Merge pull request #19 from cabb99/dev

Fix complementary strand geometry
cabb99 · Oct 31, 2023 · 2997cc1 · 2997cc1
2 parents 20b5253 + 5123b1a
commit 2997cc1
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diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -44,7 +44,7 @@ jobs:
       shell: bash -l {0}
       run: |
         conda activate open3spn2
-        pytest --skip-platform=opencl Tests/
+        pytest --skip-platform=opencl tests/
 
     - name: Slack Notification (on failure)
       if: failure()

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
-[![Actions Status](https://github.com/cabb99/open3spn2/workflows/build/badge.svg)](https://github.com/cabb99/open3spn2/actions)
+[![Actions Status](https://github.com/cabb99/open3spn2/workflows/CI/badge.svg)](https://github.com/cabb99/open3spn2/actions)
 [![Documentation Status](https://readthedocs.org/projects/open3spn2/badge/?version=latest)](https://open3spn2.readthedocs.io/en/latest/?badge=latest)
-[![Anaconda-Server Badge](https://anaconda.org/wolynes-lab/open3spn2/badges/installer/conda.svg)](https://conda.anaconda.org/wolynes-lab)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/open3spn2/badges/version.svg)](https://anaconda.org/conda-forge/open3spn2)
 
 # Open-3SPN2
 A Implementation of the 3SPN.2 and 3SPN.2C coarse-grained molecular model of DNA in OpenMM.
@@ -9,11 +9,9 @@ A Implementation of the 3SPN.2 and 3SPN.2C coarse-grained molecular model of DNA
 
 ## Installation
 
-Installation of the open3SPN2 repository is available through anaconda. Some of the dependencies  are contained in the omnia channel (openmm, pdbfixer) or in the conda-forge channel (mdtraj).
+Installation of the open3SPN2 repository is available through anaconda.
 
-```conda config --append channels conda-forge```
-
-```conda install -c wolynes-lab open3spn2```
+```conda install -c conda-forge open3spn2```
 
 For protein-DNA simulations you will also need to install [openAWSEM](https://github.com/npschafer/openawsem) and add the openAWSEM path to the `$PYTHONPATH` environment variable. In linux you can set the path variables on `~/.bashrc`.
 
@@ -30,8 +28,8 @@ If you publish any work using the open3SPN2 package, please include the followin
 Open3SPN2
 Lu, W., Bueno, C., Schafer, N. P., Moller, J., Jin, S., Chen, X., ... & Wolynes, P. G. (2021). OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PLoS computational biology, 17(2), e1008308. https://doi.org/10.1371/journal.pcbi.1008308
 
-3SPN.2
-Hinckley, D. M., Freeman, G. S., Whitmer, J. K., & De Pablo, J. J. (2013). An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization. Journal of Chemical Physics, 139(14). https://doi.org/10.1063/1.4822042
-
 3SPN.2C
 Freeman, G. S., Hinckley, D. M., Lequieu, J. P., Whitmer, J. K., & De Pablo, J. J. (2014). Coarse-grained modeling of DNA curvature. Journal of Chemical Physics, 141(16). https://doi.org/10.1063/1.4897649
+
+3SPN.2
+Hinckley, D. M., Freeman, G. S., Whitmer, J. K., & De Pablo, J. J. (2013). An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization. Journal of Chemical Physics, 139(14). https://doi.org/10.1063/1.4822042
diff --git a/Tests/test_cases.csv b/Tests/test_cases.csv
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -1,25 +1,31 @@
-Classes and functions
-===============================
+open3SPN2 Module Documentation
+==============================
 
 .. automodule:: open3SPN2
     :noindex:
-
-DNA
-------------------
+
+Classes and Functions
+---------------------
+
+DNA Class
+^^^^^^^^^^^^^^^^^^^^^^^
+
 .. autoclass:: open3SPN2.DNA
     :member-order: bysource
     :members:
 
-System
-------------------
+System Class
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
 .. autoclass:: open3SPN2.System
 
     .. automethod:: __init__
 
     .. rubric:: Methods
-    
+
 DNA Forces
-------------------
+^^^^^^^^^^
+
 .. autoclass:: open3SPN2.Bond
     :member-order: bysource
     :members:
@@ -35,7 +41,7 @@ DNA Forces
 .. autoclass:: open3SPN2.Stacking
     :member-order: bysource
     :members:
-    
+
 .. autoclass:: open3SPN2.BasePair
     :member-order: bysource
     :members:
@@ -52,8 +58,9 @@ DNA Forces
     :member-order: bysource
     :members:
 
-DNA - Protein Forces
---------------------
+DNA-Protein Forces
+^^^^^^^^^^^^^^^^^^
+
 .. autoclass:: open3SPN2.ExclusionProteinDNA
     :member-order: bysource
     :members:
@@ -62,28 +69,31 @@ DNA - Protein Forces
     :member-order: bysource
     :members:
 
-Utils
------
+Utility Functions
+^^^^^^^^^^^^^^^^^
+
 .. autofunction:: open3SPN2.parseConfigTable
-    
+
 .. autofunction:: open3SPN2.parsePDB
-    
+
 .. autofunction:: open3SPN2.fixPDB
-    
+
 .. autofunction:: open3SPN2.pdb2table
 
-Tests
------
-.. autoclass:: open3SPN2.TestEnergies
+Tests Functions
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autoclass:: tests.TestEnergies
     :member-order: bysource
     :members:
-    
-.. autofunction:: open3SPN2.test_DNA_from_xyz
-    
-.. autofunction:: open3SPN2.test_parse_xyz
-    
-.. autofunction:: open3SPN2.test_parse_log
-    
+
+.. autofunction:: tests.test_DNA_from_xyz
+
+.. autofunction:: tests.test_parse_xyz
+
+.. autofunction:: tests.test_parse_log
+
 Exceptions
-----------
-.. autoclass:: open3SPN2.DNATypeError
+^^^^^^^^^^
+
+.. autoclass:: open3SPN2.DNATypeError
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -74,7 +74,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

diff --git a/open3SPN2/3SPN2.conf b/open3SPN2/3SPN2.conf
@@ -303,32 +303,32 @@ row16   = G     G     33.17   3.86  -0.40  -0.02   -0.47    3.28
 
 # DNA-AWSEM interaction parameters
 [Protein-DNA particles]
-name    = molecule DNA      name epsilon radius cutoff mass     charge
-#unit   = nan      nan      nan  kJ/mol  nm     nm     Da        e
-row1    = DNA      A        P    0.8333  0.62   1.55    94.9696 -0.6
-row2    = DNA      A        S    0.8333  0.62   1.55    83.1104  0
-row3    = DNA      A        A    0.8333  0.62   1.55   134.122   0
-row4    = DNA      A        T    0.8333  0.62   1.55   125.1078  0
-row5    = DNA      A        G    0.8333  0.62   1.55   150.1214  0
-row6    = DNA      A        C    0.8333  0.62   1.55   110.0964  0
-row7    = DNA      B        P    0.8333  0.62   1.55    94.9696 -0.6
-row8    = DNA      B        S    0.8333  0.62   1.55    83.1104  0
-row9    = DNA      B        A    0.8333  0.62   1.55   134.122   0
-row10   = DNA      B        T    0.8333  0.62   1.55   125.1078  0
-row11   = DNA      B        G    0.8333  0.62   1.55   150.1214  0
-row12   = DNA      B        C    0.8333  0.62   1.55   110.0964  0
-row13   = DNA      B_curved P    0.8333  0.62   1.55    94.9696 -0.6
-row14   = DNA      B_curved S    0.8333  0.62   1.55    83.1104  0
-row15   = DNA      B_curved A    0.8333  0.62   1.55   134.122   0
-row16   = DNA      B_curved T    0.8333  0.62   1.55   125.1078  0
-row17   = DNA      B_curved G    0.8333  0.62   1.55   150.1214  0
-row18   = DNA      B_curved C    0.8333  0.62   1.55   110.0964  0
-row19   = Protein  Protein  CA   0.8333  0.62   1.55    12       0    #    15
-row20   = Protein  Protein  N    0       0.62   1.55     0       0    #    16
-row21   = Protein  Protein  O    0.8333  0.62   1.55    16       0    #    17
-row22   = Protein  Protein  CB   0.8333  0.62   1.55    12       1    #    18    19
-row23   = Protein  Protein  H    0       0.62   1.55     0       0
-row24   = Protein  Protein  C    0       0.62   1.55     0       0
+name    = molecule DNA      name epsilon  radius cutoff mass     charge
+#unit   = nan      nan      nan  kJ/mol   nm     nm     Da        e
+row1    = DNA      A        P    0.08333  0.62   1.55    94.9696 -0.6
+row2    = DNA      A        S    0.08333  0.62   1.55    83.1104  0
+row3    = DNA      A        A    0.08333  0.62   1.55   134.122   0
+row4    = DNA      A        T    0.08333  0.62   1.55   125.1078  0
+row5    = DNA      A        G    0.08333  0.62   1.55   150.1214  0
+row6    = DNA      A        C    0.08333  0.62   1.55   110.0964  0
+row7    = DNA      B        P    0.08333  0.62   1.55    94.9696 -0.6
+row8    = DNA      B        S    0.08333  0.62   1.55    83.1104  0
+row9    = DNA      B        A    0.08333  0.62   1.55   134.122   0
+row10   = DNA      B        T    0.08333  0.62   1.55   125.1078  0
+row11   = DNA      B        G    0.08333  0.62   1.55   150.1214  0
+row12   = DNA      B        C    0.08333  0.62   1.55   110.0964  0
+row13   = DNA      B_curved P    0.08333  0.62   1.55    94.9696 -0.6
+row14   = DNA      B_curved S    0.08333  0.62   1.55    83.1104  0
+row15   = DNA      B_curved A    0.08333  0.62   1.55   134.122   0
+row16   = DNA      B_curved T    0.08333  0.62   1.55   125.1078  0
+row17   = DNA      B_curved G    0.08333  0.62   1.55   150.1214  0
+row18   = DNA      B_curved C    0.08333  0.62   1.55   110.0964  0
+row19   = Protein  Protein  CA   0.08333  0.62   1.55    12       0    #    15
+row20   = Protein  Protein  N    0        0.62   1.55     0       0    #    16
+row21   = Protein  Protein  O    0.08333  0.62   1.55    16       0    #    17
+row22   = Protein  Protein  CB   0.08333  0.62   1.55    12       1    #    18    19
+row23   = Protein  Protein  H    0        0.62   1.55     0       0
+row24   = Protein  Protein  C    0        0.62   1.55     0       0
 
 [Sequence dependent electrostatics]
 name    = resname charge cutoff