v1.0.0

RyanZR · Jul 8, 2023 · 6b64259 · 6b64259
1 parent f975865
commit 6b64259
Showing 1 changed file with 158 additions and 0 deletions.
diff --git a/LaBOX.py b/LaBOX.py
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+#!/usr/bin/env python3
+
+#==============================================================================
+#
+#                        __        _____ _____ __ __ 
+#                       |  |   ___| __  |     |  |  |
+#                       |  |__| .|| __ -|  |  |-   -|
+#                       |_____|__||_____|_____|__|__|
+#
+#
+#   LaBOX - Gridbox size calculation for ligand docking
+#
+#   Get more information from https://github.com/RyanZR/LaBOX
+#
+#   Report bugs and issues to https://github.com/RyanZR/LaBOX/issues
+#
+#   This software is provided WITHOUT WARRANTY OF ANY KIND
+#
+#==============================================================================
+
+import os
+import sys
+import getopt
+import statistics
+
+def usage():
+    print(f'Usage')
+    print(f'╰─○ LaBOX.py [-l] <filename>')
+    print(f'')
+    print(f'Argument')
+    print(f'╰─○ Command description:')
+    print(f'        -l  ligand filename (supported: pdb, pdbqt, sdf, mol2)')
+    print(f'        -h  help')
+    print(f'        -a  about')
+    print(f'╰─○ Optional parameters:')
+    print(f'        -s  scale factor (default is 2)')
+    print(f'        -c  grid box center')
+
+def about():
+    print(f'==============================================================================')
+    print(f'                         __        _____ _____ __ __                          ')
+    print(f'                        |  |   ___| __  |     |  |  |                         ')
+    print(f'                        |  |__| .|| __ -|  |  |-   -|                         ')
+    print(f'                        |_____|__||_____|_____|__|__|                         ')
+    print(f'                                                                              ')
+    print(f'   LaBOX - Grid box size calculation for ligand docking                       ')
+    print(f'                                                                              ')
+    print(f'   Get more information from https://github.com/RyanZR/LaBOX                  ')
+    print(f'                                                                              ')
+    print(f'   Report bugs and issues to https://github.com/RyanZR/LaBOX/issues           ')
+    print(f'                                                                              ')
+    print(f'   This software is provided WITHOUT WARRANTY OF ANY KIND                     ')
+    print(f'                                                                              ')
+    print(f'==============================================================================')
+
+def file_handler(input_file):
+    ext = os.path.splitext(input_file)[-1]
+    if input_file == None:
+        print(f'LaBOX.py')
+        print(f'╰─○ Invalid file or incorrect usage')
+        sys.exit()
+    if not os.path.exists(input_file):
+        print(f'LaBOX.py')
+        print(f'╰─○ File does not exists')
+        print(f'    Is {input_file} mispelled?')
+        sys.exit()
+    if ext not in ('.pdb', 'pdbqt', '.sdf', '.mol2'):
+        print(f'LaBOX.py')
+        print(f'╰─○ File format {ext} not supported')
+        sys.exit()
+
+def get_coordinates(data, ext):
+    if ext == '.mol2':
+        commence = next(n for n, line in enumerate(data) if line.strip() != '' and line.split()[0] == '@<TRIPOS>ATOM') + 1
+        conclude = next(n for n, line in enumerate(data) if line.strip() != '' and line.split()[0] == '@<TRIPOS>BOND')
+        atoms = [line.split()[1] for line in data[commence:conclude]]
+        coord = [list(map(float, line.split()[2:5])) for line in data[commence:conclude]]
+
+    if ext == '.sdf':
+        blank = int(next(n for n, line in enumerate(data) if line.split() == []))
+        atoms = int(data[blank + 1].split()[0])
+        commence = blank + 2
+        conclude = commence + atoms
+        coord = [list(map(float, line.split()[:3])) for line in data[commence:conclude]]
+
+    if ext in ('.pdb', '.pdbqt'):
+        coord = [[float(line[31:38]), float(line[39:46]), float(line[47:54])] for line in data if line.split()[0] in ('ATOM', 'HETATM')]
+
+    xcoor, ycoor, zcoor = zip(*coord)
+    return [list(xcoor), list(ycoor), list(zcoor)]
+
+def min_max(coord: list):
+    return [min(coord), max(coord)]
+
+def center_XYZ(coord_range: list):
+    return round(statistics.mean(coord_range), 3)
+
+def length_WHD(coord_range: list, scale: float):
+    return round(abs(coord_range[0] - coord_range[1]) * scale, 3)
+
+def LaBOX(data: str, ext: str, scale: float, find_center: bool):
+    COOR = get_coordinates(data, ext)
+    X,Y,Z = COOR
+    ranges = [min_max(X), min_max(Y), min_max(Z)]
+    center = [center_XYZ(ranges[0]), center_XYZ(ranges[1]), center_XYZ(ranges[2])] 
+    bxsize = [length_WHD(ranges[0], scale), length_WHD(ranges[1], scale), length_WHD(ranges[2], scale)]
+    print(f'LaBOX.py')
+    if find_center:
+        print(f'╰─○ Grid Box Center:  X {center[0]:>8}  Y {center[1]:>8}  Z {center[2]:>8}')
+        print(f'    Grid Box Size  :  W {bxsize[0]:>8}  H {bxsize[1]:>8}  D {bxsize[2]:>8}')
+    if not find_center:
+        print(f'╰─○ Grid Box Size  :  W {bxsize[0]:>8}  H {bxsize[1]:>8}  D {bxsize[2]:>8}')
+
+def main():
+    try:
+        opts, args = getopt.getopt(
+            sys.argv[1:], 
+            ':l:s:cha', 
+            ['ligand=', 'scale=', 'center', 'help', 'about'])
+    except getopt.GetoptError as msg:
+        print(f'LaBOX.py')
+        print(f'╰─○ {msg}')
+        sys.exit()
+
+    FILENAME = None
+    FIND_CENTER = None
+    SCALE = 2
+    xcoor = None
+    ycoor = None
+    zcoor = None
+
+    if opts == []:
+        usage()
+        sys.exit()
+
+    for opt, arg in opts:
+        if opt in ('-l', '--ligand'):
+            FILENAME = arg
+        if opt in ('-s', '--scale'):
+            SCALE = arg
+            SCALE = float(SCALE)
+        if opt in ('-c', '--center'):
+            FIND_CENTER = True
+        if opt in ('-h', '--help'):
+            usage()
+            sys.exit()
+        if opt in ('-a', '--about'):
+            about()
+            sys.exit()
+
+    TARGET = FILENAME
+    file_handler(TARGET)
+    EXT = os.path.splitext(TARGET)[-1]
+    DATA = open(TARGET, 'r').readlines()
+    LaBOX(DATA, EXT, SCALE, FIND_CENTER)
+
+if __name__ == '__main__':
+    main()