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importing.py
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importing.py
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#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information.
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-*
#-* This is modified version by Koya Sakuma with foldcomp fcz loader
#-*
#Z* -------------------------------------------------------------------
if True:
import re
import os
import sys
import copy
import pymol
cmd = sys.modules["pymol.cmd"]
from . import selector
from . import colorprinting
from .cmd import _cmd, \
DEFAULT_ERROR, DEFAULT_SUCCESS, is_error, \
is_list, safe_list_eval, is_string, loadable
from .constants import _loadable
from pymol.creating import unquote
import foldcomp
def load_fcz(filename, object=None, state=0, *, _self=cmd):
with open(filename, "rb") as fcz:
fcz_binary = fcz.read()
(name, pdb) = foldcomp.decompress(fcz_binary)
if (object == None):
object = name
cmd.read_pdbstr(pdb, object)
def incentive_format_not_available_func(format=''):
raise pymol.IncentiveOnlyException(
"'%s' format not supported by this PyMOL build" % format)
from chempy import io
def filename_to_objectname(fname, *, _self=cmd):
oname, _, _, _ = filename_to_format(fname)
return _self.get_legal_name(oname)
def filename_to_format(filename):
filename = os.path.basename(filename)
pre, delim, ext = filename.rpartition('.')
if ext in ('gz', 'bz2',):
zipped = ext
pre, delim, ext = pre.rpartition('.')
else:
zipped = ''
if not pre:
pre = ext
ext = ext.lower()
if ext in ('brick', 'callback', 'cgo', 'model', 'plugin'):
# names of special loadables, not accepted as file extensions
format = ''
elif ext in ('ent', 'p5m'):
format = 'pdb'
elif ext in ('pze',):
zipped = 'gz'
format = 'pse'
elif ext in ('pzw',):
zipped = 'gz'
format = 'psw'
elif ext in ('mmd', 'out', 'dat',):
format = 'mmod'
elif ext in ('cc2',):
format = 'cc1'
elif ext in ('sd',):
format = 'sdf'
elif ext in ('rst7',):
format = 'rst'
elif ext in ('o', 'dsn6', 'omap',):
format = 'brix'
elif ext in ('maegz',):
zipped = 'gz'
format = 'mae'
elif ext in ('ph4',):
format = 'moe'
elif ext in ('spi',):
format = 'spider'
elif ext in ('pym', 'pyc',):
format = 'py'
elif ext in ('p1m', 'pim',):
format = 'pml'
elif ext in ('xml',):
format = 'pdbml'
elif ext in ('mmcif',):
format = 'cif'
elif re.match(r'pdb\d+$', ext):
format = 'pdb'
elif re.match(r'xyz_\d+$', ext):
format = 'xyz'
elif ext in ('dxbin',):
format = 'dx'
else:
format = ext
return pre, ext, format, zipped
def check_gromacs_trj_magic(filename):
colorprinting.warning('check_gromacs_trj_magic is deprecated')
return check_trj_magic(filename)[0] == 'trj'
def check_trj_magic(filename):
try:
magic = open(filename, 'rb').read(4)
if b'\xc9' in magic and b'\x07' in magic:
return 'trj', loadable.trj2
if magic in (b'CDF\001', b'CDF\002'):
return 'netcdf', loadable.plugin
except IOError as e:
print('trj magic test failed: ' + str(e))
return '', loadable.trj
def _guess_trajectory_object(candidate, _self):
# if candidate does not exist as a molecular object, return last
# structure (presumably most recently added)
onames = _self.get_object_list()
if onames and candidate not in onames:
return onames[-1]
return candidate
def auto_zoom(zoom, selection, state=0, *, _self=cmd):
if zoom > 0 or zoom < 0 and _self.get_setting_int("auto_zoom"):
_self.zoom(selection, state=state)
def set_session(session,partial=0,quiet=1,cache=1,steal=-1, *, _self=cmd):
# string implies compressed session data
if isinstance(session, bytes):
import zlib
session = io.pkl.fromString(zlib.decompress(session))
if steal<0:
steal = 1
elif steal<0:
steal = 0
# use the pymol instance to store state, not the code module
_pymol = _self._pymol
with _self.lockcm:
_cmd.set_session(_self._COb, session, int(partial), int(quiet))
try:
if 'session' not in session:
_pymol.session = pymol.Session_Storage()
elif steal:
_pymol.session = session.pop('session')
else:
_pymol.session = copy.deepcopy(session['session'])
if cache and session.get('cache'):
if steal:
_pymol._cache = session.pop('cache')
else:
_pymol._cache = copy.deepcopy(session['cache'])
error = None
for a in _pymol._session_restore_tasks:
assert a is not None
# don't stop on errors...try to complete anyway
# TODO _session_save_tasks use `is_error(<return-value>)`
# instead of `not <return-value>`
if not a(session, _self=_self):
error = f'session-restore-task "{a.__name__}" failed'
finally:
# if the movie contains commands...activate security
if _self.get_movie_locked() > 0:
_self.wizard("security")
if error:
raise pymol.CmdException(error)
def load_object(type,object,name,state=0,finish=1,discrete=0,
quiet=1,zoom=-1, *, _self=cmd):
'''
DESCRIPTION
"load_object" is a general developer function for loading Python objects
into PyMOL.
PYMOL API
cmd.load_object(type,object,name,state=0,finish=1,discrete=0,quiet=1)
type = one one of the numeric cmd.loadable types
object =
name = object name (string)
finish = perform (1) or defer (0) post-processing of structure after load
discrete = treat each state as an independent, unrelated set of atoms
quiet = suppress chatter (default is yes)
'''
with _self.lockcm:
r = _cmd.load_object(_self._COb,str(name),object,int(state)-1,
int(type),int(finish),int(discrete),
int(quiet),int(zoom))
return r
def load_brick(*arg, _self=cmd, **kw):
'''
Temporary routine for GAMESS-UK project.
'''
lst = [loadable.brick]
lst.extend(list(arg))
return _self.load_object(*lst, **kw)
def load_map(*arg, _self=cmd, **kw):
'''
Temporary routine for the Phenix project.
'''
lst = [loadable.chempymap]
lst.extend(list(arg))
return _self.load_object(*lst, **kw)
def space(space="", gamma=1.0, quiet=0, *, _self=cmd):
'''
DESCRIPTION
"space" selects a color palette (or color space).
USAGE
space space [, gamma]
ARGUMENTS
space = rgb, cmyk, or pymol: {default: rgb}
gamma = floating point gamma transformation
EXAMPLES
space rgb
space cmyk
space pymol
NOTES
Whereas computer displays use the RGB color space, computer
printers typically use the CMYK color space. The two spaces are
non-equivalent, meaning that certain RGB colors cannot be
expressed in the CMYK space and vice-versa. And as a result,
molecular graphics images prepared using RGB often turn out poorly
when converted to CMYK, with purplish blues or yellowish greens.
"space cmyk" forces PyMOL to restrict its use of the RGB color
space to subset that can be reliably converted to CMYK using
common tools such as Adobe Photoshop. Thus, what you see on the
screen is much closer to what you will get in print.
Analog video systems as well as digital video compression codecs
based on the YUV color space also have incompatibilities with RGB.
Oversaturated colors usually cause the most problems.
Although PyMOL lacks "space yuv", "space pymol" will help PyMOL
avoid oversaturated colors can cause problems when exporting
animations to video.
PYMOL API
cmd.space(string space, float gamma)
SEE ALSO
color
'''
if space == "":
filename = ""
else:
space = pymol.constants.space_sc.auto_err(space.lower(), 'space')
filename = pymol.constants.space_dict[space]
filename = _self.exp_path(filename)
with _self.lockcm:
return _cmd.load_color_table(_self._COb, filename, float(gamma),
int(quiet))
def load_callback(*arg, _self=cmd):
'''
DESCRIPTION
"load_callback" is used to load a generic Python callback object.
These objects are called every time the screen is updated and can be used
to trigger OpenGL rendering calls (such as with PyOpenGL).
PYMOL API
cmd.load_callback(object,name,state,finish,discrete)
'''
lst = [loadable.callback]
lst.extend(list(arg))
return _self.load_object(*lst)
def load_cgo(*arg, _self=cmd, **kw):
'''
DESCRIPTION
"load_cgo" is used to load a compiled graphics object, which is
actually a list of floating point numbers built using the constants
in the $PYMOL_PATH/modules/pymol/cgo.py file.
PYMOL API
cmd.load_cgo(object,name,state,finish,discrete)
'''
lst = [loadable.cgo]
lst.extend(list(arg))
if not is_list(lst[1]):
lst[1] = list(lst[1])
return _self.load_object(*lst, **kw)
def load_model(*arg, _self=cmd, **kw):
'''
DESCRIPTION
"load_model" reads a ChemPy model into an object
PYMOL API
cmd.load_model(model, object [,state [,finish [,discrete ]]])
'''
lst = [loadable.model]
lst.extend(list(arg))
return _self.load_object(*lst, **kw)
def load_traj(filename,object='',state=1,format='',interval=1,
average=1,start=1,stop=-1,max=-1,selection='all',image=1,
shift="[0.0,0.0,0.0]",plugin="", *, _self=cmd):
'''
DESCRIPTION
"load_traj" reads trajectory files.
Most of the trajectory formats listed here are supported:
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
USAGE
load_traj filename [,object [,state [,format [,interval [,average ]
[,start [,stop [,max [,selection [,image [,shift
]]]]]]]]]
ARGUMENTS
filename = str: path to trajectory file
object = str: name of the molecular object where the trajectory should be
appended as states {default: guess from filename or last object in list}
state = int: first object state to populate, or 0 to append after
last state {default: 1}
format = str: file format {default: guess from extension}
interval = int: interval to take frames from file {default: 1}
average = int: ? (trj only, possibly broken)
start = int: first frame to load from file {default: 1}
stop = int: last frame to load from file, or -1 to load all {default: -1}
max = int: maximum number of states to load, or 0 to load all {default: 0}
selection = str: atom selection to only load a subset of coordinates
{default: all}
image = 0/1: residue-based period image transformation (trj only)
shift = float-3: offset for image transformation {default: (0,0,0}
plugin = str: name of VMD plugin to use {default: guess from magic string
of from format}
NOTES
You must first load a corresponding topology file before attempting
to load a trajectory file.
PyMOL does not know how to wrap the truncated octahedron used by Amber
You will need to use the "ptraj" program first to do this.
The average option is not a running average. To perform this type of
average, use the "smooth" command after loading the trajectory file.
SEE ALSO
load
'''
with _self.lockcm:
ftype = -1
state = int(state)
interval = int(interval)
average = int(average)
start = int(start)
stop = int(stop)
max = int(max)
image = int(image)
shift = safe_list_eval(str(shift)) # dangerous
if is_list(shift):
shift = [float(shift[0]),float(shift[1]),float(shift[2])]
else:
shift = [float(shift),float(shift),float(shift)]
# preprocess selection
selection = selector.process(selection)
#
filename = unquote(filename)
noext, ext, format_guessed, zipped = filename_to_format(filename)
fname = _self.exp_path(filename)
if zipped:
raise pymol.CmdException('zipped (%s) trajectories not supported' % (zipped))
if not format:
format = format_guessed
if not plugin:
if format == 'trj':
plugin, ftype = check_trj_magic(fname)
else:
try:
ftype = int(format)
except:
plugin = _cmd.find_molfile_plugin(_self._COb, format, 0x2)
# get object name
oname = object.strip()
if not oname:
oname = _guess_trajectory_object(noext, _self)
if not len(oname): # safety
oname = 'obj01'
if ftype < 0 and not plugin:
raise pymol.CmdException("unknown format '%s'" % format)
return _cmd.load_traj(_self._COb, str(oname), fname, int(state) - 1, int(ftype),
int(interval),int(average),int(start),
int(stop),int(max),str(selection),
int(image),
float(shift[0]),float(shift[1]),
float(shift[2]),str(plugin))
def _processALN(fname,quiet=1, *, _self=cmd):
legal_dict = {}
seq_dict = {}
seq_order = []
header_seen = 0
for line in open(fname).readlines():
if not header_seen:
if line[0:7]=='CLUSTAL':
header_seen = 1
else:
key = line[0:16].strip()
if key!='':
legal_key = _self.get_legal_name(key)
if key not in legal_dict:
seq_order.append(legal_key)
legal_dict[key] = legal_key
key = legal_key
seq = line[16:].strip()
if seq != '':
seq_dict[key] = seq_dict.get(key,'') + seq
for key in seq_order:
raw_seq = seq_dict[key].replace('-','')
_self.fab(raw_seq, key, quiet=quiet)
def _processFASTA(fname, oname, quiet=1, *, _self=cmd):
legal_dict = {}
seq_dict = {}
seq_order = []
for line in open(fname).readlines():
line = line.strip()
if len(line):
if line[0:1] == '>':
key = line[1:].strip()
legal_key = _self.get_legal_name(key)
if key not in legal_dict:
seq_order.append(legal_key)
legal_dict[key] = legal_key
key = legal_key
elif key:
seq = line
if '-' in seq:
# sequence alignment
from pymol.seqalign import load_aln_multi
return load_aln_multi(fname, oname, quiet=quiet,
_self=_self)
seq_dict[key] = seq_dict.get(key,'') + seq
for key in seq_order:
raw_seq = seq_dict.get(key, '').replace('-','')
if not raw_seq:
colorprinting.warning(f'Empty sequence for key "{key}"')
continue
_self.fab(raw_seq, key, quiet=quiet)
def _processPWG(fname, *, _self=cmd):
r = DEFAULT_ERROR
import urllib.request as urllib
import shlex
try:
from .pymolhttpd import PymolHttpd
browser_flag = 0
launch_flag = 0
report_url = None
logging = 1
root = None
port = 0
wrap_native = 0
headers = []
if '://' in fname:
lines = urllib.urlopen(fname).readlines()
else:
lines = open(fname).readlines()
for line in lines:
line = line.strip()
if len(line) and line[0:1] != '#':
input = line.split(None,1)
if len(input) and input[0]!='#':
keyword = input[0].lower()
if keyword == 'port': # will be assigned dynamically if not specified
if len(input)>1:
port = int(input[1].strip())
launch_flag = 1
elif keyword == 'header':
a = shlex.split(input[1])
if len(a) != 3 or a[0] != 'add' or a[1].endswith(':'):
raise ValueError('header command must be: header add Some-Key "some value"')
headers.append(a[1:])
elif keyword == 'logging':
if len(input)>1:
logging = int(input[1].strip())
elif keyword == 'root': # must encode a valid filesystem path to local content
if len(input)>1:
root = input[1].strip()
root = _self.exp_path(root) # allow for env var substitution
if os.path.exists(root):
launch_flag = 1
else:
print("Error: requested path '%s' does not exist."%root)
else:
print("Error: missing path to root content")
elif keyword == 'browser':
# could perhaps interpret a browser name here
browser_flag = 1
elif keyword == 'launch': # launch the module named in the file (must exist!)
if len(input)>1:
mod_name = input[1]
try:
__import__(mod_name)
mod = sys.modules[mod_name]
if hasattr(mod,'__launch__'):
mod.__launch__(_self)
r = DEFAULT_SUCCESS
except:
colorprinting.print_exc()
print("Error: unable to launch web application'%s'."%mode_name)
elif keyword == 'report':
if len(input)>1:
report_url = input[1]
elif keyword == 'delete':
os.unlink(fname)
elif keyword == 'options':
# parsed during invocation
pass
elif keyword == 'wrap_native_return_types':
wrap_native = 1
else:
print("Error: unrecognized input: %s"%str(input))
if launch_flag:
server = PymolHttpd(port,root,logging,wrap_native,headers=headers)
if port == 0:
port = server.port # get the dynamically assigned port number
server.start()
if browser_flag: # fire up a local browser
import webbrowser
webbrowser.open("http://localhost:%d"%port,new=1)
r = DEFAULT_SUCCESS
else:
r = DEFAULT_SUCCESS
if report_url is not None: # report port back to server url (is this secure?)
try:
report_url = report_url + str(port)
print(" Reporting back pymol port via: '%s'"%report_url)
urllib.urlretrieve(report_url)
except:
print(" Report attempt may have failed.")
except ImportError:
colorprinting.print_exc()
if is_error(r):
print("Error: unable to handle PWG file")
return r
def _magic_check_cor_charmm(filename):
# http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/corplugin.html
# assume at least 2 title/comment lines, starting with *
with open(filename) as handle:
if (handle.readline().startswith('*') and
handle.readline().startswith('*')):
return True
return False
def _eval_func(func):
'''
Evaluate a "module:callable" signature, e.g. "os.path:dirname".
'''
if not isinstance(func, str):
return func
try:
m = __import__(func.split(':')[0])
except ImportError as e:
print(' Warning: ' + str(e))
return incentive_format_not_available_func
return eval(func.replace(':', '.'), {m.__name__: m}, {})
def load(filename, object='', state=0, format='', finish=1,
discrete=-1, quiet=1, multiplex=None, zoom=-1, partial=0,
mimic=1, object_props=None, atom_props=None, *, _self=cmd):
'''
DESCRIPTION
"load" can by used to read molecules, crystallographic maps and
other volumetric data, PyMOL sessions, and some other types of
content.
USAGE
load filename [, object [, state [, format [, finish [, discrete [, quiet
[, multiplex [, zoom [, partial [, mimic [, object_props
[, atom_props ]]]]]]]]]]]]
ARGUMENTS
filename = string: file path or URL
object = string: name of the object {default: filename prefix}
state = integer: number of the state into which
the content should be loaded, or 0 for append {default:0}
format = pdb, ccp4, etc. {default: use file extension}): format of
data file
EXAMPLES
load 1dn2.pdb
load file001.pdb, ligand
load http://delsci.com/sample.pdb
NOTES
The file extension is used to determine the format unless the
format is provided explicitly.
If an object name is specified, then the file is loaded into that
object. Otherwise, an object is created with the same name as the
file prefix.
If a state value is not specified, then the content is appended
after the last existing state (if any).
Supported molecular file formats include: pdb, mol, mol2, sdf,
xyz, and others.
Supported map formats include: xplor, ccp4, phi, and others.
All supported file formats are covered in the reference
documentation under File Formats.
PYMOL API
cmd.load(string filename, string object-name, integer state,
string format, int finish, int discrete, int quiet,
int multiplex, int zoom, int partial)
SEE ALSO
save, load_traj, fetch
'''
if object_props or atom_props:
print(' Warning: properties are not supported in Open-Source PyMOL')
with _self.lockcm:
plugin = ''
state = int(state)
finish = int(finish)
zoom = int(zoom)
discrete = int(discrete)
if multiplex is None:
multiplex=-2
# file format
try:
# user specified the type as an int
ftype = int(format)
format = loadable._reverse_lookup(format)
except ValueError:
format = str(format)
ftype = getattr(_loadable, format, -1)
if ftype in _self._load2str.values():
assert format.endswith('str')
colorprinting.warning(
' cmd.load(format="{}") is deprecated, use cmd.load_raw(format="{}")'
.format(format, format[:-3]))
return _self.load_raw(filename, format[:-3], object, state,
finish, discrete, quiet, multiplex, zoom)
filename = unquote(filename)
# analyze filename
noext, ext, format_guessed, zipped = filename_to_format(filename)
if ftype == -1:
if not format:
format = format_guessed
elif format.startswith('plugin'):
format, _, plugin = format.partition(':')
else:
ext = format
if format == 'pkl':
format = 'model' # legacy
ftype = getattr(_loadable, format, -1)
filename = _self.exp_path(filename)
# object name
object = str(object).strip()
if not object:
object = noext if noext else _self.get_unused_name('obj')
if format in ['dcd', 'dtr']:
# for trajectories, use most recently added structure
object = _guess_trajectory_object(object, _self)
# molfile plugins
if (ftype < 0 and format not in loadfunctions or
format == 'plugin' and not plugin):
plugin = _cmd.find_molfile_plugin(_self._COb, ext)
if not plugin:
raise pymol.CmdException('unsupported file type: ' + ext)
ftype = loadable.plugin
# special handling for trj files (autodetect AMBER versus GROMACS)
if ftype == loadable.trj:
plugin, ftype = check_trj_magic(filename)
if plugin:
plugin += ':2' # cPlugIOManager_traj
# special handling for cdr files (autodetect AMBER versus CHARMM)
if ftype == loadable.crd and _magic_check_cor_charmm(filename):
ftype = loadable.plugin
plugin = 'cor'
# generic forwarding to format specific load functions
func = loadfunctions.get(format, pymol.internal._load)
func = _eval_func(func)
kw_all = {
'filename': filename,
'fname': filename, # alt
'object': object,
'prefix': object, # alt
'state': state,
'format': format,
'finish': finish,
'discrete': discrete,
'quiet': quiet,
'multiplex': multiplex,
'zoom': zoom,
'partial': partial,
'mimic': mimic,
'object_props': object_props,
'atom_props': atom_props,
'_self': _self,
# for _load
'ftype': ftype,
'plugin': plugin,
'finfo': filename, # alt
'oname': object, # alt
}
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: loadfunctions[%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]
if 'contents' in sig.parameters:
kw['contents'] = _self.file_read(filename)
return func(**kw)
def load_pse(filename, partial=0, quiet=1, format='pse', *, _self=cmd):
try:
contents = _self.file_read(filename)
session = io.pkl.fromString(contents)
except AttributeError as e:
raise pymol.CmdException('PSE contains objects which cannot be unpickled (%s)' % str(e))
r = _self.set_session(session, quiet=quiet, partial=partial, steal=1)
if not partial:
_self.set("session_file",
# always use unix-like path separators
filename.replace("\\", "/"), quiet=1)
if ((format == 'psw' or
_self.get_setting_boolean("presentation")) and
_self.get_setting_boolean("presentation_auto_start")):
# set movie to first frame
if _self.get_movie_length():
_self.rewind()
# go to first scene
_self.scene("auto", "start", animate=0)
return r
def load_embedded(key=None, name=None, state=0, finish=1, discrete=1,
quiet=1, zoom=-1, multiplex=-2, object_props=None,
atom_props=None, *, _self=cmd):
'''
DESCRIPTION
"load_embedded" loads content previously defined in the current
PyMOL command script using the "embed" command.
USAGE
load_embedded [ key [, name [, state [, finish [, discrete [, quiet ]]]]]]
EXAMPLE
embed wats, pdb
HETATM 1 O WAT 1 2.573 -1.034 -1.721
HETATM 2 H1 WAT 1 2.493 -1.949 -1.992
HETATM 3 H2 WAT 1 2.160 -0.537 -2.427
HETATM 4 O WAT 2 0.705 0.744 0.160
HETATM 5 H1 WAT 2 -0.071 0.264 0.450
HETATM 6 H2 WAT 2 1.356 0.064 -0.014
embed end
load_embedded wats
NOTES
This approach only works with text data files.
'''
if object_props or atom_props:
print(' Warning: properties are not supported in Open-Source PyMOL')
list = _self._parser.get_embedded(key)
if list is None:
print("Error: embedded data '%s' not found."%key)
return DEFAULT_ERROR
if not name:
name = key if key else _self.cmd._parser.get_default_key()
return _self.load_raw(''.join(list[1]), list[0], name, state,
finish, discrete, quiet, multiplex, zoom)
def load_raw(content, format, object='', state=0, finish=1,
discrete=-1, quiet=1, multiplex=None, zoom=-1, *, _self=cmd):
'''
DESCRIPTION
API-only function for loading data from memory.
EXAMPLE
contents = open('example.mmtf', 'rb').read()
cmd.load_raw(contents, 'mmtf')
'''
if multiplex is None:
multiplex=-2
ftype = getattr(loadable, format, None)
if ftype is None:
assert format not in ('cif', 'mmtf', 'pdb', 'dx')
if not isinstance(content, bytes):
content = content.encode("utf-8")
import tempfile
fd, filename = tempfile.mkstemp()
try:
os.write(fd, content)
os.close(fd)
return _self.load(filename, object, state, format, finish,
discrete, quiet, multiplex, zoom)
finally:
os.unlink(filename)
with _self.lockcm:
return _cmd.load(_self._COb, str(object), None, content,
int(state) - 1, cmd._load2str.get(ftype, ftype),
int(finish), int(discrete),
int(quiet),int(multiplex),int(zoom))
def read_sdfstr(sdfstr,name,state=0,finish=1,discrete=1,quiet=1,
zoom=-1,multiplex=-2,object_props=None, *, _self=cmd):
'''
DESCRIPTION
"read_sdfstr" reads an MDL MOL format file as a string
PYMOL API ONLY
cmd.read_sdfstr( string molstr, string name, int state=0,
int finish=1, int discrete=1 )
NOTES
"state" is a 1-based state index for the object, or 0 to append.
"finish" is a flag (0 or 1) which can be set to zero to improve
performance when loading large numbers of objects, but you must
call "finish_object" when you are done.
"discrete" is a flag (0 or 1) which tells PyMOL that there will be
no overlapping atoms in the file being loaded. "discrete"
objects save memory but can not be edited.
'''
if object_props:
print(' Warning: properties are not supported in Open-Source PyMOL')
with _self.lockcm:
return _cmd.load(_self._COb, str(name), None, sdfstr, int(state) - 1,
loadable.sdf2str,int(finish),int(discrete),
int(quiet),int(multiplex),int(zoom))
def read_molstr(molstr,name,state=0,finish=1,discrete=1,quiet=1,
zoom=-1, *, _self=cmd):
'''
DESCRIPTION
"read_molstr" reads an MDL MOL format file as a string
PYMOL API ONLY
cmd.read_molstr( string molstr, string name, int state=0,
int finish=1, int discrete=1 )
NOTES
"state" is a 1-based state index for the object, or 0 to append.
"finish" is a flag (0 or 1) which can be set to zero to improve
performance when loading large numbers of objects, but you must
call "finish_object" when you are done.
"discrete" is a flag (0 or 1) which tells PyMOL that there will be
no overlapping atoms in the file being loaded. "discrete"
objects save memory but can not be edited.
'''
with _self.lockcm:
return _cmd.load(_self._COb, str(name), None, molstr,
int(state) - 1,
loadable.molstr,int(finish),int(discrete),
int(quiet),0,int(zoom))