier(java.lang.String fileName)
fileName
- - the name of smiles table file
delimiter - delimiting characters between records on a each line NOTE that this is not a string, the tokenizer looks for the individual characters in delimiter, not the full string itself. So the default delimiter: ' ', means ' ' or ' '.
smilesColumn - column number for the SMILES string (defaults to the first column)
nameColumn - column number for the molecule name (defaults to the second column) If set to -1 we assume that no name is available for the molecule and the name is defaulted to the smiles string
titleLine - if true, the first line is assumed to list the names of properties in order seperated by 'delimiter'. It is also assume that the 'SMILES' column and the 'name' column are not specified here if false - no title line is assumed and the properties are recorded as the 'columnX' where 'X' is the cloumn number
sanitize - if true sanitize the molecule before returning itpublic SmilesMolSupplier()
public SmilesMolSupplier(SWIGTYPE_p_std__istream inStream, boolean takeOwnership, java.lang.String delimiter, int smilesColumn, int nameColumn, boolean titleLine, boolean sanitize)
public SmilesMolSupplier(SWIGTYPE_p_std__istream inStream, boolean takeOwnership, java.lang.String delimiter, int smilesColumn, int nameColumn, boolean titleLine)
public SmilesMolSupplier(SWIGTYPE_p_std__istream inStream, boolean takeOwnership, java.lang.String delimiter, int smilesColumn, int nameColumn)
public SmilesMolSupplier(SWIGTYPE_p_std__istream inStream, boolean takeOwnership, java.lang.String delimiter, int smilesColumn)
public SmilesMolSupplier(SWIGTYPE_p_std__istream inStream, boolean takeOwnership, java.lang.String delimiter)
public SmilesMolSupplier(SWIGTYPE_p_std__istream inStream, boolean takeOwnership)
public SmilesMolSupplier(SWIGTYPE_p_std__istream inStream)
protected static long getCPtr(SmilesMolSupplier obj)
protected void finalize()
finalize
in class MolSupplier
public void delete()
delete
in class MolSupplier
public void setData(java.lang.String text, java.lang.String delimiter, int smilesColumn, int nameColumn, boolean titleLine, boolean sanitize)
public void setData(java.lang.String text, java.lang.String delimiter, int smilesColumn, int nameColumn, boolean titleLine)
public void setData(java.lang.String text, java.lang.String delimiter, int smilesColumn, int nameColumn)
public void setData(java.lang.String text, java.lang.String delimiter, int smilesColumn)
public void setData(java.lang.String text, java.lang.String delimiter)
public void setData(java.lang.String text)
public void init()
init
in class MolSupplier
public void reset()
reset
in class MolSupplier
public ROMol next()
next
in class MolSupplier
public boolean atEnd()
atEnd
in class MolSupplier
public void moveTo(long idx)
public java.lang.String getItemText(long idx)
idx
- - which item to returnpublic long length()