admin cc scripts

package/scripts/calculate_Aspaces_raw.py

-# Nico: Jan 2021
-# Uses the data calculator class to get all A spaces preprocessed data
-# Inspired from the cc pipeline
-import os
-import collections
-from chemicalchecker.util.parser import DataCalculator
-from chemicalchecker.core.preprocess import Preprocess
-from chemicalchecker.util.parser.features_A_spaces import fetch_features_A
-
-# type of data, space_name, format size
-# Note A3 contains both caffold and framework each encoded on 1024 bits, so we have 2048 total ex: f647,c92 
-# A4: supposed to be 166 groups but 152 keys are present in raw 2020_01 preprocess.h5 
-
-Aspaces= ('A1', 'A2', 'A3', 'A4', 'A5')
-
-def calculate_data_fn(space, dict_inchikey_inchi):
-    """
-    Launch the (chemistry) data calculation for one type of space
-
-    Returns: a list containing the molecular properties in dense format
-    ex: [{'inchikey': 'ASXBYYWOLISCLQ-UHFFFAOYSA-N', 'raw': ..raw_string}, {}...]
-
-    Arguments:
-    - space (str): either A1, A2, A3, A4, A5, A5
-    - dict_inchikey_inchi (dict): mapping of the molecules to calculate properties from
-
-    """
-
-    data_calculators = {
-        'A1': 'morgan_fp_r2_2048',
-        'A1': 'e3fp_3conf_1024', 
-        'A1': 'murcko_1024_cframe_1024',
-        'A1': 'maccs_keys_166',
-        'A1': 'general_physchem_properties',
-        #'chembl_target_predictions_v23_10um':'A5',
-    }
-
-    type_data= data_calculators.get(space.upper(),None)
-    assert type_data is not None, "Space "+space+" is not part of the CC A spaces!"
-
-    print("Calculating data for " + type_data)
-    parse_fn = DataCalculator.calc_fn(type_data)
-
-    for i,chunk in enumerate(parse_fn(dict_inchikey_inchi)):
-        print("CHUNK",i)
-        print(chunk)
-        if len(chunk) == 0:
-            continue
-        else:
-            return chunk
-
-    return None
-        
-
-def calculate_mol_properties(dict_inchikey_inchi):
-    """
-    Calls calculate_data_fn for all spaces
-
-    Returns: a dict containing the molecular properties in dense format for all spaces
-
-    Arguments:
-    - space (str): either A1, A2, A3, A4, A5, A5
-    - dict_inchikey_inchi (dict): mapping of the molecules to calculate properties from
-    """
-    result=dict()
-            
-    for space in Aspaces:
-        result[space]=calculate_data_fn(space, dict_inchikey_inchi=inchikey2inchi_dict)
-
-        # dictionary {'A1': [{'inchikey': 'ASXBYYWOLISCLQ-UHFFFAOYSA-N', 'raw': ..raw_string}, {}...]}
-        return result
-
-# Trying to save the result of A1 (from A1)
-
-
-def create_h5_from_inchikeys_inchi(dict_inchikey_inchi, outDir='tmp'):
-    """
-    Create the preprocessed h5 data files
-    for spaces A1 to A5 for the molecules specified in the input inchikey_inchi dictionary
-
-    Here we cannot use the predict method from Preprocess.save_output since it requires connection to the database
-    whereas we work locally.
-    """
-
-    if not os.path.exists(outDir):
-        try:
-            os.makedirs(outDir)
-        except Exception as e:
-            print("ERROR: cannot create output directory for ")
-            print(e)
-            return
-
-    outputfiles= {space: os.path.join(outDir,space+'_outsideUniv.h5') for space in Aspaces}
-    method='fit'
-    model_path='tmp'  # Dummy tmp folder
-    
-
-    # Compute the raw properties
-
-    all_properties= calculate_mol_properties(dict_inchikey_inchi)
-    all_features= fetch_features_A()
-
-    # Here we need to preprocess the dense format according to which space we have
-    for space in Aspaces:
-
-        # Dense chemical properties for all spaces
-        raw_prop= all_properties.get(space,None)
-        features= all_features.get(space, None)
-        feature_int= False if space in ('A3','A5') else True
-        discrete= False if space == 'A5' else True
-
-        if raw_prop is None or features is None:
-            print("WARNING, space",space,"properties or features is None, space skipped")
-            continue
-
-        # format the dense chemical properties in tuples (inchikey, raw_str)
-        ACTS= [(dic['inchikey'],dic['raw']) for dic in result['A1']]
-
-        if space in ('A1','A2','A3'):
-
-            # Copied from the end of A1 preprocess script
-            RAW = collections.defaultdict(list)
-            for k in ACTS:
-                if features is None:
-                    vals = [str(t) for t in k[1].split(",")]
-                else:
-                    vals = [str(t) for t in k[1].split(",") if str(t) in features]
-                RAW[str(k[0])] = vals
-
-
-        elif space == 'A4':
-            for k in ACTS:
-                if k[1] == '' or k[1] is None or k[0] is None:
-                    continue
-                if features is None:
-                    vals = [str(t) for t in k[1].split(",")]
-                else:
-                    vals = [str(t) for t in k[1].split(",") if str(t) in features]
-                RAW[str(k[0])] = vals
-
-
-        elif space == 'A5':
-            sigs = collections.defaultdict(list)
-            words = []
-            first = True
-            for k in ACTS:
-                if k[1] is None:
-                    continue
-                data = k[1].split(",")
-                vals = []
-                for d in data:
-                    ele = d.split("(")
-                    if first:
-                        words.append(str(ele[0]))
-                    vals.append(float(ele[1][:-1]))
-                sigs[str(k[0])] = vals
-                first = False
-
-            RAW=sigs
-
-        # NS: Preprocess.save_output will then convert the dense format into binary data
-        Preprocess.save_output(outputfiles[space], RAW, method, model_path, discrete, features, features_int=feature_int)
\ No newline at end of file

package/scripts/get_repo_version.py

+# Nico 11 Feb 2021
+# Put here the current CC signature repo version that can be then fetched by scripts
+
+import os
+
+CURRENT = "/aloy/web_checker/current"
+
+def cc_repo_version():
+	try:
+		return os.path.abspath(os.path.realpath(CURRENT))
+	except Exception as e:
+		print("WARNING: the cc signature repo version cannot be retrieved from", CURRENT)
+		print(e)
+		return None