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Fix truncated qhull stdio #187

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Fix truncated qhull stdio #187

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473b946
Flush qvoronoi output before reading it back
papillot Oct 7, 2026
8ddd86c
Update test references for the qvoronoi flush fix
papillot Oct 7, 2026
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1 change: 1 addition & 0 deletions src/voronoi.c
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Expand Up @@ -136,6 +136,7 @@ s_lst_vvertice *load_vvertices(s_pdb *pdb, s_fparams *params, float xshift, floa

// int status = system("qvoronoi p i Pp Fn < voro_tmp.dat > voro.tmp") ;
run_qvoronoi(fvoro, ftmp);
fflush(ftmp);
int status = M_VORONOI_SUCCESS;

if (status == M_VORONOI_SUCCESS)
Expand Down
62 changes: 33 additions & 29 deletions tests/reference_output/123abc_out/pocket25_atm.cif
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Original file line number Diff line number Diff line change
Expand Up @@ -6,21 +6,21 @@ This is a mmcif format file writen by the programm fpocket.
It represents the atoms contacted by the voronoi vertices of the pocket.

Information about the pocket 25:
0 - Pocket Score : -0.0372
1 - Drug Score : 0.0001
2 - Number of alpha spheres : 15
3 - Mean alpha-sphere radius : 4.0910
4 - Mean alpha-sphere Solvent Acc. : 0.5844
5 - Mean B-factor of pocket residues : 0.6654
6 - Hydrophobicity Score : 5.1667
7 - Polarity Score : 5
8 - Amino Acid based volume Score : 5.0000
9 - Pocket volume (Monte Carlo) : 272.5095
10 -Pocket volume (convex hull) : 4.5972
11 - Charge Score : -2
12 - Local hydrophobic density Score : 1.0000
13 - Number of apolar alpha sphere : 2
14 - Proportion of apolar alpha sphere : 0.1333
0 - Pocket Score : -0.0354
1 - Drug Score : 0.0021
2 - Number of alpha spheres : 19
3 - Mean alpha-sphere radius : 4.0159
4 - Mean alpha-sphere Solvent Acc. : 0.6640
5 - Mean B-factor of pocket residues : 0.4171
6 - Hydrophobicity Score : 28.5000
7 - Polarity Score : 3
8 - Amino Acid based volume Score : 4.1667
9 - Pocket volume (Monte Carlo) : 324.4589
10 -Pocket volume (convex hull) : 17.3477
11 - Charge Score : 0
12 - Local hydrophobic density Score : 15.0000
13 - Number of apolar alpha sphere : 16
14 - Proportion of apolar alpha sphere : 0.8421
#
loop_
_atom_site.group_PDB
Expand All @@ -39,18 +39,22 @@ _atom_site.occupancy
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_asym_id
ATOM 6291 O O ? GLU Dxp 9 ? 72.604 3.890 48.729 0.00 0 236 D
ATOM 6300 O O ? MET Dxp 10 ? 74.107 7.374 51.316 -2.14 0 237 D
ATOM 6293 C CG ? GLU Dxp 9 ? 71.423 4.039 52.375 0.00 0 236 D
ATOM 6312 O OE1 ? GLU Dxp 11 ? 77.808 6.551 52.358 0.00 0 238 D
ATOM 6299 C C ? MET Dxp 10 ? 74.371 7.293 50.096 0.00 0 237 D
ATOM 6305 N N ? GLU Dxp 11 ? 75.439 7.869 49.548 -2.19 0 238 D
ATOM 6309 C CB ? GLU Dxp 11 ? 77.861 8.128 49.916 0.00 0 238 D
ATOM 6510 C CE ? LYS Dxp 36 ? 78.782 6.894 42.671 0.00 0 263 D
ATOM 6511 N NZ ? LYS Dxp 36 ? 78.219 5.612 42.198 0.00 0 263 D
ATOM 6301 C CB ? MET Dxp 10 ? 73.225 7.186 47.771 0.00 0 237 D
ATOM 6335 O OD2 ? ASP Dxp 14 ? 78.726 9.496 45.541 -2.55 0 241 D
ATOM 6298 C CA ? MET Dxp 10 ? 73.486 6.472 49.131 0.00 0 237 D
ATOM 6491 C CZ2 ? TRP Dxp 34 ? 73.535 8.757 43.118 0.00 0 261 D
ATOM 6488 N NE1 ? TRP Dxp 34 ? 75.151 10.418 44.105 -1.09 0 261 D
ATOM 8324 C CB ? THR Dxp 268 ? 40.989 10.989 21.802 0.00 0 495 D
ATOM 8326 C CG2 ? THR Dxp 268 ? 40.062 11.269 20.618 0.00 0 495 D
ATOM 8325 O OG1 ? THR Dxp 268 ? 40.982 9.586 22.090 -1.88 0 495 D
ATOM 8296 C CA ? ALA Dxp 265 ? 40.286 11.932 26.156 0.00 0 492 D
ATOM 8125 C CD1 ? LEU Dxp 244 ? 36.891 14.630 29.976 0.00 0 471 D
ATOM 8114 C CB ? GLU Dxp 243 ? 33.026 18.463 28.302 0.00 0 470 D
ATOM 8089 O O ? LYS Dxp 240 ? 36.512 18.735 27.539 -4.29 0 467 D
ATOM 8117 O OE1 ? GLU Dxp 243 ? 32.380 17.276 25.754 0.00 0 470 D
ATOM 8298 O O ? ALA Dxp 265 ? 41.218 13.573 24.744 -0.40 0 492 D
ATOM 8299 C CB ? ALA Dxp 265 ? 39.150 12.430 27.083 0.00 0 492 D
ATOM 8126 C CD2 ? LEU Dxp 244 ? 39.085 15.575 29.317 0.00 0 471 D
ATOM 8090 C CB ? LYS Dxp 240 ? 36.370 18.986 24.210 0.00 0 467 D
ATOM 8334 C CE ? MET Dxp 269 ? 40.790 16.618 25.908 0.00 0 496 D
ATOM 8333 S SD ? MET Dxp 269 ? 40.299 17.538 24.487 0.00 0 496 D
ATOM 8331 C CB ? MET Dxp 269 ? 42.151 15.880 23.214 0.00 0 496 D
ATOM 8328 C CA ? MET Dxp 269 ? 42.550 15.278 21.865 0.00 0 496 D
ATOM 8332 C CG ? MET Dxp 269 ? 41.616 17.287 23.237 0.00 0 496 D
ATOM 8323 O O ? THR Dxp 268 ? 41.969 13.233 19.973 -1.62 0 495 D
#
60 changes: 34 additions & 26 deletions tests/reference_output/123abc_out/pocket25_env_atm.cif
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Expand Up @@ -17,30 +17,38 @@ _atom_site.occupancy
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_asym_id
ATOM 6290 C C ? GLU Dxp 9 ? 71.915 4.628 49.430 0.00 0 236 D
ATOM 6291 O O ? GLU Dxp 9 ? 72.604 3.890 48.729 0.00 0 236 D
ATOM 6292 C CB ? GLU Dxp 9 ? 70.763 3.288 51.242 0.00 0 236 D
ATOM 6293 C CG ? GLU Dxp 9 ? 71.423 4.039 52.375 0.00 0 236 D
ATOM 6297 N N ? MET Dxp 10 ? 72.265 5.885 49.709 0.00 0 237 D
ATOM 6298 C CA ? MET Dxp 10 ? 73.486 6.472 49.131 0.00 0 237 D
ATOM 6299 C C ? MET Dxp 10 ? 74.371 7.293 50.096 0.00 0 237 D
ATOM 6300 O O ? MET Dxp 10 ? 74.107 7.374 51.316 -2.14 0 237 D
ATOM 6301 C CB ? MET Dxp 10 ? 73.225 7.186 47.771 0.00 0 237 D
ATOM 6303 S SD ? MET Dxp 10 ? 72.034 9.214 46.200 0.00 0 237 D
ATOM 6304 C CE ? MET Dxp 10 ? 73.478 10.172 46.696 0.00 0 237 D
ATOM 6305 N N ? GLU Dxp 11 ? 75.439 7.869 49.548 -2.19 0 238 D
ATOM 6306 C CA ? GLU Dxp 11 ? 76.441 8.484 50.396 0.00 0 238 D
ATOM 6309 C CB ? GLU Dxp 11 ? 77.861 8.128 49.916 0.00 0 238 D
ATOM 6310 C CG ? GLU Dxp 11 ? 78.934 8.247 51.025 0.00 0 238 D
ATOM 6311 C CD ? GLU Dxp 11 ? 78.901 7.095 52.047 0.00 0 238 D
ATOM 6312 O OE1 ? GLU Dxp 11 ? 77.808 6.551 52.358 0.00 0 238 D
ATOM 6313 O OE2 ? GLU Dxp 11 ? 79.993 6.732 52.542 0.00 0 238 D
ATOM 6333 C CG ? ASP Dxp 14 ? 78.386 10.697 45.659 0.00 0 241 D
ATOM 6335 O OD2 ? ASP Dxp 14 ? 78.726 9.496 45.541 -2.55 0 241 D
ATOM 6488 N NE1 ? TRP Dxp 34 ? 75.151 10.418 44.105 -1.09 0 261 D
ATOM 6489 C CE2 ? TRP Dxp 34 ? 74.096 10.029 43.321 0.00 0 261 D
ATOM 6491 C CZ2 ? TRP Dxp 34 ? 73.535 8.757 43.118 0.00 0 261 D
ATOM 6509 C CD ? LYS Dxp 36 ? 78.417 8.015 41.707 0.00 0 263 D
ATOM 6510 C CE ? LYS Dxp 36 ? 78.782 6.894 42.671 0.00 0 263 D
ATOM 6511 N NZ ? LYS Dxp 36 ? 78.219 5.612 42.198 0.00 0 263 D
ATOM 8087 C CA ? LYS Dxp 240 ? 35.790 19.715 25.429 0.00 0 467 D
ATOM 8088 C C ? LYS Dxp 240 ? 36.703 19.593 26.682 0.00 0 467 D
ATOM 8089 O O ? LYS Dxp 240 ? 36.512 18.735 27.539 -4.29 0 467 D
ATOM 8090 C CB ? LYS Dxp 240 ? 36.370 18.986 24.210 0.00 0 467 D
ATOM 8112 C C ? GLU Dxp 243 ? 33.911 18.359 30.524 0.00 0 470 D
ATOM 8114 C CB ? GLU Dxp 243 ? 33.026 18.463 28.302 0.00 0 470 D
ATOM 8115 C CG ? GLU Dxp 243 ? 31.855 18.898 27.435 0.00 0 470 D
ATOM 8116 C CD ? GLU Dxp 243 ? 32.058 18.467 25.971 0.00 0 470 D
ATOM 8117 O OE1 ? GLU Dxp 243 ? 32.380 17.276 25.754 0.00 0 470 D
ATOM 8119 N N ? LEU Dxp 244 ? 35.188 18.111 30.233 0.00 0 471 D
ATOM 8120 C CA ? LEU Dxp 244 ? 36.034 17.247 31.068 0.00 0 471 D
ATOM 8123 C CB ? LEU Dxp 244 ? 37.398 17.066 30.398 0.00 0 471 D
ATOM 8124 C CG ? LEU Dxp 244 ? 37.965 15.640 30.361 0.00 0 471 D
ATOM 8125 C CD1 ? LEU Dxp 244 ? 36.891 14.630 29.976 0.00 0 471 D
ATOM 8126 C CD2 ? LEU Dxp 244 ? 39.085 15.575 29.317 0.00 0 471 D
ATOM 8292 C C ? GLN Dxp 264 ? 41.753 10.035 25.957 0.00 0 491 D
ATOM 8293 O O ? GLN Dxp 264 ? 42.056 10.340 24.813 0.00 0 491 D
ATOM 8295 N N ? ALA Dxp 265 ? 40.896 10.736 26.684 0.00 0 492 D
ATOM 8296 C CA ? ALA Dxp 265 ? 40.286 11.932 26.156 0.00 0 492 D
ATOM 8297 C C ? ALA Dxp 265 ? 41.301 13.030 25.810 0.00 0 492 D
ATOM 8298 O O ? ALA Dxp 265 ? 41.218 13.573 24.744 -0.40 0 492 D
ATOM 8299 C CB ? ALA Dxp 265 ? 39.150 12.430 27.083 0.00 0 492 D
ATOM 8321 C CA ? THR Dxp 268 ? 42.435 11.486 21.533 0.00 0 495 D
ATOM 8322 C C ? THR Dxp 268 ? 42.348 12.940 21.106 0.00 0 495 D
ATOM 8323 O O ? THR Dxp 268 ? 41.969 13.233 19.973 -1.62 0 495 D
ATOM 8324 C CB ? THR Dxp 268 ? 40.989 10.989 21.802 0.00 0 495 D
ATOM 8325 O OG1 ? THR Dxp 268 ? 40.982 9.586 22.090 -1.88 0 495 D
ATOM 8326 C CG2 ? THR Dxp 268 ? 40.062 11.269 20.618 0.00 0 495 D
ATOM 8327 N N ? MET Dxp 269 ? 42.706 13.838 22.024 0.00 0 496 D
ATOM 8328 C CA ? MET Dxp 269 ? 42.550 15.278 21.865 0.00 0 496 D
ATOM 8331 C CB ? MET Dxp 269 ? 42.151 15.880 23.214 0.00 0 496 D
ATOM 8332 C CG ? MET Dxp 269 ? 41.616 17.287 23.237 0.00 0 496 D
ATOM 8333 S SD ? MET Dxp 269 ? 40.299 17.538 24.487 0.00 0 496 D
ATOM 8334 C CE ? MET Dxp 269 ? 40.790 16.618 25.908 0.00 0 496 D
#
34 changes: 19 additions & 15 deletions tests/reference_output/123abc_out/pocket25_vert.pqr
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@@ -1,17 +1,21 @@
ATOM 1 O STP 25 75.274 3.616 51.622 0.00 3.95
ATOM 2 O STP 25 75.447 3.857 51.198 0.00 3.77
ATOM 3 O STP 25 77.265 3.650 48.742 0.00 4.67
ATOM 4 O STP 25 77.429 5.196 46.574 0.00 4.47
ATOM 5 O STP 25 76.872 5.560 46.252 0.00 4.27
ATOM 6 O STP 25 77.405 5.505 46.519 0.00 4.32
ATOM 7 O STP 25 76.830 5.855 46.190 0.00 4.16
ATOM 8 O STP 25 76.241 3.921 50.013 0.00 3.86
ATOM 9 O STP 25 76.891 3.834 49.144 0.00 4.31
ATOM 10 O STP 25 76.615 4.112 49.507 0.00 3.94
ATOM 11 O STP 25 76.919 4.561 46.576 0.00 4.69
ATOM 12 C STP 25 75.852 6.436 45.091 0.00 3.83
ATOM 13 C STP 25 76.021 6.874 45.250 0.00 3.78
ATOM 14 O STP 25 76.062 7.019 45.119 0.00 3.66
ATOM 15 O STP 25 75.987 6.992 45.287 0.00 3.72
ATOM 1 C STP 25 37.306 10.649 23.617 0.00 4.12
ATOM 2 O STP 25 34.891 15.746 27.462 0.00 3.40
ATOM 3 C STP 25 38.162 12.433 23.369 0.00 3.54
ATOM 4 C STP 25 36.924 15.273 26.348 0.00 3.68
ATOM 5 O STP 25 35.984 14.933 25.598 0.00 4.30
ATOM 6 O STP 25 35.896 14.879 25.845 0.00 4.26
ATOM 7 C STP 25 37.353 12.875 23.349 0.00 4.17
ATOM 8 C STP 25 37.315 15.454 26.104 0.00 3.67
ATOM 9 C STP 25 37.089 15.397 25.586 0.00 3.91
ATOM 10 C STP 25 38.261 14.808 22.014 0.00 4.21
ATOM 11 C STP 25 37.032 14.647 23.931 0.00 4.40
ATOM 12 C STP 25 37.167 15.254 25.183 0.00 3.94
ATOM 13 C STP 25 37.799 14.876 24.721 0.00 3.66
ATOM 14 C STP 25 37.439 16.076 25.622 0.00 3.41
ATOM 15 C STP 25 37.944 15.449 20.954 0.00 4.70
ATOM 16 C STP 25 38.906 14.530 21.989 0.00 3.72
ATOM 17 C STP 25 38.026 15.324 21.193 0.00 4.57
ATOM 18 C STP 25 38.196 15.118 21.517 0.00 4.37
ATOM 19 C STP 25 38.291 15.246 21.487 0.00 4.28
TER
END
71 changes: 29 additions & 42 deletions tests/reference_output/123abc_out/pocket26_atm.cif
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Expand Up @@ -6,21 +6,21 @@ This is a mmcif format file writen by the programm fpocket.
It represents the atoms contacted by the voronoi vertices of the pocket.

Information about the pocket 26:
0 - Pocket Score : -0.0384
1 - Drug Score : 0.0846
2 - Number of alpha spheres : 45
3 - Mean alpha-sphere radius : 3.7304
4 - Mean alpha-sphere Solvent Acc. : 0.4267
5 - Mean B-factor of pocket residues : 0.1353
6 - Hydrophobicity Score : 57.6667
7 - Polarity Score : 0
8 - Amino Acid based volume Score : 3.5833
9 - Pocket volume (Monte Carlo) : 229.2369
10 -Pocket volume (convex hull) : 15.0678
11 - Charge Score : 0
12 - Local hydrophobic density Score : 38.0000
13 - Number of apolar alpha sphere : 39
14 - Proportion of apolar alpha sphere : 0.8667
0 - Pocket Score : -0.0372
1 - Drug Score : 0.0001
2 - Number of alpha spheres : 15
3 - Mean alpha-sphere radius : 4.0910
4 - Mean alpha-sphere Solvent Acc. : 0.5844
5 - Mean B-factor of pocket residues : 0.6654
6 - Hydrophobicity Score : 5.1667
7 - Polarity Score : 5
8 - Amino Acid based volume Score : 5.0000
9 - Pocket volume (Monte Carlo) : 271.5010
10 -Pocket volume (convex hull) : 4.5972
11 - Charge Score : -2
12 - Local hydrophobic density Score : 1.0000
13 - Number of apolar alpha sphere : 2
14 - Proportion of apolar alpha sphere : 0.1333
#
loop_
_atom_site.group_PDB
Expand All @@ -39,31 +39,18 @@ _atom_site.occupancy
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_asym_id
ATOM 1821 C CG1 ? VAL Axp 241 ? 18.722 33.273 0.801 0.00 0 468 A
ATOM 824 N N ? LEU Axp 114 ? 19.877 26.311 -1.669 0.00 0 341 A
ATOM 818 C C ? LEU Axp 113 ? 20.351 26.072 -0.464 0.00 0 340 A
ATOM 825 C CA ? LEU Axp 114 ? 18.529 26.785 -1.887 0.00 0 341 A
ATOM 798 C CA ? ALA Axp 110 ? 24.131 27.516 -4.659 0.00 0 337 A
ATOM 1805 C CD ? PRO Axp 238 ? 21.822 33.590 -2.836 0.00 0 465 A
ATOM 1792 O O ? GLY Axp 236 ? 25.501 33.661 -3.290 -6.17 0 463 A
ATOM 801 C CB ? ALA Axp 110 ? 24.277 28.499 -5.862 0.00 0 337 A
ATOM 819 O O ? LEU Axp 113 ? 19.663 26.116 0.542 -1.07 0 340 A
ATOM 856 C CB ? ALA Axp 117 ? 16.641 27.654 2.208 0.00 0 344 A
ATOM 1539 C CG2 ? ILE Axp 205 ? 21.953 27.141 3.249 0.00 0 432 A
ATOM 1509 C CD2 ? LEU Axp 202 ? 16.995 30.754 4.286 0.00 0 429 A
ATOM 1505 O O ? LEU Axp 202 ? 21.436 31.217 5.146 -3.21 0 429 A
ATOM 820 C CB ? LEU Axp 113 ? 22.728 26.946 -0.496 0.00 0 340 A
ATOM 830 C CD1 ? LEU Axp 114 ? 17.000 29.244 -2.786 0.00 0 341 A
ATOM 2030 C CE1 ? PHE Axp 266 ? 15.255 30.669 0.284 0.00 0 493 A
ATOM 828 C CB ? LEU Axp 114 ? 18.476 27.301 -3.305 0.00 0 341 A
ATOM 1804 C CG ? PRO Axp 238 ? 21.078 33.317 -4.111 0.00 0 465 A
ATOM 1822 C CG2 ? VAL Axp 241 ? 17.795 32.913 -1.514 0.00 0 468 A
ATOM 800 O O ? ALA Axp 110 ? 21.862 27.166 -3.931 -1.07 0 337 A
ATOM 1545 C CB ? ALA Axp 206 ? 24.087 32.253 2.900 0.00 0 433 A
ATOM 1541 N N ? ALA Axp 206 ? 24.014 29.985 3.998 0.00 0 433 A
ATOM 1798 S SG ? CYS Axp 237 ? 22.030 35.316 0.634 0.00 0 464 A
ATOM 1794 C CA ? CYS Axp 237 ? 24.026 34.922 -1.329 0.00 0 464 A
ATOM 1544 O O ? ALA Axp 206 ? 26.983 31.382 2.492 -3.21 0 433 A
ATOM 1542 C CA ? ALA Axp 206 ? 24.748 30.821 3.023 0.00 0 433 A
ATOM 822 C CD1 ? LEU Axp 113 ? 25.012 27.872 -0.209 0.00 0 340 A
ATOM 6291 O O ? GLU Dxp 9 ? 72.604 3.890 48.729 0.00 0 236 D
ATOM 6300 O O ? MET Dxp 10 ? 74.107 7.374 51.316 -2.14 0 237 D
ATOM 6293 C CG ? GLU Dxp 9 ? 71.423 4.039 52.375 0.00 0 236 D
ATOM 6312 O OE1 ? GLU Dxp 11 ? 77.808 6.551 52.358 0.00 0 238 D
ATOM 6299 C C ? MET Dxp 10 ? 74.371 7.293 50.096 0.00 0 237 D
ATOM 6305 N N ? GLU Dxp 11 ? 75.439 7.869 49.548 -2.19 0 238 D
ATOM 6309 C CB ? GLU Dxp 11 ? 77.861 8.128 49.916 0.00 0 238 D
ATOM 6510 C CE ? LYS Dxp 36 ? 78.782 6.894 42.671 0.00 0 263 D
ATOM 6511 N NZ ? LYS Dxp 36 ? 78.219 5.612 42.198 0.00 0 263 D
ATOM 6301 C CB ? MET Dxp 10 ? 73.225 7.186 47.771 0.00 0 237 D
ATOM 6335 O OD2 ? ASP Dxp 14 ? 78.726 9.496 45.541 -2.55 0 241 D
ATOM 6298 C CA ? MET Dxp 10 ? 73.486 6.472 49.131 0.00 0 237 D
ATOM 6491 C CZ2 ? TRP Dxp 34 ? 73.535 8.757 43.118 0.00 0 261 D
ATOM 6488 N NE1 ? TRP Dxp 34 ? 75.151 10.418 44.105 -1.09 0 261 D
#
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