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Table 4 The number of structures and the run times are listed for MOLGEN 5.0, MAYGEN and PMG with a diverse set of molecular formulae

From: MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle

Formula

Structures (by MOLGEN and MAYGEN)

MOLGEN runtime (s)

Per structure (ms)

MAYGEN runtime (s)

Per structure (ms)

Structures (by PMG)

PMG runtime (s)

Per structure (ms)

Ratio MAYGEN/MOLGEN

Ratio PMG/MAYGEN

\(\text {C}_{10}\text {H}_{15}\text {N}\)

2,569,697

10

0.004

37

0.015

4,166,699

792

0.191

3.7

21.406

\(\text {C}_{5}\text {HFIN}_{3}\text {O}\)

2,737,786

10

0.004

21

0.008

N/A

N/A

N/A

2.1

0

\(\text {C}_{7}\text {H}_{9}\text {NO}_{2}\)

3,237,132

10

0.004

28

0.009

5,451,213

580

0.107

2.8

20.715

\(\text {C}_{9}\text {H}_{12}\text {O}_{2}\)

3,276,662

11

0.004

38

0.012

3,276,662

232

0.071

3.455

6.106

\(\text {C}_{5}\text {H}_{6}\text {N}_{2}\text {O}{3}\)

4,513,867

12

0.003

43

0.01

14,679,025

2643

0.181

3.584

61.466

\(\text {C}_{9}\text {H}_{7}\text {N}\)

2,521,767

13

0.006

22

0.009

5,076,949

484

0.096

1.693

22

\(\text {C}_{5}\text {H}_{6}\text {P}_{2}\text {S}_{3}\)

4,513,867

15

0.004

40

0.009

N/A

> 24 h

N/A

2.667

0

\(\text {C}_{5}\text {H}_{2}\text {BrClN}_{2}\text {O}_{2}\)

5,211,489

16

0.004

38

0.008

N/A

N/A

N/A

2.375

0

\(\text {C}_{9}\text {H}_{7}\text {P}\)

2,521,767

16

0.007

21

0.009

3,885,840

357

0.092

1.313

17

\(\text {C}_{11}\text {H}_{10}\)

3,614,427

20

0.006

39

0.011

3,614,427

204

0.057

1.95

5.231

\(\text {C}_{8}\text {H}_{7}\text {NO}\)

5,005,355

20

0.004

38

0.008

9,641,272

926

0.097

1.9

24.369

\(\text {C}_{5}\text {H}_{2}\text {FIO}_{2}\text {P}_{2}\)

5,211,489

20

0.004

37

0.008

N/A

N/A

N/A

1.85

0

\(\text {C}_{8}\text {H}_{5}\text {NO}\)

3,999,703

21

0.006

30

0.008

8,492,691

852

0.101

1.426

28.4

\(\text {C}_{10}\text {H}_{16}\text {S}_{2}\)

4,676,149

21

0.005

87

0.019

N/A

> 24 h

N/A

4.143

0

\(\text {C}_{9}\text {H}_{10}\text {O}_{2}\)

6,843,602

24

0.004

68

0.01

6,843,602

502

0.074

2.834

7.383

\(\text {C}_{8}\text {H}_{7}\text {PS}\)

5,005,355

24

0.005

38

0.008

51,262,825

7177

0.141

1.584

188.869

\(\text {C}_{8}\text {H}_{5}\text {PS}\)

3,999,703

25

0.007

31

0.008

44,966,952

6058

0.135

1.24

195.42

\(\text {C}_{5}\text {H}_{5}\text {N}_{3}\text {O}_{2}\)

9,390,618

26

0.003

71

0.008

70,007,293

15,845

0.227

2.731

223.17

\(\text {C}_{10}\text {H}_{13}\text {N}\)

7,122,614

27

0.004

78

0.011

12,328,415

1850

0.151

2.889

23.718

\(\text {C}_{12}\text {H}_{20}\text {O}\)

6,100,808

28

0.005

185

0.031

6,100,808

1160

0.191

6.608

6.271

\(\text {C}_{9}\text {H}_{10}\text {S}_{2}\)

6,843,602

29

0.005

68

0.01

347,718,450

79,415

0.229

2.345

1167.868

\(\text {C}_{11}\text {H}_{8}\)

4,442,438

30

0.007

46

0.011

4,442,438

296

0.067

1.534

6.435

\(\text {C}_{10}\text {H}_{10}\text {O}\)

7,288,733

30

0.005

71

0.01

7,288,733

502

0.069

2.367

7.071

\(\text {C}_{5}\text {H}_{5}\text {P}_{3}\text {S}_{2}\)

9,390,618

32

0.004

69

0.008

N/A

> 24 h

N/A

2.157

0

\(\text {C}_{7}\text {H}_{6}\text {N}_{2}\text {O}\)

10,504,307

37

0.004

77

0.008

41,261,882

5440

0.132

2.082

70.65

\(\text {C}_{10}\text {H}_{8}\text {O}\)

9,693,195

47

0.005

88

0.01

9,693,195

748

0.078

1.873

8.5

\(\text {C}_{12}\text {H}_{14}\)

11,451,841

52

0.005

158

0.014

11,451,841

864

0.076

3.039

5.469

\(\text {C}_{10}\text {H}_{11}\text {N}\)

14,778,466

57

0.004

140

0.01

27,530,678

3411

0.124

2.457

24.365

\(\text {C}_{10}\text {H}_{14}\text {O}_{2}\)

16,422,284

57

0.004

217

0.014

16,422,284

1645

0.101

3.808

7.581

\(\text {C}_{5}\text {H}_{6}\text {BrClFIN}_{2}\text {O}\)

23,955,660

57

0.003

248

0.011

N/A

N/A

N/A

4.351

0

\(\text {C}_{11}\text {H}_{14}\text {O}\)

20,354,040

76

0.004

250

0.013

20,354,040

1714

0.085

3.29

6.856

\(\text {C}_{9}\text {H}_{11}\text {NO}\)

25,895,621

86

0.004

239

0.01

46,139,031

6088

0.132

2.78

25.473

\(\text {C}_{5}\text {HFIP}_{3}\text {S}_{2}\)

22,825,473

97

0.005

178

0.008

N/A

N/A

N/A

1.836

0

\(\text {C}_{7}\text {H}_{9}\text {Br}_{2}\text {Cl}_{2}\text {PS}\)

26,610,607

109

0.005

452

0.017

N/A

N/A

N/A

4.147

0

\(\text {C}_{12}\text {H}_{18}\text {O}\)

28,140,012

114

0.005

551

0.02

28,140,012

3656

0.13

4.834

6.636

\(\text {C}_{9}\text {H}_{12}\text {F}_{2}\text {I}_{2}\text {S}\)

25,427,769

126

0.005

558

0.022

N/A

N/A

N/A

4.429

0

\(\text {C}_{10}\text {H}_{12}\text {O}_{2}\)

42,261,751

146

0.004

474

0.012

42,261,751

3692

0.088

3.247

7.79

\(\text {C}_{9}\text {H}_{9}\text {NO}\)

43,311,373

156

0.004

365

0.009

83,676,810

10,116

0.121

2.34

27.716

\(\text {C}_{11}\text {H}_{12}\text {O}\)

46,647,199

181

0.004

498

0.011

46,647,199

3818

0.082

2.752

7.667

\(\text {C}_{12}\text {H}_{10}\)

37,720,012

210

0.006

405

0.011

37,720,012

3107

0.083

1.929

7.672

\(\text {C}_{9}\text {H}_{5}\text {NO}\)

36,456,956

214

0.006

275

0.008

84,685,537

11,133

0.132

1.286

40.484

\(\text {C}_{12}\text {H}_{4}\)

16,079,924

215

0.014

366

0.023

16,079,924

3675

0.229

1.703

10.041

\(\text {C}_{9}\text {H}_{7}\text {NO}\)

49,865,161

218

0.005

407

0.009

105,236,547

11,983

0.114

1.867

29.443

\(\text {C}_{12}\text {H}_{8}\)

43,435,791

307

0.008

449

0.011

43,435,791

4147

0.096

1.463

9.237

\(\text {C}_{12}\text {H}_{6}\)

34,030,905

325

0.01

508

0.015

34,030,905

4169

0.123

1.564

8.207

\(\text {C}_{11}\text {H}_{10}\text {O}\)

79,818,477

348

0.005

765

0.01

79,818,477

6856

0.086

2.199

8.963

\(\text {C}_{10}\text {H}_{4}\text {S}_{2}\)

495,428,30

413

0.009

472

0.01

N/A

> 24 h

N/A

1.143

0

\(\text {C}_{11}\text {H}_{10}\text {S}\)

79,818,477

429

0.006

751

0.01

N/A

> 24 h

N/A

1.751

0

\(\text {C}_{10}\text {H}_{8}\text {S}_{2}\)

105,772,510

466

0.005

963

0.01

N/A

> 24 h

N/A

2.067

0

\(\text {C}_{10}\text {H}_{6}\text {S}_{2}\)

93,964,875

552

0.006

850

0.01

N/A

> 24 h

N/A

1.54

0

  1. MAYGEN always generates the same number of structures as MOLGEN. Times for Molgen were determined with the -noaromaticity flag to achieve comparability. PMG generates more structures in some cases due to different valences of S, P and N, which is why the per molecule run time is also given in milliseconds (ms)
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Journal of Cheminformatics

ISSN: 1758-2946

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