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https://github.com/Discngine/fpocket.git
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0d998c42ba |
20
INSTALL.txt
20
INSTALL.txt
@@ -1,22 +1,4 @@
|
||||
// Fpocket brought to you by Vincent Le Guilloux & Peter Schmidtke
|
||||
//
|
||||
// GNU GPL
|
||||
//
|
||||
// This file is part of the fpocket package.
|
||||
//
|
||||
// fpocket is free software: you can redistribute it and/or modify
|
||||
// it under the terms of the GNU General Public License as published by
|
||||
// the Free Software Foundation, either version 3 of the License, or
|
||||
// (at your option) any later version.
|
||||
//
|
||||
// fpocket is distributed in the hope that it will be useful,
|
||||
// but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
// GNU General Public License for more details.
|
||||
//
|
||||
// You should have received a copy of the GNU General Public License
|
||||
// along with fpocket. If not, see <http://www.gnu.org/licenses/>.
|
||||
//
|
||||
|
||||
===========================
|
||||
DEPENDENCIES :
|
||||
===========================
|
||||
|
||||
21
LICENSE
Normal file
21
LICENSE
Normal file
@@ -0,0 +1,21 @@
|
||||
MIT License
|
||||
|
||||
Copyright (c) 2020 Peter Schmidtke & Vincent Le Guilloux
|
||||
|
||||
Permission is hereby granted, free of charge, to any person obtaining a copy
|
||||
of this software and associated documentation files (the "Software"), to deal
|
||||
in the Software without restriction, including without limitation the rights
|
||||
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
copies of the Software, and to permit persons to whom the Software is
|
||||
furnished to do so, subject to the following conditions:
|
||||
|
||||
The above copyright notice and this permission notice shall be included in all
|
||||
copies or substantial portions of the Software.
|
||||
|
||||
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
||||
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
||||
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
||||
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
||||
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
||||
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
||||
SOFTWARE.
|
||||
@@ -51,7 +51,10 @@ sudo make install
|
||||
```
|
||||
|
||||
#### Compiling on Mac
|
||||
Install MacPorts https://www.macports.org/ for instance (needed for netcdf install)
|
||||
```
|
||||
sudo port install netcdf
|
||||
export LIBRARY_PATH=/opt/local/lib
|
||||
git clone https://github.com/Discngine/fpocket.git
|
||||
cd fpocket
|
||||
make ARCH=MACOSXX86_64
|
||||
@@ -133,7 +136,7 @@ Please read [CONTRIBUTING.md](https://gist.github.com/PurpleBooth/b24679402957c6
|
||||
|
||||
## License
|
||||
|
||||
This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details
|
||||
This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details
|
||||
|
||||
## Acknowledgments
|
||||
|
||||
|
||||
6101
data/sample/mdpocket/2yex.pdb
Normal file
6101
data/sample/mdpocket/2yex.pdb
Normal file
File diff suppressed because it is too large
Load Diff
2887
data/sample/mdpocket/3ot3.pdb
Normal file
2887
data/sample/mdpocket/3ot3.pdb
Normal file
File diff suppressed because it is too large
Load Diff
2850
data/sample/mdpocket/3pa3.pdb
Normal file
2850
data/sample/mdpocket/3pa3.pdb
Normal file
File diff suppressed because it is too large
Load Diff
2851
data/sample/mdpocket/3pa4.pdb
Normal file
2851
data/sample/mdpocket/3pa4.pdb
Normal file
File diff suppressed because it is too large
Load Diff
2923
data/sample/mdpocket/3tki.pdb
Normal file
2923
data/sample/mdpocket/3tki.pdb
Normal file
File diff suppressed because it is too large
Load Diff
2984
data/sample/mdpocket/4hyi.pdb
Normal file
2984
data/sample/mdpocket/4hyi.pdb
Normal file
File diff suppressed because it is too large
Load Diff
2692
data/sample/mdpocket/4rvk.pdb
Normal file
2692
data/sample/mdpocket/4rvk.pdb
Normal file
File diff suppressed because it is too large
Load Diff
2937
data/sample/mdpocket/5opb.pdb
Normal file
2937
data/sample/mdpocket/5opb.pdb
Normal file
File diff suppressed because it is too large
Load Diff
2929
data/sample/mdpocket/5opu.pdb
Normal file
2929
data/sample/mdpocket/5opu.pdb
Normal file
File diff suppressed because it is too large
Load Diff
3075
data/sample/mdpocket/5oq5.pdb
Normal file
3075
data/sample/mdpocket/5oq5.pdb
Normal file
File diff suppressed because it is too large
Load Diff
10
data/sample/mdpocket/input.txt
Normal file
10
data/sample/mdpocket/input.txt
Normal file
@@ -0,0 +1,10 @@
|
||||
2yex.pdb
|
||||
3ot3.pdb
|
||||
3pa3.pdb
|
||||
3pa4.pdb
|
||||
3tki.pdb
|
||||
4hyi.pdb
|
||||
4rvk.pdb
|
||||
5opb.pdb
|
||||
5opu.pdb
|
||||
5oq5.pdb
|
||||
2153
data/sample/mdpocket/mdpout_all_atom_pdensities.pdb
Normal file
2153
data/sample/mdpocket/mdpout_all_atom_pdensities.pdb
Normal file
File diff suppressed because it is too large
Load Diff
172597
data/sample/mdpocket/mdpout_dens_grid.dx
Normal file
172597
data/sample/mdpocket/mdpout_dens_grid.dx
Normal file
File diff suppressed because it is too large
Load Diff
184
data/sample/mdpocket/mdpout_dens_iso_8.pdb
Normal file
184
data/sample/mdpocket/mdpout_dens_iso_8.pdb
Normal file
@@ -0,0 +1,184 @@
|
||||
ATOM 1 C PTH 1 -8.641 4.782 5.052 0.00 0.00
|
||||
ATOM 2 C PTH 1 -8.641 4.782 6.052 0.00 0.00
|
||||
ATOM 3 C PTH 1 -8.641 5.782 6.052 0.00 0.00
|
||||
ATOM 4 C PTH 1 -7.641 4.782 5.052 0.00 0.00
|
||||
ATOM 5 C PTH 1 -7.641 4.782 6.052 0.00 0.00
|
||||
ATOM 6 C PTH 1 -7.641 5.782 3.052 0.00 0.00
|
||||
ATOM 7 C PTH 1 -7.641 5.782 4.052 0.00 0.00
|
||||
ATOM 8 C PTH 1 -7.641 5.782 6.052 0.00 0.00
|
||||
ATOM 9 C PTH 1 -7.641 6.782 7.052 0.00 0.00
|
||||
ATOM 10 C PTH 1 -6.641 4.782 3.052 0.00 0.00
|
||||
ATOM 11 C PTH 1 -6.641 4.782 4.052 0.00 0.00
|
||||
ATOM 12 C PTH 1 -6.641 5.782 3.052 0.00 0.00
|
||||
ATOM 13 C PTH 1 -6.641 5.782 4.052 0.00 0.00
|
||||
ATOM 14 C PTH 1 -6.641 5.782 5.052 0.00 0.00
|
||||
ATOM 15 C PTH 1 -6.641 5.782 6.052 0.00 0.00
|
||||
ATOM 16 C PTH 1 -6.641 5.782 7.052 0.00 0.00
|
||||
ATOM 17 C PTH 1 -6.641 6.782 3.052 0.00 0.00
|
||||
ATOM 18 C PTH 1 -6.641 6.782 4.052 0.00 0.00
|
||||
ATOM 19 C PTH 1 -6.641 6.782 7.052 0.00 0.00
|
||||
ATOM 20 C PTH 1 -6.641 20.782 12.052 0.00 0.00
|
||||
ATOM 21 C PTH 1 -5.641 4.782 4.052 0.00 0.00
|
||||
ATOM 22 C PTH 1 -5.641 5.782 3.052 0.00 0.00
|
||||
ATOM 23 C PTH 1 -5.641 5.782 4.052 0.00 0.00
|
||||
ATOM 24 C PTH 1 -5.641 5.782 5.052 0.00 0.00
|
||||
ATOM 25 C PTH 1 -5.641 6.782 4.052 0.00 0.00
|
||||
ATOM 26 C PTH 1 -5.641 6.782 5.052 0.00 0.00
|
||||
ATOM 27 C PTH 1 -4.641 5.782 4.052 0.00 0.00
|
||||
ATOM 28 C PTH 1 -4.641 5.782 5.052 0.00 0.00
|
||||
ATOM 29 C PTH 1 -4.641 6.782 4.052 0.00 0.00
|
||||
ATOM 30 C PTH 1 -2.641 12.782 -14.948 0.00 0.00
|
||||
ATOM 31 C PTH 1 -2.641 13.782 -14.948 0.00 0.00
|
||||
ATOM 32 C PTH 1 -2.641 13.782 -13.948 0.00 0.00
|
||||
ATOM 33 C PTH 1 -1.641 12.782 -14.948 0.00 0.00
|
||||
ATOM 34 C PTH 1 -1.641 13.782 -15.948 0.00 0.00
|
||||
ATOM 35 C PTH 1 -1.641 13.782 -14.948 0.00 0.00
|
||||
ATOM 36 C PTH 1 -0.641 11.782 -15.948 0.00 0.00
|
||||
ATOM 37 C PTH 1 -0.641 12.782 -15.948 0.00 0.00
|
||||
ATOM 38 C PTH 1 0.359 11.782 -15.948 0.00 0.00
|
||||
ATOM 39 C PTH 1 1.359 7.782 18.052 0.00 0.00
|
||||
ATOM 40 C PTH 1 1.359 7.782 19.052 0.00 0.00
|
||||
ATOM 41 C PTH 1 1.359 8.782 19.052 0.00 0.00
|
||||
ATOM 42 C PTH 1 1.359 8.782 20.052 0.00 0.00
|
||||
ATOM 43 C PTH 1 1.359 26.782 -9.948 0.00 0.00
|
||||
ATOM 44 C PTH 1 2.359 6.782 18.052 0.00 0.00
|
||||
ATOM 45 C PTH 1 2.359 7.782 18.052 0.00 0.00
|
||||
ATOM 46 C PTH 1 2.359 7.782 19.052 0.00 0.00
|
||||
ATOM 47 C PTH 1 2.359 8.782 19.052 0.00 0.00
|
||||
ATOM 48 C PTH 1 2.359 8.782 20.052 0.00 0.00
|
||||
ATOM 49 C PTH 1 3.359 4.782 17.052 0.00 0.00
|
||||
ATOM 50 C PTH 1 3.359 5.782 17.052 0.00 0.00
|
||||
ATOM 51 C PTH 1 3.359 5.782 18.052 0.00 0.00
|
||||
ATOM 52 C PTH 1 3.359 6.782 17.052 0.00 0.00
|
||||
ATOM 53 C PTH 1 3.359 6.782 18.052 0.00 0.00
|
||||
ATOM 54 C PTH 1 3.359 8.782 19.052 0.00 0.00
|
||||
ATOM 55 C PTH 1 3.359 8.782 20.052 0.00 0.00
|
||||
ATOM 56 C PTH 1 3.359 9.782 20.052 0.00 0.00
|
||||
ATOM 57 C PTH 1 3.359 19.782 -13.948 0.00 0.00
|
||||
ATOM 58 C PTH 1 3.359 19.782 -12.948 0.00 0.00
|
||||
ATOM 59 C PTH 1 3.359 20.782 -12.948 0.00 0.00
|
||||
ATOM 60 C PTH 1 3.359 21.782 -12.948 0.00 0.00
|
||||
ATOM 61 C PTH 1 3.359 21.782 -11.948 0.00 0.00
|
||||
ATOM 62 C PTH 1 4.359 4.782 16.052 0.00 0.00
|
||||
ATOM 63 C PTH 1 4.359 4.782 17.052 0.00 0.00
|
||||
ATOM 64 C PTH 1 4.359 5.782 15.052 0.00 0.00
|
||||
ATOM 65 C PTH 1 4.359 5.782 16.052 0.00 0.00
|
||||
ATOM 66 C PTH 1 4.359 5.782 17.052 0.00 0.00
|
||||
ATOM 67 C PTH 1 4.359 5.782 18.052 0.00 0.00
|
||||
ATOM 68 C PTH 1 4.359 6.782 16.052 0.00 0.00
|
||||
ATOM 69 C PTH 1 4.359 6.782 17.052 0.00 0.00
|
||||
ATOM 70 C PTH 1 4.359 8.782 19.052 0.00 0.00
|
||||
ATOM 71 C PTH 1 4.359 8.782 20.052 0.00 0.00
|
||||
ATOM 72 C PTH 1 4.359 9.782 19.052 0.00 0.00
|
||||
ATOM 73 C PTH 1 4.359 9.782 20.052 0.00 0.00
|
||||
ATOM 74 C PTH 1 4.359 20.782 -12.948 0.00 0.00
|
||||
ATOM 75 C PTH 1 4.359 21.782 -12.948 0.00 0.00
|
||||
ATOM 76 C PTH 1 5.359 4.782 15.052 0.00 0.00
|
||||
ATOM 77 C PTH 1 5.359 5.782 15.052 0.00 0.00
|
||||
ATOM 78 C PTH 1 5.359 5.782 16.052 0.00 0.00
|
||||
ATOM 79 C PTH 1 6.359 5.782 -0.948 0.00 0.00
|
||||
ATOM 80 C PTH 1 6.359 5.782 0.052 0.00 0.00
|
||||
ATOM 81 C PTH 1 6.359 5.782 1.052 0.00 0.00
|
||||
ATOM 82 C PTH 1 6.359 6.782 0.052 0.00 0.00
|
||||
ATOM 83 C PTH 1 6.359 6.782 1.052 0.00 0.00
|
||||
ATOM 84 C PTH 1 6.359 7.782 0.052 0.00 0.00
|
||||
ATOM 85 C PTH 1 6.359 7.782 1.052 0.00 0.00
|
||||
ATOM 86 C PTH 1 7.359 -0.218 -1.948 0.00 0.00
|
||||
ATOM 87 C PTH 1 7.359 0.782 -1.948 0.00 0.00
|
||||
ATOM 88 C PTH 1 7.359 5.782 -0.948 0.00 0.00
|
||||
ATOM 89 C PTH 1 7.359 5.782 0.052 0.00 0.00
|
||||
ATOM 90 C PTH 1 7.359 5.782 1.052 0.00 0.00
|
||||
ATOM 91 C PTH 1 7.359 6.782 -0.948 0.00 0.00
|
||||
ATOM 92 C PTH 1 7.359 6.782 0.052 0.00 0.00
|
||||
ATOM 93 C PTH 1 7.359 6.782 1.052 0.00 0.00
|
||||
ATOM 94 C PTH 1 7.359 6.782 16.052 0.00 0.00
|
||||
ATOM 95 C PTH 1 7.359 7.782 -0.948 0.00 0.00
|
||||
ATOM 96 C PTH 1 7.359 7.782 0.052 0.00 0.00
|
||||
ATOM 97 C PTH 1 7.359 7.782 16.052 0.00 0.00
|
||||
ATOM 98 C PTH 1 7.359 7.782 17.052 0.00 0.00
|
||||
ATOM 99 C PTH 1 7.359 8.782 17.052 0.00 0.00
|
||||
ATOM 100 C PTH 1 7.359 8.782 18.052 0.00 0.00
|
||||
ATOM 101 C PTH 1 7.359 9.782 18.052 0.00 0.00
|
||||
ATOM 102 C PTH 1 7.359 9.782 19.052 0.00 0.00
|
||||
ATOM 103 C PTH 1 8.359 -1.218 -2.948 0.00 0.00
|
||||
ATOM 104 C PTH 1 8.359 -1.218 -1.948 0.00 0.00
|
||||
ATOM 105 C PTH 1 8.359 -1.218 -0.948 0.00 0.00
|
||||
ATOM 106 C PTH 1 8.359 -0.218 -2.948 0.00 0.00
|
||||
ATOM 107 C PTH 1 8.359 -0.218 -1.948 0.00 0.00
|
||||
ATOM 108 C PTH 1 8.359 -0.218 -0.948 0.00 0.00
|
||||
ATOM 109 C PTH 1 8.359 0.782 -2.948 0.00 0.00
|
||||
ATOM 110 C PTH 1 8.359 0.782 -1.948 0.00 0.00
|
||||
ATOM 111 C PTH 1 8.359 4.782 15.052 0.00 0.00
|
||||
ATOM 112 C PTH 1 8.359 5.782 16.052 0.00 0.00
|
||||
ATOM 113 C PTH 1 8.359 6.782 -0.948 0.00 0.00
|
||||
ATOM 114 C PTH 1 8.359 6.782 16.052 0.00 0.00
|
||||
ATOM 115 C PTH 1 8.359 6.782 17.052 0.00 0.00
|
||||
ATOM 116 C PTH 1 8.359 7.782 -0.948 0.00 0.00
|
||||
ATOM 117 C PTH 1 8.359 7.782 16.052 0.00 0.00
|
||||
ATOM 118 C PTH 1 8.359 7.782 17.052 0.00 0.00
|
||||
ATOM 119 C PTH 1 8.359 8.782 -0.948 0.00 0.00
|
||||
ATOM 120 C PTH 1 8.359 8.782 18.052 0.00 0.00
|
||||
ATOM 121 C PTH 1 8.359 9.782 17.052 0.00 0.00
|
||||
ATOM 122 C PTH 1 8.359 9.782 18.052 0.00 0.00
|
||||
ATOM 123 C PTH 1 9.359 -2.218 -1.948 0.00 0.00
|
||||
ATOM 124 C PTH 1 9.359 -1.218 -2.948 0.00 0.00
|
||||
ATOM 125 C PTH 1 9.359 -1.218 -1.948 0.00 0.00
|
||||
ATOM 126 C PTH 1 9.359 -1.218 -0.948 0.00 0.00
|
||||
ATOM 127 C PTH 1 9.359 -0.218 -2.948 0.00 0.00
|
||||
ATOM 128 C PTH 1 9.359 -0.218 -1.948 0.00 0.00
|
||||
ATOM 129 C PTH 1 9.359 0.782 -2.948 0.00 0.00
|
||||
ATOM 130 C PTH 1 9.359 5.782 15.052 0.00 0.00
|
||||
ATOM 131 C PTH 1 9.359 6.782 16.052 0.00 0.00
|
||||
ATOM 132 C PTH 1 9.359 7.782 -14.948 0.00 0.00
|
||||
ATOM 133 C PTH 1 9.359 17.782 -6.948 0.00 0.00
|
||||
ATOM 134 C PTH 1 9.359 18.782 -6.948 0.00 0.00
|
||||
ATOM 135 C PTH 1 9.359 24.782 -0.948 0.00 0.00
|
||||
ATOM 136 C PTH 1 10.359 6.782 16.052 0.00 0.00
|
||||
ATOM 137 C PTH 1 10.359 7.782 16.052 0.00 0.00
|
||||
ATOM 138 C PTH 1 10.359 10.782 15.052 0.00 0.00
|
||||
ATOM 139 C PTH 1 10.359 17.782 -6.948 0.00 0.00
|
||||
ATOM 140 C PTH 1 10.359 17.782 -5.948 0.00 0.00
|
||||
ATOM 141 C PTH 1 10.359 18.782 -6.948 0.00 0.00
|
||||
ATOM 142 C PTH 1 10.359 18.782 -5.948 0.00 0.00
|
||||
ATOM 143 C PTH 1 10.359 18.782 -4.948 0.00 0.00
|
||||
ATOM 144 C PTH 1 10.359 18.782 -3.948 0.00 0.00
|
||||
ATOM 145 C PTH 1 10.359 19.782 -3.948 0.00 0.00
|
||||
ATOM 146 C PTH 1 10.359 24.782 -0.948 0.00 0.00
|
||||
ATOM 147 C PTH 1 10.359 25.782 -0.948 0.00 0.00
|
||||
ATOM 148 C PTH 1 11.359 7.782 15.052 0.00 0.00
|
||||
ATOM 149 C PTH 1 11.359 8.782 15.052 0.00 0.00
|
||||
ATOM 150 C PTH 1 11.359 9.782 15.052 0.00 0.00
|
||||
ATOM 151 C PTH 1 11.359 10.782 14.052 0.00 0.00
|
||||
ATOM 152 C PTH 1 11.359 17.782 -6.948 0.00 0.00
|
||||
ATOM 153 C PTH 1 11.359 17.782 -5.948 0.00 0.00
|
||||
ATOM 154 C PTH 1 11.359 18.782 -6.948 0.00 0.00
|
||||
ATOM 155 C PTH 1 11.359 18.782 -5.948 0.00 0.00
|
||||
ATOM 156 C PTH 1 11.359 18.782 -4.948 0.00 0.00
|
||||
ATOM 157 C PTH 1 11.359 18.782 -3.948 0.00 0.00
|
||||
ATOM 158 C PTH 1 11.359 19.782 -5.948 0.00 0.00
|
||||
ATOM 159 C PTH 1 11.359 19.782 -4.948 0.00 0.00
|
||||
ATOM 160 C PTH 1 11.359 19.782 -3.948 0.00 0.00
|
||||
ATOM 161 C PTH 1 11.359 19.782 -2.948 0.00 0.00
|
||||
ATOM 162 C PTH 1 11.359 20.782 -3.948 0.00 0.00
|
||||
ATOM 163 C PTH 1 11.359 20.782 -2.948 0.00 0.00
|
||||
ATOM 164 C PTH 1 11.359 21.782 -0.948 0.00 0.00
|
||||
ATOM 165 C PTH 1 11.359 22.782 -0.948 0.00 0.00
|
||||
ATOM 166 C PTH 1 12.359 8.782 14.052 0.00 0.00
|
||||
ATOM 167 C PTH 1 12.359 8.782 15.052 0.00 0.00
|
||||
ATOM 168 C PTH 1 12.359 9.782 15.052 0.00 0.00
|
||||
ATOM 169 C PTH 1 12.359 19.782 -4.948 0.00 0.00
|
||||
ATOM 170 C PTH 1 12.359 20.782 -2.948 0.00 0.00
|
||||
ATOM 171 C PTH 1 12.359 21.782 -1.948 0.00 0.00
|
||||
ATOM 172 C PTH 1 12.359 21.782 -0.948 0.00 0.00
|
||||
ATOM 173 C PTH 1 12.359 22.782 -1.948 0.00 0.00
|
||||
ATOM 174 C PTH 1 12.359 22.782 -0.948 0.00 0.00
|
||||
ATOM 175 C PTH 1 12.359 22.782 0.052 0.00 0.00
|
||||
ATOM 176 C PTH 1 12.359 23.782 -0.948 0.00 0.00
|
||||
ATOM 177 C PTH 1 13.359 13.782 27.052 0.00 0.00
|
||||
ATOM 178 C PTH 1 13.359 13.782 28.052 0.00 0.00
|
||||
ATOM 179 C PTH 1 13.359 22.782 -0.948 0.00 0.00
|
||||
ATOM 180 C PTH 1 14.359 17.782 -7.948 0.00 0.00
|
||||
ATOM 181 C PTH 1 15.359 16.782 -8.948 0.00 0.00
|
||||
ATOM 182 C PTH 1 15.359 16.782 -7.948 0.00 0.00
|
||||
ATOM 183 C PTH 1 15.359 17.782 -8.948 0.00 0.00
|
||||
ATOM 184 C PTH 1 15.359 17.782 -7.948 0.00 0.00
|
||||
172597
data/sample/mdpocket/mdpout_freq_grid.dx
Normal file
172597
data/sample/mdpocket/mdpout_freq_grid.dx
Normal file
File diff suppressed because it is too large
Load Diff
2593
data/sample/mdpocket/mdpout_freq_iso_0_5.pdb
Normal file
2593
data/sample/mdpocket/mdpout_freq_iso_0_5.pdb
Normal file
File diff suppressed because it is too large
Load Diff
10
data/sample/mdpocket/time.txt
Normal file
10
data/sample/mdpocket/time.txt
Normal file
@@ -0,0 +1,10 @@
|
||||
0.215480
|
||||
0.271399
|
||||
0.217237
|
||||
0.212487
|
||||
0.221198
|
||||
0.217482
|
||||
0.234323
|
||||
0.224301
|
||||
0.218361
|
||||
0.211592
|
||||
@@ -14,7 +14,7 @@ if __name__ == "__main__":
|
||||
pdbname = str(basename)+".pdb"
|
||||
pdir = "results/"+basename+"/clusterinfo.txt"
|
||||
|
||||
print pdbname+" - "+pdir+"\n"
|
||||
print(pdbname+" - "+pdir+"\n")
|
||||
|
||||
f = open(pdir)
|
||||
lines = f.readlines()
|
||||
|
||||
@@ -73,14 +73,14 @@ z=0
|
||||
y=0
|
||||
x=0
|
||||
|
||||
print "Reading the grid. Depending on the number of data points you have this might take a while...."
|
||||
print("Reading the grid. Depending on the number of data points you have this might take a while....")
|
||||
path=open(pathOutput,"w")
|
||||
|
||||
counter=1
|
||||
for count in range(n_entries/3) :
|
||||
for count in range(n_entries//3) :
|
||||
c=f.readline().split()
|
||||
if(len(c)!=3) :
|
||||
print "error reading grid data"
|
||||
print("error reading grid data")
|
||||
sys.exit("exiting the program")
|
||||
for i in range(3):
|
||||
if (iso_value<0 and float(c[i]) < iso_value) or (iso_value > 0 and float(c[i]) > iso_value) :
|
||||
@@ -98,4 +98,4 @@ for count in range(n_entries/3) :
|
||||
path.close()
|
||||
f.close()
|
||||
|
||||
print "finished writing %s"%(pathOutput)
|
||||
print("finished writing %s"%(pathOutput))
|
||||
|
||||
136
src/mdparams.c
136
src/mdparams.c
@@ -212,6 +212,8 @@ s_mdparams* get_mdpocket_args(int nargs, char **args) {
|
||||
case M_MDPAR_INPUT_FILE:
|
||||
str_list_file = optarg;
|
||||
|
||||
status++;
|
||||
|
||||
break;
|
||||
|
||||
case M_MDPAR_OUTPUT_FILE:
|
||||
@@ -246,6 +248,7 @@ s_mdparams* get_mdpocket_args(int nargs, char **args) {
|
||||
print_mdpocket_usage(stdout);
|
||||
} else {
|
||||
if (str_list_file) {
|
||||
|
||||
int res = add_list_snapshots(str_list_file, par);
|
||||
if (res <= 0) {
|
||||
fprintf(stdout, "! No data has been read.\n");
|
||||
@@ -292,97 +295,55 @@ s_mdparams* get_mdpocket_args(int nargs, char **args) {
|
||||
int: Number of file read.
|
||||
|
||||
*/
|
||||
int add_list_snapshots(char *str_list_file, s_mdparams *par) {
|
||||
FILE *f;
|
||||
int nread = 0,
|
||||
status;
|
||||
int add_list_snapshots(char *str_list_file, s_mdparams *par)
|
||||
{
|
||||
FILE *f;
|
||||
int n,
|
||||
nread = 0,
|
||||
status ;
|
||||
int nfiles=0;
|
||||
char buf[M_MAX_PDB_NAME_LEN],
|
||||
snapbuf[M_MAX_PDB_NAME_LEN*2+6];
|
||||
|
||||
char buf[M_MAX_PDB_NAME_LEN * 2 + 6],
|
||||
snapbuf[M_MAX_PDB_NAME_LEN],
|
||||
infbuf[M_MAX_PDB_NAME_LEN * 2 + 6],
|
||||
origbuf1[20],
|
||||
origbuf2[20],
|
||||
origbuf3[20],
|
||||
resbuf[20],
|
||||
extbuf1[20],
|
||||
extbuf2[20],
|
||||
extbuf3[20];
|
||||
/* Loading data. */
|
||||
f = fopen(str_list_file, "r") ;
|
||||
|
||||
if(f) {
|
||||
//first read the amount of files to read
|
||||
while(fgets(buf, 210, f)) {
|
||||
n = par->nfiles ;
|
||||
status = sscanf(buf, "%s", snapbuf) ;
|
||||
if(status < 1) {
|
||||
fprintf(stderr, "! Skipping row '%s' with bad format (status %d).\n",
|
||||
buf, status) ;
|
||||
}
|
||||
else {
|
||||
nfiles ++;
|
||||
}
|
||||
}
|
||||
fprintf(stdout,"Identified %d snapshots to analyze\n",nfiles);
|
||||
fflush(stdout);
|
||||
|
||||
/* Loading data. */
|
||||
f = fopen(str_list_file, "r");
|
||||
/*
|
||||
printf(str_list_file);
|
||||
*/
|
||||
if (f) {
|
||||
while (fgets(buf, 210, f)) {
|
||||
/*
|
||||
printf("B: %s\n" , buf);
|
||||
*/
|
||||
|
||||
status = sscanf(buf, "%s", snapbuf);
|
||||
if (status < 1) {
|
||||
|
||||
fprintf(stderr, "! Skipping row '%s' with bad format (status %d).\n",
|
||||
buf, status);
|
||||
} else {
|
||||
if (strncmp(snapbuf, "#origin", 7) == 0) {
|
||||
//status=sscanf(buf,"%s\t%d\t%d\t%d",infbuf,par->grid_origin[0],par->grid_origin[1],par->grid_origin[2]);
|
||||
status = sscanf(buf, "%s\t%s\t%s\t%s", infbuf, origbuf1, origbuf2, origbuf3);
|
||||
|
||||
if (status >= 0) {
|
||||
if (str_is_float(origbuf1, M_SIGN) && str_is_float(origbuf2, M_SIGN) && str_is_float(origbuf3, M_SIGN)) {
|
||||
par->grid_origin[0] = atof(origbuf1);
|
||||
par->grid_origin[1] = atof(origbuf2);
|
||||
par->grid_origin[2] = atof(origbuf3);
|
||||
fprintf(stdout, "Grid origin \t\t: %.3f %.3f %.3f\n", par->grid_origin[0], par->grid_origin[1], par->grid_origin[2]);
|
||||
} else {
|
||||
fprintf(stderr, "WARNING : failed to parse origin specified in the input, this calculaion will use an automatically detected origin\n");
|
||||
}
|
||||
|
||||
//
|
||||
fflush(stdout);
|
||||
} else {
|
||||
fprintf(stderr, "WARNING : failed to read the origin specified in the input file\n");
|
||||
}
|
||||
} else if (strncmp(snapbuf, "#resolution", 11) == 0) {
|
||||
//status=sscanf(buf,"%s\t%d\t%d\t%d",infbuf,par->grid_origin[0],par->grid_origin[1],par->grid_origin[2]);
|
||||
status = sscanf(buf, "%s\t%s", infbuf, resbuf);
|
||||
|
||||
if (status >= 0) {
|
||||
if (str_is_float(resbuf, M_NO_SIGN)) {
|
||||
|
||||
par->grid_spacing = atof(resbuf);
|
||||
fprintf(stdout, "Grid resolution \t: %.3f\n", par->grid_spacing);
|
||||
} else fprintf(stderr, "WARNING : failed to parse resolution specified in the input, this calculaion will use an automatically assigned resolution\n");
|
||||
|
||||
//
|
||||
fflush(stdout);
|
||||
} else fprintf(stderr, "WARNING : failed to read the resolution specified in the input file\n");
|
||||
} else if (strncmp(snapbuf, "#extent", 7) == 0) {
|
||||
//status=sscanf(buf,"%s\t%d\t%d\t%d",infbuf,par->grid_origin[0],par->grid_origin[1],par->grid_origin[2]);
|
||||
status = sscanf(buf, "%s\t%s\t%s\t%s", infbuf, extbuf1, extbuf2, extbuf3);
|
||||
|
||||
if (status >= 0) {
|
||||
if (str_is_float(extbuf1, M_NO_SIGN) && str_is_float(extbuf2, M_NO_SIGN) && str_is_float(extbuf3, M_NO_SIGN)) {
|
||||
|
||||
par->grid_extent[0] = (int) atof(extbuf1), par->grid_extent[1] = (int) atof(extbuf2), par->grid_extent[2] = (int) atof(extbuf3);
|
||||
fprintf(stdout, "Grid extent \t\t: %d %d %d\n", par->grid_extent[0], par->grid_extent[1], par->grid_extent[2]);
|
||||
} else fprintf(stderr, "WARNING : failed to parse extent specified in the input, this calculaion will use an automatically assigned grid extent\n");
|
||||
|
||||
//
|
||||
fflush(stdout);
|
||||
} else fprintf(stderr, "WARNING : failed to read the extent specified in the input file\n");
|
||||
} else {
|
||||
nread += add_snapshot(snapbuf, par);
|
||||
if(nfiles>0){
|
||||
par->fsnapshot = (char**) my_malloc( (nfiles) * sizeof (char*));
|
||||
fseek(f, 0, SEEK_SET);
|
||||
while(fgets(buf, 210, f)) {
|
||||
status = sscanf(buf, "%s", snapbuf) ;
|
||||
if(status < 1) {
|
||||
fprintf(stderr, "! Skipping row '%s' with bad format (status %d).\n",
|
||||
buf, status) ;
|
||||
}
|
||||
else {
|
||||
nread += add_snapshot(snapbuf, par) ;
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
fprintf(stderr, "! File %s doesn't exists\n", str_list_file);
|
||||
}
|
||||
fclose(f);
|
||||
return nread;
|
||||
}
|
||||
else {
|
||||
fprintf(stderr, "! File %s doesn't exists\n", str_list_file) ;
|
||||
}
|
||||
fclose(f);
|
||||
return nread ;
|
||||
}
|
||||
|
||||
/**
|
||||
@@ -406,15 +367,12 @@ int add_list_snapshots(char *str_list_file, s_mdparams *par) {
|
||||
*/
|
||||
int add_snapshot(char *snapbuf, s_mdparams *par) {
|
||||
int nm1;
|
||||
|
||||
FILE *f = fopen_pdb_check_case(snapbuf, "r");
|
||||
|
||||
if (f) {
|
||||
nm1 = par->nfiles;
|
||||
par->nfiles += 1;
|
||||
|
||||
|
||||
par->fsnapshot = (char**) my_realloc(par->fsnapshot, (par->nfiles) * sizeof (char*));
|
||||
|
||||
par->fsnapshot[nm1] = (char *) my_malloc((strlen(snapbuf) + 1) * sizeof (char));
|
||||
|
||||
strcpy(par->fsnapshot[nm1], snapbuf);
|
||||
|
||||
Reference in New Issue
Block a user