88 lines
2.6 KiB
Python
88 lines
2.6 KiB
Python
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dali_file = "dali.txt"
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pdb_dir = "dali_pdb"
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max_pairs = 10
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def fetch_pdb(pdbCode,outFile):
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try:
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import urllib.request as urllib
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except ImportError:
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import urllib
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import gzip
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import os
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remoteCode = pdbCode.upper()
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if not os.path.exists(pdb_dir):
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os.mkdir(pdb_dir)
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if not os.path.exists(outFile):
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try:
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filename = urllib.urlretrieve(
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'http://www.rcsb.org/pdb/cgi/export.cgi/' +
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remoteCode + '.pdb.gz?format=PDB&pdbId=' +
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remoteCode + '&compression=gz')[0]
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except:
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print("warning: %s not found.\n"%pdbCode)
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else:
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if (os.path.getsize(filename) > 0): # If 0, then pdb code was invalid
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try:
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abort = 0
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open(outFile, 'w').write(gzip.open(filename).read())
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print("fetched: %s"%(pdbCode))
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except IOError:
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abort = 1
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if abort:
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os.remove(outFile)
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else:
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print("warning: %s not valid.\n"%pdbCode)
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os.remove(filename)
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from pymol import cmd
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strip = lambda s: s.strip()
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import os
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seen = {}
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input = open(dali_file).readlines()
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input_state = 0
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while 1:
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try:
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line = input.pop(0)
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except IndexError:
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break
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if input_state == 0:
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if line[0:11]=='## MATRICES':
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line = input.pop(0)
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if line[0:12]==' NR. STRID1':
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input_state = 1
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elif input_state == 1:
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if strip(line)=='':
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input_state = 2
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elif line[4:5]==':':
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trg = strip(line[6:12])
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src = strip(line[13:19])
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trg_code = trg[0:4]
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src_code = src[0:4]
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if trg_code not in seen:
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trg_file = pdb_dir+os.sep+trg_code+".pdb"
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fetch_pdb(trg_code,trg_file)
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cmd.load(trg_file)
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seen[trg_code]=1
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if src_code not in seen:
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src_file = pdb_dir+os.sep+src_code+".pdb"
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fetch_pdb(src_code,src_file)
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cmd.load(src_file)
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seen[src_code]=1
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matrix = []
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for a in range(0,3):
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matrix.append(float(strip(line[29:38])))
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matrix.append(float(strip(line[39:48])))
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matrix.append(float(strip(line[49:58])))
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matrix.append(float(strip(line[59:78])))
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matrix.extend([0.0,0.0,0.0,1.0])
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max_pairs = max_pairs - 1
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if max_pairs<0:
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break
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