Merge f739fc5 into 52000c8

.gitignore

@@ -46,4 +46,8 @@ test/*.pdb
 #docs/_templates
 
 # vscode setting
-.vscode
+.vscode
+
+.DS_Store
+test/1AK4/atomic_features/test_1AK4_100w.dat
+test/2OUL/atomic_features/test_2OUL_1.dat

.travis.yml

@@ -21,33 +21,6 @@ before_install:
   - conda install -c conda-forge pytest-cov
   - conda install python=3.6
 
-  # install freesasa python bindings
-  # - pip install freesasa==2.0.3.post4 # <- doesn't work anymore
-
-  # install freesasa
-  # - conda install cython
-  # - git clone https://github.com/freesasa/freesasa-python
-  # - cd freesasa-python
-  # - git submodule update --init
-  # - USE_CYTHON=1 python setup.py build
-  # - export PYTHONPATH=$PYTHONPATH: ???
-
-  # install freesasa
-  - conda install cython
-  - sudo apt-get install -y libxml2 libxml2-dev libjson0 libjson0-dev
-  - wget http://github.com/mittinatten/freesasa/releases/download/2.0.2/freesasa-2.0.2.tar.gz
-  - mkdir freesasa
-  - tar -xvf freesasa-2.0.2.tar.gz -C freesasa --strip-components=1
-  - cd freesasa
-  - ./configure --disable-xml --disable-json --enable-python-bindings --with-python=python3.6 CFLAGS="-fPIC" --prefix=$HOME
-  - make
-  - make install
-  - cd ../
-
-
-  # install pytorch
-  - conda install pytorch=1.0 torchvision cuda80 -c soumith
-
   # codacy-coverage
   - pip install -q --upgrade pip
   - pip install -q coverage

deeprank/__init__.py

@@ -2,14 +2,18 @@
 # the warning is
 # /home/nico/anaconda3/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
 #  from ._conv import register_converters as _register_converters
+import logging
+import logging.config
+import sys
 import warnings
 
+from .config import *
 from .generate import *
 from .tools import *
 
-warnings.simplefilter(action='ignore', category=FutureWarning)
-
-
 # deep learning
 # import torch fals on Travis
 #from .learn import *
+
+warnings.simplefilter(action='ignore', category=FutureWarning)
+logging.captureWarnings(True)

deeprank/config/__init__.py

@@ -0,0 +1,17 @@
+import logging
+import logging.config
+
+from . import logger_settings
+from .chemicals import AA_codes, AA_codes_3to1, AA_codes_1to3
+from .chemicals import AA_codes_pssm_ordered
+from .chemicals import AA_properties
+
+# Debug
+DEBUG = False
+
+# Default logger
+logging.config.dictConfig(logger_settings.DEFAULT_LOGGING)
+logger = logging.getLogger('deeprank')
+
+# Default PSSM path
+PATH_PSSM_SOURCE = None

deeprank/config/chemicals.py

@@ -0,0 +1,73 @@
+# 20 standard amino acids
+# https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/iupac_aa_abbreviations.html
+_aa_standard = [
+    ('ALA', 'A'),
+    ('ARG', 'R'),
+    ('ASN', 'N'),
+    ('ASP', 'D'),
+    ('CYS', 'C'),
+    ('GLN', 'Q'),
+    ('GLU', 'E'),
+    ('GLY', 'G'),
+    ('HIS', 'H'),
+    ('ILE', 'I'),
+    ('LEU', 'L'),
+    ('LYS', 'K'),
+    ('MET', 'M'),
+    ('PHE', 'F'),
+    ('PRO', 'P'),
+    ('SER', 'S'),
+    ('THR', 'T'),
+    ('TRP', 'W'),
+    ('TYR', 'Y'),
+    ('VAL', 'V')
+    ]
+
+# nonstandard amino acids used in blast
+# https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp
+_aa_nonstadnard = [
+    ('ASX', 'B'),
+    ('GLX', 'Z'),
+    ('SEC', 'U')
+    ]
+
+# ordered amino acids according to PSSM file
+# https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#CD_PSSM
+_aa_pssm = ('A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I',
+            'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V')
+
+# ('ALA',...)
+AA_codes = tuple([i[0] for i in _aa_standard])
+
+# {'ALA': 'A', ...}
+AA_codes_3to1 = dict(_aa_standard + _aa_nonstadnard)
+
+# {'A': 'ALA', ...}
+AA_codes_1to3 = dict([i[::-1] for i in _aa_standard + _aa_nonstadnard])
+
+# AA codes ordered as PSSM header
+AA_codes_pssm_ordered = tuple([AA_codes_1to3[i] for i in _aa_pssm])
+
+# AA properties
+AA_properties = {
+    'ALA': 'apolar',
+    'GLY': 'apolar',
+    'ILE': 'apolar',
+    'LEU': 'apolar',
+    'MET': 'apolar',
+    'PHE': 'apolar',
+    'PRO': 'apolar',
+    'VAL': 'apolar',
+    'ARG': 'charged',
+    'ASP': 'charged',
+    'GLU': 'charged',
+    'LYS': 'charged',
+    'ASN': 'polar',
+    'CYS': 'polar',
+    'GLN': 'polar',
+    'HIS': 'polar',
+    'SER': 'polar',
+    'THR': 'polar',
+    'TRP': 'polar',
+    'TYR': 'polar'
+    }

deeprank/config/logger_settings.py

@@ -0,0 +1,54 @@
+# Default logging settings for DeepRank.
+DEFAULT_LOGGING = {
+    'version': 1,
+    'disable_existing_loggers': False,
+    'formatters': {
+        'brief': {
+            'format': '%(message)s',
+        },
+        'precise': {
+            'format': '%(levelname)s: %(message)s',
+        },
+    },
+    'filters': {
+        'require_debug': {
+            '()': 'deeprank.utils.logger_helper.requireDebugFilter',
+        },
+        'use_only_info_level': {
+            '()': 'deeprank.utils.logger_helper.useLevelsFilter',
+            'levels': 'INFO',   # function parameter
+        },
+        'use_only_debug_level': {
+            '()': 'deeprank.utils.logger_helper.useLevelsFilter',
+            'levels': 'DEBUG',
+        },
+    },
+    'handlers': {
+        'stdout': {
+            'level': 'INFO',
+            'formatter': 'brief',
+            'filters': ['use_only_info_level', ],
+            'class': 'logging.StreamHandler',
+            'stream': 'ext://sys.stdout',
+        },
+        'stderr': {
+            'level': 'WARNING',
+            'formatter': 'precise',
+            'class': 'logging.StreamHandler',
+            'stream': 'ext://sys.stderr',
+        },
+        'debug': {
+            'level': 'DEBUG',
+            'formatter': 'precise',
+            'filters': ['require_debug', 'use_only_debug_level'],
+            'class': 'logging.StreamHandler',
+            'stream': 'ext://sys.stderr',
+        },
+    },
+    'loggers': {
+        'deeprank': {
+            'handlers': ['stdout', 'stderr', 'debug'],
+            'level': 'DEBUG',
+        },
+    }
+}