added some output to the CG montecarlo object to look at energy decom…

…position during MC simulation

cg_pyrosetta/CG_monte_carlo.py

@@ -13,11 +13,6 @@
 import sys
 import warnings
 import cg_pyrosetta.CG_movers
-
-
-current_path = os.path.dirname(os.path.abspath(__file__))
-sys.path.insert(0, os.path.abspath(current_path + '/../PyRosetta4.modified'))
-
 import pyrosetta
 
 class Subject(ABC):
@@ -218,6 +213,9 @@ def run(self):
             if self._output is True:
                 print("Step :", self._total_trials)
                 print("Energy : ", self.get_energy())
+                print("Energy Decomposition:")
+                for scoretype in self._score.get_nonzero_weighted_scoretypes():
+                    print(str(scoretype).split(".")[-1], self._score.score_by_scoretype(self.pose, scoretype), end = " ")
                 self.pymol.apply(self.pose)
             self.notifyObservers()
 

environment.yml

@@ -1,233 +1,136 @@
-name: pyrosetta
+name: conda_pyrosetta
 channels:
-  - omnia
+  - https://conda.rosettacommons.org
   - conda-forge
+  - omnia
+  - https://levinthal:paradox@conda.rosettacommons.org
   - defaults
 dependencies:
-  - _nb_ext_conf=0.4.0=py36_1
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
   - alabaster=0.7.12=py_0
-  - ambermini=16.16.0=7
-  - anaconda-client=1.7.2=py_0
-  - appdirs=1.4.3=py_1
-  - asn1crypto=0.24.0=py36_1003
-  - astroid=2.2.5=py36_0
-  - atomicwrites=1.3.0=py_0
-  - attrs=19.1.0=py_0
-  - automat=0.7.0=py_1
-  - babel=2.7.0=py_0
-  - backcall=0.1.0=py_0
-  - bcrypt=3.1.4=py36h470a237_0
-  - blas=2.7=openblas
-  - bleach=3.1.0=py_0
-  - blosc=1.15.0=hd408876_0
-  - bzip2=1.0.6=h14c3975_5
-  - ca-certificates=2019.6.16=hecc5488_0
-  - cerberus=1.1=py36_0
-  - certifi=2019.6.16=py36_0
-  - cffi=1.12.3=py36h8022711_0
-  - cftime=1.0.3.4=py36hd352d35_1001
-  - chardet=3.0.4=py36_1003
-  - clusterutils=0.3.1=py36_1
-  - clyent=1.2.2=py_1
-  - constantly=15.1.0=py_0
-  - cryptography=2.6.1=py36h72c5cf5_0
-  - curl=7.64.1=hf8cf82a_0
-  - cycler=0.10.0=py_1
-  - cython=0.29.10=py36he1b5a44_0
-  - dataclasses=0.6=py_0
-  - dbus=1.13.6=h746ee38_0
-  - decorator=4.4.0=py_0
-  - defusedxml=0.5.0=py_1
-  - docopt=0.6.2=py_1
-  - docutils=0.14=py36_1001
-  - entrypoints=0.3=py36_1000
-  - expat=2.2.6=he6710b0_0
-  - fastcluster=1.1.25=py36h637b7d7_1000
-  - fftw3f=3.3.4=2
-  - fontconfig=2.13.0=h9420a91_0
-  - freetype=2.9.1=h8a8886c_1
-  - glib=2.56.2=hd408876_0
-  - gmp=6.1.2=h6c8ec71_1
-  - gst-plugins-base=1.14.0=hbbd80ab_1
-  - gstreamer=1.14.0=hb453b48_1
-  - hdf4=4.2.13=0
-  - hdf5=1.10.2=hba1933b_1
-  - html5lib=1.0.1=py_0
-  - hyperlink=17.3.1=py_0
-  - icu=58.2=h9c2bf20_1
-  - idna=2.8=py36_1000
-  - imagesize=1.1.0=py_0
-  - importlib_metadata=0.18=py36_0
-  - incremental=17.5.0=py_0
-  - intel-openmp=2019.3=199
-  - ipykernel=5.1.1=py36h24bf2e0_0
-  - ipython=7.5.0=py36h24bf2e0_0
-  - ipython_genutils=0.2.0=py_1
-  - ipywidgets=7.4.2=py_0
-  - isort=4.3.20=py36_0
-  - jedi=0.13.3=py36_0
-  - jinja2=2.10.1=py_0
-  - joblib=0.13.2=py_0
-  - jpeg=9b=h024ee3a_2
-  - jsonschema=3.0.1=py36_0
-  - jupyter=1.0.0=py_2
-  - jupyter_client=5.2.4=py_3
-  - jupyter_console=6.0.0=py_0
-  - jupyter_core=4.4.0=py_0
-  - kiwisolver=1.1.0=py36hc9558a2_0
-  - krb5=1.16.3=h05b26f9_1001
-  - latexcodec=1.0.7=py_0
-  - lazy-object-proxy=1.4.1=py36h516909a_0
-  - libblas=3.8.0=7_openblas
-  - libcblas=3.8.0=7_openblas
-  - libcurl=7.64.1=hda55be3_0
-  - libedit=3.1.20181209=hc058e9b_0
-  - libffi=3.2.1=hd88cf55_4
-  - libgcc=7.2.0=h69d50b8_2
-  - libgcc-ng=8.2.0=hdf63c60_1
-  - libgfortran=3.0.0=1
-  - libgfortran-ng=7.3.0=hdf63c60_0
-  - liblapack=3.8.0=7_openblas
-  - liblapacke=3.8.0=7_openblas
-  - libnetcdf=4.6.1=h5e45101_3
-  - libopenblas=0.2.20=h9ac9557_7
-  - libpng=1.6.36=hbc83047_0
-  - libsodium=1.0.16=h1bed415_0
-  - libssh2=1.8.2=h22169c7_2
-  - libstdcxx-ng=8.2.0=hdf63c60_1
-  - libuuid=1.0.3=h1bed415_2
-  - libxcb=1.13=h1bed415_1
-  - libxml2=2.9.9=he19cac6_0
-  - lzo=2.10=h49e0be7_2
-  - markupsafe=1.1.1=py36h14c3975_0
-  - matplotlib=3.1.0=py36_0
-  - matplotlib-base=3.1.0=py36h5f35d83_0
-  - mccabe=0.6.1=py_1
-  - mdtraj=1.9.3=py36h00575c5_0
-  - mistune=0.8.4=py36h14c3975_1000
-  - mkl=2018.0.3=1
-  - more-itertools=4.3.0=py36_1000
-  - mpi=1.0=mpich
-  - mpi4py=3.0.1=py36hf046da1_0
-  - mpich=3.2.1=hc99cbb1_1009
-  - msmbuilder=3.8.0=np111py36_0
-  - nb_anacondacloud=1.4.0=py36_0
-  - nb_conda=2.2.1=py36_2
-  - nb_conda_kernels=2.2.2=py36_0
-  - nbconvert=5.4.1=py_2
-  - nbformat=4.4.0=py_1
-  - nbpresent=3.0.2=py36_1
-  - ncurses=6.1=he6710b0_1
-  - netcdf4=1.3.1=py36h62672b6_4
-  - nose=1.3.7=py36_1002
-  - notebook=5.7.8=py36_1
-  - numexpr=2.6.9=py36h637b7d7_1000
-  - numpy=1.11.3=py36he5ce36f_1207
-  - numpy-base=1.14.3=py36h2b20989_0
-  - numpydoc=0.9.0=py_0
-  - openblas=0.3.5=h9ac9557_1001
-  - openmm=7.3.1=py36_cuda92_rc_2
-  - openmmtools=0.16.0=py36_0
-  - openmoltools=0.8.3=py36_0
-  - openssl=1.1.1b=h14c3975_1
-  - oset=0.1.3=py_1
-  - packaging=19.0=py_0
-  - pandas=0.23.4=py36h637b7d7_1000
-  - pandoc=2.2.3.2=0
-  - pandocfilters=1.4.2=py_1
-  - parmed=3.0.1=py36_1
-  - parso=0.4.0=py_0
-  - patsy=0.5.1=py_0
-  - pcre=8.43=he6710b0_0
-  - pdbfixer=1.5=py36_0
-  - pexpect=4.7.0=py36_0
-  - pickleshare=0.7.5=py36_1000
-  - pint=0.9=py36_2
-  - pip=19.1=py36_0
-  - plotly=3.10.0=py_0
-  - pluggy=0.12.0=py_0
-  - prometheus_client=0.6.0=py_0
-  - prompt_toolkit=2.0.9=py_0
-  - ptyprocess=0.6.0=py_1001
-  - py=1.8.0=py_0
-  - py3dmol=0.8.0=py_0
-  - pyasn1=0.4.5=py_0
-  - pyasn1-modules=0.2.5=py_0
-  - pybtex=0.22.2=py36_0
-  - pybtex-docutils=0.2.1=py36_1000
-  - pycparser=2.19=py36_1
-  - pydantic=0.29=py36_0
-  - pygments=2.4.2=py_0
-  - pyhamcrest=1.9.0=py_2
-  - pyhmc=0.1.2=py36h3010b51_1000
-  - pylint=2.3.1=py36_0
-  - pymbar=3.0.3=py36h3010b51_3
-  - pyopenssl=19.0.0=py36_0
-  - pyparsing=2.4.0=py_0
-  - pyqt=5.9.2=py36hcca6a23_0
-  - pyrsistent=0.15.2=py36h516909a_0
-  - pysocks=1.7.0=py36_0
-  - pytables=3.4.4=py36h4f72b40_1
-  - pytest=4.6.3=py36_0
-  - python=3.6.8=h0371630_0
-  - python-dateutil=2.8.0=py_0
-  - pytz=2019.1=py_0
-  - pyyaml=5.1=py36h14c3975_0
-  - pyzmq=18.0.1=py36h0e1adb2_0
-  - qcelemental=0.4.2=py_0
-  - qcportal=0.7.2=py_0
-  - qt=5.9.7=h5867ecd_1
-  - qtconsole=4.5.1=py_0
-  - readline=7.0=h7b6447c_5
-  - requests=2.22.0=py36_0
-  - retrying=1.3.3=py_2
-  - scikit-learn=0.21.2=py36h627018c_0
-  - scipy=1.2.1=py36h09a28d5_1
-  - seaborn=0.9.0=py_1
-  - send2trash=1.5.0=py_0
-  - service_identity=18.1.0=py_0
-  - setuptools=41.0.1=py36_0
-  - simplegeneric=0.8.1=py_1
-  - sip=4.19.8=py36hf484d3e_1000
-  - six=1.12.0=py36_1000
-  - snappy=1.1.7=hbae5bb6_3
-  - snowballstemmer=1.2.1=py_1
-  - sphinx=2.1.0=py_0
-  - sphinx_rtd_theme=0.4.3=py_0
-  - sphinxcontrib-applehelp=1.0.1=py_0
-  - sphinxcontrib-bibtex=0.4.2=py_0
-  - sphinxcontrib-devhelp=1.0.1=py_0
-  - sphinxcontrib-htmlhelp=1.0.2=py_0
+  - astunparse=1.6.3=pyhd8ed1ab_0
+  - attrs=21.4.0=pyhd8ed1ab_0
+  - babel=2.11.0=pyhd8ed1ab_0
+  - beautifulsoup4=4.11.1=pyha770c72_0
+  - blosc=1.21.1=h83bc5f7_3
+  - brotlipy=0.7.0=py39hb9d737c_1004
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.18.1=h7f98852_0
+  - ca-certificates=2022.9.24=ha878542_0
+  - certifi=2022.9.24=pyhd8ed1ab_0
+  - cffi=1.15.0=py39h4bc2ebd_0
+  - chardet=4.0.0=py39hf3d152e_3
+  - charset-normalizer=2.0.12=pyhd8ed1ab_0
+  - cloudpickle=2.1.0=pyhd8ed1ab_0
+  - colorama=0.4.4=pyh9f0ad1d_0
+  - conda=4.13.0=py39hf3d152e_1
+  - conda-build=3.21.9=py39hf3d152e_0
+  - conda-package-handling=1.8.1=py39hb9d737c_1
+  - cryptography=37.0.1=py39h9ce1e76_0
+  - deprecation=2.1.0=pyh9f0ad1d_0
+  - docutils=0.16=py39hf3d152e_3
+  - filelock=3.7.1=pyhd8ed1ab_0
+  - glob2=0.7=py_0
+  - hdf5=1.12.1=nompi_h4df4325_104
+  - icu=70.1=h27087fc_0
+  - idna=3.3=pyhd8ed1ab_0
+  - imagesize=1.4.1=pyhd8ed1ab_0
+  - importlib-metadata=4.11.4=py39hf3d152e_0
+  - importlib_resources=5.7.1=pyhd8ed1ab_1
+  - iniconfig=1.1.1=pyh9f0ad1d_0
+  - jinja2=3.1.2=pyhd8ed1ab_1
+  - jsonschema=4.6.0=pyhd8ed1ab_0
+  - keyutils=1.6.1=h166bdaf_0
+  - krb5=1.19.3=h08a2579_0
+  - ld_impl_linux-64=2.36.1=hea4e1c9_2
+  - libarchive=3.5.2=hada088e_2
+  - libblas=3.9.0=15_linux64_openblas
+  - libcblas=3.9.0=15_linux64_openblas
+  - libcurl=7.83.1=h2283fc2_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=12.1.0=h8d9b700_16
+  - libgfortran-ng=12.1.0=h69a702a_16
+  - libgfortran5=12.1.0=hdcd56e2_16
+  - libgomp=12.1.0=h8d9b700_16
+  - libiconv=1.16=h516909a_0
+  - liblapack=3.9.0=15_linux64_openblas
+  - liblief=0.11.5=h9c3ff4c_1
+  - libnghttp2=1.47.0=he49606f_0
+  - libnsl=2.0.0=h7f98852_0
+  - libopenblas=0.3.20=pthreads_h78a6416_0
+  - libssh2=1.10.0=ha35d2d1_2
+  - libstdcxx-ng=12.1.0=ha89aaad_16
+  - libuuid=2.32.1=h7f98852_1000
+  - libxml2=2.9.14=h22db469_0
+  - libzlib=1.2.12=h166bdaf_0
+  - lz4-c=1.9.3=h9c3ff4c_1
+  - lzo=2.10=h516909a_1000
+  - m2r2=0.3.3=pyhd8ed1ab_0
+  - markupsafe=2.1.1=py39hb9d737c_1
+  - mdtraj=1.9.7=py39h138c130_1
+  - mistune=0.8.4=py39h3811e60_1005
+  - ncurses=6.3=h27087fc_1
+  - nomkl=1.0=h5ca1d4c_0
+  - numexpr=2.8.0=py39h194a79d_102
+  - numpy=1.22.4=py39hc58783e_0
+  - openssl=3.0.7=h166bdaf_0
+  - packaging=21.3=pyhd8ed1ab_0
+  - pandas=1.4.2=py39h1832856_2
+  - patchelf=0.14.5=h58526e2_0
+  - pip=22.1.2=pyhd8ed1ab_0
+  - pkginfo=1.8.2=pyhd8ed1ab_0
+  - pluggy=1.0.0=py39hf3d152e_3
+  - psutil=5.9.1=py39hb9d737c_0
+  - py=1.11.0=pyh6c4a22f_0
+  - py-lief=0.11.5=py39he80948d_1
+  - pycosat=0.6.3=py39hb9d737c_1010
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pygments=2.13.0=pyhd8ed1ab_0
+  - pyopenssl=22.0.0=pyhd8ed1ab_0
+  - pyparsing=3.0.9=pyhd8ed1ab_0
+  - pyrosetta=2022.20+release.1eb2c32=py39_0
+  - pyrsistent=0.18.1=py39hb9d737c_1
+  - pysocks=1.7.1=py39hf3d152e_5
+  - pytables=3.7.0=py39h2669a42_0
+  - pytest=7.1.2=py39hf3d152e_0
+  - python=3.9.13=h2660328_0_cpython
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-libarchive-c=4.0=py39hf3d152e_1
+  - python_abi=3.9=2_cp39
+  - pytz=2022.1=pyhd8ed1ab_0
+  - pyyaml=6.0=py39hb9d737c_4
+  - readline=8.1=h46c0cb4_0
+  - requests=2.27.1=pyhd8ed1ab_0
+  - ripgrep=13.0.0=h2f28480_2
+  - ruamel_yaml=0.15.80=py39hb9d737c_1007
+  - scipy=1.8.1=py39he49c0e8_0
+  - setuptools=62.3.3=py39hf3d152e_0
+  - signac=1.7.0=pyhd8ed1ab_0
+  - signac-flow=0.19.0=pyhd8ed1ab_0
+  - six=1.16.0=pyh6c4a22f_0
+  - snappy=1.1.9=hbd366e4_1
+  - snowballstemmer=2.2.0=pyhd8ed1ab_0
+  - soupsieve=2.3.1=pyhd8ed1ab_0
+  - sphinx=5.0.0=pyh6c4a22f_1
+  - sphinxcontrib-applehelp=1.0.2=py_0
+  - sphinxcontrib-devhelp=1.0.2=py_0
+  - sphinxcontrib-htmlhelp=2.0.0=pyhd8ed1ab_0
   - sphinxcontrib-jsmath=1.0.1=py_0
-  - sphinxcontrib-qthelp=1.0.2=py_0
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-  - sqlite=3.28.0=h7b6447c_0
-  - statsmodels=0.9.0=py36h3010b51_1000
-  - terminado=0.8.2=py36_0
-  - testpath=0.4.2=py_1001
-  - tk=8.6.9=hed695b0_1002
-  - tornado=6.0.2=py36h516909a_0
-  - traitlets=4.3.2=py36_1000
-  - twisted=19.2.0=py36h516909a_1
-  - typed-ast=1.3.5=py36h516909a_0
-  - urllib3=1.24.3=py36_0
-  - wcwidth=0.1.7=py_1
-  - webencodings=0.5.1=py_1
-  - wheel=0.33.4=py36_0
-  - widgetsnbextension=3.4.2=py36_1000
-  - wrapt=1.11.1=py36h516909a_0
-  - xz=5.2.4=h14c3975_4
-  - yaml=0.1.7=had09818_2
-  - yank=0.23.7=py36_0
-  - zeromq=4.2.5=hf484d3e_1
-  - zipp=0.5.1=py_0
-  - zlib=1.2.11=h7b6447c_3
-  - zope=1.0=py36_1
-  - zope.interface=4.6.0=py36h14c3975_1000
-  - pip:
-    - m2r==0.2.1
-    - panedr==0.5.2
-    - pbr==5.2.1
-    - pyrosetta==2018.25+release.9d22951
-##prefix: /home/tfobe/anaconda3/envs/python36
-
+  - sphinxcontrib-qthelp=1.0.3=py_0
+  - sphinxcontrib-serializinghtml=1.1.5=pyhd8ed1ab_2
+  - sqlite=3.38.5=h4ff8645_0
+  - tk=8.6.12=h27826a3_0
+  - tomli=2.0.1=pyhd8ed1ab_0
+  - tqdm=4.64.0=pyhd8ed1ab_0
+  - tzdata=2022a=h191b570_0
+  - urllib3=1.26.9=pyhd8ed1ab_0
+  - wheel=0.37.1=pyhd8ed1ab_0
+  - xz=5.2.5=h516909a_1
+  - yaml=0.2.5=h7f98852_2
+  - zipp=3.8.0=pyhd8ed1ab_0
+  - zlib=1.2.12=h166bdaf_0
+  - zstd=1.5.2=h8a70e8d_1
+prefix: /home/tfobe/anaconda3/envs/conda_pyrosetta