Main -> Stable

README.md

@@ -48,8 +48,8 @@ For less loading time and memory footprint, a part of the cache can be loaded:
 ```python
 from rr_cache import rrCache
 
-cache = rrCache(['cid_strc'])
-cache.get_compound('MNXM2')
+cache = rrCache(["cid_strc"])
+cache.get_compound("MNXM2")
 ```
 ***From CLI***
 ```sh

environment.yaml

@@ -7,3 +7,4 @@ dependencies:
   - requests
   - rdkit
   - colored
+  - pandas

rr_cache/__main__.py

@@ -1,16 +1,18 @@
+import sys
+from json import dumps
+from logging import Logger, getLogger
+
+from brs_utils import build_args_parser
+from brs_utils import init as init_logger
+from colored import attr, fg
+
+from rr_cache.args import add_arguments
 from rr_cache.rr_cache import (
     rrCache,
 )
-from rr_cache.Args import add_arguments
-from brs_utils import init as init_logger, build_args_parser
-from logging import Logger, getLogger
-from colored import fg, attr
-from json import dumps
-from typing import (
-    List,
-)
-from .Args import CONFIG_PATH
+
 from ._version import __version__
+from .args import CONFIG_PATH
 
 
 def disable_rdkit_logging():
@@ -55,7 +57,7 @@ def entry_point():
         for dt in cspaces:
             print(f"- {dt}")
         print()
-        exit(0)
+        sys.exit(0)
 
     cache = rrCache(
         cspace=args.cspace,
@@ -88,12 +90,15 @@ def entry_point():
         )
 
 
+LOGGER = getLogger(__name__)
+
+
 def print_attr(
     cache: "rrCache",
     attr: str,
-    attr_lst: List,
+    attr_lst: list,
     do_not_dwnl_cache: bool,
-    logger: Logger = getLogger(__file__),
+    logger: Logger = LOGGER,
 ) -> None:
     cache.Load(attrs=[attr], do_not_dwnl_cache=do_not_dwnl_cache)
     if attr_lst == []:
@@ -103,9 +108,7 @@ def print_attr(
             try:
                 print(id + ":", dumps(cache.get(attr)[id], indent=4))
             except KeyError:
-                logger.error(
-                    "ID not found in rrCache('{attr}'): {id}".format(attr=attr, id=id)
-                )
+                logger.error(f"ID not found in rrCache('{attr}'): {id}")
 
 
 if __name__ == "__main__":

rr_cache/Args.py → rr_cache/args.py

@@ -5,7 +5,7 @@
 CONFIG_PATH = os_path.join(HERE, "config")
 # Default values for the arguments
 DEFAULTS = {
-    "cspace": "rr2026",
+    "cspace": "rr2026-v3.1.0",
     "databases": ["metanetx", "rhea"],
     "interactive": False,
     "do_not_dwnl_cache": False,
@@ -21,7 +21,7 @@ def add_arguments(parser: ArgumentParser) -> ArgumentParser:
         dest="cspace",
         default=DEFAULTS["cspace"],
         type=str,
-        help="chemical space to use (e.g. mnx3.1, mnx4.0...). Determines which configuration files and folders to use both the cache and the input cache (default: %(default)s).",
+        help="chemical space to use (e.g. mnx3.1, mnx4.4...). Determines which configuration files and folders to use both the cache and the input cache (default: %(default)s).",
     )
     parser.add_argument(
         "--list-chemical-spaces",

rr_cache/config/config_rr2026-v3.1.0.json

@@ -0,0 +1,77 @@
+{
+    "type": "rr2026",
+     "cache": {
+        "cid_strc": {
+            "deps": {
+                "file_deps": ["chemicals_metadata", "chem_prop.tsv"]
+            },
+            "file": {
+                "url": "",
+                "name": "cid_strc.json.gz"
+            }
+        },
+        "cid_xref": {
+            "deps": {
+                "attr_deps": [],
+                "file_deps": ["chem_xref.tsv"]
+            },
+            "file": {
+                "url": "https://gitlab.com/breakthewall/rrCache-data/-/raw/master/cache/mnx_4.4/",
+                "name": "cid_xref.json.gz"
+            }
+        },
+        "rr_reactions": {
+            "deps": {
+                "file_deps": ["templates_metadata"]
+            },
+            "file": {
+                "url": "",
+                "name": "rr_reactions.json.gz"
+            }
+        },
+        "template_reactions": {
+            "deps": {
+                "file_deps": ["templates_metadata", "reac_prop.tsv"]
+            },
+            "file": {
+                "url": "",
+                "name": "template_reactions.json.gz"
+            }
+        }
+    },
+    "sources": {
+        "mnx": {
+            "url": "https://www.metanetx.org/ftp/4.5/",
+            "files": {
+                "chem_xref.tsv": "2b88dfe3b990ee85c8d8eb51f6d7079bf042b14e4cd11a4cc6ceb841686f9ea7ef4a04358363561fbbb2187a9870a1930037a030283908788a572e7b96b91ec7",
+                "chem_prop.tsv": "00d8d09d52884961748d032288781c4d47929f12d5052b367116c411194fdfae879b15844e8a15bccd494c26702dae57fd682c3bc03b5fee3c3e92e138c1eac2",
+                "reac_prop.tsv": "1796b5d77c707d0cfbfce99cf0466ef6aff0fe61ea5ded043216aa334e5ecd1388364d214162342f470b51eca2dab4309dcec2b9e074abee47dcae974c674bd7"
+            }
+        },
+        "rr2": {
+            "url": "https://retrorules.org/dl/v3.1.0/",
+            "files": {
+                "templates_metadata": {
+                    "metanetx": "25cf9e9e4162cb9039e8692787890568c2d45e82cd2c6f28ed574a6643fc48e0b61e196b9e552419cd68dc5c86a8c2aa08c1f6731b2543e35387ebbde5587867",
+                    "rhea": "37fb906124fdb61a12b378a861341c64ecea459e8f3e8c3a5f0865290da0b712bb6b07aada4bf358ca2bdb65fd3faa5cd6acd9380ae26c64e14d6cccf70b6085",
+                    "uspto": "6aebfd43a3932b11009630a7e5fdc3e10fde9a20d9933f7792d0904c945ea1624c94a0e24a9d56d0d103b9ecfdddd1e2d8f9edb177886ecac23d5775006bc23e"
+                }
+            }
+        },
+        "rr2more": {
+            "url": "https://retrorules.org/dl/v3.0/",
+            "files": {
+                "reactions_metadata": {
+                    "metanetx": "5a61ca70e477f23a9300c3bdfb912ebd0df3a0d985a2d4b46b5a002db812ae468b9b736a72f045d022a577eeda03b81e74f6c044df5fa135dfdfc34b7e26d380",
+                    "rhea": "718295f7804b5d343c6b761550c408b9c3a6d5f1537f1f0de5858ceae6248919bd19ccb5cf4600c108e9004d20b0a4bc54f6ae85415d0dd9d964e1a12585dd10",
+                    "uspto": "4f893d0038e205ec06d66f8165000c07e17e0eb099873c252ed654c9c1cad8afa6cfbb236f60983b4d43601a71678eb469a72f53a1582914e87783c8e5ed51b8"
+                },
+                "chemicals_metadata": {
+                    "metanetx": "d0c618364af5961abb7ce99a93d29222faf3371a7270edd4667e197c87f8f2eed13d4be22a9aa03e7c4b160b424250c37c6279fe51cb68b6aae3ae968472d321",
+                    "rhea": "e46cdffb86c5ae46d3338faff720a77ca4651fe37d645b0072e7fbc78cfa19ba550ba6c2e157ceee28d09ff8e0c1fd6f18a59e6c653d1a4bfe958074f39e97c3",
+                    "uspto": "2c4aefd0c0341a2491fd1be4478092c8cfdbaf7784e5cbf982807631c5ad4c129cdbdbe9e1caebf0ae975570a004f2e498a0971c8fded386f965472bee88081b"
+                }
+            }
+        }
+    }
+}