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Merge pull request #129 from rigdenlab/changes
SIMBAD fixes and changes
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[run] | ||
branch = True | ||
source = simbad | ||
[report] | ||
exclude_lines = | ||
if self.debug: | ||
pragma: no cover | ||
raise NotImplementedError | ||
if __name__ == .__main__.: | ||
ignore_errors = True | ||
omit = | ||
simbad/*/tests/* |
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language: python | ||
os: | ||
- linux | ||
python: | ||
- "2.7" | ||
|
||
cache: pip | ||
install: | ||
- sudo apt-get update | ||
- wget https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py | ||
- python ./bootstrap.py | ||
- cctbx-python setup.py install | ||
- pip install codecov | ||
- pip install -r requirements.txt | ||
- python setup.py install | ||
script: | ||
- coverage run scripts/run_tests.py | ||
|
||
after_success: | ||
- codecov |
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# Written by: Adam Simpkin | ||
# Date: 21 July 2020 | ||
# | ||
# This script is an example of how to run the contaminant | ||
# search in SIMBAD. Various command line flags could be set | ||
# but below's example is the most basic usage and illustrates | ||
# its purporse. | ||
|
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%CCP4%\bin\simbad-contaminant.bat ^ | ||
-nproc 4 ^ | ||
-organism CHICK ^ | ||
input/2fbb.mtz |
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# Written by: Adam Simpkin | ||
# Date: 21 July 2020 | ||
# | ||
# This script is an example of how to run the lattice search | ||
# SIMBAD. Various command line flags could be set but below's | ||
# example is the most basic usage and illustrates its purpose. | ||
|
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%CCP4%\bin\simbad-lattice.bat ^ | ||
input/1dtx.mtz |
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# Written by: Adam Simpkin | ||
# Date: 21 July 2020 | ||
# | ||
# This script is an example of how to run the a MoRDa search in | ||
# SIMBAD. Various command line flags could be set but below's | ||
# example is the most basic usage and illustrates its purpose | ||
#. | ||
# Note: the MoRDa database needs to be installed separately. | ||
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set morda_db="<PATH TO MORDA DB>" | ||
set nproc=4 | ||
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%CCP4%\bin\simbad-morda ^ | ||
-morda_db %morda_db% ^ | ||
-nproc %nproc% ^ | ||
input/1dtx.mtz |
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% 29968670 | ||
@Article{pmid29968670, | ||
Author="Simpkin, Adam J. and Simkovic, Felix and Thomas, Jens M. H. and Savko, Martin and Lebedev, Andrey and Uski, Ville and Ballard, Charles and Wojdyr, Marcin and Wu, Rui and Sanishvili, Ruslan and Xu, Yibin and Lisa, Mar{\'\i}a-Natalia and Buschiazzo, Alejandro and Shepard, William and Rigden, Daniel J. and Keegan, Ronan M.", | ||
Title="{{\it SIMBAD}: a sequence-independent molecular-replacement pipeline}", | ||
Journal="Acta Crystallographica Section D", | ||
Year="2018", | ||
Volume="74", | ||
Number="7", | ||
Pages="595--605", | ||
Month="Jul", | ||
Doi={10.1107/S2059798318005752}, | ||
Url={https://doi.org/10.1107/S2059798318005752}, | ||
} | ||
|
||
% 31909738 | ||
@Article{pmid31909738, | ||
Author="Simpkin, Adam J. and Simkovic, Felix and Thomas, Jens M. H. and Savko, Martin and Lebedev, Andrey and Uski, Ville and Ballard, Charles C. and Wojdyr, Marcin and Shepard, William and Rigden, Daniel J. and Keegan, Ronan M.", | ||
Title="{Using {\it Phaser} and ensembles to improve the performance of {\it SIMBAD}}", | ||
Journal="Acta Crystallographica Section D", | ||
Year="2020", | ||
Volume="76", | ||
Number="1", | ||
Pages="1--8", | ||
Month="Jan", | ||
Doi={10.1107/S2059798319015031}, | ||
Url={https://doi.org/10.1107/S2059798319015031}, | ||
} |
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PMID- 29968670 | ||
AU - A. J. SIMPKIN | ||
AU - F. SIMKOVIC | ||
AU - J. J. THOMAS | ||
AU - M. SAVKO | ||
AU - A. LEBEDEV | ||
AU - V. USKI | ||
AU - C. BALLARD | ||
AU - M. WOJDYR | ||
AU - R. WU | ||
AU - R. SANISHVILI | ||
AU - Y. XU | ||
AU - L. MARIA-NATALIA | ||
AU - A. BUSCHIAZZO | ||
AU - W. SHEPARD | ||
AU - D. J. RIGDEN | ||
AU - R. M. KEEGAN | ||
TI - SIMBAD: a sequence-independent molecular-replacement pipeline | ||
SO - Acta Crystallographica Section D 2018;74(7):595-605 | ||
UR - https://doi.org/10.1107/S2059798318005752 | ||
N1 - doi:10.1107/S2059798318005752 | ||
|
||
PMID- 31909738 | ||
AU - A. J. SIMPKIN | ||
AU - F. SIMKOVIC | ||
AU - J. J. THOMAS | ||
AU - M. SAVKO | ||
AU - A. LEBEDEV | ||
AU - V. USKI | ||
AU - C. BALLARD | ||
AU - M. WOJDYR | ||
AU - W. SHEPARD | ||
AU - D. J. RIGDEN | ||
AU - R. M. KEEGAN | ||
TI - Using Phaser and ensembles to improve the performance of SIMBAD | ||
SO - Acta Crystallographica Section D 2020;76(1):1-8 | ||
UR - https://doi.org/10.1107/S2059798319015031 | ||
N1 - doi:10.1107/S2059798319015031 |
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