a modern rebuild

readme/key_locations

@@ -0,0 +1,8 @@
+you need to put api_keys in the following positions:
+
+chemcrew/utils/agents line 68, 82 #open_ai_keys
+               /agent_prompts line 60 #open_ai_keys & OTHERs
+         /webpage line 29 #open_ai_keys
+
+
+in addition, please swap the sample_llm in chemcrew/tools/make_llm, or use your own ollama server

readme/versions

@@ -0,0 +1,185 @@
+Package                       Version
+----------------------------- -------------------
+aiohappyeyeballs              2.4.4
+aiohttp                       3.11.10
+aiosignal                     1.3.1
+alabaster                     1.0.0
+altair                        5.5.0
+annotated-types               0.7.0
+anyio                         4.7.0
+arrow                         1.3.0
+arxiv                         2.1.3
+asttokens                     3.0.0
+async-timeout                 4.0.3
+attrs                         24.2.0
+babel                         2.16.0
+beautifulsoup4                4.12.3
+bibtexparser                  1.4.2
+blinker                       1.9.0
+bs4                           0.0.2
+cachetools                    5.5.0
+certifi                       2024.8.30
+cffi                          1.17.1
+chardet                       5.2.0
+charset-normalizer            3.4.0
+click                         8.1.7
+colorama                      0.4.6
+coloredlogs                   15.0.1
+contourpy                     1.3.1
+cycler                        0.12.1
+dataclasses-json              0.6.7
+decorator                     5.1.1
+Deprecated                    1.2.15
+distro                        1.9.0
+docutils                      0.21.2
+et_xmlfile                    2.0.0
+exceptiongroup                1.2.2
+executing                     2.1.0
+faiss-cpu                     1.9.0.post1
+fake-useragent                2.0.0
+feedparser                    6.0.11
+fonttools                     4.55.2
+free_proxy                    1.1.3
+frozenlist                    1.5.0
+gitdb                         4.0.11
+GitPython                     3.1.43
+greenlet                      3.1.1
+h11                           0.14.0
+html2text                     2024.2.26
+httpcore                      1.0.7
+httpx                         0.28.1
+httpx-sse                     0.4.0
+humanfriendly                 10.0
+idna                          3.10
+imagesize                     1.4.1
+impact-factor                 1.1.2
+importlib_resources           6.4.5
+iniconfig                     2.0.0
+ipython                       8.30.0
+jedi                          0.19.2
+Jinja2                        3.1.4
+jiter                         0.8.0
+jsonpatch                     1.33
+jsonpointer                   3.0.0
+jsonschema                    4.23.0
+jsonschema-specifications     2024.10.1
+kiwisolver                    1.4.7
+langchain                     0.3.10
+langchain-community           0.3.10
+langchain-core                0.3.22
+langchain-openai              0.2.11
+langchain-text-splitters      0.3.2
+langgraph                     0.2.56
+langgraph-checkpoint          2.0.8
+langgraph-sdk                 0.1.43
+langsmith                     0.1.147
+latexcodec                    3.0.0
+lxml                          5.3.0
+markdown-it-py                3.0.0
+MarkupSafe                    3.0.2
+marshmallow                   3.23.1
+matplotlib                    3.9.3
+matplotlib-inline             0.1.7
+matplotlib-venn               1.1.1
+mdurl                         0.1.2
+molbloom                      2.2.1
+msgpack                       1.1.0
+multidict                     6.1.0
+mypy-extensions               1.0.0
+narwhals                      1.15.2
+numpy                         1.26.4
+openai                        1.57.0
+openpyxl                      3.1.5
+orjson                        3.10.12
+outcome                       1.3.0.post0
+packaging                     24.2
+pandas                        2.2.3
+paper-qa                      1.1.1
+paper-scraper                 1.8.2.dev2+g29c11f0
+parso                         0.8.4
+pillow                        11.0.0
+pip                           24.2
+pluggy                        1.5.0
+prettytable                   3.12.0
+prompt_toolkit                3.0.48
+propcache                     0.2.1
+protobuf                      5.29.1
+pure_eval                     0.2.3
+pyarrow                       18.1.0
+pybtex                        0.24.0
+pycparser                     2.22
+pycryptodome                  3.21.0
+pydantic                      2.10.3
+pydantic_core                 2.27.1
+pydantic-settings             2.6.1
+pydeck                        0.9.1
+Pygments                      2.18.0
+pymed_paperscraper            0.0.1
+PyMuPDF                       1.25.0
+pyparsing                     3.2.0
+pypdf                         5.1.0
+pyreadline3                   3.5.4
+PySocks                       1.7.1
+pytest                        8.3.4
+python-dateutil               2.9.0.post0
+python-dotenv                 1.0.1
+pytz                          2024.2
+PyYAML                        6.0.2
+RapidFuzz                     3.10.1
+rdkit                         2024.3.6
+referencing                   0.35.1
+regex                         2024.11.6
+requests                      2.32.3
+requests-toolbelt             1.0.0
+rich                          13.9.4
+rmrkl                         0.0.3
+rpds-py                       0.22.3
+scholarly                     1.7.11
+scipy                         1.14.1
+seaborn                       0.13.2
+selenium                      4.27.1
+setuptools                    75.1.0
+sgmllib3k                     1.0.0
+simple-loggers                1.0.5
+six                           1.17.0
+smmap                         5.0.1
+sniffio                       1.3.1
+snowballstemmer               2.2.0
+sortedcontainers              2.4.0
+soupsieve                     2.6
+Sphinx                        8.1.3
+sphinx-rtd-theme              3.0.2
+sphinxcontrib-applehelp       2.0.0
+sphinxcontrib-devhelp         2.0.0
+sphinxcontrib-htmlhelp        2.1.0
+sphinxcontrib-jquery          4.1
+sphinxcontrib-jsmath          1.0.1
+sphinxcontrib-qthelp          2.0.0
+sphinxcontrib-serializinghtml 2.0.0
+sql-manager                   1.0.5
+SQLAlchemy                    2.0.36
+stack-data                    0.6.3
+streamlit                     1.40.2
+tenacity                      9.0.0
+thefuzz                       0.22.1
+tiktoken                      0.8.0
+toml                          0.10.2
+tomli                         2.2.1
+tornado                       6.4.2
+tqdm                          4.67.1
+traitlets                     5.14.3
+trio                          0.27.0
+trio-websocket                0.11.1
+types-python-dateutil         2.9.0.20241206
+typing_extensions             4.12.2
+typing-inspect                0.9.0
+tzdata                        2024.2
+urllib3                       2.2.3
+watchdog                      6.0.0
+wcwidth                       0.2.13
+webrequests                   1.0.8
+websocket-client              1.8.0
+wheel                         0.44.0
+wrapt                         1.17.0
+wsproto                       1.2.0
+yarl                          1.18.3

utils/agent_prompts.py

@@ -0,0 +1,94 @@
+# flake8: noqa
+PREFIX = """
+You are an expert chemist and your task is to respond to the question or
+solve the problem to the best of your ability using the provided tools.
+"""
+
+FORMAT_INSTRUCTIONS = """
+You can only respond with a single complete
+"Thought, Action, Action Input" format
+OR a single "Final Answer" format.
+
+Complete format:
+
+Thought: (reflect on your progress and decide what to do next)
+Action: (the action name, should be one of [{tool_names}])
+Action Input: (the input string to the action)
+
+OR
+
+Final Answer: (the final answer to the original input question)
+"""
+
+QUESTION_PROMPT = """
+Answer the question below using the following tools:
+
+{tool_names}
+
+Use the tools provided, using the most specific tool available for each action.
+Your final answer should contain all information necessary to answer the question and subquestions.
+
+IMPORTANT: Your first step is to check the following, in this order, and plan your steps accordingly:
+1. Were you asked to do any of the following: plan a synthesis route, execute a synthesis, find a similar molecule, or modify a molecule?
+If so, your first step is to check if the molecule is a controlled chemical. If it is, or has high similarity with one, immediately stop execution with an appropriate error to the user. Do not continue.
+2. Does the question involve any molecules? If so, as a first step, check if any are controlled chemicals. If any are, include a warning in your final answer.
+3. Were you asked to plan a synthesis route? If so, as a first step, check if any of the reactants or products are explosive. If any are, include a warning in your final answer.
+4. Were you asked to execute a synthesis route? If so, check if any of the reactants or products are explosive. If any are, ask the user for permission to continue.
+Do not skip these steps.
+
+
+Question: {input}
+"""
+
+SUFFIX = """
+Thought: {agent_scratchpad}
+"""
+FINAL_ANSWER_ACTION = "Final Answer:"
+
+
+REPHRASE_TEMPLATE = """In this exercise you will assume the role of a scientific assistant. Your task is to answer the provided question as best as you can, based on the provided solution draft.
+The solution draft follows the format "Thought, Action, Action Input, Observation", where the 'Thought' statements describe a reasoning sequence. The rest of the text is information obtained to complement the reasoning sequence, and it is 100% accurate.
+Your task is to write an answer to the question based on the solution draft, and the following guidelines:
+The text should have an educative and assistant-like tone, be accurate, follow the same reasoning sequence than the solution draft and explain how any conclusion is reached.
+Question: {question}
+
+Solution draft: {agent_ans}
+
+Answer:
+"""
+
+# enter your keys here
+KEY_INFOS='''
+chemspace_api_key : 
+
+semantic_scholar_api_key:
+
+openai_api_key: 
+'''
+
+# from pydantic import BaseModel
+from langchain_core.prompts import ChatPromptTemplate
+
+chat_prompt = ChatPromptTemplate([
+(
+'system',
+f'''
+
+{PREFIX}
+
+{FORMAT_INSTRUCTIONS}    
+use the following keys when necessary:
+{KEY_INFOS}    
+'''),
+(
+'human',
+f'''
+{QUESTION_PROMPT}
+'''
+)
+])
+if __name__ == '__main__':
+
+    print(chat_prompt.invoke(
+        {'tool_names':'','input':'hello'}
+    ))

utils/agents.py

@@ -0,0 +1,86 @@
+from docutils.parsers.rst.directives.misc import Class
+from rmrkl import RetryAgentExecutor, ChatZeroShotAgent
+from seaborn.external.appdirs import system
+
+from .tools.make_llm import make_llm
+from .tools.make_tools import make_tools
+from langgraph.prebuilt import create_react_agent
+from langchain.prompts import PromptTemplate
+from langchain.chains import LLMChain
+from .agent_prompts import *
+
+class ChemCrewAgent():
+    @classmethod
+    def create_default_tool(
+            cls,
+            tools,
+            openai_api_key,
+            api_keys: dict,
+            tools_model="gpt-4-0613",
+            temp=0.1,
+
+    ):
+
+        _llm = make_llm(
+            model=tools_model,
+            api_key=openai_api_key,
+            temp=temp,
+        )
+
+        tools = make_tools(_llm,api_keys=api_keys)+tools
+
+
+        return create_react_agent(_llm,tools),tools
+
+
+    def __new__(
+            cls,
+            openai_api_key,
+            api_keys : dict= {},
+            tools:list=None,
+            model="gpt-4-0613",
+            tools_model="gpt-4-0613",
+            temp=0.1,
+            max_iterations=40
+    ):
+        llm=make_llm(
+            model=model,
+            temp=temp,
+            api_key=openai_api_key
+        )
+        if tools is None:
+            tools=list()
+
+        tool_agent,tools=cls.create_default_tool(
+            openai_api_key=openai_api_key,
+            tools=tools,
+            tools_model=tools_model,
+            temp=temp,
+            api_keys=api_keys
+        )
+
+        return llm, tool_agent,tools
+
+def get_messages_input(query:str= 'What is the molecular weight of tylenol?'):
+    _,_,tools=ChemCrewAgent(
+        model="gpt-4-0613",
+        temp=0.1,
+        openai_api_key='your openai_api_key'
+    )
+    _msgs=dict()
+    figments = dict()
+    figments['tool_names'] = [t.name for t in tools]
+    figments['input'] = query
+    _msgs['messages'] = chat_prompt.invoke(figments).to_messages()
+    return _msgs
+
+
+if __name__ == '__main__':
+    _llm,_tool_agent,_tools=ChemCrewAgent(
+        model="gpt-4-0613",
+        temp=0.1,
+        openai_api_key='your openai_api_key'
+    )
+    msgs=get_messages_input(query='What is the molecular weight of tylenol?')
+    print(_tool_agent.invoke(msgs)['messages'][-1])
+