1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
|
#include <RDGeneral/test.h>
#include <stdlib.h>
#include <stdio.h>
#include <GraphMol/GraphMol.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/SequenceParsers.h>
#include <GraphMol/FileParsers/SequenceWriters.h>
#define VERBOSE
static void testToPDB(const RDKit::ROMol &mol) {
std::string pdb = RDKit::MolToPDBBlock(mol);
printf(" PDB:\n%s\n", pdb.c_str());
}
static void testToSmiles(const RDKit::ROMol &mol) {
std::string smi = RDKit::MolToSmiles(mol, true);
printf(" Smiles: %s\n", smi.c_str());
}
static void testToSequence(const RDKit::ROMol &mol) {
std::string seq = RDKit::MolToSequence(mol);
printf(" Sequence: %s\n", seq.c_str());
}
static void testToHELM(const RDKit::ROMol &mol) {
std::string helm = RDKit::MolToHELM(mol);
printf(" HELM: %s\n", helm.c_str());
}
static void testSeq(const char *seq) {
RDKit::RWMol *mol = RDKit::SequenceToMol(seq);
testToSequence(*mol);
testToHELM(*mol);
testToSmiles(*mol);
testToPDB(*mol);
delete mol;
}
static void testHELM(const char *helm) {
RDKit::RWMol *mol = RDKit::HELMToMol(helm);
TEST_ASSERT(mol);
testToSequence(*mol);
testToHELM(*mol);
testToSmiles(*mol);
testToPDB(*mol);
delete mol;
}
static void testPDB(const char *pdb) {
RDKit::RWMol *mol = RDKit::PDBBlockToMol(pdb);
testToSequence(*mol);
testToHELM(*mol);
testToSmiles(*mol);
testToPDB(*mol);
delete mol;
}
static void testPDB() {
testPDB(
"ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 23 OD1 GLU A 3 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 24 OD2 GLU A 3 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00\n"
"ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00\n"
"CONECT 1 2\n"
"CONECT 2 1 3\n"
"CONECT 3 2 4 4 5\n"
"CONECT 4 3 3\n"
"CONECT 5 3 6\n"
"CONECT 6 5 7 9\n"
"CONECT 7 6 8 8 16\n"
"CONECT 8 7 7\n"
"CONECT 9 6 10\n"
"CONECT 10 9 11\n"
"CONECT 11 10 12\n"
"CONECT 12 11 13\n"
"CONECT 13 12 14 14 15\n"
"CONECT 14 13 13\n"
"CONECT 15 13\n"
"CONECT 16 7 17\n"
"CONECT 17 16 18 20\n"
"CONECT 18 17 19 19 25\n"
"CONECT 19 18 18\n"
"CONECT 20 17 21\n"
"CONECT 21 20 22\n"
"CONECT 22 21 23 23 24\n"
"CONECT 23 22 22\n"
"CONECT 24 22\n"
"CONECT 25 18 26\n"
"CONECT 26 25 27\n"
"CONECT 27 26 28 28 29\n"
"CONECT 28 27 27\n"
"CONECT 29 27\n"
"END\n");
}
int main() {
testSeq("GREG");
// The following is the sequence of crambin from 1CRN
testSeq("TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN");
testHELM("PEPTIDE1{G.R.E.G}$$$$");
// The following is the HELM for oxytocin
testHELM("PEPTIDE1{C.Y.I.Q.N.C.P.L.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$");
// The following is the HELM for gramicidin S
testHELM(
"PEPTIDE1{L.[dF].P.V.[Orn].L.[dF].P.V.[Orn]}$"
"PEPTIDE1,PEPTIDE1,10:R2-1:R1$$$");
// The following tests GREG from PDB file
testPDB();
return 0;
}
|
