Search is not available for this dataset
text stringlengths 75 104k |
|---|
def statuses(ctx, page):
"""Get job statuses.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon job -j 2 statuses
```
"""
user, project_name, _job = get_job_or_local(ctx.obj.get('project'), ctx.obj.get('job'))
page = page or 1
try:
r... |
def resources(ctx, gpu):
"""Get job resources.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon job -j 2 resources
```
For GPU resources
\b
```bash
$ polyaxon job -j 2 resources --gpu
```
"""
user, project_name, _job = get_job... |
def logs(ctx, past, follow, hide_time):
"""Get job logs.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon job -j 2 logs
```
\b
```bash
$ polyaxon job logs
```
"""
user, project_name, _job = get_job_or_local(ctx.obj.get('project'), ... |
def outputs(ctx):
"""Download outputs for job.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon job -j 1 outputs
```
"""
user, project_name, _job = get_job_or_local(ctx.obj.get('project'), ctx.obj.get('job'))
try:
PolyaxonClient().job.d... |
def pprint(value):
"""Prints as formatted JSON"""
click.echo(
json.dumps(value,
sort_keys=True,
indent=4,
separators=(',', ': '))) |
def login(token, username, password):
"""Login to Polyaxon."""
auth_client = PolyaxonClient().auth
if username:
# Use username / password login
if not password:
password = click.prompt('Please enter your password', type=str, hide_input=True)
password = password.strip(... |
def whoami():
"""Show current logged Polyaxon user."""
try:
user = PolyaxonClient().auth.get_user()
except (PolyaxonHTTPError, PolyaxonShouldExitError, PolyaxonClientException) as e:
Printer.print_error('Could not load user info.')
Printer.print_error('Error message `{}`.'.format(e))... |
def build(ctx, project, build): # pylint:disable=redefined-outer-name
"""Commands for build jobs."""
ctx.obj = ctx.obj or {}
ctx.obj['project'] = project
ctx.obj['build'] = build |
def get(ctx):
"""Get build job.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon build -b 1 get
```
\b
```bash
$ polyaxon build --build=1 --project=project_name get
```
"""
user, project_name, _build = get_build_or_local(ctx.obj.ge... |
def delete(ctx):
"""Delete build job.
Uses [Caching](/references/polyaxon-cli/#caching)
Example:
\b
```bash
$ polyaxon build delete
```
\b
```bash
$ polyaxon build -b 2 delete
```
"""
user, project_name, _build = get_build_or_local(ctx.obj.get('project'), ctx.obj.... |
def update(ctx, name, description, tags):
"""Update build.
Uses [Caching](/references/polyaxon-cli/#caching)
Example:
\b
```bash
$ polyaxon build -b 2 update --description="new description for my build"
```
"""
user, project_name, _build = get_build_or_local(ctx.obj.get('project')... |
def stop(ctx, yes):
"""Stop build job.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon build stop
```
\b
```bash
$ polyaxon build -b 2 stop
```
"""
user, project_name, _build = get_build_or_local(ctx.obj.get('project'), ctx.obj.ge... |
def bookmark(ctx):
"""Bookmark build job.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon build bookmark
```
\b
```bash
$ polyaxon build -b 2 bookmark
```
"""
user, project_name, _build = get_build_or_local(ctx.obj.get('project'),... |
def resources(ctx, gpu):
"""Get build job resources.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon build -b 2 resources
```
For GPU resources
\b
```bash
$ polyaxon build -b 2 resources --gpu
```
"""
user, project_name, _bui... |
def init(project, polyaxonfile):
"""Initialize a new polyaxonfile specification."""
user, project_name = get_project_or_local(project)
try:
project_config = PolyaxonClient().project.get_project(user, project_name)
except (PolyaxonHTTPError, PolyaxonShouldExitError, PolyaxonClientException) as e:... |
def run(ctx, project, file, name, tags, description, ttl, u, l): # pylint:disable=redefined-builtin
"""Run polyaxonfile specification.
Examples:
\b
```bash
$ polyaxon run -f file -f file_override ...
```
Upload before running
\b
```bash
$ polyaxon run -f file -u
```
... |
def bookmark(ctx, username): # pylint:disable=redefined-outer-name
"""Commands for bookmarks."""
ctx.obj = ctx.obj or {}
ctx.obj['username'] = username |
def projects(ctx, page):
"""List bookmarked projects for user.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon bookmark projects
```
\b
```bash
$ polyaxon bookmark -u adam projects
```
"""
user = get_username_or_local(ctx.obj.get(... |
def _remove_trailing_spaces(line):
"""Remove trailing spaces unless they are quoted with a backslash."""
while line.endswith(' ') and not line.endswith('\\ '):
line = line[:-1]
return line.replace('\\ ', ' ') |
def find_matching(cls, path, patterns):
"""Yield all matching patterns for path."""
for pattern in patterns:
if pattern.match(path):
yield pattern |
def is_ignored(cls, path, patterns):
"""Check whether a path is ignored. For directories, include a trailing slash."""
status = None
for pattern in cls.find_matching(path, patterns):
status = pattern.is_exclude
return status |
def _matches_patterns(path, patterns):
"""Given a list of patterns, returns a if a path matches any pattern."""
for glob in patterns:
try:
if PurePath(path).match(glob):
return True
except TypeError:
pass
return False |
def _ignore_path(cls, path, ignore_list=None, white_list=None):
"""Returns a whether a path should be ignored or not."""
ignore_list = ignore_list or []
white_list = white_list or []
return (cls._matches_patterns(path, ignore_list) and
not cls._matches_patterns(path, whit... |
def group(ctx, project, group): # pylint:disable=redefined-outer-name
"""Commands for experiment groups."""
ctx.obj = ctx.obj or {}
ctx.obj['project'] = project
ctx.obj['group'] = group |
def get(ctx):
"""Get experiment group by uuid.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon group -g 13 get
```
"""
user, project_name, _group = get_project_group_or_local(ctx.obj.get('project'),
... |
def delete(ctx):
"""Delete experiment group.
Uses [Caching](/references/polyaxon-cli/#caching)
"""
user, project_name, _group = get_project_group_or_local(ctx.obj.get('project'),
ctx.obj.get('group'))
if not click.confirm("Are sure you wa... |
def update(ctx, name, description, tags):
"""Update experiment group.
Uses [Caching](/references/polyaxon-cli/#caching)
Example:
\b
```bash
$ polyaxon group -g 2 update --description="new description for this group"
```
\b
```bash
$ polyaxon update --tags="foo, bar"
```
... |
def stop(ctx, yes, pending):
"""Stop experiments in the group.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples: stop only pending experiments
\b
```bash
$ polyaxon group stop --pending
```
Examples: stop all unfinished
\b
```bash
$ polyaxon group stop
```
... |
def bookmark(ctx):
"""Bookmark group.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
\b
```bash
$ polyaxon group bookmark
```
\b
```bash
$ polyaxon group -g 2 bookmark
```
"""
user, project_name, _group = get_project_group_or_local(ctx.obj.get('projec... |
def config(list): # pylint:disable=redefined-builtin
"""Set and get the global configurations."""
if list:
_config = GlobalConfigManager.get_config_or_default()
Printer.print_header('Current config:')
dict_tabulate(_config.to_dict()) |
def get(keys):
"""Get the global config values by keys.
Example:
\b
```bash
$ polyaxon config get host http_port
```
"""
_config = GlobalConfigManager.get_config_or_default()
if not keys:
return
print_values = {}
for key in keys:
if hasattr(_config, key):
... |
def set(verbose, # pylint:disable=redefined-builtin
host,
http_port,
ws_port,
use_https,
verify_ssl):
"""Set the global config values.
Example:
\b
```bash
$ polyaxon config set --hots=localhost http_port=80
```
"""
_config = GlobalConfigManager.... |
def activate(username):
"""Activate a user.
Example:
\b
```bash
$ polyaxon user activate david
```
"""
try:
PolyaxonClient().user.activate_user(username)
except (PolyaxonHTTPError, PolyaxonShouldExitError, PolyaxonClientException) as e:
Printer.print_error('Could no... |
def delete(username):
"""Delete a user.
Example:
\b
```bash
$ polyaxon user delete david
```
"""
try:
PolyaxonClient().user.delete_user(username)
except (PolyaxonHTTPError, PolyaxonShouldExitError, PolyaxonClientException) as e:
Printer.print_error('Could not delete... |
def deploy(file, manager_path, check, dry_run): # pylint:disable=redefined-builtin
"""Deploy polyaxon."""
config = read_deployment_config(file)
manager = DeployManager(config=config,
filepath=file,
manager_path=manager_path,
... |
def teardown(file): # pylint:disable=redefined-builtin
"""Teardown a polyaxon deployment given a config file."""
config = read_deployment_config(file)
manager = DeployManager(config=config, filepath=file)
exception = None
try:
if click.confirm('Would you like to execute pre-delete hooks?', ... |
def create_tarfile(files, project_name):
"""Create a tar file based on the list of files passed"""
fd, filename = tempfile.mkstemp(prefix="polyaxon_{}".format(project_name), suffix='.tar.gz')
with tarfile.open(filename, "w:gz") as tar:
for f in files:
tar.add(f)
yield filename
... |
def url(ctx):
"""Prints the tensorboard url for project/experiment/experiment group.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples for project tensorboards:
\b
```bash
$ polyaxon tensorboard url
```
\b
```bash
$ polyaxon tensorboard -p mnist url
```
Exam... |
def start(ctx, file): # pylint:disable=redefined-builtin
"""Start a tensorboard deployment for project/experiment/experiment group.
Project tensorboard will aggregate all experiments under the project.
Experiment group tensorboard will aggregate all experiments under the group.
Experiment tensorboar... |
def stop(ctx, yes):
"""Stops the tensorboard deployment for project/experiment/experiment group if it exists.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples: stopping project tensorboard
\b
```bash
$ polyaxon tensorboard stop
```
Examples: stopping experiment group tensor... |
def check_cli_version():
"""Check if the current cli version satisfies the server requirements"""
if not CliConfigManager.should_check():
return
server_version = get_server_version()
current_version = get_current_version()
CliConfigManager.reset(current_version=current_version,
... |
def version(cli, platform):
"""Print the current version of the cli and platform."""
version_client = PolyaxonClient().version
cli = cli or not any([cli, platform])
if cli:
try:
server_version = version_client.get_cli_version()
except AuthorizationError:
session_e... |
def dashboard(yes, url):
"""Open dashboard in browser."""
dashboard_url = "{}/app".format(PolyaxonClient().api_config.http_host)
if url:
click.echo(dashboard_url)
sys.exit(0)
if not yes:
click.confirm('Dashboard page will now open in your browser. Continue?',
... |
def grant(username):
"""Grant superuser role to a user.
Example:
\b
```bash
$ polyaxon superuser grant david
```
"""
try:
PolyaxonClient().user.grant_superuser(username)
except (PolyaxonHTTPError, PolyaxonShouldExitError, PolyaxonClientException) as e:
Printer.print... |
def revoke(username):
"""Revoke superuser role to a user.
Example:
\b
```bash
$ polyaxon superuser revoke david
```
"""
try:
PolyaxonClient().user.revoke_superuser(username)
except (PolyaxonHTTPError, PolyaxonShouldExitError, PolyaxonClientException) as e:
Printer.p... |
def url(ctx):
"""Prints the notebook url for this project.
Uses [Caching](/references/polyaxon-cli/#caching)
Example:
\b
```bash
$ polyaxon notebook url
```
"""
user, project_name = get_project_or_local(ctx.obj.get('project'))
try:
response = PolyaxonClient().project.g... |
def start(ctx, file, u): # pylint:disable=redefined-builtin
"""Start a notebook deployment for this project.
Uses [Caching](/references/polyaxon-cli/#caching)
Example:
\b
```bash
$ polyaxon notebook start -f file -f file_override ...
```
Example: upload before running
\b
``... |
def stop(ctx, commit, yes):
"""Stops the notebook deployment for this project if it exists.
Uses [Caching](/references/polyaxon-cli/#caching)
"""
user, project_name = get_project_or_local(ctx.obj.get('project'))
if not yes and not click.confirm("Are sure you want to stop notebook "
... |
def cli(context, verbose):
""" Polyaxon CLI tool to:
* Parse, Validate, and Check Polyaxonfiles.
* Interact with Polyaxon server.
* Run and Monitor experiments.
Check the help available for each command listed below.
"""
configure_logger(verbose or GlobalConfigManager.get_val... |
def check(self):
"""Add platform specific checks"""
if not self.is_valid:
raise PolyaxonDeploymentConfigError(
'Deployment type `{}` not supported'.format(self.deployment_type))
check = False
if self.is_kubernetes:
check = self.check_for_kubernetes... |
def install(self):
"""Install polyaxon using the current config to the correct platform."""
if not self.is_valid:
raise PolyaxonDeploymentConfigError(
'Deployment type `{}` not supported'.format(self.deployment_type))
if self.is_kubernetes:
self.install_o... |
def upgrade(self):
"""Upgrade deployment."""
if not self.is_valid:
raise PolyaxonDeploymentConfigError(
'Deployment type `{}` not supported'.format(self.deployment_type))
if self.is_kubernetes:
self.upgrade_on_kubernetes()
elif self.is_docker_comp... |
def teardown(self, hooks=True):
"""Teardown Polyaxon."""
if not self.is_valid:
raise PolyaxonDeploymentConfigError(
'Deployment type `{}` not supported'.format(self.deployment_type))
if self.is_kubernetes:
self.teardown_on_kubernetes(hooks=hooks)
... |
def project(ctx, project): # pylint:disable=redefined-outer-name
"""Commands for projects."""
if ctx.invoked_subcommand not in ['create', 'list']:
ctx.obj = ctx.obj or {}
ctx.obj['project'] = project |
def create(ctx, name, description, tags, private, init):
"""Create a new project.
Uses [Caching](/references/polyaxon-cli/#caching)
Example:
\b
```bash
$ polyaxon project create --name=cats-vs-dogs --description="Image Classification with DL"
```
"""
try:
tags = tags.split... |
def list(page): # pylint:disable=redefined-builtin
"""List projects.
Uses [Caching](/references/polyaxon-cli/#caching)
"""
user = AuthConfigManager.get_value('username')
if not user:
Printer.print_error('Please login first. `polyaxon login --help`')
page = page or 1
try:
r... |
def get(ctx):
"""Get info for current project, by project_name, or user/project_name.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
To get current project:
\b
```bash
$ polyaxon project get
```
To get a project by name
\b
```bash
$ polyaxon project get... |
def delete(ctx):
"""Delete project.
Uses [Caching](/references/polyaxon-cli/#caching)
"""
user, project_name = get_project_or_local(ctx.obj.get('project'))
if not click.confirm("Are sure you want to delete project `{}/{}`".format(user, project_name)):
click.echo('Existing without deleting ... |
def update(ctx, name, description, tags, private):
"""Update project.
Uses [Caching](/references/polyaxon-cli/#caching)
Example:
\b
```bash
$ polyaxon update foobar --description="Image Classification with DL using TensorFlow"
```
\b
```bash
$ polyaxon update mike1/foobar --d... |
def groups(ctx, query, sort, page):
"""List experiment groups for this project.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
Get all groups:
\b
```bash
$ polyaxon project groups
```
Get all groups with with status {created or running}, and
creation date betwee... |
def experiments(ctx, metrics, declarations, independent, group, query, sort, page):
"""List experiments for this project.
Uses [Caching](/references/polyaxon-cli/#caching)
Examples:
Get all experiments:
\b
```bash
$ polyaxon project experiments
```
Get all experiments with with ... |
def git(ctx, url, private, sync): # pylint:disable=assign-to-new-keyword
"""Set/Sync git repo on this project.
Uses [Caching](/references/polyaxon-cli/#caching)
Example:
\b
```bash
$ polyaxon project git --url=https://github.com/polyaxon/polyaxon-quick-start
```
\b
```bash
$... |
def ci(ctx, enable, disable): # pylint:disable=assign-to-new-keyword
"""Enable/Disable CI on this project.
Uses [Caching](/references/polyaxon-cli/#caching)
Example:
\b
```bash
$ polyaxon project ci --enable
```
\b
```bash
$ polyaxon project ci --disable
```
"""
... |
def download(ctx):
"""Download code of the current project."""
user, project_name = get_project_or_local(ctx.obj.get('project'))
try:
PolyaxonClient().project.download_repo(user, project_name)
except (PolyaxonHTTPError, PolyaxonShouldExitError, PolyaxonClientException) as e:
Printer.prin... |
def write(self,file,optstring="",quote=False):
"""write the 'object' line; additional args are packed in string"""
classid = str(self.id)
if quote: classid = '"'+classid+'"'
# Only use a *single* space between tokens; both chimera's and pymol's DX parser
# does not properly imple... |
def edges(self):
"""Edges of the grid cells, origin at centre of 0,0,..,0 grid cell.
Only works for regular, orthonormal grids.
"""
return [self.delta[d,d] * numpy.arange(self.shape[d]+1) + self.origin[d]\
- 0.5*self.delta[d,d] for d in range(self.rank)] |
def write(self, file):
"""Write the *class array* section.
Parameters
----------
file : file
Raises
------
ValueError
If the `dxtype` is not a valid type, :exc:`ValueError` is
raised.
"""
if self.type not in self.dx_typ... |
def write(self, filename):
"""Write the complete dx object to the file.
This is the simple OpenDX format which includes the data into
the header via the 'object array ... data follows' statement.
Only simple regular arrays are supported.
The format should be compatible with VM... |
def read(self,file):
"""Read DX field from file.
dx = OpenDX.field.read(dxfile)
The classid is discarded and replaced with the one from the file.
"""
DXfield = self
p = DXParser(file)
p.parse(DXfield) |
def sorted_components(self):
"""iterator that returns (component,object) in id order"""
for component, object in \
sorted(self.components.items(),
key=lambda comp_obj: comp_obj[1].id):
yield component, object |
def histogramdd(self):
"""Return array data as (edges,grid), i.e. a numpy nD histogram."""
shape = self.components['positions'].shape
edges = self.components['positions'].edges()
hist = self.components['data'].array.reshape(shape)
return (hist,edges) |
def value(self,ascode=None):
"""Return text cast to the correct type or the selected type"""
if ascode is None:
ascode = self.code
return self.cast[ascode](self.text) |
def initialize(self):
"""Initialize the corresponding DXclass from the data.
class = DXInitObject.initialize()
"""
return self.DXclasses[self.type](self.id,**self.args) |
def parse(self,DXfield):
"""Parse the dx file and construct a DX field object with component classes.
A :class:`field` instance *DXfield* must be provided to be
filled by the parser::
DXfield_object = OpenDX.field(*args)
parse(DXfield_object)
A tokenizer turns th... |
def __general(self):
"""Level-0 parser and main loop.
Look for a token that matches a level-1 parser and hand over control."""
while 1: # main loop
try:
tok = self.__peek() # only peek, apply_parser() will consume
except... |
def __comment(self):
"""Level-1 parser for comments.
pattern: #.*
Append comment (with initial '# ' stripped) to all comments.
"""
tok = self.__consume()
self.DXfield.add_comment(tok.value())
self.set_parser('general') |
def __object(self):
"""Level-1 parser for objects.
pattern: 'object' id 'class' type ...
id ::= integer|string|'"'white space string'"'
type ::= string
"""
self.__consume() # 'object'
classid = self.__consume().text
word = self.__con... |
def __gridpositions(self):
"""Level-2 parser for gridpositions.
pattern:
object 1 class gridpositions counts 97 93 99
origin -46.5 -45.5 -48.5
delta 1 0 0
delta 0 1 0
delta 0 0 1
"""
try:
tok = self.__consume()
except DXParserN... |
def __gridconnections(self):
"""Level-2 parser for gridconnections.
pattern:
object 2 class gridconnections counts 97 93 99
"""
try:
tok = self.__consume()
except DXParserNoTokens:
return
if tok.equals('counts'):
shape = []
... |
def __array(self):
"""Level-2 parser for arrays.
pattern:
object 3 class array type double rank 0 items 12 data follows
0 2 0
0 0 3.6
0 -2.0 1e-12
+4.534e+01 .34534 0.43654
attribute "dep" string "positions"
"""
try:
tok = self... |
def __field(self):
"""Level-2 parser for a DX field object.
pattern:
object "site map 1" class field
component "positions" value 1
component "connections" value 2
component "data" value 3
"""
try:
tok = self.__consume()
except DXParser... |
def use_parser(self,parsername):
"""Set parsername as the current parser and apply it."""
self.__parser = self.parsers[parsername]
self.__parser() |
def __tokenize(self,string):
"""Split s into tokens and update the token buffer.
__tokenize(string)
New tokens are appended to the token buffer, discarding white
space. Based on http://effbot.org/zone/xml-scanner.htm
"""
for m in self.dx_regex.finditer(string.strip()):... |
def __refill_tokenbuffer(self):
"""Add a new tokenized line from the file to the token buffer.
__refill_tokenbuffer()
Only reads a new line if the buffer is empty. It is safe to
call it repeatedly.
At end of file, method returns empty strings and it is up to
__peek and... |
def read(self, filename):
"""Populate the instance from the plt file *filename*."""
from struct import calcsize, unpack
if not filename is None:
self.filename = filename
with open(self.filename, 'rb') as plt:
h = self.header = self._read_header(plt)
ne... |
def _read_header(self, pltfile):
"""Read header bytes, try all possibilities for byte order/size/alignment."""
nheader = struct.calcsize(self._headerfmt)
names = [r.key for r in self._header_struct]
binheader = pltfile.read(nheader)
def decode_header(bsaflag='@'):
h =... |
def ndmeshgrid(*arrs):
"""Return a mesh grid for N dimensions.
The input are N arrays, each of which contains the values along one axis of
the coordinate system. The arrays do not have to have the same number of
entries. The function returns arrays that can be fed into numpy functions
so that they ... |
def resample(self, edges):
"""Resample data to a new grid with edges *edges*.
This method creates a new grid with the data from the current
grid resampled to a regular grid specified by *edges*. The
order of the interpolation is set by
:attr:`Grid.interpolation_spline_order`: c... |
def resample_factor(self, factor):
"""Resample to a new regular grid.
Parameters
----------
factor : float
The number of grid cells are scaled with `factor` in each
dimension, i.e., ``factor * N_i`` cells along each
dimension i.
Returns
... |
def _update(self):
"""compute/update all derived data
Can be called without harm and is idem-potent.
Updates these attributes and methods:
:attr:`origin`
the center of the cell with index 0,0,0
:attr:`midpoints`
centre coordinate of each grid c... |
def interpolated(self):
"""B-spline function over the data grid(x,y,z).
The :func:`interpolated` function allows one to obtain data
values for any values of the coordinates::
interpolated([x1,x2,...],[y1,y2,...],[z1,z2,...]) -> F[x1,y1,z1],F[x2,y2,z2],...
The interpolation ... |
def load(self, filename, file_format=None):
"""Load saved (pickled or dx) grid and edges from <filename>.pickle
Grid.load(<filename>.pickle)
Grid.load(<filename>.dx)
The load() method calls the class's constructor method and
completely resets all values, based on the load... |
def _load_cpp4(self, filename):
"""Initializes Grid from a CCP4 file."""
ccp4 = CCP4.CCP4()
ccp4.read(filename)
grid, edges = ccp4.histogramdd()
self.__init__(grid=grid, edges=edges, metadata=self.metadata) |
def _load_dx(self, filename):
"""Initializes Grid from a OpenDX file."""
dx = OpenDX.field(0)
dx.read(filename)
grid, edges = dx.histogramdd()
self.__init__(grid=grid, edges=edges, metadata=self.metadata) |
def _load_plt(self, filename):
"""Initialize Grid from gOpenMol plt file."""
g = gOpenMol.Plt()
g.read(filename)
grid, edges = g.histogramdd()
self.__init__(grid=grid, edges=edges, metadata=self.metadata) |
def export(self, filename, file_format=None, type=None, typequote='"'):
"""export density to file using the given format.
The format can also be deduced from the suffix of the filename
though the *format* keyword takes precedence.
The default format for export() is 'dx'. Use 'dx' for
... |
def _export_python(self, filename, **kwargs):
"""Pickle the Grid object
The object is dumped as a dictionary with grid and edges: This
is sufficient to recreate the grid object with __init__().
"""
data = dict(grid=self.grid, edges=self.edges, metadata=self.metadata)
wit... |
def _export_dx(self, filename, type=None, typequote='"', **kwargs):
"""Export the density grid to an OpenDX file.
The file format is the simplest regular grid array and it is
also understood by VMD's and Chimera's DX reader; PyMOL
requires the dx `type` to be set to "double".
F... |
def centers(self):
"""Returns the coordinates of the centers of all grid cells as an
iterator."""
for idx in numpy.ndindex(self.grid.shape):
yield self.delta * numpy.array(idx) + self.origin |
def check_compatible(self, other):
"""Check if *other* can be used in an arithmetic operation.
1) *other* is a scalar
2) *other* is a grid defined on the same edges
:Raises: :exc:`TypeError` if not compatible.
"""
if not (numpy.isreal(other) or self == other):
... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.