OEBitVector

class OEBitVector

This class represents OEBitVector.

The OEBitVector class is used to represent a resizable bitmap. These are commonly used to store fingerprints in cheminformatics.

Constructors

OEBitVector()
OEBitVector(unsigned int size)
OEBitVector(const OEBitVector &src)

When constructed with a size argument, this specifies the initial number of bits in the OEBitVector. When constructed without an argument, the default number of bits is architecture dependent, 32 bits on 32-bit hosts and 64 bits on 64-bit hosts. Initially, all the bits are set to zero.

OEBitVector(OERandom &rand, unsigned int size)

Creates a OEBitVector with size bits randomly initialized from the rand object.

OEBitVector(const unsigned char *data, unsigned int size)

Using this constructor is equivalent to creating a default constructed OEBitVector and then immediately calling OEBitVector.SetData with the data and size arguments.

operator<

bool operator<(const OEBitVector &other) const

operator=

OEBitVector &operator=(const OEBitVector &src)

operator&=

OEBitVector &operator&=(const OEBitVector &)

operator-=

OEBitVector &operator-=(const OEBitVector &)

operator[]

bool operator[](unsigned int bit) const

operator^=

OEBitVector &operator^=(unsigned int bit)
OEBitVector &operator^=(const OEBitVector &)

operator|=

OEBitVector &operator|=(unsigned int bit)
OEBitVector &operator|=(const OEBitVector &)

ClearBits

void ClearBits()

Clears all of the bits of the OEBitVector to zero.

CountBits

unsigned int CountBits() const

Counts the number of bits that are set to one, in the OEBitVector object.

FirstBit

int FirstBit() const

Returns the index of the first bit, i.e. the set bit with the lowest index, in the OEBitVector. Bit position indices are numbered from zero, and have a maximum of OEBitVector.GetSize -1. If the OEBitVector has no bits set, i.e. OEBitVector.IsEmpty returns true, this method return will return the value -1.

FromHexString

void FromHexString(const char *bvs)
void FromHexString(const std::string &bvs)

Converts a hexadecimal string, in either upper, lower or mixed case, into an OEBitVector. Each valid hexadecimal digit (0-9, a-f, A-F) translates to four bits in the OEBitVector. Note: Because OEBitVectors may have a length not divisible by four, the last character of an OEChem-generated hexadecimal string may be a non-hex digit encoding the correct length of the OEBitVector. Don’t worry if you see a non-hex digit at the end of a hexadecimal string.

See also

GetData

const unsigned char *GetData() const

Returns a pointer to the internal storage of the OEBitVector‘s bitmap. This pointer to a sequence of at least (OEBitVector.GetSize +7)/8 consecutive bytes. Bit index zero corresponds to the least significant bit of the first byte. All bits beyond OEBitVector.GetSize in the last byte are guaranteed to be zero. The OEBitVector.GetData method always returns a valid non-NULL pointer even if the number of bits is zero.

GetSize

unsigned int GetSize() const

Returns the size, in bits, of the OEBitVector. An OEBitVector may potentially contain zero bits.

IsBitOn

bool IsBitOn(unsigned int bit) const

Tests whether the bit as the specified position/index of an OEBitVector is set. Bit position indices are numbered from zero, and have a maximum of OEBitVector.GetSize -1. This method returns false for all indices greater than or equal to OEBitVector.GetSize.

IsEmpty

bool IsEmpty() const

Returns true if all the bits of an OEBitVector are zero. This is equivalent to, but much more efficient than, testing that OEBitVector.CountBits == 0. An OEBitVector of zero size is considered empty.

LastBit

int LastBit() const

Returns the index of the last bit, i.e. the set bit with the highest index, in the OEBitVector. Bit position indices are numbered from zero, and have a maximum of OEBitVector.GetSize -1. If the OEBitVector has no bits set, i.e. OEBitVector.IsEmpty returns true, this method return will return the value -1.

NegateBits

void NegateBits()

Inverts all of the bits of an OEBitVector.

NextBit

int NextBit(unsigned int) const

Returns the next set bit after the specified bit position, i.e. the set bit with the lowest index greater than the argument. If there are no such set bits, or the value of bit is greater than or equal to OEBitVector.GetSize, this method returns the value -1.

PrevBit

int PrevBit(unsigned int) const

Returns the previous set bit before the specified bit position, i.e. the set bit with the highest index less than the argument. If there are no such set bits, this method returns the value -1. If the specified value of bit is greater than or equal to OEBitVector.GetSize, this method returns the same values as OEBitVector.LastBit.

SetBitOff

void SetBitOff(unsigned int bit)

Clears the bit at the specified bit position/index of an OEBitVector. Bit position indices are numbered from zero, and have a maximum of OEBitVector.GetSize -1. If the value of ‘bit’ is greater than or equal to OEBitVector.GetSize, the bitmap is resized to ‘bit’+1 bits. All of the new bits are initialized to zero.

SetBitOn

void SetBitOn(unsigned int bit)

Tests whether the bit as the specified position/index of an OEBitVector is set. Bit position indices are numbered from zero, and have a maximum of OEBitVector.GetSize -1. This method returns false for all indices greater than or equal to OEBitVector.GetSize.

SetData

void SetData(const unsigned char *data, unsigned int nbits)

Initialize the OEBitVector by the binary data pointed to by data, possibly resizing the OEBitVector to accommodate the nbits of data. data should point to at least nbits/8 bytes of data. If a non-multiple of 8 bits is to be copied it is the users responsibility to make sure the remainder of bits in the last byte are zeroed out.

SetRangeOff

void SetRangeOff(unsigned int start, unsigned int end)

SetRangeOn

void SetRangeOn(unsigned int start, unsigned int end)

SetSize

void SetSize(unsigned int bits)

Resizes an OEBitVector to the specified number of bits. A size argument of zero is allowed. If this method increases the size of an OEBitVector all of the new bit positions are initialized to zero.

ToHexString

void ToHexString(std::string &bvs) const

Generates a hexadecimal string representation of an OEBitVector. Each “nibble” of four bits is converted into an uppercase hexadecimal character.

../../_images/OEBitVector_ToHexString.png

The interpretation of the four-bit long “nibble”-s (big-endian system)

The four-bit long “nibble” shown above is encoded as hexadecimal ‘A’:

\(0 * 2^0 + 1 * 2^1 + 0 * 2^2 + 1 * 2^3 = 0 + 2 + 0 + 8 = 10 (dec) = A (hex)\)

Because OEBitVectors may have a length that is not a multiple of four, an extra non-hexadecimal digit is added to the end of the string to encode the correct OEBitVector length.

Interpretation of last character
last character number of extra bits
‘J’ 0
‘G’ 1
‘H’ 2
‘I’ 3

For example, if the size of the bit-vector is 8 (multiple of four), then the last character of the returned string will be ‘J’. If the size of the bit-vector is 9, then the last character will be ‘I’, since there will be three extra bits to add up to a number that can be multiplied by four.

See also

ToggleBit

void ToggleBit(unsigned int bit)

Inverts the bit at the specified bit position/index of an OEBitVector. Bit position indices are numbered from zero, and have a maximum of OEBitVector.GetSize -1. If the value of ‘bit’ is greater than or equal to OEBitVector.GetSize, the bitmap is resized to ‘bit’+1 bits. All of the new bits other than the one specified in the argument, i.e. the last, are initialized to zero.