WIP #25

update/sdfwip.py

@@ -0,0 +1,52 @@
+import time
+import logging
+import mmap
+from collections import deque
+
+
+def find_structures_line_ranges(file_path):
+    structures_ranges = {}
+    with open(file_path, "r") as file:
+        mmapped_file = mmap.mmap(file.fileno(), 0, access=mmap.ACCESS_READ)
+        start_line = 1
+        prev_line = prev_prev_line = b''
+        for line_number, line in enumerate(iter(mmapped_file.readline, b""), start=1):
+            if line.startswith(b"$$$$"):
+                end_line = line_number
+                identifier = prev_prev_line.strip().decode()  # Use the value two lines above as the identifier
+                structures_ranges[identifier] = (start_line, end_line)
+                start_line = line_number + 1
+            prev_prev_line, prev_line = prev_line, line
+    return structures_ranges, mmapped_file
+
+
+def read_selected_ranges(mmapped_file, ranges_to_read):
+    selected_lines = deque()
+    for start, end in ranges_to_read:
+        selected_lines.append(mmapped_file[start:end].decode())
+    return selected_lines
+
+
+def main():
+    file_path = "data/lotus.sdf"
+    structures_ranges, mmapped_file = find_structures_line_ranges(file_path)
+    # print(structures_ranges)
+
+    # Admitting the indices are already available
+    start_time = time.time()
+    # TODO this will allow to get the ranges from a (list of) SID(s)
+    ranges_to_read = [structures_ranges[key] for key in list(structures_ranges.keys())[:100000]]
+
+    if ranges_to_read:
+        selected_lines = read_selected_ranges(mmapped_file, ranges_to_read)
+    else:
+        logging.info("No '$$$$' occurrences found in the file.")
+
+    end_time = time.time()
+    logging.info(f"Time taken to get the blocks: {end_time - start_time} seconds")
+    # print(selected_lines)
+
+
+if __name__ == "__main__":
+    logging.basicConfig(level=logging.INFO)
+    main()