def multisave(filename, pattern="all", state=-1,
append=0, format='', quiet=1, _self=cmd):
'''
DESCRIPTION
"multisave" will save a multi-entry PDB file.
Every object in the given selection (pattern) will have a HEADER and a
CRYST (if symmetry is defined) record, and is terminated with END.
Loading such a multi-entry PDB file into PyMOL will load each entry
as a separate object.
This behavior is different to the "save" command, where a multi-object
selection is written "flat" to a PDB file, without HEADER or CRYST
records.
ARGUMENTS
filename = string: file path to be written
pattern = str: atom selection (before 1.8.4: object name pattern)
state = int: object state (-1=current, 0=all) {default: -1}
append = 0/1: append to existing file {default: 0}
format = str: file format {default: guess from extension, or 'pdb'}
'''
from pymol.importing import filename_to_format
_, _, format_guessed, zipped = filename_to_format(filename)
if zipped:
raise pymol.CmdException(zipped + ' not supported with multisave')
if not format:
format = format_guessed or 'pdb'
if format == 'pmo':
raise pymol.CmdException('pmo format not supported anymore')
if format not in ('pdb', 'cif'):
raise pymol.CmdException(format + ' format not supported with multisave')
s = get_str(format, pattern, state, '', -1, 1, quiet, _self)
if s is None:
if _self._raising(): raise QuietException
return DEFAULT_ERROR
filename = _self.exp_path(filename)
with open(filename, 'a' if int(append) else 'w') as handle:
handle.write(s)
return DEFAULT_SUCCESS
def multisave(filename, pattern="all", state=-1,
append=0, format='', quiet=1, _self=cmd):
'''
DESCRIPTION
"multisave" will save a multi-entry PDB file.
Every object in the given selection (pattern) will have a HEADER and a
CRYST (if symmetry is defined) record, and is terminated with END.
Loading such a multi-entry PDB file into PyMOL will load each entry
as a separate object.
This behavior is different to the "save" command, where a multi-object
selection is written "flat" to a PDB file, without HEADER or CRYST
records.
ARGUMENTS
filename = string: file path to be written
pattern = str: atom selection (before 1.8.4: object name pattern)
state = int: object state (-1=current, 0=all) {default: -1}
append = 0/1: append to existing file {default: 0}
format = str: file format {default: guess from extension, or 'pdb'}
'''
from pymol.importing import filename_to_format
_, _, format_guessed, zipped = filename_to_format(filename)
if zipped:
raise pymol.CmdException(zipped + ' not supported with multisave')
if not format:
format = format_guessed or 'pdb'
if format == 'pmo':
raise pymol.CmdException('pmo format not supported anymore')
if format not in ('pdb', 'cif'):
raise pymol.CmdException(format + ' format not supported with multisave')
s = get_str(format, pattern, state, '', -1, 1, quiet, _self)
if s is None:
if _self._raising(): raise QuietException
return DEFAULT_ERROR
filename = _self.exp_path(filename)
with open(filename, 'a' if int(append) else 'w') as handle:
handle.write(s)
return DEFAULT_SUCCESS
def ext_get_primary(ext):
r'''
If `ext` is an alias for another extension, return the other, otherwise return `ext`
'''
try:
from pymol import importing
except ImportError:
print('import pymol failed')
return ext
return importing.filename_to_format('.' + ext)[2]
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, cif, 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
'''
quiet = int(quiet)
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
# analyze filename
from pymol.importing import filename_to_format, _eval_func
_, _, format_guessed, zipped = filename_to_format(filename)
filename = _self.exp_path(filename)
# file format
if not format:
if not format_guessed:
raise pymol.CmdException('Unrecognized file format')
format = format_guessed
# PyMOL session
if format in (
'pse',
'psw',
):
_self.set(
"session_file",
# always use unix-like path separators
filename.replace("\\", "/"),
quiet=1)
if not quiet:
print(" Save: Please wait -- writing session file...")
func_type4 = {
'mmod': io.mmd.toFile,
'pkl': io.pkl.toFile, # binary pickle
'pkla': lambda model, filename: io.pkl.toFile(
model, filename, bin=0), # ascii pickle
}
contents = None
if format in savefunctions:
# generic forwarding to format specific save functions
func = savefunctions[format]
func = _eval_func(func)
kw_all = {
'filename': filename,
'selection': selection,
'name': selection, # alt (get_ccp4str)
'state': state,
'format': format,
'ref': ref,
'ref_state': ref_state,
'quiet': quiet,
'partial': partial,
'_self': _self,
}
import inspect
sig = inspect.signature(func, follow_wrapped=False)
kw = {}
for n, param in sig.parameters.items():
if param.kind == inspect.Parameter.VAR_KEYWORD:
kw = kw_all
break
if param.kind == inspect.Parameter.VAR_POSITIONAL:
print('FIXME: savefunctions[%s]: *args' % (format))
elif param.kind == inspect.Parameter.POSITIONAL_ONLY:
raise Exception('positional-only arguments not supported')
elif n in kw_all:
kw[n] = kw_all[n]
contents = func(**kw)
if 'filename' in sig.parameters:
# assume function wrote directly to file and returned a status
return contents
elif format in func_type4:
func_type4[format](_self.get_model(selection, state, ref,
ref_state), filename)
r = DEFAULT_SUCCESS
else:
raise pymol.CmdException('File format not supported for export')
# function returned sequence of strings or bytes
if isinstance(contents, (tuple, list)) and contents:
contents = contents[0][:0].join(contents)
if cmd.is_string(contents):
if not isinstance(contents, bytes):
contents = contents.encode()
if zipped == 'gz':
import gzip
fopen = gzip.open
else:
fopen = open
if zipped == 'bz2':
import bz2
contents = bz2.compress(contents)
with fopen(filename, 'wb') as handle:
handle.write(contents)
r = DEFAULT_SUCCESS
if _self._raising(r): raise QuietException
if not quiet:
if r == DEFAULT_SUCCESS:
print(' Save: wrote "' + filename + '".')
else:
print(' Save-Error: no file written')
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, sdf, pkl, pkla, mmd, out,
dat, mmod, cif, 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
'''
quiet = int(quiet)
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
# analyze filename
from pymol.importing import filename_to_format, _eval_func
_, _, format_guessed, zipped = filename_to_format(filename)
filename = _self.exp_path(filename)
# file format
if not format:
if not format_guessed:
raise pymol.CmdException('Unrecognized file format')
format = format_guessed
# PyMOL session
if format in ('pse', 'psw',):
_self.set("session_file",
# always use unix-like path separators
filename.replace("\\", "/"), quiet=1)
if not quiet:
print(" Save: Please wait -- writing session file...")
func_type4 = {
'mmod': io.mmd.toFile,
'pkl': io.pkl.toFile, # binary pickle
'pkla': lambda model, filename: io.pkl.toFile(model, filename, bin=0), # ascii pickle
}
contents = None
if format in savefunctions:
# generic forwarding to format specific save functions
func = savefunctions[format]
func = _eval_func(func)
kw = {
'filename': filename,
'selection': selection,
'name': selection, # alt (get_ccp4str)
'state': state,
'format': format,
'ref': ref,
'ref_state': ref_state,
'quiet': quiet,
'partial': partial,
'_self': _self,
}
import inspect
spec = inspect.getargspec(func)
if spec.varargs:
print('FIXME: savefunctions[%s]: *args' % (format))
if not spec.keywords:
kw = dict((n, kw[n]) for n in spec.args if n in kw)
contents = func(**kw)
if 'filename' in spec.args:
# assume function wrote directly to file and returned a status
return contents
elif format in func_type4:
func_type4[format](_self.get_model(selection, state, ref, ref_state), filename)
r = DEFAULT_SUCCESS
else:
raise pymol.CmdException('File format not supported for export')
# function returned sequence of strings or bytes
if isinstance(contents, (tuple, list)) and contents:
contents = contents[0][:0].join(contents)
if cmd.is_string(contents):
if not isinstance(contents, bytes):
contents = contents.encode()
if zipped == 'gz':
import gzip
fopen = gzip.open
else:
fopen = open
if zipped == 'bz2':
import bz2
contents = bz2.compress(contents)
with fopen(filename, 'wb') as handle:
handle.write(contents)
r = DEFAULT_SUCCESS
if _self._raising(r,_self): raise QuietException
if not quiet:
if r == DEFAULT_SUCCESS:
print(' Save: wrote "' + filename + '".')
else:
print(' Save-Error: no file written')
return r
