def data_from_sdf(sdf_file_path):
mol_dict = {}
row_id_list = []
row_id_dict = {}
col_id_list = []
col_id_dict = {}
# first pass, load the identifiers, MOL files, and tag names
col = 0
sdf = SDF(sdf_file_path)
while 1:
rec = sdf.read()
if not rec:
break
mol = rec.get('MOL')
# get the unique identifier
mol_id = mol[0].strip()
# store the MOL record
mol_dict[mol_id] = ''.join(mol)
# add row (assuming mol_id is unique)
row_id_list.append(mol_id)
row_id_dict[mol_id] = None
# add column (if new)
for key in rec.kees:
if key != 'MOL':
if key not in col_id_dict:
col_id_list.append(key)
col_id_dict[key] = None
# second pass, read the actual data into the table structure
content = {}
sdf = SDF(sdf_file_path)
while 1:
rec = sdf.read()
if not rec:
break
mol_id = rec.get('MOL')[0].strip()
for key in rec.kees:
if key != 'MOL':
content[ (mol_id,key) ] = rec.get(key)[0].strip()
return {
'content' : content,
'row_id_list' : row_id_list,
'col_id_list' : col_id_list,
'mol_dict' : mol_dict
}
def data_from_sdf(sdf_file_path):
mol_dict = {}
row_id_list = []
row_id_dict = {}
col_id_list = []
col_id_dict = {}
# first pass, load the identifiers, MOL files, and tag names
col = 0
sdf = SDF(sdf_file_path)
while 1:
rec = sdf.read()
if not rec:
break
mol = rec.get('MOL')
# get the unique identifier
mol_id = mol[0].strip()
# store the MOL record
mol_dict[mol_id] = ''.join(mol)
# add row (assuming mol_id is unique)
row_id_list.append(mol_id)
row_id_dict[mol_id] = None
# add column (if new)
for key in rec.kees:
if key != 'MOL':
if key not in col_id_dict:
col_id_list.append(key)
col_id_dict[key] = None
# second pass, read the actual data into the table structure
content = {}
sdf = SDF(sdf_file_path)
while 1:
rec = sdf.read()
if not rec:
break
mol_id = rec.get('MOL')[0].strip()
for key in rec.kees:
if key != 'MOL':
content[(mol_id, key)] = rec.get(key)[0].strip()
return {
'content': content,
'row_id_list': row_id_list,
'col_id_list': col_id_list,
'mol_dict': mol_dict
}
def save(filename,
selection='(all)',
state=-1,
format='',
ref='',
ref_state=-1,
quiet=1,
partial=0,
_self=cmd):
'''
DESCRIPTION
"save" writes content to a file.
USAGE
save filename [, selection [, state [, format ]]]
ARGUMENTS
filename = string: file path to be written
selection = string: atoms to save {default: (all)}
state = integer: state to save {default: -1 (current state)}
PYMOL API
cmd.save(string file, string selection, int state, string format)
NOTES
The file format is automatically chosen if the extesion is one of
the supported output formats: pdb, pqr, mol, pkl, mmd, mmod, pov,
png, pse, aln, obj, mtl, or wrl.
If the file format is not recognized, then a PDB file is written
by default.
For molecular files and where applicable and supported:
* if state = -1 (default), then only the current state is written.
* if state = 0, then a multi-state output file is written.
SEE ALSO
load, get_model
'''
# preprocess selection
input_selection = selection
selection = selector.process(input_selection)
#
r = DEFAULT_ERROR
lc_filename = string.lower(filename)
if format == '':
format = 'unknown'
# refactor following if/elif cascade
# with a dictionary lookup
if re.search("\.pdb$|\.ent$", lc_filename):
format = 'pdb'
elif re.search("\.pqr$", lc_filename):
format = 'pqr'
elif re.search("\.mol$", lc_filename):
format = 'mol'
elif re.search("\.sdf$", lc_filename):
format = 'sdf'
elif re.search("\.pkl$", lc_filename):
format = 'pkl'
elif re.search("\.pkl$", lc_filename):
format = 'pkla'
elif re.search("\.mmd$", lc_filename):
format = 'mmod'
elif re.search("\.out$", lc_filename):
format = 'mmod'
elif re.search("\.dat$", lc_filename):
format = 'mmod'
elif re.search("\.mmod$", lc_filename):
format = 'mmod'
elif re.search("\.pmo$", lc_filename):
format = 'pmo'
elif re.search("\.pov$", lc_filename):
format = 'pov'
elif re.search("\.png$", lc_filename):
format = 'png'
elif re.search("\.pse$|\.psw$", lc_filename):
format = 'pse'
elif re.search("\.aln$", lc_filename):
format = 'aln'
elif re.search("\.fasta$", lc_filename):
format = 'fasta'
elif re.search("\.obj$", lc_filename):
format = 'obj'
elif re.search("\.mtl$", lc_filename):
format = 'mtl'
elif re.search("\.wrl$", lc_filename):
format = 'wrl'
elif re.search("\.idtf$", lc_filename):
format = 'idtf'
elif re.search("\.mol2$", lc_filename):
format = 'mol2'
else:
format = str(format)
if format == 'unknown':
if not quiet:
print " Save-Warning: Unrecognized file type -- defaulting to PDB format."
format = 'pdb'
filename = _self.exp_path(filename)
if format == 'pdb': # standard PDB file
f = open(filename, "w")
if f:
st = ''
try:
_self.lock(_self)
st = _cmd.get_pdb(_self._COb, "(" + str(selection) + ")",
int(state) - 1, 0, str(ref),
int(ref_state) - 1, int(quiet))
if st != None:
r = DEFAULT_SUCCESS
finally:
_self.unlock(r, _self=_self)
f.write(st)
f.close()
if not quiet:
print " Save: wrote \"" + filename + "\"."
elif format == 'aln':
st = ''
try:
_self.lock(_self)
st = _cmd.get_seq_align_str(_self._COb, str(selection),
int(state) - 1, 0, int(quiet))
if st != None:
r = DEFAULT_SUCCESS
finally:
_self.unlock(r, _self)
if st != None:
f = open(filename, "w")
f.write(st)
f.close()
if not quiet:
print " Save: wrote \"" + filename + "\"."
else:
r = DEFAULT_ERROR
elif format == 'fasta':
st = _self.get_fastastr(selection)
if st != None:
r = DEFAULT_SUCCESS
f = open(filename, "w")
f.write(st)
f.close()
if not quiet:
print " Save: wrote \"" + filename + "\"."
else:
r = DEFAULT_ERROR
elif format == 'pqr': # PQR (modified PDB file)
f = open(filename, "w")
if f:
st = ''
try:
_self.lock(_self)
st = _cmd.get_pdb(_self._COb, "(" + str(selection) + ")",
int(state) - 1, 1, str(ref),
int(ref_state) - 1, int(quiet))
if st != None:
r = DEFAULT_SUCCESS
finally:
_self.unlock(r, _self)
f.write(st)
f.close()
if not quiet:
print " Save: wrote \"" + filename + "\"."
elif format == 'pkl': # python binary
io.pkl.toFile(_self.get_model(selection, state, ref, ref_state),
filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \"" + filename + "\"."
elif format == 'pkla': # ascii override
io.pkl.toFile(_self.get_model(selection, state, ref, ref_state),
filename,
bin=0)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \"" + filename + "\"."
elif format == 'pse': # PyMOL session
filename = filename.replace(
"\\", "/") # always use unix-like path separators
_self.set("session_file", filename, quiet=1)
if '(' in input_selection: # ignore selections
input_selection = ''
if not quiet:
print " Save: Please wait -- writing session file..."
io.pkl.toFile(
_self.get_session(str(input_selection), int(partial),
int(quiet)), filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \"" + filename + "\"."
elif format == 'mmod': # macromodel
io.mmd.toFile(_self.get_model(selection, state, ref, ref_state),
filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \"" + filename + "\"."
elif format == 'sdf':
state = int(state)
if state == 0:
first_state = 1
last_state = cmd.count_states(selection)
else:
first_state = state
last_state = state
sdf = SDF(filename, 'w')
for state in range(first_state, last_state + 1):
rec = SDFRec(
io.mol.toList(
_self.get_model(selection, state, ref, ref_state)) +
["$$$$\n"])
sdf.write(rec)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote %d states to \"%s\"." % (
1 + last_state - first_state, filename)
elif format == 'mol':
io.mol.toFile(_self.get_model(selection, state, ref, ref_state),
filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \"" + filename + "\"."
elif format == "mol2":
state = int(state)
if state == 0:
first_state = 1
last_state = cmd.count_states(selection)
else:
first_state = state
last_state = state
recList = []
for state in range(first_state, last_state + 1):
# assign_atom_types selection, format [ mol2, macromodel ], state, quiet
assign_atom_types(selection, "mol2", state, 1, _self)
recList.extend(
io.mol2.toList(_self.get_model(selection, state, ref,
ref_state),
selection=selection,
state=state))
m = MOL2(cmd=cmd)
m.strToFile(recList, filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote %d states to \"%s\"." % (
1 + last_state - first_state, filename)
elif format == 'png':
r = _self.png(filename, quiet=quiet)
# refactor below to lift repeated code
elif format == 'pov':
tup = _self.get_povray()
f = open(filename, "w")
f.write(tup[0])
f.write(tup[1])
f.flush()
f.close()
if not quiet:
print " Save: wrote \"" + filename + "\"."
r = DEFAULT_SUCCESS
elif format == 'obj':
tup = _self.get_mtl_obj()
f = open(filename, "w")
f.write(tup[1])
f.flush()
f.close()
r = DEFAULT_SUCCESS
elif format == 'mtl':
tup = _self.get_mtl_obj()
f = open(filename, "w")
f.write(tup[0])
f.flush()
f.close()
r = DEFAULT_SUCCESS
elif format == 'wrl':
txt = _self.get_vrml()
f = open(filename, "w")
f.write(txt)
f.flush()
f.close()
if not quiet:
print " Save: wrote \"" + filename + "\"."
r = DEFAULT_SUCCESS
elif format == 'idtf':
tup = _self.get_idtf()
f = open(filename, "w")
f.write(tup[0])
f.write(tup[1])
f.flush()
f.close()
if not quiet:
fov = float(cmd.get("field_of_view"))
dist = cmd.get_view()[11]
print " 3Daac=%3.1f, 3Droll=0, 3Dc2c=0 0 1, 3Droo=%1.2f, 3Dcoo=0 0 %1.2f" % (
fov, -dist, dist)
print " Save: wrote \"" + filename + "\"."
r = DEFAULT_SUCCESS
if _self._raising(r, _self): raise QuietException
return r
def save(filename, selection='(all)', state=-1, format='', ref='',
ref_state=-1, quiet=1, partial=0,_self=cmd):
'''
DESCRIPTION
"save" writes content to a file.
USAGE
save filename [, selection [, state [, format ]]]
ARGUMENTS
filename = string: file path to be written
selection = string: atoms to save {default: (all)}
state = integer: state to save {default: -1 (current state)}
PYMOL API
cmd.save(string file, string selection, int state, string format)
NOTES
The file format is automatically chosen if the extesion is one of
the supported output formats: pdb, pqr, mol, pkl, mmd, mmod, pov,
png, pse, aln, obj, mtl, or wrl.
If the file format is not recognized, then a PDB file is written
by default.
For molecular files and where applicable and supported:
* if state = -1 (default), then only the current state is written.
* if state = 0, then a multi-state output file is written.
SEE ALSO
load, get_model
'''
# preprocess selection
input_selection = selection
selection = selector.process(input_selection)
#
r = DEFAULT_ERROR
lc_filename=string.lower(filename)
if format=='':
format = 'unknown'
# refactor following if/elif cascade
# with a dictionary lookup
if re.search("\.pdb$|\.ent$",lc_filename):
format = 'pdb'
elif re.search("\.pqr$",lc_filename):
format = 'pqr'
elif re.search("\.mol$",lc_filename):
format = 'mol'
elif re.search("\.sdf$",lc_filename):
format = 'sdf'
elif re.search("\.pkl$",lc_filename):
format = 'pkl'
elif re.search("\.pkl$",lc_filename):
format = 'pkla'
elif re.search("\.mmd$",lc_filename):
format = 'mmod'
elif re.search("\.out$",lc_filename):
format = 'mmod'
elif re.search("\.dat$",lc_filename):
format = 'mmod'
elif re.search("\.mmod$",lc_filename):
format = 'mmod'
elif re.search("\.pmo$",lc_filename):
format = 'pmo'
elif re.search("\.pov$",lc_filename):
format = 'pov'
elif re.search("\.png$",lc_filename):
format = 'png'
elif re.search("\.pse$|\.psw$",lc_filename):
format = 'pse'
elif re.search("\.aln$",lc_filename):
format = 'aln'
elif re.search("\.fasta$",lc_filename):
format = 'fasta'
elif re.search("\.obj$",lc_filename):
format = 'obj'
elif re.search("\.mtl$",lc_filename):
format = 'mtl'
elif re.search("\.wrl$",lc_filename):
format = 'wrl'
elif re.search("\.idtf$",lc_filename):
format = 'idtf'
elif re.search("\.mol2$",lc_filename):
format = 'mol2'
else:
format = str(format)
if format=='unknown':
if not quiet:
print " Save-Warning: Unrecognized file type -- defaulting to PDB format."
format='pdb'
filename = _self.exp_path(filename)
if format=='pdb': # standard PDB file
f=open(filename,"w")
if f:
st = ''
try:
_self.lock(_self)
st = _cmd.get_pdb(_self._COb,"("+str(selection)+")",int(state)-1,0,
str(ref),int(ref_state)-1,int(quiet))
if st != None:
r = DEFAULT_SUCCESS
finally:
_self.unlock(r,_self=_self)
f.write(st)
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='aln':
st = ''
try:
_self.lock(_self)
st = _cmd.get_seq_align_str(_self._COb,str(selection),int(state)-1,0,int(quiet))
if st != None:
r = DEFAULT_SUCCESS
finally:
_self.unlock(r,_self)
if st!=None:
f=open(filename,"w")
f.write(st)
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
else:
r = DEFAULT_ERROR
elif format=='fasta':
st = _self.get_fastastr(selection)
if st != None:
r = DEFAULT_SUCCESS
f=open(filename,"w")
f.write(st)
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
else:
r = DEFAULT_ERROR
elif format=='pqr': # PQR (modified PDB file)
f=open(filename,"w")
if f:
st = ''
try:
_self.lock(_self)
st = _cmd.get_pdb(_self._COb,"("+str(selection)+")",int(state)-1,1,
str(ref),int(ref_state)-1,int(quiet))
if st != None:
r = DEFAULT_SUCCESS
finally:
_self.unlock(r,_self)
f.write(st)
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='pkl': # python binary
io.pkl.toFile(_self.get_model(selection,state,ref,ref_state),filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='pkla': # ascii override
io.pkl.toFile(_self.get_model(selection,state,ref,ref_state),filename,bin=0)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='pse': # PyMOL session
filename = filename.replace("\\","/") # always use unix-like path separators
_self.set("session_file",filename,quiet=1)
if '(' in input_selection: # ignore selections
input_selection=''
if not quiet:
print " Save: Please wait -- writing session file..."
io.pkl.toFile(_self.get_session(str(input_selection),int(partial),int(quiet)),filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='mmod': # macromodel
io.mmd.toFile(_self.get_model(selection,state,ref,ref_state),filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='sdf':
state = int(state)
if state==0:
first_state = 1
last_state = cmd.count_states(selection)
else:
first_state = state
last_state = state
sdf = SDF(filename,'w')
for state in range(first_state, last_state+1):
rec = SDFRec(io.mol.toList(_self.get_model(selection,state,ref,ref_state))
+ ["$$$$\n"])
sdf.write(rec)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote %d states to \"%s\"."%(1+last_state-first_state,filename)
elif format=='mol':
io.mol.toFile(_self.get_model(selection,state,ref,ref_state),filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=="mol2":
state = int(state)
if state==0:
first_state = 1
last_state = cmd.count_states(selection)
else:
first_state = state
last_state = state
recList=[]
for state in range(first_state, last_state+1):
# assign_atom_types selection, format [ mol2, macromodel ], state, quiet
assign_atom_types(selection, "mol2", state, 1, _self)
recList.extend(io.mol2.toList(_self.get_model(selection,state,ref,ref_state),selection=selection,state=state))
m = MOL2(cmd=cmd)
m.strToFile(recList,filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote %d states to \"%s\"."%(1+last_state-first_state,filename)
elif format=='png':
r = _self.png(filename,quiet=quiet)
# refactor below to lift repeated code
elif format=='pov':
tup = _self.get_povray()
f=open(filename,"w")
f.write(tup[0])
f.write(tup[1])
f.flush()
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
r = DEFAULT_SUCCESS
elif format=='obj':
tup = _self.get_mtl_obj()
f=open(filename,"w")
f.write(tup[1])
f.flush()
f.close()
r = DEFAULT_SUCCESS
elif format=='mtl':
tup = _self.get_mtl_obj()
f=open(filename,"w")
f.write(tup[0])
f.flush()
f.close()
r = DEFAULT_SUCCESS
elif format=='wrl':
txt = _self.get_vrml()
f=open(filename,"w")
f.write(txt)
f.flush()
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
r = DEFAULT_SUCCESS
elif format=='idtf':
tup = _self.get_idtf()
f=open(filename,"w")
f.write(tup[0]);
f.write(tup[1]);
f.flush()
f.close()
if not quiet:
fov = float(cmd.get("field_of_view"))
dist = cmd.get_view()[11]
print " 3Daac=%3.1f, 3Droll=0, 3Dc2c=0 0 1, 3Droo=%1.2f, 3Dcoo=0 0 %1.2f"%(fov,-dist,dist)
print " Save: wrote \""+filename+"\"."
r = DEFAULT_SUCCESS
if _self._raising(r,_self): raise QuietException
return r
def load_annotated_sdf(filename, object=None, state=1, discrete=1, _self=cmd):
pymol = _self._pymol
cmd = _self
# get object name from file prefix
if object == None:
object = re.sub(r"\.[sS][dD][fF]$", "", filename)
# open the SD file
inp_sdf = SDF(filename)
# create a persistent place to store the annotations
if not hasattr(pymol.session, 'annotation'):
pymol.session.annotation = {}
# create a state-indexed dictionary for this object
state_dict = {}
pymol.session.annotation[object] = state_dict
while 1:
# get next record
sdf_rec = inp_sdf.read()
# if at end of list, break out of loop
if not sdf_rec: break
# get the MOL portion of the record
mol_list = sdf_rec.get('MOL')
# load it into PyMOL
cmd.read_molstr(string.join(mol_list, ''),
object,
state,
finish=0,
discrete=discrete)
# populate with tuple containing ordered list of keys
# and associated data dictionary
anno_list = ["\\955" + object]
for key in sdf_rec.kees:
if (key != 'MOL'):
data = sdf_rec.data[key]
print key, data
anno_list.append(
" \\595%s: \\559%s" %
(key, string.join(map(string.strip, sdf_rec.data[key]))))
state_dict[state] = anno_list
# increment the state index
state = state + 1
if state > 1:
cmd.zoom(object)
cmd.finish_object(object)
def load_annotated_sdf(filename, object=None, state=1, discrete=1, _self=cmd):
pymol=_self._pymol
cmd=_self
# get object name from file prefix
if object==None:
object = re.sub(r"\.[sS][dD][fF]$","",filename)
# open the SD file
inp_sdf = SDF(filename)
# create a persistent place to store the annotations
if not hasattr(pymol.session,'annotation'):
pymol.session.annotation = {}
# create a state-indexed dictionary for this object
state_dict = {}
pymol.session.annotation[object] = state_dict
while 1:
# get next record
sdf_rec = inp_sdf.read()
# if at end of list, break out of loop
if not sdf_rec: break
# get the MOL portion of the record
mol_list = sdf_rec.get('MOL')
# load it into PyMOL
cmd.read_molstr(''.join(mol_list),object,
state,finish=0,discrete=discrete)
# populate with tuple containing ordered list of keys
# and associated data dictionary
anno_list = [ "\\955"+object ]
for key in sdf_rec.kees:
if (key!='MOL'):
data = sdf_rec.data[key]
print(key,data)
anno_list.append(" \\595%s: \\559%s"%(
key,
' '.join(map(str.strip, sdf_rec.data[key]))))
state_dict[state] = anno_list
# increment the state index
state = state + 1
if state > 1:
cmd.zoom(object)
cmd.finish_object(object)
def save(filename, selection='(all)', state=-1, format='', ref='',
ref_state=-1, quiet=1, partial=0,_self=cmd):
'''
DESCRIPTION
"save" writes content to a file.
USAGE
save filename [, selection [, state [, format ]]]
ARGUMENTS
filename = string: file path to be written
selection = string: atoms to save {default: (all)}
state = integer: state to save {default: -1 (current state)}
PYMOL API
cmd.save(string file, string selection, int state, string format)
NOTES
The file format is automatically chosen if the extesion is one of
the supported output formats: pdb, pqr, mol, sdf, pkl, pkla, mmd, out,
dat, mmod, pmo, pov, png, pse, psw, aln, fasta, obj, mtl, wrl, dae, idtf,
or mol2.
If the file format is not recognized, then a PDB file is written
by default.
For molecular files and where applicable and supported:
* if state = -1 (default), then only the current state is written.
* if state = 0, then a multi-state output file is written.
SEE ALSO
load, get_model
'''
import cPickle
import gzip
do_gzip = False
# preprocess selection
input_selection = selection
selection = selector.process(input_selection)
#
r = DEFAULT_ERROR
lc_filename=string.lower(filename)
if format=='':
format = 'unknown'
# refactor following if/elif cascade
# with a dictionary lookup
if re.search("\.pdb$|\.ent$",lc_filename):
format = 'pdb'
elif re.search("\.cif$",lc_filename):
format = 'cif'
elif re.search("\.pqr$",lc_filename):
format = 'pqr'
elif re.search("\.mol$",lc_filename):
format = 'mol'
elif re.search("\.sdf$",lc_filename):
format = 'sdf'
elif re.search("\.pkl$",lc_filename):
format = 'pkl'
elif re.search("\.xyz$",lc_filename):
format = 'xyz'
elif re.search("\.mmd$",lc_filename):
format = 'mmod'
elif re.search("\.out$",lc_filename):
format = 'mmod'
elif re.search("\.dat$",lc_filename):
format = 'mmod'
elif re.search("\.mmod$",lc_filename):
format = 'mmod'
elif re.search("\.pmo$",lc_filename):
format = 'pmo'
elif re.search("\.pov$",lc_filename):
format = 'pov'
elif re.search("\.png$",lc_filename):
format = 'png'
elif re.search("\.pse$|\.psw$",lc_filename):
format = 'pse'
elif re.search("\.pze$|\.pzw$",lc_filename):
do_gzip = True
format = 'pse'
elif re.search("\.aln$",lc_filename):
format = 'aln'
elif re.search("\.fasta$",lc_filename):
format = 'fasta'
elif re.search("\.obj$",lc_filename):
format = 'obj'
elif re.search("\.mtl$",lc_filename):
format = 'mtl'
elif re.search("\.wrl$",lc_filename):
format = 'wrl'
elif re.search("\.dae$",lc_filename):
format = 'dae'
elif re.search("\.idtf$",lc_filename):
format = 'idtf'
elif re.search("\.mol2$",lc_filename):
format = 'mol2'
else:
format = str(format)
if format=='unknown':
if not quiet:
print " Save-Warning: Unrecognized file type -- defaulting to PDB format."
format='pdb'
filename = _self.exp_path(filename)
if format=='pdb': # standard PDB file
f=open(filename,"w")
if f:
st = ''
try:
_self.lock(_self)
st = _cmd.get_pdb(_self._COb,"("+str(selection)+")",int(state)-1,0,
str(ref),int(ref_state)-1,int(quiet))
if st != None:
r = DEFAULT_SUCCESS
finally:
_self.unlock(r,_self=_self)
f.write(st)
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
if format=='cif': # mmCIF
with open(filename, "w") as f:
st = get_cifstr(selection, state, int(quiet), _self=_self)
f.write(st)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='aln':
st = ''
try:
_self.lock(_self)
st = _cmd.get_seq_align_str(_self._COb,str(selection),int(state)-1,0,int(quiet))
if st != None:
r = DEFAULT_SUCCESS
finally:
_self.unlock(r,_self)
if st!=None:
f=open(filename,"w")
f.write(st)
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
else:
r = DEFAULT_ERROR
elif format=='fasta':
st = _self.get_fastastr(selection)
if st != None:
r = DEFAULT_SUCCESS
f=open(filename,"w")
f.write(st)
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
else:
r = DEFAULT_ERROR
elif format=='pqr': # PQR (modified PDB file)
f=open(filename,"w")
if f:
st = ''
try:
_self.lock(_self)
st = _cmd.get_pdb(_self._COb,"("+str(selection)+")",int(state)-1,1,
str(ref),int(ref_state)-1,int(quiet))
if st != None:
r = DEFAULT_SUCCESS
finally:
_self.unlock(r,_self)
f.write(st)
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='pkl': # python binary
io.pkl.toFile(_self.get_model(selection,state,ref,ref_state),filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='pkla': # ascii override
io.pkl.toFile(_self.get_model(selection,state,ref,ref_state),filename,bin=0)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='pse': # PyMOL session
filename = filename.replace("\\","/") # always use unix-like path separators
_self.set("session_file",filename,quiet=1)
if '(' in input_selection: # ignore selections
input_selection=''
if not quiet:
print " Save: Please wait -- writing session file..."
session = _self.get_session(input_selection, partial, quiet)
contents = cPickle.dumps(session, 1)
with (gzip.open if do_gzip else open)(filename, 'wb') as handle:
handle.write(contents)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=='mmod': # macromodel
io.mmd.toFile(_self.get_model(selection,state,ref,ref_state),filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format == 'xyz':
state = int(state)
buf = []
for i, (selection, state) in enumerate(
pymol.selecting.objsele_state_iter(selection, state)):
n_atoms_i = len(buf)
buf.append('') # natoms (deferred)
buf.append('') # comment
n = _self.iterate_state(state, selection,
'_buf.append("%s %f %f %f" % (elem, x, y, z))',
space={'_buf': buf})
buf[n_atoms_i] = str(n)
with open(filename, 'w') as handle:
print >> handle, '\n'.join(buf)
if not quiet:
print " Save: wrote %d states to \"%s\"." % (i + 1, filename)
elif format=='sdf':
state = int(state)
sdf = SDF(filename,'w')
for i, (selection, state) in enumerate(
pymol.selecting.objsele_state_iter(selection, state)):
rec = SDFRec(io.mol.toList(_self.get_model(selection,state,ref,ref_state))
+ ["$$$$\n"])
sdf.write(rec)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote %d states to \"%s\"." % (i + 1, filename)
elif format=='mol':
io.mol.toFile(_self.get_model(selection,state,ref,ref_state),filename)
r = DEFAULT_SUCCESS
if not quiet:
print " Save: wrote \""+filename+"\"."
elif format=="mol2":
state = int(state)
recList = []
entrycount = 0
for osele, ostate in pymol.selecting.objsele_state_iter(selection, state):
assign_atom_types(osele, "mol2", ostate, 1, _self)
recList.extend(io.mol2.toList(_self.get_model(osele,
ostate, ref, ref_state), selection=osele, state=ostate))
entrycount += 1
m = MOL2(cmd=cmd)
m.strToFile(recList,filename)
r = DEFAULT_SUCCESS
if not quiet:
print ' Save: wrote %d entries to "%s".' % (entrycount, filename)
elif format=='png':
r = _self.png(filename,quiet=quiet)
# refactor below to lift repeated code
elif format=='pov':
tup = _self.get_povray()
f=open(filename,"w")
f.write(tup[0])
f.write(tup[1])
f.flush()
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
r = DEFAULT_SUCCESS
elif format=='obj':
tup = _self.get_mtl_obj()
f=open(filename,"w")
f.write(tup[1])
f.flush()
f.close()
r = DEFAULT_SUCCESS
elif format=='mtl':
tup = _self.get_mtl_obj()
f=open(filename,"w")
f.write(tup[0])
f.flush()
f.close()
r = DEFAULT_SUCCESS
elif format=='wrl':
txt = _self.get_vrml()
f=open(filename,"w")
f.write(txt)
f.flush()
f.close()
if not quiet:
print " Save: wrote \""+filename+"\"."
r = DEFAULT_SUCCESS
elif format=='dae':
txt = _self.get_collada()
if txt:
with open(filename, "w") as f:
f.write(txt)
if not quiet:
print " Save: wrote \""+filename+"\"."
r = DEFAULT_SUCCESS
elif not quiet:
print " COLLADA export failed, no file written"
elif format=='idtf':
tup = _self.get_idtf()
f=open(filename,"w")
f.write(tup[0]);
f.write(tup[1]);
f.flush()
f.close()
if not quiet:
fov = float(cmd.get("field_of_view"))
dist = cmd.get_view()[11]
print " 3Daac=%3.1f, 3Droll=0, 3Dc2c=0 0 1, 3Droo=%1.2f, 3Dcoo=0 0 %1.2f"%(fov,-dist,dist)
print " Save: wrote \""+filename+"\"."
r = DEFAULT_SUCCESS
if _self._raising(r,_self): raise QuietException
return r
