Package schrodinger :: Package utils :: Module pymol :: Class PymolInstance

Class PymolInstance

object --+
         |
        PymolInstance

Known Subclasses:

PymolScriptInstance

Represents a remote PyMOL instance (controlled via a one-way pipe)

Acts like a proxy to the cmd module, without return values on function calls (which would actually be very usefull).

See also: PyMOL XMLRPC server (pymol -R)

Instance Methods

[hide private]

__init__(self, pymol_command='pymol')
x.__init__(...) initializes x; see help(type(x)) for signature

_initPipe(self)
Set up self._pipe

_hangingStdinWorkaround(self)
workaround for PYMOL-234 PYMOL-246 PYMOL-508 PYMOL-510

dict

_getEnviron(self)
The SCHRODINGER environment may be incompatible with PyMOL.

__getattr__(self, name)

str

get_legal_name(self, name)
Replacement for cmd.get_legal_name

str

get_unused_name(self, name, alwaysnumber=1)
Replacement for cmd.get_unused_name, does not talk back to PyMOL but maintains it's own set of already used names.

sendVersionCheck(self)
Print a warning on the PyMOL log window if PyMOL version is too old.

bool

do(self, cmmd)
Send command to PyMOL

close(self)
Quit PyMOL

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

_re_illegal = re.compile(r'[^-\.\w]')

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, pymol_command=`'pymol'`)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

pymol_command (str) - path to pymol executable

Overrides: object.__init__

_getEnviron(self)

The SCHRODINGER environment may be incompatible with PyMOL. This method provides a cleaned environment dictionary for the pymol subprocess.

Returns: dict

get_legal_name(self, name)

Replacement for cmd.get_legal_name

Parameters:

name (str) - name candidate

Returns: str

legal PyMOL object name

get_unused_name(self, name, alwaysnumber=1)

Replacement for cmd.get_unused_name, does not talk back to PyMOL but maintains it's own set of already used names.

This is only necessary because the the pipe cannot return values.

Parameters:

name (str) - name candidate
alwaysnumber (bool) - if False, only append a number if name already exists

Returns: str

unused legal PyMOL object name

do(self, cmmd)

Send command to PyMOL

Parameters:

cmmd (str) - PyMOL command

Returns: bool

True on success and False on error

Class PymolInstance

__init__(self, pymol_command='pymol') (Constructor)

_getEnviron(self)

get_legal_name(self, name)

get_unused_name(self, name, alwaysnumber=1)

do(self, cmmd)

init(self, pymol_command=`'pymol'`)
(Constructor)