SOURSOP 2.0.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- soursop/__init__.py +42 -0
- soursop/_internal_data.py +1408 -0
- soursop/_version.py +1 -0
- soursop/configs.py +33 -0
- soursop/data/SASA_SUMMARY.csv +20 -0
- soursop/data/bbseg2.dat +36 -0
- soursop/data/phi_excluded_volume_tripeptides.pickle +0 -0
- soursop/data/psi_excluded_volume_tripeptides.pickle +0 -0
- soursop/data/test_data/all_residues_AA.pdb +339 -0
- soursop/data/test_data/all_residues_AA.xtc +0 -0
- soursop/data/test_data/cap_tests/ACD_start_1.pdb +48 -0
- soursop/data/test_data/cap_tests/ACD_start_10.pdb +48 -0
- soursop/data/test_data/cap_tests/ACE_NH2.pdb +87 -0
- soursop/data/test_data/cap_tests/ACE_NME.pdb +90 -0
- soursop/data/test_data/cap_tests/ACE_NME_multichain.pdb +264 -0
- soursop/data/test_data/cap_tests/ACE_NME_start_at_5.pdb +90 -0
- soursop/data/test_data/cap_tests/ACE_UCAP.pdb +85 -0
- soursop/data/test_data/cap_tests/FOR_NH2.pdb +84 -0
- soursop/data/test_data/cap_tests/FOR_NME.pdb +87 -0
- soursop/data/test_data/cap_tests/FOR_UCAP.pdb +82 -0
- soursop/data/test_data/cap_tests/UCAP_NH2.pdb +83 -0
- soursop/data/test_data/cap_tests/UCAP_NME.pdb +86 -0
- soursop/data/test_data/cap_tests/UCAP_UCAP.pdb +81 -0
- soursop/data/test_data/cap_tests/__START.pdb +48 -0
- soursop/data/test_data/ctl9_AA.pdb +1486 -0
- soursop/data/test_data/ctl9_AA.xtc +0 -0
- soursop/data/test_data/ctl9_AA_reference.pkl +0 -0
- soursop/data/test_data/gromacs1chain/top.pdb +945 -0
- soursop/data/test_data/gromacs1chain/traj.xtc +0 -0
- soursop/data/test_data/gromacs2chains/top.pdb +964 -0
- soursop/data/test_data/gromacs2chains/traj.xtc +0 -0
- soursop/data/test_data/gs6_AA.dcd +0 -0
- soursop/data/test_data/gs6_AA.pdb +86 -0
- soursop/data/test_data/gs6_AA.xtc +0 -0
- soursop/data/test_data/gs6_AA_reference.pkl +0 -0
- soursop/data/test_data/gs6_distance_map_mean.npy +0 -0
- soursop/data/test_data/gs6_distance_map_std.npy +0 -0
- soursop/data/test_data/gs6_invalid_r1.pdb +86 -0
- soursop/data/test_data/ntl9_AA.pdb +914 -0
- soursop/data/test_data/ntl9_AA.xtc +0 -0
- soursop/data/test_data/ntl9_AA_reference.pkl +0 -0
- soursop/data/test_data/ntl9_distance_map_mean.npy +0 -0
- soursop/data/test_data/ntl9_distance_map_std.npy +0 -0
- soursop/data/test_data/pre_data/PRE_109_unweighted.csv +92 -0
- soursop/data/test_data/pre_data/PRE_119_unweighted.csv +92 -0
- soursop/data/test_data/pre_data/PRE_149_unweighted.csv +92 -0
- soursop/data/test_data/pre_data/PRE_61_unweighted.csv +92 -0
- soursop/data/test_data/pre_data/PRE_74_unweighted.csv +92 -0
- soursop/data/test_data/pre_data/PRE_96_unweighted.csv +92 -0
- soursop/data/test_data/sampling_quality/EV/1/__START.pdb +35 -0
- soursop/data/test_data/sampling_quality/EV/1/__traj.xtc +0 -0
- soursop/data/test_data/sampling_quality/EV/2/__START.pdb +35 -0
- soursop/data/test_data/sampling_quality/EV/2/__traj.xtc +0 -0
- soursop/data/test_data/sampling_quality/EV/3/__START.pdb +35 -0
- soursop/data/test_data/sampling_quality/EV/3/__traj.xtc +0 -0
- soursop/data/test_data/sampling_quality/WT/1/__START.pdb +35 -0
- soursop/data/test_data/sampling_quality/WT/1/__traj.xtc +0 -0
- soursop/data/test_data/sampling_quality/WT/2/__START.pdb +35 -0
- soursop/data/test_data/sampling_quality/WT/2/__traj.xtc +0 -0
- soursop/data/test_data/sampling_quality/WT/3/__START.pdb +35 -0
- soursop/data/test_data/sampling_quality/WT/3/__traj.xtc +0 -0
- soursop/data/test_data/sigA_CG.pdb +206 -0
- soursop/data/test_data/sigA_CG.xtc +0 -0
- soursop/data/test_data/sigA_CG_reference.pkl +0 -0
- soursop/data/test_data/swan_trajectories/Ash1.pdb +328 -0
- soursop/data/test_data/swan_trajectories/Ash1.xtc +0 -0
- soursop/data/test_data/swan_trajectories/alpha_syn.pdb +528 -0
- soursop/data/test_data/swan_trajectories/alpha_syn.xtc +0 -0
- soursop/data/test_data/swan_trajectories/helix.pdb +190 -0
- soursop/data/test_data/swan_trajectories/helix.xtc +0 -0
- soursop/data/test_data/synth_1_CG.pdb +78 -0
- soursop/data/test_data/synth_1_CG.xtc +0 -0
- soursop/data/test_data/synth_1_CG_reference.pkl +0 -0
- soursop/plugins/__init__.py +4 -0
- soursop/plugins/sparrow_plugin/__init__.py +94 -0
- soursop/soursop.py +86 -0
- soursop/ssbme.py +1805 -0
- soursop/sscoper.py +1507 -0
- soursop/ssdata.py +202 -0
- soursop/ssexceptions.py +52 -0
- soursop/sshdx.py +359 -0
- soursop/ssio.py +62 -0
- soursop/ssmutualinformation.py +170 -0
- soursop/ssnmr.py +2272 -0
- soursop/sspolymer.py +53 -0
- soursop/sspre.py +286 -0
- soursop/ssprotein.py +6110 -0
- soursop/sssampling.py +1684 -0
- soursop/sstools.py +346 -0
- soursop/sstrajectory.py +1467 -0
- soursop/ssutils.py +1050 -0
- soursop/tests/__init__.py +3 -0
- soursop/tests/build_reference/__init__.py +0 -0
- soursop/tests/build_reference/build_references.py +797 -0
- soursop/tests/conftest.py +173 -0
- soursop/tests/test_caps.py +88 -0
- soursop/tests/test_reference_observables.py +294 -0
- soursop/tests/test_scratchpad.ipynb +892 -0
- soursop/tests/test_soursop.py +47 -0
- soursop/tests/test_ssbme.py +368 -0
- soursop/tests/test_sscoper.py +319 -0
- soursop/tests/test_sshdx.py +133 -0
- soursop/tests/test_ssmutual_information.py +28 -0
- soursop/tests/test_ssnmr.py +917 -0
- soursop/tests/test_ssnmr_extended.py +61 -0
- soursop/tests/test_sspre.py +35 -0
- soursop/tests/test_ssproteins.py +1191 -0
- soursop/tests/test_sssampling.py +109 -0
- soursop/tests/test_sstrajectory.py +1045 -0
- soursop/tests/test_ssutils.py +43 -0
- soursop/tests/test_swan.py +195 -0
- soursop/tests/test_weights.py +787 -0
- soursop-2.0.0.dist-info/METADATA +198 -0
- soursop-2.0.0.dist-info/RECORD +117 -0
- soursop-2.0.0.dist-info/WHEEL +5 -0
- soursop-2.0.0.dist-info/licenses/LICENSE +57 -0
- soursop-2.0.0.dist-info/top_level.txt +1 -0
soursop/__init__.py
ADDED
|
@@ -0,0 +1,42 @@
|
|
|
1
|
+
## _____ ____ _ _ _____ _____ ____ _____
|
|
2
|
+
## / ____|/ __ \| | | | __ \ / ____|/ __ \| __ \
|
|
3
|
+
## | (___ | | | | | | | |__) | (___ | | | | |__) |
|
|
4
|
+
## \___ \| | | | | | | _ / \___ \| | | | ___/
|
|
5
|
+
## ____) | |__| | |__| | | \ \ ____) | |__| | |
|
|
6
|
+
## |_____/ \____/ \____/|_| \_\_____/ \____/|_|
|
|
7
|
+
|
|
8
|
+
## Alex Holehouse (Pappu Lab and Holehouse Lab) and Jared Lalmansing (Pappu lab)
|
|
9
|
+
## Simulation analysis package
|
|
10
|
+
## Copyright 2014 - 2026
|
|
11
|
+
##
|
|
12
|
+
|
|
13
|
+
import os
|
|
14
|
+
|
|
15
|
+
# Generate _version.py if missing and in the Read the Docs environment
|
|
16
|
+
if os.getenv("READTHEDOCS") == "True" and not os.path.isfile("../soursop/_version.py"):
|
|
17
|
+
import versioningit
|
|
18
|
+
|
|
19
|
+
__version__ = versioningit.get_version("../")
|
|
20
|
+
else:
|
|
21
|
+
from soursop._version import __version__
|
|
22
|
+
|
|
23
|
+
# The git revision is derived from the version string written by versioningit
|
|
24
|
+
# (see soursop.soursop.version_git_revision). Guarded so a partially-built or
|
|
25
|
+
# source checkout still imports cleanly.
|
|
26
|
+
try:
|
|
27
|
+
from soursop.soursop import version_git_revision as _version_git_revision
|
|
28
|
+
|
|
29
|
+
__git_revision__ = _version_git_revision()
|
|
30
|
+
except Exception: # pragma: no cover - defensive fallback
|
|
31
|
+
__git_revision__ = "unknown"
|
|
32
|
+
|
|
33
|
+
# code that allows access to the data directory
|
|
34
|
+
_ROOT = os.path.abspath(os.path.dirname(__file__))
|
|
35
|
+
|
|
36
|
+
|
|
37
|
+
def get_data(path):
|
|
38
|
+
return os.path.join(_ROOT, "data", path)
|
|
39
|
+
|
|
40
|
+
|
|
41
|
+
def get_version():
|
|
42
|
+
return "%s - %s" % (str(__version__), str(__git_revision__))
|