parsing formula

.gitignore

@@ -0,0 +1 @@
+__pycache__

app.py

@@ -2,40 +2,131 @@ import altair as alt
 import molmass
 import gradio as gr
 import pandas as pd
+import re
 
-def ms(formula):
-    mf = molmass.Formula(formula)
-    return mf.spectrum().dataframe().round(4).query("Fraction > .001").drop(columns=["Fraction"])
+# def ms(formula):
+#     mf = molmass.Formula(formula)
+#     return mf.spectrum().dataframe().round(4).query("Fraction > .001").drop(columns=["Fraction"])
 
-def plot_ms(spec_df):
-    chart = alt.Chart(spec_df).mark_bar().encode(
-        x=alt.X("m\/z:O").title('mz'),
-        y=alt.Y("Intensity\ %:Q").title("relative intensity (%)")
-    )
-    return chart
+# def plot_ms(spec_df):
+#     chart = alt.Chart(spec_df).mark_bar().encode(
+#         x=alt.X("m\/z:O").title('mz'),
+#         y=alt.Y("Intensity\ %:Q").title("relative intensity (%)")
+#     )
+#     return chart
+
+
+example1 = """# Lines starting with '#' are comments
+# Lines with "=" are fragment definitions
+Azide = H2NCH(CH2CH2N3)COOH 
+Alkyne = HCCCH2NH2
+Click = Azide + Alkyne
+Click - H+
+Click + H+
+Click + Na+
+Click + 2H+
+2*Click + H+
+"""
+
+example2 = """NH4+"""
+examples_dict = {
+    "addition": example1,
+    "substitution": example2,
+}
+
+def make_formula(line):
+    """Recursively splits line on ' + ' and ' - ' (signs padded with spaces) to construct formula.
+
+    Parsing precedence:
+    1) '+' over '-'
+    2) if a group is recognized as a key in GROUPS, the GROUPS[line] value is returned
+    
+    Don't go crazy, it's not a full string calculator.
+    """
+    if " + " in line:
+        term1, term2 = line.split(" + ", maxsplit=1)
+        return make_formula(term1) + make_formula(term2)
+    elif " - " in line:
+        term1, term2 = line.split(" - ", maxsplit=1)
+        return make_formula(term1) - make_formula(term2)
+    else:
+        group_lookup = molmass.GROUPS.get(line)
+        return group_lookup or molmass.Formula(line)
+
+
+class FormulaBox:
+    """Parsing formulabox"""
+    
+    def __init__(self, inputs, **kwargs):
+        self.min_intensity = kwargs.get("min_intensity") or 1e-4
+        self.lines = inputs.split("\n")
+        self.ions = {}
+        self.parse()
+
+
+    def parse(self):
+        """lines are either definitions ('=') or ions (no '=')"""
+        for _line in self.lines:
+            line = re.sub("\s+", "", _line)
+            if line == "" or line.startswith("#"):
+                continue
+            elif "=" in line:
+                self.add_group(line)
+            else:
+                self.ions[line] = make_formula(_line)
+        return
+
+    def add_group(self, line):
+        alias, value = line.split("=")
+        # self.groups[alias] = make_formula(value)
+        molmass.GROUPS[alias] = make_formula(value)
+        # GROUPS.update(**self.groups)
+        return
+
+    def get_spectra(self):
+        self.spectra = {
+            k: v.spectrum(min_intensity=self.min_intensity)
+            for k, v in self.ions.items()
+        }
+        return
+    
+    @property
+    def df(self):
+        frame = pd.DataFrame([
+            {
+                "molecule": k,
+                "mf": v.formula,
+                "charge": v.charge,
+                "monoisotopic_mass": v.monoisotopic_mass,
+                "mz": v.spectrum(min_intensity=1e-4).peak.mz,
+                "top_isotope_fraction": v.spectrum(min_intensity=1e-4).peak.fraction,
+            }
+            for k, v in self.ions.items()
+        ]).round(5)
+        return frame
+
+    def spectra(self):
+        return
+
+fb1 = FormulaBox(example1)
 
 
 with gr.Blocks() as demo:
-    example_mf = "FmocCysGlyLysCONH2"
-    formula = gr.Textbox(label="formula", value=example_mf)
     with gr.Row():
-        example_ms = ms(example_mf)
-        example_plot = plot_ms(example_ms)
-        spec_df = gr.Dataframe(value=example_ms, label="MS")
-        spec_plot = gr.Plot(value=example_plot, label="MS")
+        with gr.Column(scale=1):
+            formula_box = gr.Textbox(value=example1, lines=12, max_lines=256, label="FormulaBox")
+            btn = gr.Button("Submit")
+        with gr.Column(scale=2):
+            # examples = gr.Examples(examples=["addition", "substitution"], inputs=formula_box, run_on_click=True, fn=get_example)
+            # examples2 = gr.Examples(examples=[example1, example2], inputs=formula_box, run_on_click=True, fn=lambda x:x, preprocess=get_example)
+            ms_df_box = gr.Dataframe(value=fb1.df, label="MS DF")
     
-    @gr.on(triggers=[formula.submit], inputs=[formula], outputs=[spec_df])
-    def calc_ms(formula):
+    @gr.on(triggers=[formula_box.blur, btn.click], inputs=[formula_box], outputs=[ms_df_box])
+    def make_ms_df(formula_box):
         try:
-            return ms(formula)
+            fb = FormulaBox(formula_box)
+            return fb.df
         except Exception as e:
             return pd.DataFrame({"error": [e.__str__()]})
 
-    @gr.on(triggers=[formula.submit], inputs=[spec_df], outputs=[spec_plot])
-    def calc_plot(spec_df):
-        try:
-            return plot_ms(spec_df)
-        except Exception:
-            return example_plot.properties(width=480, height=240)
-
 demo.launch()