def get_names(type='public_objects',enabled_only=0,selection="",_self=cmd):
'''
DESCRIPTION
"get_names" returns a list of object and/or selection names.
PYMOL API
cmd.get_names( [string: "objects"|"selections"|"all"|"public_objects"|"public_selections"] )
NOTES
The default behavior is to return only object names.
SEE ALSO
get_type, count_atoms, count_states
'''
selection = selector.process(selection)
# this needs to be replaced with a flag & masking scheme...
if type=='objects':
mode = 1
elif type=='selections':
mode = 2
elif type=='all':
mode = 0
elif type=='public':
mode = 3
elif type=='public_objects':
mode = 4
elif type=='public_selections':
mode = 5
elif type=='public_nongroup_objects':
mode = 6
elif type=='public_group_objects':
mode = 7
elif type=='nongroup_objects':
mode = 8
elif type=='group_objects':
mode = 9
else:
raise pymol.CmdException("unknown type: '{}'".format(type))
with _self.lockcm:
r = _cmd.get_names(_self._COb,int(mode),int(enabled_only),str(selection))
return r
def color_by_area(sele, mode="molecular", state=0, palette='rainbow', _self=cmd):
"""
DESCRIPTION
Colors molecule by surface area
ARGUMENTS
sele = str: atom selection
mode = str: "molecular" {default} or "solvent"
"""
asa = 1 if mode=="solvent" else 0
tmpObj = _self.get_unused_name("_tmp")
tmpSel = _self.get_unused_name("_sel")
orgSel = _self.get_unused_name("_org")
orgN = _self.select(orgSel, sele, 0)
_self.create(tmpObj, "byobj ?%s & ! solvent" % (orgSel), zoom=0)
tmpN = _self.select(tmpSel, '?%s in ?%s' % (tmpObj, orgSel), 0)
try:
if orgN != tmpN:
raise pymol.CmdException('color_by_area failed')
_self.set("dot_solvent", asa, tmpObj)
_self.set("dot_density", 3, tmpObj)
l = []
_self.get_area(tmpSel, load_b=1)
_self.spectrum("b", palette, tmpSel)
_self.iterate(tmpSel, "l_a(color)", space={'l_a': l.append})
_self.alter(orgSel, "color=l_n()", space={'l_n': getattr(iter(l), _next_method_name)})
_self.recolor(orgSel)
finally:
_self.delete(tmpSel)
_self.delete(tmpObj)
_self.delete(orgSel)
def alignto(target='',
method="cealign",
selection='',
quiet=1,
_self=cmd,
**kwargs):
"""
DESCRIPTION
"alignto" aligns all other loaded objects to the target
using the specified alignment algorithm.
USAGE
alignto target [, method [, quiet ]]
NOTES
Available alignment methods are "align", "super" and "cealign".
EXAMPLE
# fetch some calmodulins
fetch 1cll 1sra 1ggz 1k95, async=0
# align them to 1cll using cealign
alignto 1cll, method=cealign
alignto 1cll, object=all_to_1cll
SEE ALSO
extra_fit, align, super, cealign, fit, rms, rms_cur, intra_fit
"""
if not selection:
names = cmd.get_names("public_objects", 1)
if not names:
raise pymol.CmdException('no public objects')
selection = '%' + ' %'.join(names)
return extra_fit(selection, target, method, 0, quiet, _self, **kwargs)
def system(command, async_=0, _self=cmd, **kwargs):
'''
DESCRIPTION
"system" executes a command in a subshell under Unix or Windows.
USAGE
system command
PYMOL API
cmd.system(string command,int async=0)
NOTES
async can only be specified from the Python level (not the command language)
if async is 0 (default), then the result code from "system" is returned in r
if async is 1, then the command is run in a separate thread whose object is
returned
SEE ALSO
ls, cd, pwd
'''
async_ = int(kwargs.pop('async', async_))
if kwargs:
raise pymol.CmdException('unknown argument: ' + ', '.join(kwargs))
r = None
if async_:
r = threading.Thread(target=_cmd.system,args=(str(command),1))
r.start()
else:
r = _cmd.system(_self._COb,str(command),0)
return r # special meaning
def get_gltf(filename, quiet=1, *, _self=cmd):
'''
DESCRIPTION
"get_gltf" saves a gltf file representing the content
currently displayed.
PYMOL API
cmd.get_gltf()
'''
import shutil
exe = shutil.which('collada2gltf') or shutil.which('COLLADA2GLTF-bin')
if exe is None:
raise pymol.CmdException('could not find collada2gltf')
# https://github.com/schrodinger/pymol-open-source/issues/107
_self.set('collada_geometry_mode', 1, quiet=quiet)
r = _self.get_collada()
# write collada file
with open(filename, 'w') as handle:
handle.write(r)
import subprocess
result = subprocess.call([exe, '-i', filename, '-o', filename])
# convert collada file to gltf by using collada2gltf binary
if not quiet:
if result == 0:
print(' Save: wrote "' + filename + '".')
else:
print(' Save-Error: no file written')
return result
def cd(dir="~",complain=1,quiet=1):
'''
DESCRIPTION
"cd" changes the current working directory.
USAGE
cd <path>
SEE ALSO
pwd, ls, system
'''
dir = exp_path(dir)
try:
os.chdir(dir) # raises on error
if not quiet:
print(" cd: now in %s" % getcwdu())
except BaseException as e:
if complain:
raise pymol.CmdException(str(e))
return DEFAULT_SUCCESS
def fab(input,name=None,mode='peptide',resi=1,chain='',segi='',state=-1,
dir=1,hydro=-1,ss=0,async_=-1,quiet=1,_self=cmd, **kwargs):
'''
DESCRIPTION
Build a peptide
ARGUMENTS
input = str: sequence in one-letter code
name = str: name of object to create {default: }
ss = int: Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat
EXAMPLE
fab ACDEFGH
fab ACDEFGH, helix, ss=1
'''
async_ = int(kwargs.pop('async', async_))
if kwargs:
raise pymol.CmdException('unknown argument: ' + ', '.join(kwargs))
if async_ < 1:
r = _fab(input,name,mode,resi,chain,segi,
state,dir,hydro,ss,quiet,_self)
else:
fab_thread = threading.Thread(target=_fab, args=(input,name,mode,
resi,chain,
segi,state,dir,
hydro,ss,quiet,_self))
fab_thread.setDaemon(1)
fab_thread.start()
r = DEFAULT_SUCCESS
return r
def attach_fragment(selection, fragment, hydrogen, anchor, *, _self=cmd):
'''
ARGUMENTS
selection = str: Name of a single-atom selection. If no such named
selection exists, then create a new object with name `fragment`.
fragment = str: fragment name to load from fragment library
hydrogen = int: atom ID in fragment to fuse
anchor = int: (unused)
'''
remove_hydrogens = _self.get_setting_boolean("auto_remove_hydrogens")
if selection not in _self.get_names("selections"):
if fragment in _self.get_names("objects"):
raise pymol.CmdException("an object with that name already exists")
_self.fragment(fragment)
if remove_hydrogens:
_self.remove(f"(hydro and {fragment})")
else:
fragment_label = _self.get_unused_name(_prefix + "_attach_fragment")
_self.fragment(fragment, fragment_label, origin=0)
try:
_self.fuse(f"{fragment_label} and id {hydrogen}", f"({selection})",
1)
if remove_hydrogens:
_self.remove("(hydro and pkmol)")
elif _self.count_atoms('hydro and (neighbor pk2)'):
_self.h_fill()
finally:
_self.delete(fragment_label)
def dumpexcel(selection='all',
props='chain segi resi resn name b q',
state=STATELESS):
'''
DESCRIPTION
Open a new Excel spreadsheet with atom property data from the given
selection.
'''
try:
import xlwings
except ImportError:
raise pymol.CmdException('Requires xlwings (conda install xlwings)')
try:
sheet = xlwings.Book().sheets[0]
except IndexError:
sheet = None
if not isinstance(props, (list, tuple)):
props = props.split()
table = [props]
kwargs = {
'expression': '_append((' + ','.join(props) + '))',
'space': {
'_append': table.append
},
}
if state == STATELESS:
pymol.cmd.iterate(selection, **kwargs)
else:
pymol.cmd.iterate_state(state, selection, **kwargs)
xlwings.view(table, sheet)
def get_gltf(filename, quiet=1, _self=cmd):
'''
DESCRIPTION
"get_gltf" saves a gltf file representing the content
currently displayed.
PYMOL API
cmd.get_gltf()
'''
from distutils.spawn import find_executable
exe = find_executable('collada2gltf')
if exe is None:
raise pymol.CmdException('could not find collada2gltf')
COLLADA_VERSION = 2
r = _self.get_collada(COLLADA_VERSION)
# write collada file
with open(filename, 'w') as handle:
handle.write(r)
import subprocess
result = subprocess.call([exe, '-i', filename, '-o', filename])
# convert collada file to gltf by using collada2gltf binary
if not quiet:
if result == 0:
print(' Save: wrote "' + filename + '".')
else:
print(' Save-Error: no file written')
return result
def get_stereo_labels_schrodinger(molstr):
'''R/S labels with SCHRODINGER backend
'''
if 'SCHRODINGER' not in os.environ:
raise pymol.CmdException('SCHRODINGER environment variable not set')
import subprocess
import tempfile
schrun = os.path.join(os.environ['SCHRODINGER'], 'run')
script = os.path.join(os.path.dirname(__file__), 'schrodinger-helper.py')
filename = tempfile.mktemp('.mol')
args = [schrun, script, filename]
env = dict(os.environ)
env.pop('PYTHONEXECUTABLE', '') # messes up on Mac
with open(filename, 'w') as handle:
handle.write(molstr)
try:
p = subprocess.Popen(
args,
env=env,
universal_newlines=True,
stdin=subprocess.PIPE, # Windows fix
stderr=subprocess.PIPE, # Windows fix
stdout=subprocess.PIPE)
stdout, stderr = p.communicate()
finally:
os.unlink(filename)
if stderr:
print(stderr)
return stdout.splitlines()
def ramp_new(name,
map_name,
range=[-1.0, 0.0, 1.0],
color=['red', [1.0, 1.0, 1.0], 'blue'],
state=1,
selection='',
beyond=2.0,
within=6.0,
sigma=2.0,
zero=1,
quiet=1,
_self=cmd):
'''
DESCRIPTION
"ramp_new" creates a color ramp based on a map potential value or
based on proximity to a molecular object.
USAGE
ramp_new name, map_name [, range [, color [, state [, selection [,
beyond [, within [, sigma [, zero ]]]]]]]]
ARGUMENTS
name = string: name of the ramp object
map_name = string: name of the map (for potential) or molecular
object (for proximity)
range = list: values corresponding to slots in the ramp
color = list: colors corresponding to slots in the ramp
state = integer: state identifier
selection = selection: for automatic ranging
beyond = number: with automatic ranging, are we excluding
values beyond a certain distance from the selection?
within = number: with automatic ranging, are we only including
valuess within a certain distance from the selection?
sigma = number: with automatic ranging, how many standard
deviations from the mean do we go?
zero = integer: with automatic ranging, do we force the central
value to be zero?
EXAMPLES
ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
NOTES
Color ramps are extremely powerful but complicated to use.
In the simplest case, they can be used to color representations
based on the potential values found in a map object at the
corresponding positions in space.
In another simple case, representations can be colored based on
proximity to a target. Note that since ramp targets must
themselves be real objects (not merely selections), the "create"
command may be needed in order to generate an appropriate target.
In more complicated cases, they can be used to color
representations on one object based atoms found in another.
Ramps can operate recursively. In other words, the output color
from one ramp can be used as the input color for another. For
example, you could color by map potential within a certain
distance of the target object, beyond which, a uniform color is applied.
PYMOL API
def ramp_new(string name, string map_name, list range, list color,
int state, string selection, float beyond, float
within, float sigma, int zero, int quiet)
SEE ALSO
ramp_update, load, color, create, slice, gradient
'''
r = DEFAULT_ERROR
safe_color = str(color).strip()
if (safe_color[0:1] == "["): # looks like a list
color = safe_alpha_list_eval(str(safe_color))
else: # looks like a literal
color = str(color)
new_color = []
# preprocess selection
if selection != '':
selection = selector.process(selection)
# coerce range
try:
if isinstance(range, str):
range = safe_list_eval(range)
range = list(map(float, range))
except:
raise pymol.CmdException('invalid range')
if is_list(color):
for a in color:
if not is_list(a):
new_color.append(list(_self.get_color_tuple(
a, 4))) # incl negative RGB special colors
else:
new_color.append(a)
elif is_string(color):
new_color = ramp_spectrum_dict[ramp_spectrum_sc.auto_err(
str(color), 'ramp color spectrum')]
else:
new_color = int(color)
try:
_self.lock(_self)
r = _cmd.ramp_new(_self._COb, str(name), str(map_name), range,
new_color,
int(state) - 1, str(selection), float(beyond),
float(within), float(sigma), int(zero),
int(quiet))
_self._invalidate_color_sc(_self)
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
def map_generate(name,
reflection_file,
amplitudes,
phases,
weights="None",
reso_low=50.0,
reso_high=1.0,
quiet=1,
zoom=1,
_self=cmd):
'''
DESCRIPTION
"map_generate" generates a map object from a PDB object or selection and
reflection data.
Experimental use with caution.
USAGE
map_generate name, reflection_file, amplitudes, phases, weights [,
reso_low [, reso_high ]]
ARGUMENTS
name = string: name of the map object to create or modify
reflection_file = string: name of reflection file on disk; if None, then
PyMOL attempts to download the CIF file from the PDB.
Default = None; attempt to download from PDB.
amplitudes = string: fully qualified apmlitudes column name. Properly
qualified names are: project/crysta/column. For example,
KINASE/cryastl1/FWT.
phases = string: fully qualified phases column name. Properly
qualified names are: project/crystal/column. For example,
KINASE/crystal1/DELPHWT.
weights = string: fully qualified phases column name. Properly
qualified names are: project/crystal/column. For example,
KINASE/crystal1/FOM.
reso_low = float : minimum resolution; if set to equal max_reso, then
reso_low and reso_high will be read from the reflection file.
reso_high = float : maximum resolution; if set to equal min_reso then
reso_low and reso_high will be read from the reflection file.
NOTES
This function can be used to synthesize x-ray maps from the reflection data.
Supported reflection file formats are "mtz". Other formats coming soon.
New in PyMOL v1.4 for Mac and Linux.
'''
import subprocess
exe = 'mtz2ccp4_px'
quiet = int(quiet)
r = DEFAULT_ERROR
try:
_self.lock(_self)
if not os.path.isfile(reflection_file):
print(
" MapGenerate-Error: Could not find file '%s'.\n Please check the filename and try again."
% reflection_file)
raise pymol.CmdException
# TODO: work for CIF, MTZ, and CNS
from . import headering
mtzFile = headering.MTZHeader(reflection_file)
# FORMAT: crystal/dataset/column
_, datasetName, ampColName = ('//' + amplitudes).rsplit('/', 2)
# if datasetName is empty, take any dataset that has ampColName
for dataset in list(mtzFile.datasets.values()):
if (not datasetName or dataset["name"] == datasetName) and \
ampColName in dataset["cols"]:
break
else:
raise pymol.CmdException("no dataset found")
cellX, cellY, cellZ = dataset['x'], dataset['y'], dataset['z']
cellAlpha, cellBeta, cellGamma = dataset['alpha'], dataset[
'beta'], dataset['gamma']
if reso_low == reso_high:
reso_low, reso_high = mtzFile.reso_min, mtzFile.reso_max
space_group = mtzFile.space_group
phases = phases.rsplit('/', 1)[-1]
if not phases:
raise pymol.CmdException("phase name missing")
if weights and weights != "None":
weights = weights.rsplit('/', 1)[-1]
if not weights:
raise pymol.CmdException(
"Improperly formatted weights name")
else:
weights = ''
if not quiet:
print('Info: Generating map from columns', ampColName, phases,
weights)
print('Info: Resolution limits low=%.2f high=%.2f' %
(reso_low, reso_high))
tempFile = tempfile.NamedTemporaryFile(delete=False)
tempFileName = tempFile.name
tempFile.close()
r = _cmd.map_generate(_self._COb, str(name), str(reflection_file),
str(tempFileName), str(ampColName),
str(phases), str(weights), float(reso_low),
float(reso_high), str(space_group),
float(cellX), float(cellY), float(cellZ),
float(cellAlpha), float(cellBeta),
float(cellGamma), int(quiet), int(zoom))
# With NO_MMLIBS the C function call returns None.
# Try standalone executable instead.
if r is None:
args = [
str(arg) for arg in [
exe, space_group, cellX, cellY, cellZ, cellAlpha,
cellBeta, cellGamma, reso_high, reso_low,
reflection_file, ampColName, phases, weights,
tempFileName
]
]
subprocess.check_call(args)
r = tempFileName
if r != None:
if not quiet:
print("Loading map '%s'" % (name))
r = _self.load(r, name, format="ccp4", finish=1)
else:
print(' Error: Map generation failed')
os.remove(tempFileName)
except OSError as e:
raise pymol.CmdException('cannot run %s: %s' % (exe, e))
except subprocess.CalledProcessError as e:
raise pymol.CmdException('%s failed: %s' % (exe, e))
except ImportError:
print(
" MapGenerate-Error: Cannot import headering module. Cannot read MTZ file or make map."
)
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return name
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 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 = _self.get_str(format, pattern, state, '', -1, 1, quiet)
if s is None:
raise QuietException
filename = _self.exp_path(filename)
with open(filename, 'a' if int(append) else 'w') as handle:
handle.write(s)
return DEFAULT_SUCCESS
def png(filename,
width=0,
height=0,
dpi=-1.0,
ray=0,
quiet=1,
prior=0,
format=0,
*,
_self=cmd):
'''
DESCRIPTION
"png" saves a PNG format image file of the current display.
USAGE
png filename [, width [, height [, dpi [, ray]]]]
ARGUMENTS
filename = string: file path to be written
width = integer or string: width in pixels (without units), inches (in)
or centimeters (cm). If unit suffix is given, dpi argument is required
as well. If only one of width or height is given, the aspect ratio of
the viewport is preserved. {default: 0 (current)}
height = integer or string: height (see width) {default: 0 (current)}
dpi = float: dots-per-inch {default -1.0 (unspecified)}
ray = 0 or 1: should ray be run first {default: 0 (no)}
EXAMPLES
png image.png
png image.png, dpi=300
png image.png, 10cm, dpi=300, ray=1
NOTES
PNG is the only image format supported by PyMOL.
SEE ALSO
mpng, save
PYMOL API
cmd.png(string filename, int width, int height, float dpi,
int ray, int quiet)
'''
ray = int(ray)
PRIOR_TRY = -1
PRIOR_NO = 0
PRIOR_YES = 1
prior = int(prior)
assert prior in (PRIOR_TRY, PRIOR_YES, PRIOR_NO)
FORMAT_GUESS = -1
FORMAT_PNG = 0
FORMAT_PPM = 1
if format == 'png':
format = FORMAT_PNG
assert format in (FORMAT_PNG, FORMAT_PPM, FORMAT_GUESS)
if format == FORMAT_GUESS:
if filename and filename.endswith(".ppm"):
format = FORMAT_PPM
else:
format = FORMAT_PNG
if filename and not filename.startswith('\x01'):
if format == FORMAT_PNG and not filename.endswith(".png"):
filename += ".png"
filename = cmd.exp_path(filename)
dpi = float(dpi)
if dpi < 0:
dpi = _self.get_setting_float('image_dots_per_inch')
width = _unit2px(width, dpi)
height = _unit2px(height, dpi)
def func():
with _self.lockcm:
return _cmd.png(_self._COb, filename, int(width), int(height),
dpi, ray, int(quiet), prior, format)
if prior:
# fetch the prior image, without doing any work (fast-path / non-GLUT thread-safe)
r = func()
if r:
return r
if prior != PRIOR_TRY:
raise pymol.CmdException("no prior image available")
print("no prior image available, fall back to rendering")
prior = PRIOR_NO
if ray:
return func()
return _self._call_with_opengl_context(func)
def _get_mtl_obj(format, _self):
# TODO mtl not implemented, always returns empty string
if format == 'mtl':
raise pymol.CmdException('.MTL export not implemented')
i = {'mtl': 0, 'obj': 1}.get(format)
return _self.get_mtl_obj()[i]
def clean(selection,
present='',
state=-1,
fix='',
restrain='',
method='mmff',
async_=0,
save_undo=1,
message=None,
_self=cmd_module,
**kwargs):
'''
DESCRIPTION
Note: This operation is limited to 999 atoms.
Run energy minimization on the given selection, using an MMFF94
force field.
ARGUMENTS
selection = str: atom selection to minimize
present = str: selection of fixed atoms to restrain the minimization
state = int: object state {default: -1 (current)}
fix = UNUSED
restraing = UNUSED
method = UNUSED
async = 0/1: run in separate thread {default: 0}
save_undo = UNUSED
message = Message to display during async minimization
EXAMPLE
# minimize ligand in binding pocket
clean organic, all within 8 of organic
'''
if int(state) == 0:
raise pymol.CmdException('cleaning all states not supported')
async_ = int(kwargs.pop('async', async_))
if kwargs:
raise pymol.CmdException('unknown argument: ' + ', '.join(kwargs))
args = (selection, present, state, fix, restrain, method, save_undo,
message, _self)
if not async_:
return _clean(*args)
else:
try:
t = threading.Thread(target=_clean, args=args)
t.setDaemon(1)
t.start()
except:
traceback.print_exc()
return 0
def focal_blur(aperture=2.0,
samples=10,
ray=0,
filename='',
quiet=1,
_self=cmd):
'''
DESCRIPTION
Creates fancy figures by introducing a focal blur to the image.
The object at the origin will be in focus.
USAGE
focal_blur [ aperture [, samples [, ray [, filename ]]]]
ARGUMENTS
aperture = float: aperture angle in degrees {default: 2.0}
samples = int: number of images for averaging {default: 10}
ray = 0/1: {default: 0}
filename = str: write image to file {default: temporary}
AUTHORS
Jarl Underhaug, Jason Vertrees and Thomas Holder
EXAMPLES
focal_blur 3.0, 50
'''
from tempfile import mkdtemp
from shutil import rmtree
from math import sin, cos, pi, sqrt
try:
import Image
except ImportError:
try:
from PIL import Image
except ImportError:
raise pymol.CmdException(
"Python Image Library (PIL) not available")
aperture, samples = float(aperture), int(samples)
ray, quiet = int(ray), int(quiet)
avg = None
handle_list = []
# make sure we have a still image
_self.mstop()
_self.unset('rock')
_self.unset('text')
# we need at least two samples
if samples < 2:
raise pymol.CmdException("need samples > 1")
# Get the orientation of the camera and the light
view = _self.get_view()
lights_names = [
'light', 'light2', 'light3', 'light4', 'light5', 'light6',
'light7', 'light8', 'light9'
]
lights = [
_self.get_setting_tuple(lights_names[i])[1]
for i in range(_self.get_setting_int('light_count') - 1)
]
# Create a temporary directory
tmpdir = mkdtemp()
try:
# Rotate the camera and the light in order to create the blur
for frame in range(samples):
# Populate angles as Fermat's spiral
theta = frame * pi * 110.0 / 144.0
radius = 0.5 * aperture * sqrt(frame / float(samples - 1))
x = cos(theta) * radius
y = sin(theta) * radius
xr = x / 180.0 * pi
yr = y / 180.0 * pi
# Rotate the camera
_self.turn('x', x)
_self.turn('y', y)
# Rotate the light
for light, light_name in zip(lights, lights_names):
ly = light[1] * cos(xr) - light[2] * sin(xr)
lz = light[2] * cos(xr) + light[1] * sin(xr)
lx = light[0] * cos(yr) + lz * sin(yr)
lz = lz * cos(yr) - lx * sin(yr)
_self.set(light_name, [lx, ly, lz])
# Save the image to temporary directory
curFile = "%s/frame-%04d.png" % (tmpdir, frame)
_self.png(curFile, ray=ray, quiet=1)
if not quiet:
print(" Created frame %i/%i (%0.0f%%)" %
(frame + 1, samples, 100 * (frame + 1) / samples))
# Create the average/blured image
handle = open(curFile, "rb")
handle_list.append(handle)
img = Image.open(handle)
avg = Image.blend(avg, img, 1.0 / (frame + 1)) if avg else img
del img
# Return the camera and the light to the original orientation
_self.set_view(view)
for light, light_name in zip(lights, lights_names):
_self.set(light_name, light)
if not filename:
filename = '%s/avg.png' % (tmpdir)
# Load the blured image
avg.save(filename)
_self.load(filename)
finally:
del avg
# needed for Windows
for handle in handle_list:
handle.close()
# Delete the temporary files
rmtree(tmpdir)
def extra_fit(selection='(all)',
reference='',
method='align',
zoom=1,
quiet=0,
*,
_self=cmd,
**kwargs):
'''
DESCRIPTION
Like "intra_fit", but for multiple objects instead of
multiple states.
ARGUMENTS
selection = string: atom selection of multiple objects {default: all}
reference = string: reference object name {default: first object in selection}
method = string: alignment method (command that takes "mobile" and "target"
arguments, like "align", "super", "cealign" {default: align}
... extra arguments are passed to "method"
SEE ALSO
align, super, cealign, intra_fit, util.mass_align
'''
zoom, quiet = int(zoom), int(quiet)
sele_name = _self.get_unused_name('_')
_self.select(sele_name, selection, 0)
models = _self.get_object_list(sele_name)
if not reference:
reference = models[0]
models = models[1:]
elif reference in models:
models.remove(reference)
else:
_self.select(sele_name, reference, merge=1)
if _self.is_string(method):
if method in _self.keyword:
method = _self.keyword[method][0]
else:
raise pymol.CmdException(method, 'Unknown method')
for model in models:
x = method(mobile='?%s & ?%s' % (sele_name, model),
target='?%s & ?%s' % (sele_name, reference),
**kwargs)
if not quiet:
if _self.is_sequence(x):
print('%-20s RMSD = %8.3f (%d atoms)' %
(model, x[0], x[1]))
elif isinstance(x, float):
print('%-20s RMSD = %8.3f' % (model, x))
elif isinstance(x, dict) and 'RMSD' in x:
natoms = x.get('alignment_length', 0)
suffix = (' (%s atoms)' % natoms) if natoms else ''
print('%-20s RMSD = %8.3f' % (model, x['RMSD']) + suffix)
else:
print('%-20s' % (model, ))
if zoom:
_self.zoom(sele_name)
_self.delete(sele_name)
def callout(name,
label,
pos='',
screen='auto',
state=-1,
color='front',
quiet=1,
_wiz=0,
_self=cmd):
'''
DESCRIPTION
Create a new screen-stabilized callout object.
ARGUMENTS
name = str: object name
label = str: label text
pos = str or list: anchor in model space as 3-float coord list or atom
selection. If empty, don't draw an arrow. {default: }
screen = str or list: position on screen as 2-float list between [-1,-1]
(lower left) and [1,1] (upper right) or "auto" for smart placement.
{default: auto}
'''
state, quiet = int(state), int(quiet)
sele = ''
if state == -1:
state = _self.get_setting_int('state')
if isinstance(pos, basestring):
if ',' in pos:
pos = _self.safe_list_eval(pos)
else:
sele, pos = pos, None
if isinstance(screen, basestring):
if screen == 'auto':
screen = (0.0, 0.0)
else:
screen = _self.safe_list_eval(screen)
if len(screen) == 2:
screen += (0.0, )
elif len(screen) != 3:
raise pymol.CmdException('invalid screen argument')
if isinstance(screen[0], int):
relative_mode = 2 # pixels
else:
relative_mode = 1 # [-1.0 .. +1.0]
if not name:
name = _self.get_unused_name('callout', 1)
_self.pseudoatom(name,
sele,
'CALL',
'CAL',
str(_self.count_atoms('?' + name) + 1),
'C',
'CALL',
'PS',
0.5,
color=color,
label=label,
pos=pos,
state=state,
quiet=quiet)
expr = ('('
's["label_relative_mode"],'
's["label_connector"],'
's["label_connector_color"],'
's["label_color"],'
') = (%d, %s, "default", "default",)' % (
relative_mode,
bool(pos or sele),
))
expr_state = ('(' 's["label_screen_point"],' ') = (%s,)' % (screen, ))
_self.alter("last " + name, expr)
_self.alter_state(state, "last " + name, expr_state)
if int(_wiz):
_self.wizard('labeledit', 'last ' + name)
def load_mtz_cctbx(filename,
prefix='',
amplitudes='',
phases='',
quiet=1,
_self=pymol.cmd):
'''
DESCRIPTION
Load maps from an MTZ file, using iotbx (via "cctbx.python").
Map objects will be named: <prefix>_<amplitudes>_<phases>
ARGUMENTS
filename = str: path to mtz file
prefix = str: object name prefix for new map objects
amplitudes = str: amplitudes column label (optional). If not given,
load all maps. If given, the 'phases' argument is required as well.
phases = str: phases column label (required if and only if
amplitudes is given as well)
'''
import subprocess
import shutil
if not prefix:
prefix = os.path.basename(filename).rpartition('.')[0]
args = [filename, prefix, amplitudes, phases]
try:
# try with "cctbx.python"
process = subprocess.Popen(['cctbx.python', this_file] + args,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = process.communicate()
if stderr:
raise pymol.CmdException(stderr)
outdir = stdout.strip()
if not isinstance(outdir, str):
outdir = outdir.decode()
except OSError:
try:
# try inside this Python interpreter
outdir = mtz2ccp4maps(*args)
except ImportError:
raise pymol.CmdException(
"can't import iotbx and can't run cctbx.python")
# normalization is done by apply_sigma_scaling()
normalize = _self.get_setting_int('normalize_ccp4_maps')
if normalize:
_self.set('normalize_ccp4_maps', 0)
for mapfilename in os.listdir(outdir):
_self.load(os.path.join(outdir, mapfilename), quiet=quiet)
if normalize:
_self.set('normalize_ccp4_maps', normalize)
shutil.rmtree(outdir)
def set_key(key, fn=None, arg=(), kw={}, _self=cmd):
'''
DESCRIPTION
"set_key" binds a specific python function to a key press.
New in PyMOL 1.6.1: second argument can also be a string in PyMOL
command syntax.
USAGE
set_key key, command
EXAMPLE
set_key F1, as cartoon, polymer; as sticks, organic
PYMOL API (ONLY)
cmd.set_key( string key, function fn, tuple arg=(), dict kw={})
PYTHON EXAMPLE
from pymol import cmd
def color_blue(object): cmd.color("blue",object)
cmd.set_key( 'F1' , color_blue, ( "object1" ) )
// would turn object1 blue when the F1 key is pressed and
cmd.set_key( 'F2' , color_blue, ( "object2" ) )
// would turn object2 blue when the F2 key is pressed.
cmd.set_key( 'CTRL-C' , cmd.zoom )
cmd.set_key( 'ALT-A' , cmd.turn, ('x',90) )
KEYS WHICH CAN BE REDEFINED
F1 to F12
left, right, pgup, pgdn, home, insert
CTRL-A to CTRL-Z
ALT-0 to ALT-9, ALT-A to ALT-Z
SEE ALSO
button, alias
'''
if fn is None:
def decorator(func):
set_key(key, func, arg, kw, _self)
return func
return decorator
if is_string(fn):
if arg or kw:
raise ValueError('arg and kw must be empty if fn is string')
else:
fn = (fn, arg, kw)
mod, _, pat = key.rpartition('-')
if mod not in internal.modifier_keys:
raise pymol.CmdException("not a valid modifier key: '%s'." % mod)
if len(pat) > 1:
if pat[0] != 'F':
pat = pat.lower()
key = pat if not mod else (mod + '-' + pat)
if pat not in internal.special_key_names:
raise pymol.CmdException("special '%s' key not found." % pat)
elif not mod:
raise pymol.CmdException("Can't map regular letters.")
elif mod == 'SHFT':
raise pymol.CmdException("Can't map regular letters with SHFT.")
_self.key_mappings[key] = fn
return DEFAULT_SUCCESS
def assign_stereo(selection='all',
state=-1,
method='',
quiet=1,
prop='stereo',
_self=cmd):
'''
DESCRIPTION
Assign "stereo" atom property (R/S stereochemistry).
Requires either a Schrodinger Suite installation (SCHRODINGER
environment variable set) or RDKit (rdkit Python module).
USAGE
assign_stereo [selection [, state [, method ]]]
ARGUMENTS
selection = str: atom selection {default: all}
state = int: object state {default: -1 (current)}
method = schrodinger or rdkit: {default: try both}
'''
state, quiet = int(state), int(quiet)
# method check
if method and method not in methods:
raise pymol.CmdException("method '{}' not in {}".format(
method, list(methods)))
# alt code check
alt_codes = set()
cmd.iterate('({})&!alt ""'.format(selection),
'alt_codes.add(alt)',
space={'alt_codes': alt_codes})
if len(alt_codes) > 1:
alt_codes = sorted(alt_codes)
selection = '({}) & alt +{}'.format(selection, alt_codes[0])
print(' Warning: only using first alt code of: {}'.format(alt_codes))
molstr = _self.get_str('mol', selection, state)
if method:
labels = methods[method](molstr)
else:
for method in ('rdkit', 'schrodinger'):
try:
labels = methods[method](molstr)
except BaseException as e:
print(' Method "{}" not available ({})'.format(
method,
str(e).strip()))
else:
print(' Using method={}'.format(method))
break
else:
raise pymol.CmdException('need SCHRODINGER or rdkit')
# apply new labels
_self.alter_state(state,
selection,
prop + ' = next(label_iter)',
space={
'label_iter': iter(labels),
'next': next
})
def elbow_angle(obj, light='L', heavy='H', limit_l=107, limit_h=113, draw=0):
"""
DESCRIPTION
Calculates the integer elbow angle of an antibody Fab complex and
optionally draws a graphical representation of the vectors used to
determine the angle.
ARGUMENTS
obj = string: object
light/heavy = strings: chain ID of light and heavy chains, respectively
limit_l/limit_h = integers: residue numbers of the last residue in the
light and heavy chain variable domains, respectively
draw = boolean: Choose whether or not to draw the angle visualization
REQUIRES: com.py, transformations.py, numpy (see above)
"""
# store current view
orig_view = cmd.get_view()
limit_l = int(limit_l)
limit_h = int(limit_h)
draw = int(draw)
# for temp object names
tmp_prefix = "tmp_elbow_"
prefix = tmp_prefix + obj + '_'
# names
vl = prefix + 'VL'
vh = prefix + 'VH'
cl = prefix + 'CL'
ch = prefix + 'CH'
# selections
vl_sel = 'polymer and %s and chain %s and resi 1-%i' % (obj, light,
limit_l)
vh_sel = 'polymer and %s and chain %s and resi 1-%i' % (obj, heavy,
limit_h)
cl_sel = 'polymer and %s and chain %s and not resi 1-%i' % (obj, light,
limit_l)
ch_sel = 'polymer and %s and chain %s and not resi 1-%i' % (obj, heavy,
limit_h)
v_sel = '((' + vl_sel + ') or (' + vh_sel + '))'
c_sel = '((' + cl_sel + ') or (' + ch_sel + '))'
# create temp objects
cmd.create(vl, vl_sel)
cmd.create(vh, vh_sel)
cmd.create(cl, cl_sel)
cmd.create(ch, ch_sel)
# superimpose vl onto vh, calculate axis and angle
Rv = calc_super_matrix(vl, vh)
angle_v, direction_v, point_v = transformations.rotation_from_matrix(Rv)
# superimpose cl onto ch, calculate axis and angle
Rc = calc_super_matrix(cl, ch)
angle_c, direction_c, point_c = transformations.rotation_from_matrix(Rc)
# delete temporary objects
cmd.delete(vl)
cmd.delete(vh)
cmd.delete(cl)
cmd.delete(ch)
# if dot product is positive, angle is acute
if (numpy.dot(direction_v, direction_c) > 0):
direction_c = direction_c * -1 # ensure angle is > 90 (need to standardize this)
# TODO: make both directions point away from the elbow axis.
elbow = int(
numpy.degrees(numpy.arccos(numpy.dot(direction_v, direction_c))))
# while (elbow < 90):
# elbow = 180 - elbow # limit to physically reasonable range
# compare the direction_v and direction_c axes to the vector defined by
# the C-alpha atoms of limit_l and limit_h of the original fab
hinge_l_sel = "%s//%s/%s/CA" % (obj, light, limit_l)
hinge_h_sel = "%s//%s/%s/CA" % (obj, heavy, limit_h)
try:
hinge_l = cmd.get_atom_coords(hinge_l_sel)
hinge_h = cmd.get_atom_coords(hinge_h_sel)
except pymol.CmdException:
# Either hinge_l_sel or hinge_h_sel atom did not exist.
raise pymol.CmdException(
'Unable to calculate elbow angle. Please check '
'your limit and chain selections and try again.')
hinge_vec = numpy.array(hinge_h) - numpy.array(hinge_l)
test = numpy.dot(hinge_vec, numpy.cross(direction_v, direction_c))
if (test > 0):
elbow = 360 - elbow
print(" Elbow angle: %i degrees" % elbow)
if (draw == 1):
# there is probably a more elegant way to do this, but
# it works so I'm not going to mess with it for now
pre = obj + '_elbow_'
# draw hinge vector
cmd.pseudoatom(pre + "hinge_l", pos=hinge_l)
cmd.pseudoatom(pre + "hinge_h", pos=hinge_h)
cmd.distance(pre + "hinge_vec", pre + "hinge_l", pre + "hinge_h")
cmd.set("dash_gap", 0)
# draw the variable domain axis
com_v = COM(v_sel)
start_v = [a - 10 * b for a, b in zip(com_v, direction_v)]
end_v = [a + 10 * b for a, b in zip(com_v, direction_v)]
cmd.pseudoatom(pre + "start_v", pos=start_v)
cmd.pseudoatom(pre + "end_v", pos=end_v)
cmd.distance(pre + "v_vec", pre + "start_v", pre + "end_v")
# draw the constant domain axis
com_c = COM(c_sel)
start_c = [a - 10 * b for a, b in zip(com_c, direction_c)]
end_c = [a + 10 * b for a, b in zip(com_c, direction_c)]
cmd.pseudoatom(pre + "start_c", pos=start_c)
cmd.pseudoatom(pre + "end_c", pos=end_c)
cmd.distance(pre + "c_vec", pre + "start_c", pre + "end_c")
# customize appearance
cmd.hide("labels", pre + "hinge_vec")
cmd.hide("labels", pre + "v_vec")
cmd.hide("labels", pre + "c_vec")
cmd.color("green", pre + "hinge_l")
cmd.color("red", pre + "hinge_h")
cmd.color("black", pre + "hinge_vec")
cmd.color("black", pre + "start_v")
cmd.color("black", pre + "end_v")
cmd.color("black", pre + "v_vec")
cmd.color("black", pre + "start_c")
cmd.color("black", pre + "end_c")
cmd.color("black", pre + "c_vec")
# draw spheres
cmd.show("spheres", pre + "hinge_l or " + pre + "hinge_h")
cmd.show("spheres", pre + "start_v or " + pre + "start_c")
cmd.show("spheres", pre + "end_v or " + pre + "end_c")
cmd.set("sphere_scale", 2)
cmd.set("dash_gap", 0, pre + "hinge_vec")
cmd.set("dash_width", 5)
cmd.set("dash_radius", 0.3)
# group drawing objects
cmd.group(pre, pre + "*")
# restore original view
cmd.set_view(orig_view)
return 0
def attach_amino_acid(selection,amino_acid,center=0,animate=-1,object="",hydro=-1,ss=-1,_self=cmd):
'''
ARGUMENTS
selection = str: named selection of single N or C atom
amino_acid = str: fragment name to load from fragment library
center = bool: center on new terminus (pk1)
animate = int: animate centering
object = str: name of new object (if selection is none)
hydro = int (-1/0/1): keep hydrogens
ss = int: Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat
'''
# global ___total, ___seg1, ___seg2, ___seg3, ___pass, ___last
# ___mark0 = ___time()
# ___mark1 = ___time()
# ___mark2 = ___time()
# ___entry = ___time()
r = DEFAULT_SUCCESS
ss = int(ss)
center = int(center)
if hydro<0:
hydro = not int(_self.get_setting_boolean("auto_remove_hydrogens"))
if (selection not in _self.get_names('all')
if selection == 'pk1' # legacy, calling functions should pass '?pk1'
else _self.count_atoms(selection) == 0):
if object == "":
object = amino_acid
# create new object
if amino_acid in _self.get_names("objects"):
raise pymol.CmdException("an object with that name already exists")
r = _self.fragment(amino_acid,object)
if not hydro:
_self.remove("(hydro and %s)"%object)
if _self.count_atoms("((%s) and name C)"%object):
_self.edit("((%s) and name C)"%object)
elif _self.count_atoms("((%s) and name N)"%object):
_self.edit("((%s) and name N)"%object)
elif _self.select(tmp_connect,"(%s) & elem N,C"%selection) != 1:
_self.delete(tmp_wild)
raise pymol.CmdException("invalid connection point: must be one atom, name N or C.")
elif amino_acid in ["nhh","nme"] and _self.select(tmp_connect,"(%s) & elem C"%selection) != 1:
_self.delete(tmp_wild)
raise pymol.CmdException("invalid connection point: must be C for residue '%s'"%(amino_acid))
elif amino_acid in ["ace"] and _self.select(tmp_connect,"(%s) & elem N"%selection) != 1:
_self.delete(tmp_wild)
raise pymol.CmdException("invalid connection point: must be N for residue '%s'"%(amino_acid))
else:
if ss<0:
ss = _self.get_setting_int("secondary_structure")
if ss:
if ss==1: # helix
phi=-57.0
psi=-47.0
elif ss==2: # antipara-beta
phi=-139.0
psi=135.0
elif ss==3: # para-beta
phi=-119.0
psi=113.0
else:
phi=180.0
psi=180.0
_self.fragment(amino_acid,tmp_editor, origin=0)
if _self.count_atoms("elem N",domain=tmp_connect):
tmp = [ None ]
_self.iterate(tmp_connect,"tmp[0]=resv", space={ 'tmp' : tmp })
tmp[0] = str(tmp[0]-1) # counting down
_self.alter(tmp_editor,"resi=tmp[0]",space={ 'tmp' : tmp})
_self.set_geometry(tmp_connect, 3, 3) # make nitrogen planar
_self.fuse("(%s and name C)"%(tmp_editor),tmp_connect,2)
_self.select(tmp_domain, "byresi (pk1 | pk2)")
if not hydro:
_self.remove("(pkmol and hydro)")
if ((_self.select(tmp1,"?pk1",domain=tmp_domain)==1) and
(_self.select(tmp2,"?pk2",domain=tmp_domain)==1)):
if ((_self.select(tmp3,"(name CA,CH3 & nbr. ?pk1)",domain=tmp_domain)==1) and
(_self.select(tmp4,"(name CA,CH3 & nbr. ?pk2)",domain=tmp_domain)==1)):
_self.set_dihedral(tmp4,tmp2,tmp1,tmp3,180.0)
if hydro:
_self.h_fix(tmp2) # fix hydrogen position
if ss:
if amino_acid[0:3]!='pro':
if ((_self.select(tmp4,
"(!(resn PRO) & name C & nbr. (name CA & nbr. "+tmp2+"))",
domain=tmp_domain)==1) and
(_self.select(tmp3,
"(!(resn PRO) & name CA & nbr. "+tmp2+")",
domain=tmp_domain)==1)):
_self.set_dihedral( # PHI
tmp4, # C
tmp3, # CA
tmp2, # N
tmp1, # C
phi)
if ((_self.select(tmp4,"(name N & nbr. (name CA & nbr. "+tmp1+"))",
domain=tmp_domain)==1) and
(_self.select(tmp3,"(name CA & nbr. "+tmp1+")",domain=tmp_domain)==1)):
_self.set_dihedral( # PSI (n-1)
tmp2, # N
tmp1, # C
tmp3, # CA
tmp4, # N
psi)
sele = ("(name N & (byres nbr. %s) &! (byres %s))"% (tmp_connect,tmp_connect))
if _self.select(tmp1,sele,domain=tmp_domain):
_self.edit(tmp1)
if center:
_self.center(tmp1,animate=animate)
elif _self.count_atoms("elem C",domain=tmp_connect): # forward
tmp = [ None ]
_self.iterate(tmp_connect,"tmp[0]=resv", space={ 'tmp' : tmp })
tmp[0] = str(tmp[0]+1) # counting up
_self.alter(tmp_editor,"resi=tmp[0]",space={ 'tmp' : tmp})
_self.set_geometry(tmp_editor + " & name N", 3, 3) # make nitrogen planar
_self.fuse("(%s and name N)"%tmp_editor,tmp_connect,2)
_self.select(tmp_domain, "byresi (pk1 | pk2)")
if not hydro:
_self.remove("(pkmol and hydro)")
if (( _self.select(tmp1,"?pk1",domain=tmp_domain)==1) and
( _self.select(tmp2,"?pk2",domain=tmp_domain)==1)):
# ___mark1 = ___time()
if ((_self.select(tmp3,"(name CA,CH3 & nbr. ?pk1)",domain=tmp_domain)==1) and
(_self.select(tmp4,"(name CA,CH3 & nbr. ?pk2)",domain=tmp_domain)==1)):
_self.set_dihedral(tmp4,tmp2,tmp1,tmp3,180.0)
if hydro:
_self.h_fix("pk1") # fix hydrogen position
if ss:
if hydro and amino_acid[0:3]=='nhh': # fix amide hydrogens
if ((_self.select(tmp3,"(name H1 & nbr. "+tmp1+")",domain=tmp_domain)==1) and
(_self.select(tmp4,"(name O & nbr. "+tmp2+")",domain=tmp_domain)==1)):
_self.set_dihedral(
tmp4, # O
tmp2, # C
tmp1, # N
tmp3, # H1
180)
if amino_acid[0:3]!='pro':
if ((_self.select(tmp3,"(name CA & nbr. "+tmp1+")",domain=tmp_domain)==1) and
(_self.select(tmp4,"(name C & nbr. (name CA & nbr. "+tmp1+"))",domain=tmp_domain)==1)):
_self.set_dihedral( # PHI
tmp2, # C
tmp1, # N
tmp3, # CA
tmp4, # C
phi)
if ((_self.select(tmp3,"(name CA & nbr. "+tmp2+")",domain=tmp_domain)==1) and
(_self.select(tmp4,"(name N & nbr. (name CA & nbr. "+tmp2+"))",domain=tmp_domain)==1)):
_self.set_dihedral( # PSI (n-1)
tmp4, # N
tmp3, # CA
tmp2, # C
tmp1, # N
psi)
# ___mark2 = ___time()
sele = ("(name C & (byres nbr. %s) & !(byres %s))"% (tmp_connect,tmp_connect))
if _self.select(tmp1,sele,domain=tmp_domain):
_self.edit(tmp1)
if center:
_self.center(tmp1,animate=animate)
else:
_self.unpick()
elif _self.count_atoms("((%s) and elem H)"%selection):
_self.delete(tmp_wild)
raise pymol.CmdException("please pick a nitrogen or carbonyl carbon to grow from.")
else:
_self.delete(tmp_wild)
raise pymol.CmdException("unable to attach fragment.")
_self.delete(tmp_wild)
# ___exit = ___time()
# ___seg1 = ___seg1 + ___mark1 - ___entry
# ___seg2 = ___seg2 + ___mark2 - ___mark1
# ___seg3 = ___seg3 + ___exit - ___mark2
# ___total = ___total + ___exit - ___entry
# ___pass = ___pass + 1
# print "%0.3f %0.3f %0.3f / %0.3f + %0.3f + %0.3f = %0.3f vs %0.3f"%(___seg1/___total,___seg2/___total,___seg3/___total,
# ___seg1/___pass, ___seg2/___pass, ___seg3/___pass,
# ___total/___pass, (___time()-___last) - (___exit - ___entry))
# ___last = ___time()
return r