Merge pull request #24 from yuzie007/fetch-transformations-k

Fetch transformations to k-subgroups etc.

ikdsplit/__init__.py

@@ -5,7 +5,6 @@
 import ikdsplit.converter
 import ikdsplit.filler
 import ikdsplit.regressor
-import ikdsplit.runner
 import ikdsplit.sorter
 import ikdsplit.splitter
 
@@ -18,7 +17,6 @@ def main() -> None:
 
     commands = {
         "split": ikdsplit.splitter,
-        "run": ikdsplit.runner,
         "convert": ikdsplit.converter,
         "fill": ikdsplit.filler,
         "regress": ikdsplit.regressor,

ikdsplit/database/fetch_transformations_k.py

@@ -0,0 +1,57 @@
+"""Fetch Wycksplit from the Bilbao Crystallographic Server."""
+
+import time
+import urllib
+
+import pandas as pd
+
+
+def fetch_transformation(spg_sup: int, spg_sub: int, index: int) -> None:
+    """Get transformation."""
+    url = "https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-tranmax?"
+    query = {"super": spg_sup, "sub": spg_sub, "index": index}
+    url += urllib.parse.urlencode(query)
+    transformations = pd.read_html(url)[1]
+    s = transformations.loc[0]["Transformation Matrix"]
+    ts = s.split()
+    d = {}
+    d["supergroup"] = spg_sup
+    d["subgroup"] = spg_sub
+    d["Pxx"] = ts[0]
+    d["Pxy"] = ts[1]
+    d["Pxz"] = ts[2]
+    d["Pyx"] = ts[4]
+    d["Pyy"] = ts[5]
+    d["Pyz"] = ts[6]
+    d["Pzx"] = ts[8]
+    d["Pzy"] = ts[9]
+    d["Pzz"] = ts[10]
+    d["px"] = ts[3]
+    d["py"] = ts[7]
+    d["pz"] = ts[11]
+    return d
+
+
+def run() -> None:
+    """Run."""
+    ds = []
+    df = pd.read_csv("loss_of_centrings.csv")
+    for supergroup, groups in df.groupby("supergroup"):
+        print(f"{supergroup:03d}")
+        url = "https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-lxi?"
+        query = {"gnum": supergroup}
+        url += urllib.parse.urlencode(query)
+        subgroups = pd.read_html(url)[1]
+        isin = groups["subgroup"].to_numpy()
+        subgroups = subgroups[subgroups["IT number"].isin(isin)]
+        for d in subgroups.to_dict(orient="records"):
+            subgroup = d["IT number"]
+            index = d["Index"]
+            print(f"-> {subgroup:03d}")
+            ds.append(fetch_transformation(supergroup, subgroup, index))
+            time.sleep(5)
+    pd.DataFrame(ds).to_csv("transformations_k.csv", index=False)
+
+
+if __name__ == "__main__":
+    run()

ikdsplit/database/loss_of_centrings.csv

@@ -0,0 +1,212 @@
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