def fetch_scop(code, name='', **kwargs): if name == '': name = code kwargs['async'] = 0 r = fetch(code[1:5], name, **kwargs) if cmd.is_error(r): return r try: import Bio.SCOP import MySQLdb conn = MySQLdb.connect(**mysql_kwargs) scop = Bio.SCOP.Scop(db_handle=conn) d = scop.getDomainBySid(code) if len(d.residues.fragments) > 0: rsele = '' for frag in d.residues.fragments: chain, start, stop = frag rsele += ' (chain ' + chain if start and stop: rsele += ' and resi %s-%s' % (start, stop) rsele += ')' cmd.remove(name + ' and not (' + rsele + ')') except: print(' Warning: SCOP domain resiude range handling failed') return -1
def fetch_cath(code, name='', **kwargs): if name == '': name = code r = fetch(code[:4], name, async=0, **kwargs) if cmd.is_error(r): return r if code[5:7] == '00': if code[4] != '0': cmd.remove(name + ' and not chain ' + code[4]) else: try: if len(cath_domains) == 0: cath_parse_domall() d = cath_domains[code] rsele = '' for frag in d: chain, start, stop = frag rsele += ' (chain ' + chain if start and stop: rsele += ' and resi %s-%s' % (start, stop) rsele += ')' cmd.remove(name + ' and not (' + rsele + ')') except: print ' Warning: CATH domain resiude range handling failed' return -1
def fetch_scop(code, name="", **kwargs): if name == "": name = code r = fetch(code[1:5], name, async=0, **kwargs) if cmd.is_error(r): return r try: import Bio.SCOP import MySQLdb conn = MySQLdb.connect(**mysql_kwargs) scop = Bio.SCOP.Scop(db_handle=conn) d = scop.getDomainBySid(code) if len(d.residues.fragments) > 0: rsele = "" for frag in d.residues.fragments: chain, start, stop = frag rsele += " (chain " + chain if start and stop: rsele += " and resi %s-%s" % (start, stop) rsele += ")" cmd.remove(name + " and not (" + rsele + ")") except: print " Warning: SCOP domain resiude range handling failed" return -1
def fetch_cath(code, name='', **kwargs): if name == '': name = code kwargs['async'] = 0 r = fetch(code[:4], name, **kwargs) if cmd.is_error(r): return r if code[5:7] == '00': if code[4] != '0': cmd.remove(name + ' and not chain ' + code[4]) else: try: if len(cath_domains) == 0: cath_parse_domall() d = cath_domains[code] rsele = '' for frag in d: chain, start, stop = frag rsele += ' (chain ' + chain if start and stop: rsele += ' and resi %s-%s' % (start, stop) rsele += ')' cmd.remove(name + ' and not (' + rsele + ')') except: print(' Warning: CATH domain resiude range handling failed') return -1
def fetch_cath(code, name="", **kwargs): if name == "": name = code r = fetch(code[:4], name, async=0, **kwargs) if cmd.is_error(r): return r if code[5:7] == "00": if code[4] != "0": cmd.remove(name + " and not chain " + code[4]) else: try: if len(cath_domains) == 0: cath_parse_domall() d = cath_domains[code] rsele = "" for frag in d: chain, start, stop = frag rsele += " (chain " + chain if start and stop: rsele += " and resi %s-%s" % (start, stop) rsele += ")" cmd.remove(name + " and not (" + rsele + ")") except: print " Warning: CATH domain resiude range handling failed" return -1
def fetch_chain(code, name='', **kwargs): if name == '': name = code chain = code[4] if len(code) == 5 else code[5] r = fetch(code[:4], name, async=0, **kwargs) if cmd.is_error(r): return r cmd.remove(name + ' and not chain ' + chain)
def fetch_chain(code, name='', *, _self=cmd, **kwargs): if name == '': name = code chain = code[4] if len(code) == 5 else code[5] kwargs['async'] = 0 r = fetch(code[:4], name, **kwargs) if cmd.is_error(r): return r _self.remove(name + ' and not chain ' + chain)
def x(st): print st cmd.set("raise_exceptions", 0) valu = eval(st) print valu if cmd.is_error(valu): cmd.set("raise_exceptions", 1) try: print eval(st) except pymol.CmdException: print "CmdException raised." except cmd.QuietException: print "QuietException raised."
def x(st): print st cmd.set("raise_exceptions",0) valu = eval(st) print valu if cmd.is_error(valu): cmd.set("raise_exceptions",1) try: print eval(st) except pymol.CmdException: print "CmdException raised." except cmd.QuietException: print "QuietException raised."