is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| dali.py (pymol-v1.8.6.0.tar.bz2) | : | dali.py (pymol-v2.1.0.tar.bz2) |
|---|
| | |
| dali_file = "dali.txt" | | dali_file = "dali.txt" |
| | |
| pdb_dir = "dali_pdb" | | pdb_dir = "dali_pdb" |
| | |
| max_pairs = 10 | | max_pairs = 10 |
| | |
| def fetch_pdb(pdbCode,outFile): | | def fetch_pdb(pdbCode,outFile): |
|
| import urllib | | try: |
| | import urllib.request as urllib |
| | except ImportError: |
| | import urllib |
| | |
| import gzip | | import gzip |
| import os | | import os |
|
| import string | | |
| | |
|
| remoteCode = string.upper(pdbCode) | | remoteCode = pdbCode.upper() |
| if not os.path.exists(pdb_dir): | | if not os.path.exists(pdb_dir): |
| os.mkdir(pdb_dir) | | os.mkdir(pdb_dir) |
| if not os.path.exists(outFile): | | if not os.path.exists(outFile): |
| try: | | try: |
| filename = urllib.urlretrieve( | | filename = urllib.urlretrieve( |
| 'http://www.rcsb.org/pdb/cgi/export.cgi/' + | | 'http://www.rcsb.org/pdb/cgi/export.cgi/' + |
| remoteCode + '.pdb.gz?format=PDB&pdbId=' + | | remoteCode + '.pdb.gz?format=PDB&pdbId=' + |
| remoteCode + '&compression=gz')[0] | | remoteCode + '&compression=gz')[0] |
| except: | | except: |
|
| print "warning: %s not found.\n"%pdbCode | | print("warning: %s not found.\n"%pdbCode) |
| else: | | else: |
| if (os.path.getsize(filename) > 0): # If 0, then pdb code was invali
d | | if (os.path.getsize(filename) > 0): # If 0, then pdb code was invali
d |
| try: | | try: |
| abort = 0 | | abort = 0 |
| open(outFile, 'w').write(gzip.open(filename).read()) | | open(outFile, 'w').write(gzip.open(filename).read()) |
|
| print "fetched: %s"%(pdbCode) | | print("fetched: %s"%(pdbCode)) |
| except IOError: | | except IOError: |
| abort = 1 | | abort = 1 |
| if abort: | | if abort: |
| os.remove(outFile) | | os.remove(outFile) |
| else: | | else: |
|
| print "warning: %s not valid.\n"%pdbCode | | print("warning: %s not valid.\n"%pdbCode) |
| os.remove(filename) | | os.remove(filename) |
| | |
| from pymol import cmd | | from pymol import cmd |
|
| from string import strip | | strip = lambda s: s.strip() |
| import os | | import os |
| | |
| seen = {} | | seen = {} |
| input = open(dali_file).readlines() | | input = open(dali_file).readlines() |
| input_state = 0 | | input_state = 0 |
| while 1: | | while 1: |
| try: | | try: |
| line = input.pop(0) | | line = input.pop(0) |
| except IndexError: | | except IndexError: |
| break | | break |
| | |
| skipping to change at line 64 | | skipping to change at line 67 |
|---|
| if line[0:12]==' NR. STRID1': | | if line[0:12]==' NR. STRID1': |
| input_state = 1 | | input_state = 1 |
| elif input_state == 1: | | elif input_state == 1: |
| if strip(line)=='': | | if strip(line)=='': |
| input_state = 2 | | input_state = 2 |
| elif line[4:5]==':': | | elif line[4:5]==':': |
| trg = strip(line[6:12]) | | trg = strip(line[6:12]) |
| src = strip(line[13:19]) | | src = strip(line[13:19]) |
| trg_code = trg[0:4] | | trg_code = trg[0:4] |
| src_code = src[0:4] | | src_code = src[0:4] |
|
| if not seen.has_key(trg_code): | | if trg_code not in seen: |
| trg_file = pdb_dir+os.sep+trg_code+".pdb" | | trg_file = pdb_dir+os.sep+trg_code+".pdb" |
| fetch_pdb(trg_code,trg_file) | | fetch_pdb(trg_code,trg_file) |
| cmd.load(trg_file) | | cmd.load(trg_file) |
| seen[trg_code]=1 | | seen[trg_code]=1 |
|
| if not seen.has_key(src_code): | | if src_code not in seen: |
| src_file = pdb_dir+os.sep+src_code+".pdb" | | src_file = pdb_dir+os.sep+src_code+".pdb" |
| fetch_pdb(src_code,src_file) | | fetch_pdb(src_code,src_file) |
| cmd.load(src_file) | | cmd.load(src_file) |
| seen[src_code]=1 | | seen[src_code]=1 |
| matrix = [] | | matrix = [] |
| for a in range(0,3): | | for a in range(0,3): |
| matrix.append(float(strip(line[29:38]))) | | matrix.append(float(strip(line[29:38]))) |
| matrix.append(float(strip(line[39:48]))) | | matrix.append(float(strip(line[39:48]))) |
| matrix.append(float(strip(line[49:58]))) | | matrix.append(float(strip(line[49:58]))) |
| matrix.append(float(strip(line[59:78]))) | | matrix.append(float(strip(line[59:78]))) |
| | | |
| End of changes. 9 change blocks. |
|---|
| 9 lines changed or deleted | | 12 lines changed or added |
|---|
"Fossies" - the Fresh Open Source Software Archive 