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cffi_test.c
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cffi_test.c
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/*
Copyright (C) 2021 Greg Landrum
@@ 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 <stdio.h>
#include <string.h>
#include <stdlib.h>
#ifdef WIN32
#ifndef _USE_MATH_DEFINES
#define _USE_MATH_DEFINES
#define _DEFINED_USE_MATH_DEFINES
#endif
#endif
#include <math.h>
#ifdef _DEFINED_USE_MATH_DEFINES
#undef _DEFINED_USE_MATH_DEFINES
#undef _USE_MATH_DEFINES
#endif
#include "cffiwrapper.h"
#ifdef NDEBUG
#undef NDEBUG
#endif
#include <assert.h>
static const char molblock_native_wedging[] =
"\n\
MJ201100 \n\
\n\
18 21 0 0 1 0 0 0 0 0999 V2000\n\
-0.8540 -1.4441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-0.3019 -0.8310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.5185 -0.9172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.8540 -0.1635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.6825 0.6434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-0.1379 0.7296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-0.5504 1.4441 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
-0.4734 -0.0239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.2409 0.3885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-1.6609 -1.2726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-2.2130 -1.8857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-1.9580 -2.6703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-1.1511 -2.8419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-0.5990 -2.2287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-3.0201 -1.7143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-3.5720 -2.3275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-3.3171 -3.1121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-2.5100 -3.2835 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
2 3 1 0 0 0 0\n\
4 3 1 0 0 0 0\n\
4 5 1 0 0 0 0\n\
6 5 1 0 0 0 0\n\
6 7 1 1 0 0 0\n\
6 8 1 0 0 0 0\n\
8 9 1 1 0 0 0\n\
8 2 1 0 0 0 0\n\
4 9 1 1 0 0 0\n\
2 1 1 1 0 0 0\n\
10 11 1 0 0 0 0\n\
11 12 2 0 0 0 0\n\
12 13 1 0 0 0 0\n\
13 14 2 0 0 0 0\n\
1 10 2 0 0 0 0\n\
1 14 1 0 0 0 0\n\
15 16 2 0 0 0 0\n\
16 17 1 0 0 0 0\n\
11 15 1 0 0 0 0\n\
17 18 2 0 0 0 0\n\
12 18 1 0 0 0 0\n\
M END\n";
static const char quinoline_scaffold[] =
"\n\
MJ201100 \n\
\n\
10 11 0 0 1 0 0 0 0 0999 V2000\n\
-8.1001 2.8219 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
-8.8145 2.4094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-8.8145 1.5843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-8.1001 1.1718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-7.3856 1.5843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-7.3856 2.4094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-6.6711 1.1718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-5.9566 1.5842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-5.9566 2.4092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-6.6711 2.8218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
2 3 1 0 0 0 0\n\
3 4 2 0 0 0 0\n\
4 5 1 0 0 0 0\n\
5 6 2 0 0 0 0\n\
7 8 2 0 0 0 0\n\
8 9 1 0 0 0 0\n\
9 10 2 0 0 0 0\n\
5 7 1 0 0 0 0\n\
10 6 1 0 0 0 0\n\
1 2 2 0 0 0 0\n\
6 1 1 0 0 0 0\n\
M END\n";
void find_wedged_bonds(char *molblock, int *have1, int *have6) {
molblock = strdup(molblock);
assert(molblock);
size_t molblock_len = strlen(molblock);
char *line_start = molblock;
char *line_end = strpbrk(line_start, "\n");
int line_num = 0;
unsigned int i;
unsigned int j;
unsigned int s;
unsigned int e;
int n_atoms = -1;
int n_bonds = -1;
int b[4];
*have1 = 0;
*have6 = 0;
while (line_end) {
*line_end = '\0';
if (line_num == 3) {
assert(strlen(line_start) > 6);
line_start[6] = '\0';
sscanf(&line_start[3], "%d", &n_bonds);
line_start[3] = '\0';
sscanf(line_start, "%d", &n_atoms);
assert(n_atoms >= 0 && n_bonds >= 0);
} else if (line_num > 3 + n_atoms && line_num < 4 + n_atoms + n_bonds) {
for (i = 0; i < 4; ++i) {
j = 3 - i;
s = j * 3;
e = (j + 1) * 3;
line_start[e] = '\0';
sscanf(&line_start[s], "%d", &b[j]);
}
assert(b[0] >= 1 && b[0] <= n_atoms);
assert(b[1] >= 1 && b[1] <= n_atoms);
assert(b[2] == 1 || b[2] == 2);
assert(b[3] == 0 || b[3] == 1 || b[3] == 6);
if (b[3] == 1) {
*have1 = 1;
}
if (b[3] == 6) {
*have6 = 1;
}
}
line_start = line_end + 1;
if (line_start >= molblock + molblock_len) {
break;
}
line_end = strpbrk(line_start, "\n");
if (!line_end) {
line_end = molblock + molblock_len;
}
++line_num;
}
free(molblock);
}
int extract_bond_coords(char *svg, char *bond, double *coord1, double *coord2) {
svg = strdup(svg);
assert(svg);
char *line = strtok(svg, "\n");
char *str = NULL;
double dummy[2];
coord1 = coord1 ? coord1 : dummy;
coord2 = coord2 ? coord2 : dummy;
while (line) {
str = strstr(line, bond);
if (str) {
str = strstr(str, "M ");
}
if (str) {
assert(sscanf(str, "M %lf,%lf L %lf,%lf", &coord1[0], &coord1[1],
&coord2[0], &coord2[1]) == 4);
break;
}
line = strtok(NULL, "\n");
}
free(svg);
return (str ? 1 : 0);
}
double angle_deg_between_vectors(double *v1, double *v2) {
return 180 / M_PI *
acos((v1[0] * v2[0] + v1[1] * v2[1]) /
sqrt((v1[0] * v1[0] + v1[1] * v1[1]) *
(v2[0] * v2[0] + v2[1] * v2[1])));
}
void test_io() {
char *pkl;
size_t pkl_size;
size_t pkl2_size;
char *pkl2;
printf("--------------------------\n");
printf(" test_io\n");
pkl = get_mol("c1cc(O)ccc1", &pkl_size, "");
assert(pkl);
assert(pkl_size > 0);
char *smiles = get_smiles(pkl, pkl_size, NULL);
assert(!strcmp(smiles, "Oc1ccccc1"));
free(smiles);
smiles = NULL;
smiles = get_cxsmiles(pkl, pkl_size, NULL);
assert(!strcmp(smiles, "Oc1ccccc1"));
free(smiles);
smiles = NULL;
char *json = get_json(pkl, pkl_size, NULL);
assert(strstr(json, "rdkitjson"));
pkl2 = get_mol(json, &pkl2_size, "");
assert(pkl2);
assert(pkl2_size > 0);
smiles = get_smiles(pkl2, pkl2_size, NULL);
assert(!strcmp(smiles, "Oc1ccccc1"));
free(smiles);
smiles = NULL;
free(pkl2);
pkl2 = NULL;
free(json);
json = NULL;
//---------
// failures
// kekulization
pkl2 = get_mol("c1cccc1", &pkl2_size, "");
assert(pkl2 == NULL);
assert(!pkl2_size);
// bad input
pkl2 = get_mol("foo", &pkl2_size, "");
assert(pkl2 == NULL);
assert(!pkl2_size);
// valence
pkl2 = get_mol("CO(C)C", &pkl2_size, "");
assert(pkl2 == NULL);
assert(!pkl2_size);
// bad molblock
pkl2 = get_mol(
" Mrv1921 05042106432D\n\
\n\
2 1 0 0 0 0 999 V2000\n\
-7.3214 3.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-6.6070 4.1625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
1 2 1 0 0 0 0\n\
M END",
&pkl2_size, "");
assert(pkl2 == NULL);
assert(!pkl2_size);
//---------
// options
pkl2 = get_mol("[H]C", &pkl2_size, "{\"removeHs\":false}");
assert(pkl2 != NULL);
assert(pkl2_size);
smiles = get_smiles(pkl2, pkl2_size, NULL);
assert(!strcmp(smiles, "[H]C"));
free(smiles);
smiles = NULL;
free(pkl2);
pkl2 = NULL;
pkl2 = get_mol("[H]C", &pkl2_size, NULL);
assert(pkl2 != NULL);
assert(pkl2_size);
free(pkl2);
pkl2 = NULL;
smiles = get_smiles(pkl, pkl_size, "{\"canonical\":false}");
assert(!strcmp(smiles, "c1cc(O)ccc1"));
free(smiles);
smiles = NULL;
//---------
// mol block
char *molblock = get_molblock(NULL, pkl_size, NULL);
assert(!molblock);
molblock = get_molblock(pkl, 0, NULL);
assert(!molblock);
molblock = get_molblock(pkl, pkl_size, NULL);
pkl2 = get_mol(molblock, &pkl2_size, "");
assert(pkl2);
assert(pkl2_size > 0);
smiles = get_smiles(pkl2, pkl2_size, NULL);
assert(!strcmp(smiles, "Oc1ccccc1"));
free(smiles);
smiles = NULL;
free(pkl2);
pkl2 = NULL;
free(molblock);
molblock = NULL;
pkl2 = get_mol(molblock_native_wedging, &pkl2_size, "");
assert(pkl2);
assert(pkl2_size > 0);
molblock = get_molblock(pkl2, pkl2_size, NULL);
assert(strstr(molblock, "4 3 1 6"));
assert(!strstr(molblock, "H "));
free(molblock);
molblock = get_molblock(pkl2, pkl2_size, "{\"useMolBlockWedging\":true}");
assert(!strstr(molblock, "4 3 1 6"));
assert(strstr(molblock, "6 7 1 1"));
assert(!strstr(molblock, "H "));
free(molblock);
molblock = get_molblock(pkl2, pkl2_size, "{\"addChiralHs\":true}");
assert(strstr(molblock, "H "));
free(molblock);
// Here we want to test that the original molblock wedging is preserved and
// inverted as the coordinates are rigid-body rotated
size_t scaffold_pkl_size;
int have1;
int have6;
char *scaffold = get_mol(quinoline_scaffold, &scaffold_pkl_size, NULL);
assert(set_2d_coords_aligned(&pkl2, &pkl2_size, scaffold, scaffold_pkl_size,
"{\"acceptFailure\":false,\"alignOnly\":true}",
NULL));
molblock = get_molblock(pkl2, pkl2_size, "{\"useMolBlockWedging\":true}");
find_wedged_bonds(molblock, &have1, &have6);
assert(!have1 && have6);
assert(!strstr(molblock, "4 3 1 6"));
assert(strstr(molblock, "6 7 1 6"));
assert(!strstr(molblock, "H "));
free(molblock);
free(pkl2);
// Here we want to test that the original molblock wedging gets cleared
// and hence wedging is recomputed as the coordinates are re-generated
pkl2 = get_mol(molblock_native_wedging, &pkl2_size, "");
assert(pkl2);
assert(pkl2_size > 0);
assert(set_2d_coords_aligned(&pkl2, &pkl2_size, scaffold, scaffold_pkl_size,
"{\"acceptFailure\":false}", NULL));
molblock = get_molblock(pkl2, pkl2_size, "{\"useMolBlockWedging\":true}");
find_wedged_bonds(molblock, &have1, &have6);
assert(have1 && have6);
free(molblock);
free(pkl2);
free(scaffold);
molblock = get_v3kmolblock(pkl, pkl_size, NULL);
pkl2 = get_mol(molblock, &pkl2_size, "");
assert(pkl2);
assert(pkl2_size > 0);
smiles = get_smiles(pkl2, pkl2_size, NULL);
assert(!strcmp(smiles, "Oc1ccccc1"));
free(smiles);
smiles = NULL;
free(pkl2);
pkl2 = NULL;
free(molblock);
molblock = NULL;
molblock = get_v3kmolblock(pkl, pkl_size, "{\"kekulize\":false}");
assert(strstr(molblock, "M V30 1 4 1 2"));
free(molblock);
molblock = NULL;
#ifdef RDK_BUILD_INCHI_SUPPORT
//---------
// InChI
char *inchi = get_inchi(pkl, pkl_size, NULL);
assert(!strcmp(inchi, "InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H"));
free(inchi);
inchi = get_inchikey_for_inchi("InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H");
assert(!strcmp(inchi, "ISWSIDIOOBJBQZ-UHFFFAOYSA-N"));
free(inchi);
inchi = get_inchi(pkl, pkl_size, "{\"options\":\"/FixedH\"}");
assert(!strcmp(inchi, "InChI=1/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H"));
free(inchi);
molblock = get_molblock(pkl, pkl_size, NULL);
inchi = get_inchi_for_molblock(molblock, NULL);
assert(!strcmp(inchi, "InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H"));
free(inchi);
inchi = get_inchi_for_molblock(molblock, "{\"options\":\"/FixedH\"}");
assert(!strcmp(inchi, "InChI=1/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H"));
free(inchi);
free(molblock);
#endif
//---------
// queries
char *smarts = get_smarts(pkl, pkl_size, NULL);
assert(!strcmp(smarts, "[#6]1:[#6]:[#6](-[#8]):[#6]:[#6]:[#6]:1"));
pkl2 = get_qmol(smarts, &pkl2_size, "");
assert(pkl2);
free(smarts);
smarts = get_smarts(pkl2, pkl2_size, NULL);
assert(!strcmp(smarts, "[#6]1:[#6]:[#6](-[#8]):[#6]:[#6]:[#6]:1"));
free(smarts);
free(pkl2);
free(pkl);
pkl = NULL;
printf(" done\n");
printf("--------------------------\n");
}
void test_svg() {
char *pkl;
size_t pkl_size;
printf("--------------------------\n");
printf(" test_svg\n");
pkl = get_mol("c1cc(O)ccc1", &pkl_size, "");
assert(pkl);
assert(pkl_size > 0);
char *svg = get_svg(pkl, pkl_size, "{\"width\":350,\"height\":300}");
assert(strstr(svg, "width='350px'"));
assert(strstr(svg, "height='300px'"));
assert(strstr(svg, "</svg>"));
free(svg);
svg = get_svg(pkl, pkl_size, "{\"atoms\": [0, 1, 2], \"width\":127}");
assert(strstr(svg, "fill:#FF7F7F"));
assert(strstr(svg, "width='127px'"));
assert(strstr(svg, "</svg>"));
free(svg);
svg = get_svg(
pkl, pkl_size,
"{\"highlightAtomColors\":{"
"\"0\": [1.0, 0.0, 0.0],"
"\"1\": [1.0, 0.0, 0.0],"
"\"2\": [1.0, 0.0, 0.0],"
"\"3\": [0.0, 1.0, 0.0],"
"\"4\": [1.0, 0.0, 0.0],"
"\"5\": [1.0, 0.0, 0.0],"
"\"6\": [1.0, 0.0, 0.0]"
"}, \"highlightBondColors\":{"
"\"2\": [0.0, 0.7, 0.9]"
"}, \"highlightAtomRadii\":{"
"\"0\": 0.1,"
"\"1\": 0.1,"
"\"2\": 0.1,"
"\"3\": 0.8,"
"\"4\": 0.1,"
"\"5\": 0.1,"
"\"6\": 0.1"
"}, \"atoms\": [0, 1, 2, 3, 4, 5, 6], \"bonds\": [2], \"width\":127}");
assert(!strstr(svg, "fill:#FF7F7F"));
assert(strstr(svg, "fill:#FF0000"));
assert(strstr(svg, "fill:#00FF00"));
assert(strstr(svg, "fill:#00B2E5"));
assert(strstr(svg, "width='127px'"));
assert(strstr(svg, "</svg>"));
free(svg);
free(pkl);
pkl = get_mol(molblock_native_wedging, &pkl_size, "");
assert(pkl);
assert(pkl_size > 0);
char *svg1 = get_svg(pkl, pkl_size, "{\"width\":350,\"height\":300}");
assert(strstr(svg1, "width='350px'"));
assert(strstr(svg1, "height='300px'"));
assert(strstr(svg1, "</svg>"));
assert(strstr(svg1, "atom-17"));
assert(strstr(svg1, "atom-18"));
assert(strstr(svg1, "atom-19"));
char *svg2 = get_svg(
pkl, pkl_size,
"{\"width\":350,\"height\":300,\"useMolBlockWedging\":true,\"wedgeBonds\":false,\"addChiralHs\":false}");
assert(strstr(svg2, "width='350px'"));
assert(strstr(svg2, "height='300px'"));
assert(strstr(svg2, "</svg>"));
assert(strstr(svg2, "atom-17"));
assert(!strstr(svg2, "atom-18"));
assert(!strstr(svg2, "atom-19"));
free(svg1);
free(svg2);
free(pkl);
printf(" done\n");
printf("--------------------------\n");
}
unsigned int count_occurrences(const char *str, const char *substr) {
unsigned int count = 0;
const char *from = str;
while (from = strstr(from, substr)) {
++count;
++from;
}
return count;
}
void test_rxn_svg() {
char *pkl;
size_t pkl_size;
printf("--------------------------\n");
printf(" test_rxn_svg\n");
pkl = get_rxn("[CH3:1][OH:2]>>[CH2:1]=[OH0:2]", &pkl_size, "");
assert(pkl);
assert(pkl_size > 0);
char *svg = get_rxn_svg(pkl, pkl_size, "{\"width\":350,\"height\":300}");
assert(strstr(svg, "width='350px'"));
assert(strstr(svg, "height='300px'"));
assert(strstr(svg, "</svg>"));
free(pkl);
pkl = get_rxn(
"$RXN\n\
\n\
RDKit\n\
\n\
1 1\n\
$MOL\n\
\n\
RDKit 2D\n\
\n\
2 1 0 0 0 0 0 0 0 0999 V2000\n\
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n\
1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0\n\
1 2 6 0\n\
V 1 [C&H3:1]\n\
V 2 [O&H1:2]\n\
M END\n\
$MOL\n\
\n\
RDKit 2D\n\
\n\
2 1 0 0 0 0 0 0 0 0999 V2000\n\
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n\
1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0\n\
1 2 2 0\n\
V 1 [C&H2:1]\n\
V 2 [O&H0:2]\n\
M END",
&pkl_size, "");
char *svg_from_block = get_rxn_svg(pkl, pkl_size, "");
assert(strstr(svg, "</svg>"));
assert(count_occurrences(svg, "<path") > 0);
assert(count_occurrences(svg, "<path") ==
count_occurrences(svg_from_block, "<path"));
free(svg);
free(svg_from_block);
free(pkl);
printf(" done\n");
printf("--------------------------\n");
}
void test_flexicanvas() {
char *pkl;
size_t pkl_size;
printf("--------------------------\n");
printf(" test_flexicanvas\n");
pkl = get_mol("CCCC", &pkl_size, "");
assert(pkl);
assert(pkl_size > 0);
char *svg = get_svg(pkl, pkl_size, "{\"width\":-1,\"height\":-1}");
assert(strstr(svg, "width='87px'"));
assert(strstr(svg, "height='19px'"));
assert(strstr(svg, "</svg>"));
free(svg);
free(pkl);
pkl = NULL;
printf(" done\n");
printf("--------------------------\n");
}
void test_substruct() {
printf("--------------------------\n");
printf(" test_substruct\n");
char *mpkl;
size_t mpkl_size;
mpkl = get_mol("Cl[C@H](F)C[C@H](F)Cl", &mpkl_size, "");
char *qpkl;
size_t qpkl_size;
qpkl = get_qmol("Cl[C@@H](F)C", &qpkl_size, "");
char *json = get_substruct_match(mpkl, mpkl_size, qpkl, qpkl_size, "");
assert(!strcmp(json, "{\"atoms\":[0,1,2,3],\"bonds\":[0,1,2]}"));
free(json);
json = get_substruct_matches(mpkl, mpkl_size, qpkl, qpkl_size, "");
assert(!strcmp(json,
"[{\"atoms\":[0,1,2,3],\"bonds\":[0,1,2]},{\"atoms\":[6,4,5,3]"
",\"bonds\":[5,4,3]}]"));
free(json);
// make sure using parameters works
json = get_substruct_match(mpkl, mpkl_size, qpkl, qpkl_size,
"{\"useChirality\":true}");
assert(!strcmp(json, "{\"atoms\":[6,4,5,3],\"bonds\":[5,4,3]}"));
free(json);
json = get_substruct_matches(mpkl, mpkl_size, qpkl, qpkl_size,
"{\"useChirality\":true}");
assert(!strcmp(json, "[{\"atoms\":[6,4,5,3],\"bonds\":[5,4,3]}]"));
free(json);
free(mpkl);
mpkl = NULL;
free(qpkl);
qpkl = NULL;
printf(" done\n");
printf("--------------------------\n");
}
void test_descriptors() {
printf("--------------------------\n");
printf(" test_descriptors\n");
char *mpkl;
size_t mpkl_size;
mpkl = get_mol("c1nccc(O)c1", &mpkl_size, "");
char *descrs = get_descriptors(mpkl, mpkl_size);
assert(strstr(descrs, "lipinskiHBA"));
assert(strstr(descrs, "NumAliphaticRings"));
assert(strstr(descrs, "chi3v"));
assert(strstr(descrs, "amw"));
free(descrs);
free(mpkl);
mpkl = NULL;
printf(" done\n");
printf("--------------------------\n");
}
void test_fingerprints() {
printf("--------------------------\n");
printf(" test_fingerprints\n");
assert(!get_morgan_fp(NULL, 0, NULL));
char *mpkl;
size_t mpkl_size;
mpkl = get_mol("c1nccc(O)c1", &mpkl_size, "");
const char *mfp_json = "{\"radius\":2,\"nBits\":1024}";
char *fp = get_morgan_fp(mpkl, mpkl_size, mfp_json);
assert(strlen(fp) == 1024);
free(fp);
fp = get_morgan_fp(mpkl, mpkl_size, "{\"radius\":1,\"nBits\":64}");
assert(!strcmp(
fp, "0011000000100000010000100000000000001001010000000000000000100000"));
free(fp);
fp = get_morgan_fp(mpkl, mpkl_size, "{\"radius\":2,\"nBits\":64}");
assert(!strcmp(
fp, "0011000000100000010000100000000000001001010000000010000010100001"));
free(fp);
size_t nbytes;
assert(!get_morgan_fp_as_bytes(NULL, 0, &nbytes, NULL));
fp = get_morgan_fp_as_bytes(mpkl, mpkl_size, &nbytes,
"{\"radius\":2,\"nBits\":64}");
assert(nbytes == 8);
free(fp);
assert(!get_rdkit_fp(NULL, 0, NULL));
fp = get_rdkit_fp(mpkl, mpkl_size, "{\"nBits\":64}");
assert(!strcmp(
fp, "1111011000111100011011011111011001111111110010000111000011111111"));
free(fp);
fp = get_rdkit_fp(mpkl, mpkl_size, "{\"nBits\":64,\"maxPath\":4}");
assert(!strcmp(
fp, "1111011000110000010001010111000001101011100010000001000011100011"));
free(fp);
assert(!get_rdkit_fp_as_bytes(NULL, 0, &nbytes, NULL));
fp = get_rdkit_fp_as_bytes(mpkl, mpkl_size, &nbytes, "{\"nBits\":64}");
assert(nbytes == 8);
free(fp);
assert(!get_pattern_fp(NULL, 0, NULL));
fp = get_pattern_fp(mpkl, mpkl_size, "{\"nBits\":64}");
assert(!strcmp(
fp, "1011111111111111110011011111011001011110111101111110101111010011"));
free(fp);
assert(!get_pattern_fp_as_bytes(NULL, 0, &nbytes, NULL));
fp = get_pattern_fp_as_bytes(mpkl, mpkl_size, &nbytes, "{\"nBits\":64}");
assert(nbytes == 8);
free(fp);
fp = get_pattern_fp(mpkl, mpkl_size,
"{\"nBits\":64,\"tautomericFingerprint\":true}");
assert(!strcmp(
fp, "1011111111111111110011111111011101011111111101111111111111011011"));
free(fp);
assert(!get_topological_torsion_fp(NULL, 0, NULL));
fp = get_topological_torsion_fp(mpkl, mpkl_size, "{\"nBits\":64}");
assert(!strcmp(
fp, "1100000000000000000000000000000000000000000011000000000011001100"));
free(fp);
assert(!get_topological_torsion_fp_as_bytes(NULL, 0, &nbytes, NULL));
fp = get_topological_torsion_fp_as_bytes(mpkl, mpkl_size, &nbytes,
"{\"nBits\":64}");
assert(nbytes == 8);
free(fp);
assert(!get_atom_pair_fp(NULL, 0, NULL));
fp = get_atom_pair_fp(mpkl, mpkl_size, "{\"nBits\":64}");
assert(!strcmp(
fp, "0000000000000000000000001110111011101100000000000000000011001100"));
free(fp);
fp = get_atom_pair_fp(mpkl, mpkl_size, "{\"nBits\":64,\"minLength\":2}");
assert(!strcmp(
fp, "0000000000000000000000001000111011100000000000000000000011001100"));
free(fp);
fp = get_atom_pair_fp(mpkl, mpkl_size, "{\"nBits\":64,\"maxLength\":2}");
assert(!strcmp(
fp, "0000000000000000000000001110111011001100000000000000000011000000"));
free(fp);
assert(!get_atom_pair_fp_as_bytes(NULL, 0, &nbytes, NULL));
fp = get_atom_pair_fp_as_bytes(mpkl, mpkl_size, &nbytes, "{\"nBits\":64}");
assert(nbytes == 8);
free(fp);
assert(!get_maccs_fp(NULL, 0));
fp = get_maccs_fp(mpkl, mpkl_size);
assert(!strcmp(
fp,
"00000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000001100000000000000100000001000001000000000101000100000000100001000111110"));
free(fp);
assert(!get_maccs_fp_as_bytes(NULL, 0, &nbytes));
fp = get_maccs_fp_as_bytes(mpkl, mpkl_size, &nbytes);
assert(nbytes == 21);
free(fp);
#ifdef RDK_BUILD_AVALON_SUPPORT
assert(!get_avalon_fp(NULL, 0, NULL));
fp = get_avalon_fp(mpkl, mpkl_size, "{\"nBits\":64}");
assert(!strcmp(
fp, "0001000001100011110001011100011100000110100010001110110001110011"));
free(fp);
assert(!get_avalon_fp_as_bytes(NULL, 0, nbytes, NULL));
fp = get_avalon_fp_as_bytes(mpkl, mpkl_size, &nbytes, "{\"nBits\":64}");
assert(nbytes == 8);
free(fp);
#endif
free(mpkl);
mpkl = NULL;
printf(" done\n");
printf("--------------------------\n");
}
void test_modifications() {
printf("--------------------------\n");
printf(" test_modifications\n");
char *mpkl;
size_t mpkl_size;
mpkl = get_mol("CCC", &mpkl_size, "");
assert(add_hs(&mpkl, &mpkl_size) > 0);
char *ctab = get_molblock(mpkl, mpkl_size, NULL);
assert(strstr(ctab, " H "));
free(ctab);
assert(remove_all_hs(&mpkl, &mpkl_size) > 0);
ctab = get_molblock(mpkl, mpkl_size, NULL);
assert(!strstr(ctab, " H "));
free(ctab);
free(mpkl);
mpkl = NULL;
printf(" done\n");
printf("--------------------------\n");
}
float **_get_coord_array(char *mpkl, size_t mpkl_size) {
char *molblock = get_molblock(mpkl, mpkl_size, NULL);
assert(molblock);
size_t molblock_len = strlen(molblock);
char *line_start = molblock;
char *line_end = strpbrk(line_start, "\n");
int line_num = 0;
float **res = NULL;
unsigned int i;
unsigned int j;
unsigned int s;
unsigned int e;
unsigned int atom_num = 0;
int n_atoms = 0;
while (line_end) {
*line_end = '\0';
if (line_num == 3) {
assert(strlen(line_start) > 3);
line_start[3] = '\0';
sscanf(line_start, "%d", &n_atoms);
if (n_atoms) {
res = (float **)malloc((n_atoms + 1) * sizeof(float *));
assert(res);
res[n_atoms] = NULL;
for (i = 0; i < n_atoms; ++i) {
res[i] = (float *)malloc(3 * sizeof(float));
assert(res[i]);
}
}
} else if (line_num > 3 && line_num < 4 + n_atoms && res) {
for (i = 0; i < 3; ++i) {
j = 2 - i;
s = j * 10;
e = (j + 1) * 10;
line_start[e] = '\0';
sscanf(&line_start[s], "%f", &res[atom_num][j]);
}
++atom_num;
}
line_start = line_end + 1;
if (line_start >= molblock + molblock_len) {
break;
}
line_end = strpbrk(line_start, "\n");
if (!line_end) {
line_end = molblock + molblock_len;
}
++line_num;
}
free(molblock);
return res;
}
void _free_coord_array(float **coord_array) {
size_t i = 0;
if (coord_array) {
while (coord_array[i]) {
free(coord_array[i++]);
}
free(coord_array);
}
}
float _sq_dist(float *xyz1, float *xyz2) {
float sqd = 0.;
unsigned int i;
for (i = 0; i < 3; ++i) {
sqd += (xyz1[i] - xyz2[i]) * (xyz1[i] - xyz2[i]);
}
return sqd;
}
void test_coords() {
printf("--------------------------\n");
printf(" test_coords\n");
char *mpkl;
size_t mpkl_size;
char *mpkl2;
size_t mpkl2_size;
char *mpkl3;
size_t mpkl3_size;
mpkl = get_mol("C1CNC1CC", &mpkl_size, "");
char *cxsmi = get_cxsmiles(mpkl, mpkl_size, NULL);
// no cxsmiles yet
assert(!strstr(cxsmi, "|"));
prefer_coordgen(0);
set_2d_coords(&mpkl, &mpkl_size);
free(cxsmi);
cxsmi = get_cxsmiles(mpkl, mpkl_size, NULL);
// since we have coords there's something there:
assert(strstr(cxsmi, "|"));
#ifdef RDK_BUILD_COORDGEN_SUPPORT
prefer_coordgen(1);
set_2d_coords(&mpkl, &mpkl_size);
prefer_coordgen(0);
char *cxsmi2 = get_cxsmiles(mpkl, mpkl_size, NULL);
assert(strstr(cxsmi2, "|"));
assert(strcmp(cxsmi, cxsmi2));
free(cxsmi2);
#endif
free(cxsmi);
// aligned
char *tpkl;
size_t tpkl_size;
char *tpkl2;
size_t tpkl2_size;
char *tpkl3;
size_t tpkl3_size;
tpkl = get_mol(
"\n\
Mrv2102 04062106432D\n\
\n\
0 0 0 0 0 999 V3000\n\
M V30 BEGIN CTAB\n\
M V30 COUNTS 6 6 0 0 0\n\
M V30 BEGIN ATOM\n\
M V30 1 R# 0 2.1032 0 0 RGROUPS=(1 1)\n\
M V30 2 C 0 0.5632 0 0\n\
M V30 3 C 1.0889 -0.5258 0 0\n\
M V30 4 C 0 -1.6147 0 0\n\
M V30 5 N -1.0889 -0.5258 0 0\n\
M V30 6 R# 2.6289 -0.5258 0 0 RGROUPS=(1 2)\n\
M V30 END ATOM\n\
M V30 BEGIN BOND\n\
M V30 1 1 1 2\n\
M V30 2 1 2 3\n\
M V30 3 1 3 4\n\
M V30 4 1 4 5\n\
M V30 5 1 2 5\n\
M V30 6 1 3 6\n\
M V30 END BOND\n\
M V30 END CTAB\n\
M END\n",
&tpkl_size, "");
assert(!set_2d_coords_aligned(&mpkl, &mpkl_size, tpkl, tpkl_size,
"{\"acceptFailure\":false}", NULL));
char *match_json;
assert(set_2d_coords_aligned(
&mpkl, &mpkl_size, tpkl, tpkl_size,
"{\"allowRGroups\":true,\"acceptFailure\":false}", &match_json));
assert(!strcmp(match_json, "{\"atoms\":[4,3,0,1,2],\"bonds\":[3,5,0,1,2]}"));
free(match_json);
assert(set_2d_coords_aligned(
&mpkl, &mpkl_size, tpkl, tpkl_size,
"{\"allowRGroups\":true,\"acceptFailure\":false,\"alignOnly\":true}",
&match_json));
assert(!strcmp(match_json, "{\"atoms\":[4,3,0,1,2],\"bonds\":[3,5,0,1,2]}"));
free(match_json);
free(tpkl);
// Github #4121: set_2d_coords_aligned crashes if template mol has no
// conformer
tpkl = get_mol("C1CNC1", &tpkl_size, NULL);
assert(!set_2d_coords_aligned(&mpkl, &mpkl_size, tpkl, tpkl_size, "", NULL));
free(tpkl);
// 3D
assert(add_hs(&mpkl, &mpkl_size));
assert(set_3d_coords(&mpkl, &mpkl_size, "") > 0);
char *cxsmi3 = get_cxsmiles(mpkl, mpkl_size, NULL);
assert(set_3d_coords(&mpkl, &mpkl_size, "{\"randomSeed\":123}") > 0);
assert(has_coords(mpkl, mpkl_size) == 3);
assert(set_3d_coords(&mpkl, &mpkl_size,
"{\"randomSeed\":123,\"coordMap\":{\"3\":[0,0,0],\"4\":["
"0,0,1.5],\"5\":[0,1.5,1.5]}}") > 0);
assert(has_coords(mpkl, mpkl_size) == 3);
cxsmi = get_cxsmiles(mpkl, mpkl_size, NULL);
// since we have coords there's something there:
assert(strstr(cxsmi, "|"));
// coords generated with two different seeds differ:
assert(strcmp(cxsmi, cxsmi3));
free(cxsmi3);
free(cxsmi);
free(mpkl);
mpkl = NULL;
// test set_2d_coords_aligned
tpkl = get_mol(
"\n\
RDKit 2D\n\
\n\
6 6 0 0 0 0 0 0 0 0999 V2000\n\
-13.7477 6.3036 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n\
-13.7477 4.7567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-12.6540 3.6628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-13.7477 2.5691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-14.8414 3.6628 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
-11.1071 3.6628 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n\
1 2 1 0\n\
2 3 1 0\n\
3 4 1 0\n\
4 5 1 0\n\
2 5 1 0\n\
3 6 1 0\n\
M RGP 2 1 1 6 2\n\
M END\n",
&tpkl_size, "");
mpkl = get_mol(
"\n\
RDKit 2D\n\
\n\
18 22 0 0 0 0 0 0 0 0999 V2000\n\
4.3922 -1.5699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
2.9211 -2.0479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
2.5995 -0.5349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
3.3731 0.8046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
4.8441 1.2825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
4.0704 -0.0568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
1.8666 0.7748 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.7736 -0.3197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.7749 -1.8666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-0.7718 -1.8679 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
-0.7731 -0.3208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-1.8679 0.7718 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n\
-4.0718 -0.0598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-4.3933 -1.5729 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-2.9222 -2.0509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-2.6008 -0.5379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\