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rdkit/Code/DataStructs/Utils.cpp
Ricardo Rodriguez 7b7a8a4e17 Refactor iostreams includes (#8846) 
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
2025-10-08 16:08:01 +02:00

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// $Id$
//
// Copyright (c) 2002-20`0 greg Landrum, Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "BitVects.h"
#include "BitVectUtils.h"
#include <RDGeneral/Invariant.h>
//! Convert a SparseBitVector to an ExplicitBitVector
ExplicitBitVect *convertToExplicit(const SparseBitVect *sbv) {
unsigned int sl = sbv->getNumBits();
auto *ebv = new ExplicitBitVect(sl);
const IntSet *bset = sbv->getBitSet();
for (int it : *bset) {
ebv->setBit(it);
}
return ebv;
}
void a2b(const char *, char *);
//! \brief Construct a BitVect from the ASCII representation of a
//! Daylight fingerprint string
template <typename T>
void FromDaylightString(T &sbv, const std::string &s) {
sbv.clearBits();
size_t length = s.length();
size_t nBits;
if (s[length - 1] == '\n') {
length -= 1;
}
// 4 bytes in the ascii correspond to 3 bytes in the binary
// plus there's one extra ascii byte for the pad marker
length -= 1;
nBits = (3 * length / 4) * 8;
switch (s[length]) {
case '1':
nBits -= 16;
break;
case '2':
nBits -= 8;
break;
case '3':
break;
default:
throw "ValueError bad daylight fingerprint string";
}
size_t i = 0, nBitsDone = 0;
while (i < length) {
char bytes[3];
a2b(s.c_str() + i, bytes);
for (size_t j = 0; j < 3 && nBitsDone < nBits; j++) {
unsigned char query = 0x80;
for (size_t k = 0; k < 8; k++) {
if (bytes[j] & query) {
sbv.setBit(nBitsDone);
}
query >>= 1;
nBitsDone++;
}
}
i += 4;
}
}
template RDKIT_DATASTRUCTS_EXPORT void FromDaylightString(SparseBitVect &sbv,
const std::string &s);
template RDKIT_DATASTRUCTS_EXPORT void FromDaylightString(ExplicitBitVect &sbv,
const std::string &s);
//! \brief Construct a BitVect from the ASCII representation of a
//! BitString
template <typename T>
void FromBitString(T &sbv, const std::string &s) {
PRECONDITION(s.length() <= sbv.getNumBits(), "bad bitvect length");
sbv.clearBits();
for (unsigned int i = 0; i < sbv.getNumBits(); ++i) {
if (s[i] == '1') {
sbv.setBit(i);
}
}
}
template RDKIT_DATASTRUCTS_EXPORT void FromBitString(SparseBitVect &sbv,
const std::string &s);
template RDKIT_DATASTRUCTS_EXPORT void FromBitString(ExplicitBitVect &sbv,
const std::string &s);
//! converts 4 ascii bytes at a4 to 3 binary bytes
/*!
THE FOLLOWING IS TAKEN FROM THE DAYLIGHT CONTRIB PROGRAM
ascii2bits.c
*********************************************************************
*** a2b - converts 4 ascii bytes at a4 to 3 binary
*** bytes at b3.
***
*** ASCII: |=======+=======+=======+=======| etc.
*** ^
*** becomes... 3 <-> 4
*** v
*** BINARY: |=====+=====+=====+=====| etc.
********************************************************************
*/
void a2b(const char *a4, char *b3) {
int i;
char byte = 0x00, b = 0x00;
/*********************************************
*** Use the Daylight mapping to convert each
*** ascii char to its 6-bit code.
***
*** a4: |xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx (printable)
*** |=======+=======+=======+=======|
*** becomes...
*** a4: |00xxxxxx00xxxxxx00xxxxxx00xxxxxx
*** |=======+=======+=======+=======|
*********************************************/
for (i = 0; i < 4; ++i) {
switch (a4[i]) {
case '.':
byte = 0x00;
break; /* 00 = __000000 */
case '+':
byte = 0x01;
break; /* 01 = __000001 */
case '0':
byte = 0x02;
break; /* 02 = __000010 */
case '1':
byte = 0x03;
break; /* 03 = __000011 */
case '2':
byte = 0x04;
break; /* 04 = __000100 */
case '3':
byte = 0x05;
break; /* 05 = __000101 */
case '4':
byte = 0x06;
break; /* 06 = __000110 */
case '5':
byte = 0x07;
break; /* 07 = __000111 */
case '6':
byte = 0x08;
break; /* 08 = __001000 */
case '7':
byte = 0x09;
break; /* 09 = __001001 */
case '8':
byte = 0x0a;
break; /* 10 = __001010 */
case '9':
byte = 0x0b;
break; /* 11 = __001011 */
case 'A':
byte = 0x0c;
break; /* 12 = __001100 */
case 'B':
byte = 0x0d;
break; /* 13 = __001101 */
case 'C':
byte = 0x0e;
break; /* 14 = __001110 */
case 'D':
byte = 0x0f;
break; /* 15 = __001111 */
case 'E':
byte = 0x10;
break; /* 16 = __010000 */
case 'F':
byte = 0x11;
break; /* 17 = __010001 */
case 'G':
byte = 0x12;
break; /* 18 = __010010 */
case 'H':
byte = 0x13;
break; /* 19 = __010011 */
case 'I':
byte = 0x14;
break; /* 20 = __010100 */
case 'J':
byte = 0x15;
break; /* 21 = __010101 */
case 'K':
byte = 0x16;
break; /* 22 = __010110 */
case 'L':
byte = 0x17;
break; /* 23 = __010111 */
case 'M':
byte = 0x18;
break; /* 24 = __011000 */
case 'N':
byte = 0x19;
break; /* 25 = __011001 */
case 'O':
byte = 0x1a;
break; /* 26 = __011010 */
case 'P':
byte = 0x1b;
break; /* 27 = __011011 */
case 'Q':
byte = 0x1c;
break; /* 28 = __011100 */
case 'R':
byte = 0x1d;
break; /* 29 = __011101 */
case 'S':
byte = 0x1e;
break; /* 30 = __011110 */
case 'T':
byte = 0x1f;
break; /* 31 = __011111 */
case 'U':
byte = 0x20;
break; /* 32 = __100000 */
case 'V':
byte = 0x21;
break; /* 33 = __100001 */
case 'W':
byte = 0x22;
break; /* 34 = __100010 */
case 'X':
byte = 0x23;
break; /* 35 = __100011 */
case 'Y':
byte = 0x24;
break; /* 36 = __100100 */
case 'Z':
byte = 0x25;
break; /* 37 = __100101 */
case 'a':
byte = 0x26;
break; /* 38 = __100110 */
case 'b':
byte = 0x27;
break; /* 39 = __100111 */
case 'c':
byte = 0x28;
break; /* 40 = __101000 */
case 'd':
byte = 0x29;
break; /* 41 = __101001 */
case 'e':
byte = 0x2a;
break; /* 42 = __101010 */
case 'f':
byte = 0x2b;
break; /* 43 = __101011 */
case 'g':
byte = 0x2c;
break; /* 44 = __101100 */
case 'h':
byte = 0x2d;
break; /* 45 = __101101 */
case 'i':
byte = 0x2e;
break; /* 46 = __101110 */
case 'j':
byte = 0x2f;
break; /* 47 = __101111 */
case 'k':
byte = 0x30;
break; /* 48 = __110000 */
case 'l':
byte = 0x31;
break; /* 49 = __110001 */
case 'm':
byte = 0x32;
break; /* 50 = __110010 */
case 'n':
byte = 0x33;
break; /* 51 = __110011 */
case 'o':
byte = 0x34;
break; /* 52 = __110100 */
case 'p':
byte = 0x35;
break; /* 53 = __110101 */
case 'q':
byte = 0x36;
break; /* 54 = __110110 */
case 'r':
byte = 0x37;
break; /* 55 = __110111 */
case 's':
byte = 0x38;
break; /* 56 = __111000 */
case 't':
byte = 0x39;
break; /* 57 = __111001 */
case 'u':
byte = 0x3a;
break; /* 58 = __111010 */
case 'v':
byte = 0x3b;
break; /* 59 = __111011 */
case 'w':
byte = 0x3c;
break; /* 60 = __111100 */
case 'x':
byte = 0x3d;
break; /* 61 = __111101 */
case 'y':
byte = 0x3e;
break; /* 62 = __111110 */
case 'z':
byte = 0x3f;
break; /* 63 = __111111 */
}
/*********************************************
*** Now copy the 4x6=24 bits from a4 to b3.
***
*** a4: |--000000--111111--222222--333333
*** |=======+=======+=======+=======|
***
*** b3: |000000111111222222333333
*** |=====+=====+=====+=====|
*********************************************/
switch (i) {
case 0:
b3[0] = (byte << 2); /*** 6 bits into 1st byte ***/
break;
case 1:
b3[0] |= ((b = byte) >> 4); /*** 2 bits into 1st byte ***/
b3[1] = ((b = byte) << 4); /*** 4 bits into 2nd byte ***/
break;
case 2:
b3[1] |= ((b = byte) >> 2); /*** 4 bits into 2nd byte ***/
b3[2] = ((b = byte) << 6); /*** 2 bits into 3rd byte ***/
break;
case 3:
b3[2] |= byte; /*** 6 bits into 3rd byte ***/
break;
}
}
return;
}
// Demo Data:
// 256 bits:
//.b7HEa..ccc+gWEIr89.8lV8gOF3aXFFR.+Ps.mZ6lg.2
//
// 00000010 01110010 01010011 01000010 01100000
// 00000000 10100010 10001010 00000001 10110010
// 00100100 00010100 11011100 10100010 11000000
// 00101011 00011000 01001010 10110001 10100100
// 01000101 10011010 00110100 01010001 01110100
// 00000000 01011011 11100000 00001100 10100101
// 00100011 00011011
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