|
3 | 3 | import getopt |
4 | 4 | import shutil |
5 | 5 | import numpy as np |
| 6 | +import argparse |
6 | 7 |
|
7 | 8 | from urllib.request import urlopen |
8 | 9 | from io import StringIO |
9 | | -from pkaani.pkaani import calculate_pka |
| 10 | + |
10 | 11 | from pkaani.prep_pdb import prep_pdb |
11 | 12 |
|
| 13 | +class MyParser(argparse.ArgumentParser): |
| 14 | + def error(self, message): |
| 15 | + sys.stderr.write('error: %s\n' % message) |
| 16 | + usage_pkaani() |
| 17 | + sys.exit(2) |
| 18 | + |
| 19 | + |
12 | 20 | def usage_pkaani(): |
13 | | - """ |
14 | | - Show how to use this program! |
15 | | - """ |
16 | | - print(""" |
| 21 | + """ |
| 22 | + Show how to use this program! |
| 23 | + """ |
| 24 | + |
| 25 | + print(""" |
17 | 26 | Example usages: |
18 | 27 |
|
19 | 28 | * If PDB file doesnt exist, it is downloaded and prepared for pKa calculations. |
20 | 29 |
|
21 | | - pkaani -i 1BNZ |
22 | | - pkaani -i 1BNZ.pdb |
| 30 | + pkaani -i 1BNZ |
| 31 | + pkaani -i 1BNZ.pdb |
23 | 32 |
|
24 | 33 | * Multiple files can be given as inputs |
25 | 34 |
|
26 | | - pkaani -i 1BNZ,1E8L |
| 35 | + pkaani -i 1BNZ,1E8L |
27 | 36 |
|
28 | 37 | * If a specific directory is wanted: |
29 | 38 |
|
30 | | - pkaani -i path_to_file/1BNZ |
31 | | - pkaani -i path_to_file/1BNZ,path_to_file/1E8L |
| 39 | + pkaani -i path_to_file/1BNZ |
| 40 | + pkaani -i path_to_file/1BNZ,path_to_file/1E8L |
32 | 41 |
|
33 | 42 |
|
34 | 43 | Arguments: -i: Input files. Inputs can be given with or without |
35 | | - file extension (.pdb). If PDB file is under a |
36 | | - specific directory (or will be downloaded) the path |
37 | | - can also be given as path_to_file/PDBFILE. |
38 | | - Multiple PDB files can be given |
39 | | - by using "," as separator (i.e. pkaani -i 1BNZ,1E8L). |
| 44 | + file extension (.pdb). If PDB file is under a |
| 45 | + specific directory (or will be downloaded) the path |
| 46 | + can also be given as path_to_file/PDBFILE. |
| 47 | + Multiple PDB files can be given |
| 48 | + by using "," as separator (i.e. pkaani -i 1BNZ,1E8L |
| 49 | + or pkaani -i myFile1.pdb,myFile2.pdb). |
40 | 50 | """) |
41 | 51 |
|
42 | | -def handle_arguments_pkaani(): |
43 | | - inp_file = None |
44 | | - prep_files = None |
| 52 | +def validate_args(): |
| 53 | + parser = MyParser(description="Given a PDB, find the pKa of the titratable amino acids") |
| 54 | + parser.add_argument("-i", "--input_file_list", type=str, help="Comma-separated list of input files", required=True) |
45 | 55 |
|
46 | | - try: |
47 | | - opts, args = getopt.getopt(sys.argv[1:], "hi:", ["help","inp="]) |
48 | | - except getopt.GetoptError: |
49 | | - usage_pkaani() |
50 | | - sys.exit(-1) |
51 | | - |
52 | | - for opt, arg in opts: |
53 | | - |
| 56 | + args = parser.parse_args() |
| 57 | + return args |
54 | 58 |
|
55 | | - if opt in ('-h', "--help"): |
56 | | - usage_pkaani() |
57 | | - sys.exit(-1) |
58 | | - |
59 | | - elif opt in ("-i", "--inp"): |
60 | | - inp_file=[x.strip() for x in arg.split(',')] |
61 | | - |
62 | | - else: |
63 | | - assert False, usage_pkaani() |
64 | 59 |
|
65 | | - if inp_file is None: |
66 | | - usage_pkaani() |
67 | | - sys.exit(-1) |
68 | | - # Input PDB file is mandatory! |
69 | | - if len(inp_file)==0: # is None: |
70 | | - print("@> ERROR: A PDB file is mandatory!") |
71 | | - usage_pkaani() |
72 | | - sys.exit(-1) |
| 60 | +def main(): |
| 61 | + args = validate_args() |
73 | 62 |
|
74 | | - return inp_file |
| 63 | + if len(args.input_file_list) != 0: |
| 64 | + input_files = [x.strip() for x in args.input_file_list.split(',')] |
75 | 65 |
|
76 | | -def main(): |
| 66 | + pdbfiles=np.array(input_files) |
| 67 | + |
| 68 | + #first prepare PDB files for pkaani |
| 69 | + for inputpdb in pdbfiles: |
| 70 | + pdbid=inputpdb.rsplit('.', 1)[0] |
| 71 | + pdbfile=pdbid+".pdb" |
| 72 | + file_exist=True |
| 73 | + if not os.path.exists(pdbfile): |
| 74 | + file_exist=False |
| 75 | + base=os.path.basename(pdbfile) |
| 76 | + dpdbid=base.rsplit('.', 1)[0] |
| 77 | + |
| 78 | + print("File %s is not accessible" % pdbfile) |
| 79 | + print("Downloading : http://www.rcsb.org/pdb/files/%s.pdb" % dpdbid) |
| 80 | + |
| 81 | + url = 'http://www.rcsb.org/pdb/files/%s.pdb' % dpdbid |
| 82 | + |
| 83 | + file = urlopen(url) |
| 84 | + contents = file.read().decode('utf-8') |
| 85 | + file.close() |
| 86 | + file = StringIO(contents) |
| 87 | + |
| 88 | + outfile=pdbfile |
| 89 | + |
| 90 | + with open(outfile, 'w') as f2: |
| 91 | + for line in contents: |
| 92 | + f2.write(line) |
| 93 | + |
| 94 | + prep_pdb(pdbfile) |
| 95 | + file_exist=True |
| 96 | + |
| 97 | + #CALCULATER PKA |
| 98 | + from pkaani.pkaani import calculate_pka |
| 99 | + pkadict=calculate_pka(pdbfiles,writefile=True) |
77 | 100 |
|
78 | | - input_files = handle_arguments_pkaani() |
79 | | - pdbfiles=np.array(input_files) |
80 | | - |
81 | | - #first prepare PDB files for pkaani |
82 | | - for inputpdb in pdbfiles: |
83 | | - pdbid=inputpdb.rsplit('.', 1)[0] |
84 | | - pdbfile=pdbid+".pdb" |
85 | | - file_exist=True |
86 | | - if not os.path.exists(pdbfile): |
87 | | - file_exist=False |
88 | | - base=os.path.basename(pdbfile) |
89 | | - dpdbid=base.rsplit('.', 1)[0] |
90 | | - |
91 | | - print("File %s is not accessible" % pdbfile) |
92 | | - print("Downloading : http://www.rcsb.org/pdb/files/%s.pdb" % dpdbid) |
93 | | - |
94 | | - url = 'http://www.rcsb.org/pdb/files/%s.pdb' % dpdbid |
95 | | - |
96 | | - file = urlopen(url) |
97 | | - contents = file.read().decode('utf-8') |
98 | | - file.close() |
99 | | - file = StringIO(contents) |
100 | | - |
101 | | - outfile=pdbfile |
102 | | - |
103 | | - with open(outfile, 'w') as f2: |
104 | | - for line in contents: |
105 | | - f2.write(line) |
106 | | - |
107 | | - prep_pdb(pdbfile) |
108 | | - file_exist=True |
109 | | - |
110 | | - #CALCULATER PKA |
111 | | - pkadict=calculate_pka(pdbfiles,writefile=True) |
112 | | - |
113 | | - #RENAME FILES PROPERLY |
114 | | - for inputpdb in pdbfiles: |
115 | | - pdbid=inputpdb.rsplit('.', 1)[0] |
116 | | - pdbfile=pdbid+".pdb" |
117 | | - |
118 | | - if os.path.exists(pdbfile): |
119 | | - oldf=pdbfile |
120 | | - newf=pdbid+"_pkaani.pdb" |
121 | | - os.rename(oldf,newf) |
122 | | - if file_exist: |
123 | | - oldf=pdbid+"_0.pdb" |
124 | | - newf=pdbfile |
125 | | - os.rename(pdbid+"_0.pdb",pdbfile) |
| 101 | + #RENAME FILES PROPERLY |
| 102 | + for inputpdb in pdbfiles: |
| 103 | + pdbid=inputpdb.rsplit('.', 1)[0] |
| 104 | + pdbfile=pdbid+".pdb" |
| 105 | + |
| 106 | + if os.path.exists(pdbfile): |
| 107 | + oldf=pdbfile |
| 108 | + newf=pdbid+"_pkaani.pdb" |
| 109 | + os.rename(oldf,newf) |
| 110 | + if file_exist: |
| 111 | + oldf=pdbid+"_0.pdb" |
| 112 | + newf=pdbfile |
| 113 | + os.rename(pdbid+"_0.pdb",pdbfile) |
126 | 114 |
|
127 | 115 |
|
128 | 116 |
|
129 | 117 | if __name__ == "__main__": |
130 | | - main() |
131 | | - |
132 | | - |
| 118 | + main() |
| 119 | + |
| 120 | + |
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