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added python3 compatibility (for dlpisces.py and download_pdbs.py), f…
…ixed numerous packaging bugs preventing pip installation, and made the code slightly more modular.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,218 @@ | ||
| #!/usr/bin/env python | ||
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| """ | ||
| Typical usage (example): | ||
| dlpdbfile.py < list_of_pdb_codes.txt | ||
| Where the input file contains a list of pdb-codes, one per line: | ||
| 100d | ||
| 101d | ||
| 102d | ||
| 103d | ||
| 104d | ||
| 107d | ||
| 108d | ||
| 109d | ||
| Every line in this file contains a 4-letter pdb identifier. | ||
| Each 4-letter pdb code is compared with a list of pdb codes downloaded so far | ||
| (which is initially read from the file "pdbs_most_recent.txt", if present). | ||
| If it is new 4-letter pdb code, then the corresponding pdb file is downloaded, | ||
| and appended to the end of the "pdbs_most_recent.txt" file. | ||
| The corresponding DSSP file is also downloaded, if available. | ||
| """ | ||
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| # author: Andrew Jewett | ||
| g_program_name = __file__.split('/')[-1] | ||
| g_date_str = '2021-1-24' | ||
| g_version_str = '0.6.0' | ||
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| import sys, urllib, urllib.request, random, time, gzip | ||
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| def FileExists(fname): | ||
| try: | ||
| file = open(fname, 'r') | ||
| except IOError: | ||
| exists = False | ||
| else: | ||
| exists = True | ||
| return exists | ||
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| def ExtractFileName(url): | ||
| # The name of the file we create will be the same as the last few | ||
| # characters of the URL. (Whatever comes after the last '/' character.) | ||
| out_fname = url | ||
| slash_loc = out_fname.rfind('/') | ||
| if (slash_loc >= 0): # if '/' was found, then remove text preceeding '/' | ||
| out_fname = out_fname[slash_loc+1:] | ||
| if (out_fname == ''): | ||
| sys.stderr.write('Error: filename difficult to determine from URL:\n' +\ | ||
| ' \"'+url+'\"\n') | ||
| sys.exit(-1) | ||
| return out_fname | ||
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| # This function downloads a file from a URL, and (if requested by the user) | ||
| # prints out a warning message if there was a problem. | ||
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| import os | ||
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| def DownloadFileTo(url, file_name, verbose_mode = True): | ||
| # Open the input file (at url) for reading | ||
| # Simple way: | ||
| # in_file = urllib.urlopen(url) | ||
| # But the web site may return garbage if the file doesn't exist. | ||
| # Instead, we check for errors first: | ||
| try: in_file = urllib.request.urlopen(url) | ||
| except urllib.error.URLError as e: | ||
| if (verbose_mode): | ||
| sys.stderr.write(str(e)+'\n') | ||
| sys.stderr.write(' omitting file \"'+file_name+'\"\n') | ||
| else: | ||
| if (verbose_mode): | ||
| sys.stderr.write('downloading file \"'+file_name+'\"\n') | ||
| # Open the output file for writing | ||
| out_file = open(file_name, 'wb') | ||
| out_file.write(in_file.read()) | ||
| out_file.close() | ||
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| # This version infers the file name from the URL. | ||
| def DownloadFile(url, verbose_mode = True): | ||
| DownloadFileTo(url, ExtractFileName(url), verbose_mode) | ||
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| # Read in the list of PDB files already downloaded: | ||
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| pdbs_old = set([]) | ||
| try: | ||
| pdbs_old_file = open('pdbs_old.txt', 'r') | ||
| for pdb_code in pdbs_old_file: | ||
| pdb_code = pdb_code.strip()#eliminate trailing and preceeding whitespace | ||
| pdb_code = pdb_code.lower()#pdb codes are case-insensitive | ||
| if (len(pdb_code) != 4): | ||
| sys.stderr.write('Error in in \"pdbs_old.txt\":\n') | ||
| sys.stderr.write(' Invalid PDB-code: \"'+pdb_code+'\"\n') | ||
| exit(-1) | ||
| pdbs_old.add(pdb_code) | ||
| pdbs_old_file.close() | ||
| except IOError: | ||
| pass | ||
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| def main(): | ||
| # Here we keep track of the list of pdb files which | ||
| # i) are in the current list of pdb files requested in | ||
| # sys.stdin | ||
| # ii) are in the current list, but are not downloaded yet | ||
| # (new pdb files) | ||
| pdbs_current_file = open('pdbs_most_recent.txt', 'w') | ||
| pdbs_current = set([]) #entire list of pdb codes requested | ||
| pdbs_new = set([]) #a list of new pdb codes requested that were not in the old list | ||
| pdbs_old_file = open('pdbs_old.txt', 'a') | ||
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| for line in sys.stdin: | ||
| line = line.strip() | ||
| if len(line) == 0: | ||
| continue | ||
| pdb_code = line.lower() #(pdb codes are case-insensitive) | ||
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| if (pdb_code in pdbs_new): | ||
| sys.stderr.write(pdb_code+' appears redundantly. skipping\n') | ||
| elif (pdb_code in pdbs_old): | ||
| if (not (pdb_code in pdbs_current)): | ||
| sys.stderr.write(pdb_code+' downloaded already. skipping.\n') | ||
| pdbs_current.add(pdb_code) | ||
| pdbs_current_file.write(pdb_code+'\n') | ||
| pdbs_current_file.flush() #<- necessary in case we get interrupted | ||
| else: | ||
| sys.stderr.write(pdb_code+' appears redundantly. skipping\n') | ||
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| else: | ||
| #Download the corresponding pdb file | ||
| file_name = pdb_code+'.pdb.gz' # <- these are compressed files | ||
| url = 'http://www.rcsb.org/pdb/files/'+file_name | ||
| # Note, if the URL above files, try this one instead: | ||
| # url = 'https://files.rcsb.org/download/'+file_name | ||
| DownloadFileTo(url, file_name) | ||
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| #Unzip the pdb file: | ||
| with gzip.open(file_name, 'rb') as f: | ||
| file_content = f.read() | ||
| f.close() | ||
| f = open(pdb_code+'.pdb', 'wb') | ||
| f.write(file_content) | ||
| if not FileExists(pdb_code+'.pdb'): | ||
| sys.stderr.write('Error: A problem occured when trying to download PDB code \"'+pdb_code+'\"\n' | ||
| ' Delete this entry from the file \"pdbs_old.txt\", and rerun '+g_program_name+'\n') | ||
| sys.exit(-1) | ||
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| #Optional: Download the corresponding DSSP file | ||
| url = 'ftp://ftp.cmbi.ru.nl/pub/molbio/data/dssp/'+pdb_code+'.dssp' | ||
| DownloadFile(url) | ||
| if not FileExists(pdb_code+'.dssp'): | ||
| sys.stderr.write(" (The old DSSP PDB is server flaking out again.\n" | ||
| " Don't worry. DSSP files are not needed.)\n") | ||
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| #Keep track of the the pdbs we have downloaded so far: | ||
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| pdbs_current.add(pdb_code) | ||
| pdbs_current_file.write(pdb_code+'\n') | ||
| pdbs_current_file.flush() #<- necessary in case we get interrupted | ||
| pdbs_old_file.write(pdb_code+'\n') | ||
| pdbs_old_file.flush() #<- necessary in case we get interrupted | ||
| pdbs_new.add(pdb_code) | ||
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| pdbs_current_file.close() | ||
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| def ChainFromPDBfile(chainID, pdb_file): | ||
| for line in pdb_file: | ||
| line_type = line[0:6] | ||
| if line_type in set(['ATOM ', 'HETATM', 'ANISOU', 'SIGATM', 'SIGUIJ']): | ||
| if line[21:22] == chainID: | ||
| yield line | ||
| elif line_type == "HET ": | ||
| if line[12:13] == chainID: | ||
| yield line | ||
| elif line_type == "HELIX ": | ||
| initChainID = line[19:20] | ||
| endChainID = line[31:32] | ||
| if (initChainID == chainID) or (endChainID == chainID): | ||
| yield line | ||
| elif line_type == "SHEET ": | ||
| initChainID = line[21:22] | ||
| endChainID = line[32:33] | ||
| if (initChainID == chainID) or (endChainID == chainID): | ||
| yield line | ||
| elif line_type == "TURN ": | ||
| initChainID = line[19:20] | ||
| endChainID = line[30:31] | ||
| if (initChainID == chainID) or (endChainID == chainID): | ||
| yield line | ||
| elif line_type == "SEQRES": | ||
| if line[11:12] == chainID: | ||
| yield line | ||
| elif line_type == "TER ": | ||
| ter_chainID = line[21:22] | ||
| if (ter_chainID == chainID) or (ter_chainID == " "): | ||
| yield line | ||
| else: | ||
| yield line | ||
| return | ||
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| if __name__ == "__main__": | ||
| main() |
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