Feat/updates configs + README updates

README.md

@@ -69,8 +69,16 @@ docker run -i -t -p 8888:8888 rdkit-lwreg /bin/bash -c "\
 ## Very basic usage demo
 
 ### Command line
+Using the default configuration options:
+```
+% lwreg initdb --confirm=yes                          # initialization with default config
+```
+Instead using the interactive configuration:
+```
+% lwreg interactive-config                            # interactive configuration, add host, user, password to config.json afterwards
+% lwreg --config config.json initdb --confirm=yes     # initialization with config.json
+```
 ```
-% lwreg initdb --confirm=yes
 % lwreg register --smiles CCOCC
 1
 % lwreg register --smiles CCOCCC
@@ -89,15 +97,28 @@ ERROR:root:Compound already registered
 ```
 >>> import lwreg
 
->>> from lwreg import utils
-
+>>> from lwreg import utils, helpers
+```
+Using the default configuration options:
+```
+# default config 
 >>> lwreg.set_default_config(utils.defaultConfig())   # you generally will want to provide more information about the database
 
 >>> lwreg.initdb()
 This will destroy any existing information in the registration database.
   are you sure? [yes/no]: yes
 True
+```
+Instead using the interactive configuration:
+```
+>>> config = helpers.interactive_config()   # interactive configuration
 
+>>> lwreg.initdb(config=config)
+This will destroy any existing information in the registration database.
+  are you sure? [yes/no]: yes
+True
+```
+```
 >>> lwreg.register(smiles='CCO')
 1
 

lwreg/helpers.py

@@ -11,7 +11,7 @@ def interactive_config():
     config["dbtype"] = input("Choose your database type: ([sqlite3], postgresql) ") or "sqlite3"
     if config["dbtype"] not in ["sqlite3","postgresql"]:
         raise ValueError('Selected option is invalid')
-    config["standardization"] = input("Choose your standardization: (none, sanitize, [fragment], charge, tautomer, super, canonicalize) ") or "fragment"
+    config["standardization"] = input("Choose your standardization: (none, sanitize, [fragment], charge, tautomer, super, overlappingAtoms, polymer) ") or "fragment"
     if config["standardization"] not in utils.standardizationOptions.keys():
         raise ValueError('Selected option is invalid')
     Hs_option = input("Do you want to remove Hs? ([yes]/no) ") or "yes"
@@ -36,7 +36,7 @@ def interactive_config():
         numConfDigits_opt = input("How many conformer digits would you like to include? ([3]) ") or "3"
         if numConfDigits_opt:
             config["numConformerDigits"] = int(numConfDigits_opt)
-        invariantConfs = input("Would you like to register your conformers as translationally and rotationally invariant? ([yes]/no)") or "yes"
+        invariantConfs = input("Would you like to register your conformers as translationally and rotationally invariant? (yes/[no])") or "no"
         if invariantConfs == "yes":
             config["standardization"] = [config["standardization"],"canonicalize"]
     elif conf_option: 

lwreg/utils.py

@@ -32,6 +32,8 @@
     'tautomer': standardization_lib.TautomerParent(),
     'super': standardization_lib.SuperParent(),
     'canonicalize': standardization_lib.CanonicalizeOrientation(),
+    'overlappingAtoms': standardization_lib.OverlappingAtomsCheck(),
+    'polymer': standardization_lib.PolymerCheck()
 }
 
 _defaultConfig = {