def testMAEName(self):
import gzip
from epymol import mae
name = 'a.b.c'
filename = 'PYMOL-771-example.mae.gz'
contents = gzip.open(filename).read()
mae.read_maestr(contents, name)
v = cmd.get_object_list()
self.assertEqual(v, [name])
def testMAEName(self):
import gzip
from epymol import mae
name = 'a.b.c'
filename = 'PYMOL-771-example.mae.gz'
contents = gzip.open(filename).read()
mae.read_maestr(contents, name)
v = cmd.get_object_list()
self.assertEqual(v, [name])
def _load(oname,finfo,state,ftype,finish,discrete,
quiet=1,multiplex=0,zoom=-1,mimic=1,
plugin='',
object_props=None,
atom_props=None, _self=cmd):
# WARNING: internal routine, subject to change
# caller must already hold API lock
# NOTE: state index assumes 1-based state
r = DEFAULT_ERROR
size = 0
if ftype not in (loadable.model,loadable.brick):
if ftype == loadable.r3d:
from . import cgo
obj = cgo.from_r3d(finfo)
if is_ok(obj):
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.cgo,
int(finish),int(discrete),int(quiet),
int(zoom))
else:
print("Load-Error: Unable to open file '%s'."%finfo)
elif ftype == loadable.cc1: # ChemDraw 3D
obj = chempy.io.cc1.fromFile(finfo)
if obj:
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.model,
int(finish),int(discrete),
int(quiet),int(zoom))
elif ftype == loadable.moe:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import moe
moe_str = _self.file_read(finfo)
r = moe.read_moestr(moe_str,str(oname),int(state),
int(finish),int(discrete),int(quiet),int(zoom),_self=_self)
# END PROPRIETARY CODE SEGMENT
except ImportError:
raise pymol.IncentiveOnlyException(".MOE format not supported by this PyMOL build.")
elif ftype == loadable.mae:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import mae
mae_str = _self.file_read(finfo)
r = mae.read_maestr(mae_str,str(oname),
int(state),
int(finish),int(discrete),
int(quiet),int(zoom),int(multiplex),
int(mimic),
_self=_self)
# END PROPRIETARY CODE SEGMENT
except ImportError:
raise pymol.IncentiveOnlyException(".MAE format not supported by this PyMOL build.")
else:
if ftype in _load2str and ('://' in finfo
or cmd.gz_ext_re.search(finfo)
or any(c > '~' for c in finfo) # ascii check
):
# NOTE: we could safely always do this, not only for URLs and
# compressed files. But I don't want to change the old behavior
# that regular files are read from the C function.
finfo = _self.file_read(finfo)
ftype = _load2str[ftype]
r = _cmd.load(_self._COb,str(oname),finfo,int(state)-1,int(ftype),
int(finish),int(discrete),int(quiet),
int(multiplex),int(zoom), plugin, object_props)
else:
try:
x = chempy.io.pkl.fromFile(finfo)
if isinstance(x, (list, tuple)):
for a in x:
r = _cmd.load_object(_self._COb,str(oname),a,int(state)-1,
int(ftype),0,int(discrete),int(quiet),
int(zoom))
if(state>0):
state = state + 1
_cmd.finish_object(_self._COb,str(oname))
else:
r = _cmd.load_object(_self._COb,str(oname),x,
int(state)-1,int(ftype),
int(finish),int(discrete),
int(quiet),int(zoom))
except:
# traceback.print_exc()
print("Load-Error: Unable to load file '%s'." % finfo)
return r
def _load(oname,finfo,state,ftype,finish,discrete,
quiet=1,multiplex=0,zoom=-1,mimic=1,
_self=cmd):
# WARNING: internal routine, subject to change
# caller must already hold API lock
# NOTE: state index assumes 1-based state
r = DEFAULT_ERROR
size = 0
if ftype not in (loadable.model,loadable.brick):
if ftype == loadable.r3d:
import cgo
obj = cgo.from_r3d(finfo)
if is_ok(obj):
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.cgo,
int(finish),int(discrete),int(quiet),
int(zoom))
else:
print "Load-Error: Unable to open file '%s'."%finfo
elif ftype == loadable.cc1: # ChemDraw 3D
obj = io.cc1.fromFile(finfo)
if obj:
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.model,
int(finish),int(discrete),
int(quiet),int(zoom))
elif ftype == loadable.moe:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import moe
if (string.find(finfo,":")>1):
import urllib
moe_file = urllib.urlopen(finfo)
else:
moe_file = open(finfo)
moe_str = moe_file.read()
moe_file.close()
r = moe.read_moestr(moe_str,str(oname),int(state),
int(finish),int(discrete),int(quiet),int(zoom),_self=_self)
# END PROPRIETARY CODE SEGMENT
except ImportError:
print "Error: .MOE format not supported by this PyMOL build."
if _self._raising(-1,_self): raise pymol.CmdException
elif ftype == loadable.mae:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import mae
if (string.find(finfo,":")>1):
import urllib
mae_file = urllib.urlopen(finfo)
else:
mae_file = open(finfo)
mae_str = mae_file.read()
mae_file.close()
r = mae.read_maestr(mae_str,str(oname),
int(state),
int(finish),int(discrete),
int(quiet),int(zoom),int(multiplex),
int(mimic),
_self=_self)
# END PROPRIETARY CODE SEGMENT
except ValueError:
print "Error: .MAE format not supported by this PyMOL build."
if _self._raising(-1,_self): raise pymol.CmdException
else:
if ftype in _load2str.keys() and (string.find(finfo,":")>1):
gz = re.search("\.gz$",finfo,re.I)
try:
import urllib
tmp_file = urllib.urlopen(finfo)
except:
print "Error: unable to open the URL:\nError: %s"%finfo
# traceback.print_exc()
return 0
finfo = tmp_file.read()
if gz:
import StringIO
fakestream = StringIO.StringIO(finfo)
import gzip
finfo = gzip.GzipFile(fileobj=fakestream).read()
ftype = _load2str[ftype]
tmp_file.close()
elif ftype in _load2str.keys() and re.search("\.gz$",finfo,re.I):
import gzip
finfo = gzip.open(finfo).read()
ftype = _load2str[ftype]
r = _cmd.load(_self._COb,str(oname),finfo,int(state)-1,int(ftype),
int(finish),int(discrete),int(quiet),
int(multiplex),int(zoom))
else:
try:
x = io.pkl.fromFile(finfo)
if isinstance(x,types.ListType) or isinstance(x,types.TupleType):
for a in x:
r = _cmd.load_object(_self._COb,str(oname),a,int(state)-1,
int(ftype),0,int(discrete),int(quiet),
int(zoom))
if(state>0):
state = state + 1
_cmd.finish_object(_self._COb,str(oname))
else:
r = _cmd.load_object(_self._COb,str(oname),x,
int(state)-1,int(ftype),
int(finish),int(discrete),
int(quiet),int(zoom))
except:
# traceback.print_exc()
print "Load-Error: Unable to load file '%s'." % finfo
return r
def _load(oname,finfo,state,ftype,finish,discrete,
quiet=1,multiplex=0,zoom=-1,mimic=1,
_self=cmd):
# WARNING: internal routine, subject to change
# caller must already hold API lock
# NOTE: state index assumes 1-based state
r = DEFAULT_ERROR
size = 0
if ftype not in (loadable.model,loadable.brick):
if ftype == loadable.r3d:
import cgo
obj = cgo.from_r3d(finfo)
if is_ok(obj):
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.cgo,
int(finish),int(discrete),int(quiet),
int(zoom))
else:
print "Load-Error: Unable to open file '%s'."%finfo
elif ftype == loadable.cc1: # ChemDraw 3D
obj = io.cc1.fromFile(finfo)
if obj:
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.model,
int(finish),int(discrete),
int(quiet),int(zoom))
elif ftype == loadable.moe:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import moe
moe_str = _self.file_read(finfo)
r = moe.read_moestr(moe_str,str(oname),int(state),
int(finish),int(discrete),int(quiet),int(zoom),_self=_self)
# END PROPRIETARY CODE SEGMENT
except ImportError:
print "Error: .MOE format not supported by this PyMOL build."
if _self._raising(-1,_self): raise pymol.CmdException
elif ftype == loadable.mae:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import mae
mae_str = _self.file_read(finfo)
r = mae.read_maestr(mae_str,str(oname),
int(state),
int(finish),int(discrete),
int(quiet),int(zoom),int(multiplex),
int(mimic),
_self=_self)
# END PROPRIETARY CODE SEGMENT
except ValueError:
print "Error: .MAE format not supported by this PyMOL build."
if _self._raising(-1,_self): raise pymol.CmdException
else:
if ftype in _load2str and ('://' in finfo or cmd.gz_ext_re.search(finfo)):
# NOTE: we could safely always do this, not only for URLs and
# compressed files. But I don't want to change the old behavior
# that regular files are read from the C function.
finfo = _self.file_read(finfo)
ftype = _load2str[ftype]
r = _cmd.load(_self._COb,str(oname),finfo,int(state)-1,int(ftype),
int(finish),int(discrete),int(quiet),
int(multiplex),int(zoom))
else:
try:
x = io.pkl.fromFile(finfo)
if isinstance(x,types.ListType) or isinstance(x,types.TupleType):
for a in x:
r = _cmd.load_object(_self._COb,str(oname),a,int(state)-1,
int(ftype),0,int(discrete),int(quiet),
int(zoom))
if(state>0):
state = state + 1
_cmd.finish_object(_self._COb,str(oname))
else:
r = _cmd.load_object(_self._COb,str(oname),x,
int(state)-1,int(ftype),
int(finish),int(discrete),
int(quiet),int(zoom))
except:
# traceback.print_exc()
print "Load-Error: Unable to load file '%s'." % finfo
return r
