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Discngine / fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
MIT License
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qhull input error #25

Open pslacerda opened 4 years ago

pslacerda commented 4 years ago

dpocket from master failed with attached PDB file. Ligand resn is DIE.

Having 8433 objects in memory
<dpocket>s 282/4195 - ../RawData/pdbbind/3f33/3f33
[3f33.zip](https://github.com/Discngine/fpocket/files/4262386/3f33.zip)

_complex.pdb:Having 8433 objects in memory
QH6013 qhull input error: input is less than 3-dimensional since it has the same x coordinate

While executing: rbox D3 | qconvex FS
Options selected for Qhull 2015.2 2016/01/18:
  run-id 1496072203  FSize  _pre-merge  _zero-centrum  _max-width 1.9
  Error-roundoff 4.1e-14  _one-merge 2.9e-13  _near-inside 1.5e-12
  Visible-distance 8.3e-14  U-coplanar-distance 8.3e-14  Width-outside 1.7e-13
  _wide-facet 5e-13
QH6154 Qhull precision error: Initial simplex is flat (facet 1 is coplanar with the interior point)

While executing: rbox D3 | qconvex FS
Options selected for Qhull 2015.2 2016/01/18:
  run-id 1496072203  FSize  _pre-merge  _zero-centrum  _max-width 1.9
  Error-roundoff 4.1e-14  _one-merge 2.9e-13  _near-inside 1.5e-12
  Visible-distance 8.3e-14  U-coplanar-distance 8.3e-14  Width-outside 1.7e-13
  _wide-facet 5e-13

precision problems (corrected unless 'Q0' or an error)
      2 flipped facets
      4 degenerate hyperplanes recomputed with gaussian elimination
      8 nearly singular or axis-parallel hyperplanes
      4 zero divisors during back substitute
      4 zero divisors during gaussian elimination

The input to qhull appears to be less than 3 dimensional, or a
computation has overflowed.

Qhull could not construct a clearly convex simplex from points:
- p2(v3):   -46    -0     0
- p1(v2):   -46    -0     0
- p8(v1):   -44     0     0
- p0(v0):   -46    -0     0

The center point is coplanar with a facet, or a vertex is coplanar
with a neighboring facet.  The maximum round off error for
computing distances is 4.1e-14.  The center point, facets and distances
to the center point are as follows:

center point   -45.83        0        0

facet p1 p8 p0 distance=    0
facet p2 p8 p0 distance=    0
facet p2 p1 p0 distance= -0.28
facet p2 p1 p8 distance=    0

These points either have a maximum or minimum x-coordinate, or
they maximize the determinant for k coordinates.  Trial points
are first selected from points that maximize a coordinate.

The min and max coordinates for each dimension are:
  0:     -46.3  -2.225e-308  difference= 46.3
  1:        -0        -0  difference=    0
  2:         0         0  difference=    0

If the input should be full dimensional, you have several options that
may determine an initial simplex:
  - use 'QJ'  to joggle the input and make it full dimensional
  - use 'QbB' to scale the points to the unit cube
  - use 'QR0' to randomly rotate the input for different maximum points
  - use 'Qs'  to search all points for the initial simplex
  - use 'En'  to specify a maximum roundoff error less than 4.1e-14.
  - trace execution with 'T3' to see the determinant for each point.

If the input is lower dimensional:
  - use 'QJ' to joggle the input and make it full dimensional
  - use 'Qbk:0Bk:0' to delete coordinate k from the input.  You should
    pick the coordinate with the least range.  The hull will have the
    correct topology.
  - determine the flat containing the points, rotate the points
    into a coordinate plane, and delete the other coordinates.
  - add one or more points to make the input full dimensional.
QH6154 Qhull precision error: Initial simplex is flat (facet 1 is coplanar with the interior point)

While executing: rbox D3 | qconvex FS
Options selected for Qhull 2015.2 2016/01/18:
  run-id 1496072203  FSize  _pre-merge  _zero-centrum  _max-width 1.9
  Error-roundoff 4.1e-14  _one-merge 2.9e-13  _near-inside 1.5e-12
  Visible-distance 8.3e-14  U-coplanar-distance 8.3e-14  Width-outside 1.7e-13
  _wide-facet 5e-13

The input to qhull appears to be less than 3 dimensional, or a
computation has overflowed.

Qhull could not construct a clearly convex simplex from points:
- p2(v3):    44    -0     0
- p1(v2):    44    -0     0
- p8(v1):    46     0    -0
- p0(v0):    44    -0     0

The center point is coplanar with a facet, or a vertex is coplanar
with a neighboring facet.  The maximum round off error for
computing distances is 4.1e-14.  The center point, facets and distances
to the center point are as follows:

center point    44.87        0        0

facet p1 p8 p0 distance=    0
facet p2 p8 p0 distance=    0
facet p2 p1 p0 distance= -0.28
facet p2 p1 p8 distance=    0

These points either have a maximum or minimum x-coordinate, or
they maximize the determinant for k coordinates.  Trial points
are first selected from points that maximize a coordinate.

The min and max coordinates for each dimension are:
  0:     44.39      46.3  difference= 1.917
  1:        -0        -0  difference=    0
  2:         0         0  difference=    0

If the input should be full dimensional, you have several options that
may determine an initial simplex:
  - use 'QJ'  to joggle the input and make it full dimensional
  - use 'QbB' to scale the points to the unit cube
  - use 'QR0' to randomly rotate the input for different maximum points
  - use 'Qs'  to search all points for the initial simplex
  - use 'En'  to specify a maximum roundoff error less than 4.1e-14.
  - trace execution with 'T3' to see the determinant for each point.

If the input is lower dimensional:
  - use 'QJ' to joggle the input and make it full dimensional
  - use 'Qbk:0Bk:0' to delete coordinate k from the input.  You should
    pick the coordinate with the least range.  The hull will have the
    correct topology.
  - determine the flat containing the points, rotate the points
    into a coordinate plane, and delete the other coordinates.
  - add one or more points to make the input full dimensional.
QH6013 qhull input error: input is less than 3-dimensional since it has the same x coordinate

While executing: rbox D3 | qconvex FS
Options selected for Qhull 2015.2 2016/01/18:
  run-id 1496072203  FSize  _pre-merge  _zero-centrum  _max-width 1.9
  Error-roundoff 4.1e-14  _one-merge 2.9e-13  _near-inside 1.5e-12
  Visible-distance 8.3e-14  U-coplanar-distance 8.3e-14  Width-outside 1.7e-13
  _wide-facet 5e-13
QH6013 qhull input error: input is less than 3-dimensional since it has the same x coordinate

While executing: rbox D3 | qconvex FS
Options selected for Qhull 2015.2 2016/01/18:
  run-id 1496072203  FSize  _pre-merge  _zero-centrum  _max-width 1.9
  Error-roundoff 4.1e-14  _one-merge 2.9e-13  _near-inside 1.5e-12
  Visible-distance 8.3e-14  U-coplanar-distance 8.3e-14  Width-outside 1.7e-13
  _wide-facet 5e-13
sorting atoms and vertices or something like this 
sort finished
pschmidtke commented 4 years ago

can you run this through a normal fpocket though?

manaryna commented 4 years ago

I'm having the same issue but in mdpocket.

analysing snapshot 156QH6114 qhull precision error: initial simplex is not convex. Distance=-15 While executing: rbox D3 | qvoronoi p i Pp Qz Qt Options selected for Qhull 2015.2 2016/01/18: run-id 650992928 voronoi _bbound-last _coplanar-keep points incidence Pprecision-ignore Qz-infinity-point Qtriangulate _pre-merge _zero-centrum Pgood _max-width 1e+37 Error-roundoff 2e+22 _one-merge 1.8e+23 _near-inside 9e+23 Visible-distance 1.2e+23 U-coplanar-distance 1.2e+23 Width-outside 2.4e+23 _wide-facet 7.2e+23 The input to qhull appears to be less than 4 dimensional, or a computation has overflowed. Qhull could not construct a clearly convex simplex from points: - p2818(v4): 12 39 16 5.8e-35 - p4674(v3): 3.4 -11 1e+37 3e+36 - p384(v2): -19 -33 4.6 4.5e-35 - p4675(v1): 1e+37 1e+37 1e+37 9.1e+36 - p462(v0): -35 -27 15 6.5e-35 The center point is coplanar with a facet, or a vertex is coplanar with a neighboring facet. The maximum round off error for computing distances is 2e+22. The center point, facets and distances to the center point are as follows: center point 1.994e+36 1.994e+36 3.988e+36 2.417e+36 facet p4674 p384 p4675 p462 distance= -3e+20 facet p2818 p384 p4675 p462 distance= -7.3e+35 facet p2818 p4674 p4675 p462 distance= -1.5e+20 facet p2818 p4674 p384 p462 distance= -1.1e+36 facet p2818 p4674 p384 p4675 distance= -5.9e+20 These points either have a maximum or minimum x-coordinate, or they maximize the determinant for k coordinates. Trial points are first selected from points that maximize a coordinate. The min and max coordinates for each dimension are: 0: -34.83 9.969e+36 difference= 9.969e+36 1: -33.44 9.969e+36 difference= 9.969e+36 2: -39.12 9.969e+36 difference= 9.969e+36 3: 8.352e-53 9.969e+36 difference= 9.969e+36 If the input should be full dimensional, you have several options that may determine an initial simplex: - use 'QJ' to joggle the input and make it full dimensional - use 'QbB' to scale the points to the unit cube - use 'QR0' to randomly rotate the input for different maximum points - use 'Qs' to search all points for the initial simplex - use 'En' to specify a maximum roundoff error less than 2e+22. - trace execution with 'T3' to see the determinant for each point. If the input is lower dimensional: - use 'QJ' to joggle the input and make it full dimensional - use 'Qbk:0Bk:0' to delete coordinate k from the input. You should pick the coordinate with the least range. The hull will have the correct topology. - determine the flat containing the points, rotate the points into a coordinate plane, and delete the other coordinates. - add one or more points to make the input full dimensional. Segmentation fault (core dumped)