Moved prompts and methods keywords to a dedicated file

prompts.py

@@ -0,0 +1,150 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""A collection of various PDB-related prompts
+"""
+
+# A list of abbreviated names and synonyms
+# for various biophysical methonds
+# that are typically used for integrative modeling
+
+METHODS_KEYWORDS = {
+    'CX-MS': [
+        'cross-link', 'crosslink',
+        'XL-MS', 'CX-MS', 'CL-MS', 'XLMS', 'CXMS', 'CLMS',
+        "chemical crosslinking mass spectrometry",
+        'photo-crosslinking', 'crosslinking restraints',
+        'crosslinking-derived restraints', 'chemical crosslinking',
+        'in vivo crosslinking', 'crosslinking data',
+    ],
+
+    'HDX': [
+        'Hydrogen–deuterium exchange mass spectrometry',
+        'Hydrogen/deuterium exchange mass spectrometry'
+        'HDX', 'HDXMS', 'HDX-MS',
+    ],
+
+    'EPR': [
+        'electron paramagnetic resonance spectroscopy',
+        'EPR', 'DEER',
+        "Double electron electron resonance spectroscopy",
+    ],
+
+    'FRET': [
+        'FRET',
+        "forster resonance energy transfer",
+        "fluorescence resonance energy transfer",
+    ],
+
+    'AFM': [
+        'AFM',  "atomic force microscopy",
+    ],
+
+    'SAS': [
+        'SAS', 'SAXS', 'SANS', "Small angle solution scattering",
+        "solution scattering", "SEC-SAXS", "SEC-SAS", "SASBDB",
+        "Small angle X-ray scattering", "Small angle neutron scattering",
+    ],
+
+    '3DGENOME': [
+        'HiC', 'Hi-C', "chromosome conformation capture",
+    ],
+
+    'Y2H': [
+        'Y2H',
+        "yeast two-hybrid",
+    ],
+
+    'DNA_FOOTPRINTING': [
+        "DNA Footprinting",
+        "hydroxyl radical footprinting",
+    ],
+
+    'XRAY_TOMOGRAPHY': [
+        "soft x-ray tomography",
+    ],
+
+    'FTIR': [
+        "FTIR", "Infrared spectroscopy",
+        "Fourier-transform infrared spectroscopy",
+    ],
+
+    'FLUORESCENCE': [
+        "Fluorescence imaging",
+        "fluorescence microscopy", "TIRF",
+    ],
+
+    'EVOLUTION': [
+        'coevolution', "evolutionary covariance",
+    ],
+
+    'PREDICTED': [
+        "predicted contacts",
+    ],
+
+    'INTEGRATIVE': [
+        "integrative structure", "hybrid structure",
+        "integrative modeling", "hybrid modeling",
+    ],
+
+    'SHAPE': [
+        'Hydroxyl Acylation analyzed by Primer Extension',
+    ]
+}
+
+
+def keywords_dict_to_string(keywords: dict) -> str:
+    """
+    Convert dictionary with method keywords and synonyms
+    to a string
+
+    Example:
+
+        keywords = {
+            'AFM': [
+                'AFM',  "atomic force microscopy",
+            ],
+
+            'SAS': [
+                'SAS', "solution scattering",
+            ],
+        }
+
+    Result:
+
+        'AFM (AFM, atomic force microscopy) or SAS (SAS, solution scattering)'
+    """
+
+    methods_string = ''
+    for i, (k, v) in enumerate(keywords.items()):
+        if i > 0:
+            methods_string += ' or '
+        methods_string += f'{k} ({", ".join(v)})'
+
+    return methods_string
+
+def get_qbi_hackathon_prompt(keywords: dict) -> str:
+    """
+    Returns a prompt that was initially developed
+    during the QBI Hackathon.
+    """
+
+    if len(keywords) == 0:
+        raise(ValueError("Keywords dict can't be empty"))
+
+    methods_string = keywords_dict_to_string(keywords)
+
+    prompt = (
+        "You are reading a materials and methods section "
+        "of a scientific paper. "
+        f"Here is the list of methods {methods_string}.\n\n"
+        "Did the authors use any of them? "
+        "Answer Yes or No, followed by the name(s) of methods. "
+        "Use only abbreviations."
+    )
+
+    return prompt
+
+if __name__ == '__main__':
+    # Just call an example function
+    print(get_qbi_hackathon_prompt(METHODS_KEYWORDS))