choderalab/yank-0.25.2.zip
choderalab-yank-8c7bf01
.gitattributes
97 Bytes
.gitignore
426 Bytes
.travis.yml
3.4 kB
Dockerfile
480 Bytes
LICENSE
1.1 kB
README.md
1.8 kB
Yank
__init__.py
308 Bytes
analyze.py
51.7 kB
cli.py
3.0 kB
commands
__init__.py
229 Bytes
analyze.py
15.9 kB
cite.py
1.5 kB
cleanup.py
1.6 kB
help.py
1.6 kB
platforms.py
1.3 kB
script.py
6.9 kB
selftest.py
9.0 kB
status.py
4.8 kB
experiment.py
147.5 kB
pipeline.py
115.2 kB
reports
YANK_Health_Report_Example.ipynb
1.2 MB
YANK_Health_Report_Template.ipynb
24.1 kB
__init__.py
404 Bytes
notebook.py
34.9 kB
restraints.py
118.4 kB
schema
__init__.py
364 Bytes
validator.py
25.2 kB
tests
__init__.py
0 Bytes
data
README.md
1.1 kB
abl-imatinib-explicit
2HYY-pdbfixer.pdb
344.0 kB
STI02.mol2
6.9 kB
benzene-toluene-explicit
benzene.frcmod
178 Bytes
benzene.gaff.mol2
1.4 kB
benzene.tripos.mol2
1.3 kB
complex.inpcrd
79.3 kB
complex.prmtop
359.6 kB
solvent.inpcrd
76.7 kB
solvent.prmtop
346.5 kB
toluene.frcmod
178 Bytes
toluene.tripos.mol2
1.6 kB
benzene-toluene-standard-state
README.md
794 Bytes
standard_state_complex.inpcrd
1.1 kB
standard_state_complex.prmtop
17.7 kB
standard_state_complex_boxless.inpcrd
1.0 kB
standard_state_complex_nan.inpcrd
995 Bytes
p-xylene-gromacs-example
complex.gro
2.7 MB
complex.top
750.1 kB
solvent.gro
95.8 kB
solvent.top
476 Bytes
top
charmm36.ff
atomtypes.atp
21.0 kB
cmap.itp
41.4 kB
ffbonded.itp
825.2 kB
ffnonbonded.itp
1.4 MB
forcefield.doc
6.5 kB
forcefield.itp
435 Bytes
gb.itp
2.7 kB
ions.itp
1.7 kB
merged.arn
92 Bytes
merged.c.tdb
1.1 kB
merged.hdb
8.5 kB
merged.n.tdb
1.4 kB
merged.r2b
198 Bytes
merged.rtp
735.5 kB
merged.vsd
5.2 kB
nbfix.itp
1.1 kB
spc.itp
619 Bytes
spce.itp
625 Bytes
tip3p.itp
1.0 kB
tip4p.itp
1.2 kB
watermodels.dat
221 Bytes
p-xyle.itp
4.7 kB
p-xylene-implicit
181L-pdbfixer.pdb
104.7 kB
p-xylene.mol2
1.9 kB
toluene-explicit
solvent.pdb
318.5 kB
solvent.xml
955.1 kB
vacuum.pdb
1.0 kB
vacuum.xml
13.2 kB
test_analyze.py
33.4 kB
test_cli.py
7.1 kB
test_examples.py
4.0 kB
test_experiment.py
149.3 kB
test_pipeline.py
16.1 kB
test_restraints.py
28.2 kB
test_schema.py
1.7 kB
test_utils.py
15.2 kB
test_yank.py
34.3 kB
utils.py
69.1 kB
yank.py
67.0 kB
devtools
README.md
2.3 kB
conda-recipe
README.md
731 Bytes
build.sh
285 Bytes
meta.yaml
596 Bytes
travis-ci
build_docs.sh
573 Bytes
install.sh
1.2 kB
oe_license.txt.enc
6.6 kB
set_doc_version.py
583 Bytes
update_versions_json.py
778 Bytes
docs
Makefile
5.8 kB
_static
custom.css
750 Bytes
toggle_sections.js
1.3 kB
yank.jpg
56.3 kB
yank.png
171.3 kB
yankIcon.png
6.9 kB
_templates
layout.html
158 Bytes
page.html
876 Bytes
acknowledgments.rst
939 Bytes
algorithms.rst
47.4 kB
analysis.rst
11.8 kB
api
analysis_api.rst
84 Bytes
experiment_api.rst
89 Bytes
index.rst
822 Bytes
mpi_api.rst
75 Bytes
multistate_api
analyzers_api.rst
106 Bytes
index.rst
617 Bytes
pipeline_api.rst
85 Bytes
restraints_api.rst
89 Bytes
utils_api.rst
79 Bytes
yank_api.rst
77 Bytes
benchmarks.rst
578 Bytes
building_docs.rst
1.6 kB
conf.py
9.3 kB
examples
all-ligand-explicit.rst
8.5 kB
freesolv-imp-exp.rst
2.9 kB
host-guest-implicit.rst
6.8 kB
hydration-phenol-explicit.rst
5.8 kB
index.rst
1.8 kB
p-xylene-explicit.rst
17.1 kB
faq.rst
3.4 kB
index.rst
2.9 kB
installation.rst
14.7 kB
ncfile-header.txt
4.2 kB
quickstart.rst
1.1 kB
references.bib
19.7 kB
references.rst
3.1 kB
requirements.txt
38 Bytes
running.rst
16.8 kB
site-resources
drawiodiagrams
README.md
1.0 kB
YANKRestraintFlowChartDiagram.xml
3.0 kB
YANKUMLClassDiagram.xml
7.3 kB
YankTCycleDiagram.xml
827.8 kB
images
YANKRestraintFlowChart.png
168.5 kB
YANKTC-Complete.png
1.5 MB
YANKTC-Stage1.png
754.4 kB
YANKTC-Stage2.png
954.5 kB
YANKTC-Stage3.png
1.4 MB
YANKUMLClassDiagram.png
203.5 kB
tutorial-files
implicit2_stock.yaml
2.2 kB
sphinxext
notebook_sphinxext.py
5.9 kB
store_format.rst
355 Bytes
style.dontbuild
4.7 kB
theory.rst
6.8 kB
tutorial.rst
26.0 kB
versions_div_theme
README.md
188 Bytes
__init__.py
267 Bytes
footer.html
75 Bytes
layout.html
142 Bytes
static
css
versions_div.css
283 Bytes
js
versions.js
828 Bytes
theme.conf
97 Bytes
versions.html
499 Bytes
whatsnew.rst
31.6 kB
yamlpages
combinatorial.rst
1.1 kB
cookbook.rst
7.3 kB
experiments.rst
4.3 kB
index.rst
8.7 kB
mcmc.rst
4.0 kB
molecules.rst
16.2 kB
options.rst
24.1 kB
protocols.rst
10.2 kB
samplers.rst
12.5 kB
solvents.rst
10.7 kB
systems.rst
6.5 kB
version.rst
397 Bytes
yank-yaml-cookbook
README.md
221 Bytes
all-options.yaml
5.5 kB
combinatorial-experiment.yaml
14.1 kB
setup.py
5.1 kB