schrodinger.application.desmond.meta module

Module for all metadynamics backend functionality

schrodinger.application.desmond.meta.get_backend()

A convenience function to see if we’re running under job control. If so, return a _Backend object. Otherwise, return None.

class schrodinger.application.desmond.meta.CV(dim, width, wall, floor)

Bases: object

base class for collective variable

__init__(dim, width, wall, floor)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvid)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n base class for collective variable\n ', '__init__': <function CV.__init__>, 'getMExpr': <function CV.getMExpr>, '__dict__': <attribute '__dict__' of 'CV' objects>, '__weakref__': <attribute '__weakref__' of 'CV' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVrgyr(atomlist, width)

Bases: schrodinger.application.desmond.meta.CV

Radius of Gyration Collective Variable

cvrgyr_template = '\n#radius of gyration definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_cog = center_of_geometry(%(cvname)s_sel);\n%(cvname)s_coord_range = series (i=0:length(%(cvname)s_sel))\n norm2(min_image(pos(%(cvname)s_sel[i])-%(cvname)s_cog));\n%(cvname)s=sqrt(%(cvname)s_coord_range/length(%(cvname)s_sel));\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n'

__init__(atomlist, width)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n Radius of Gyration Collective Variable\n ', 'cvrgyr_template': '\n#radius of gyration definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_cog = center_of_geometry(%(cvname)s_sel);\n%(cvname)s_coord_range = series (i=0:length(%(cvname)s_sel))\n norm2(min_image(pos(%(cvname)s_sel[i])-%(cvname)s_cog));\n%(cvname)s=sqrt(%(cvname)s_coord_range/length(%(cvname)s_sel));\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n', '__init__': <function CVrgyr.__init__>, 'getMExpr': <function CVrgyr.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVrgyr_mass(atomlist, width)

Bases: schrodinger.application.desmond.meta.CV

Radius of Gyration Collective Variable

cvrgyr_mass_template = '\n#mass-weighted radius of gyration definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_com = center_of_mass(%(cvname)s_sel);\n%(cvname)s_coord_range = series (i=0:length(%(cvname)s_sel))\n mass(%(cvname)s_sel[i])*norm2(min_image(pos(%(cvname)s_sel[i])-%(cvname)s_com));\n%(cvname)s=sqrt(%(cvname)s_coord_range/sum(mass(%(cvname)s_sel)));\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n\n'

__init__(atomlist, width)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n Radius of Gyration Collective Variable\n ', 'cvrgyr_mass_template': '\n#mass-weighted radius of gyration definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_com = center_of_mass(%(cvname)s_sel);\n%(cvname)s_coord_range = series (i=0:length(%(cvname)s_sel))\n mass(%(cvname)s_sel[i])*norm2(min_image(pos(%(cvname)s_sel[i])-%(cvname)s_com));\n%(cvname)s=sqrt(%(cvname)s_coord_range/sum(mass(%(cvname)s_sel)));\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n\n', '__init__': <function CVrgyr_mass.__init__>, 'getMExpr': <function CVrgyr_mass.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVrmsd(atomlist, xyz_coords_ref, width, rmsd_weights=None, superpos_weights=None)

Bases: schrodinger.application.desmond.meta.CV

rmsd collective variable

cvrmsd_template = '\n# rmsd definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_ref = array( %(xyz_ref)s );\n%(cvname)s = rmsd( %(cvname)s_ref, %(cvname)s_sel );\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n'

cvrmsd_weights_template = '\n# rmsd definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_ref = array( %(xyz_ref)s );\n%(cvname)s_rmsd_weights = array( %(rmsd_weights)s );\n%(cvname)s_superpos_weights = array( %(superpos_weights)s );\n%(cvname)s = rmsd( %(cvname)s_ref, %(cvname)s_sel, %(cvname)s_rmsd_weights, %(cvname)s_superpos_weights );\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n'

__init__(atomlist, xyz_coords_ref, width, rmsd_weights=None, superpos_weights=None)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n rmsd collective variable\n ', 'cvrmsd_template': '\n# rmsd definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_ref = array( %(xyz_ref)s );\n%(cvname)s = rmsd( %(cvname)s_ref, %(cvname)s_sel );\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n', 'cvrmsd_weights_template': '\n# rmsd definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_ref = array( %(xyz_ref)s );\n%(cvname)s_rmsd_weights = array( %(rmsd_weights)s );\n%(cvname)s_superpos_weights = array( %(superpos_weights)s );\n%(cvname)s = rmsd( %(cvname)s_ref, %(cvname)s_sel, %(cvname)s_rmsd_weights, %(cvname)s_superpos_weights );\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n', '__init__': <function CVrmsd.__init__>, 'getMExpr': <function CVrmsd.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVrmsd_symm(atomlist, xyz_coords_ref_list, width)

Bases: schrodinger.application.desmond.meta.CV

rmsd collective variable

cvrmsd_setup_template = '\n# setting up rmsd_symm with total of %(nconfs)s conformations\n%(cvname)s_sel = %(atomlist)s;\n\n'

cvrmsd_conf_template = '\n# rmsd_symm definition #%(confnum)s\n%(cvname)s_ref_%(confnum)s = array( %(xyz_ref)s );\n%(cvname)s_%(confnum)s = rmsd( %(cvname)s_ref_%(confnum)s, %(cvname)s_sel );\n'

cvrmsd_template = '\n%(cvname)s = min( array( %(confs)s ));\nprint ("%(cvname)s", %(cvname)s );\n# the width for %(cvname)s will be set to: %(width)s\n'

__init__(atomlist, xyz_coords_ref_list, width)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n rmsd collective variable\n ', 'cvrmsd_setup_template': '\n# setting up rmsd_symm with total of %(nconfs)s conformations\n%(cvname)s_sel = %(atomlist)s;\n\n', 'cvrmsd_conf_template': '\n# rmsd_symm definition #%(confnum)s\n%(cvname)s_ref_%(confnum)s = array( %(xyz_ref)s );\n%(cvname)s_%(confnum)s = rmsd( %(cvname)s_ref_%(confnum)s, %(cvname)s_sel );\n', 'cvrmsd_template': '\n%(cvname)s = min( array( %(confs)s ));\nprint ("%(cvname)s", %(cvname)s );\n# the width for %(cvname)s will be set to: %(width)s\n', '__init__': <function CVrmsd_symm.__init__>, 'getMExpr': <function CVrmsd_symm.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVwhim(atomlist, eigval, width)

Bases: schrodinger.application.desmond.meta.CV

whim collective variable

cvwhim_template = '\n#whim definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_whim = whim(%(cvname)s_sel, mass(%(cvname)s_sel));\n%(cvname)s = %(cvname)s_whim[%(eigval)i];\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n'

__init__(atomlist, eigval, width)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n whim collective variable\n ', 'cvwhim_template': '\n#whim definition\n%(cvname)s_sel = %(atomlist)s;\n%(cvname)s_whim = whim(%(cvname)s_sel, mass(%(cvname)s_sel));\n%(cvname)s = %(cvname)s_whim[%(eigval)i];\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n', '__init__': <function CVwhim.__init__>, 'getMExpr': <function CVwhim.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVzdist0(atomlist, width)

Bases: schrodinger.application.desmond.meta.CV

This collective variable reports an absolute Z-distance from the simulation box origin (Z==0). This cv is useful when for membrane penetration studies.

cvzdist0_template = '\n# Z-dist definition\n%(cvname)s_g0 = center_of_mass ( %(atomlist)s );\n%(cvname)s_z = %(cvname)s_g0[2];\n%(cvname)s = sqrt(%(cvname)s_z^2);\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n'

__init__(atomlist, width)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n This collective variable reports an absolute Z-distance from the simulation box\n origin (Z==0). This cv is useful when for membrane penetration studies.\n ', 'cvzdist0_template': '\n# Z-dist definition\n%(cvname)s_g0 = center_of_mass ( %(atomlist)s );\n%(cvname)s_z = %(cvname)s_g0[2];\n%(cvname)s = sqrt(%(cvname)s_z^2);\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n', '__init__': <function CVzdist0.__init__>, 'getMExpr': <function CVzdist0.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVzdist(atomlist, width, wall, floor)

Bases: schrodinger.application.desmond.meta.CV

This collective variable reports an absolute Z-distance. this CV is used for membrane penetration studies.

cvzdist_template = '\n# Z-dist definition\n%(cvname)s_g0 = center_of_mass ( %(atomlist)s );\n%(cvname)s = %(cvname)s_g0[2];\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n'

cvdist_wall_template = '\n# the upper bound, wall params for %(cvname)s are: width is 0.2;\n# location at %(wall)f; hight is 1000\n%(cvname)s_wall = 1000 / (1 + exp(( %(wall)f - %(cvname)s) / 0.2) );\n'

cvdist_floor_template = "\n# lower bound wall or 'floor' params for %(cvname)s are: width is 0.2;\n# location at %(floor)f; # hight is 1000\n%(cvname)s_floor = 1000 / (1 + exp((%(cvname)s - %(floor)f) / 0.2) );\n"

__init__(atomlist, width, wall, floor)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n This collective variable reports an absolute Z-distance.\n this CV is used for membrane penetration studies.\n ', 'cvzdist_template': '\n# Z-dist definition\n%(cvname)s_g0 = center_of_mass ( %(atomlist)s );\n%(cvname)s = %(cvname)s_g0[2];\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n', 'cvdist_wall_template': '\n# the upper bound, wall params for %(cvname)s are: width is 0.2;\n# location at %(wall)f; hight is 1000\n%(cvname)s_wall = 1000 / (1 + exp(( %(wall)f - %(cvname)s) / 0.2) );\n', 'cvdist_floor_template': "\n# lower bound wall or 'floor' params for %(cvname)s are: width is 0.2;\n# location at %(floor)f; # hight is 1000\n%(cvname)s_floor = 1000 / (1 + exp((%(cvname)s - %(floor)f) / 0.2) );\n", '__init__': <function CVzdist.__init__>, 'getMExpr': <function CVzdist.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVDist(p0, p1, width, wall, floor)

Bases: schrodinger.application.desmond.meta.CV

distance collective variable

cvdist_template = '\n# distance definition\n%(cvname)s_p0 = %(p0_atomsel)s;\n%(cvname)s_p1 = %(p1_atomsel)s;\n%(cvname)s = dist(%(cvname)s_p0, %(cvname)s_p1);\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n'

cvdist_grp_template = '\n# distance definition for group of atoms\n%(cvname)s_g0 = center_of_mass ( %(p0_atomsel)s );\n%(cvname)s_g1 = center_of_mass ( %(p1_atomsel)s );\n%(cvname)s = norm(min_image(%(cvname)s_g0 - %(cvname)s_g1));\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n'

cvdist_wall_template = '\n# the upper bound, wall params for %(cvname)s are: width is 0.2;\n# location at %(wall)f; hight is 1000\n%(cvname)s_wall = 1000 / (1 + exp(( %(wall)f - %(cvname)s) / 0.2) );\n'

cvdist_floor_template = "\n# lower bound wall or 'floor' params for %(cvname)s are: width is 0.2;\n# location at %(floor)f; # hight is 1000\n%(cvname)s_floor = 1000 / (1 + exp((%(cvname)s - %(floor)f) / 0.2) );\n\n"

__init__(p0, p1, width, wall, floor)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n distance collective variable\n ', 'cvdist_template': '\n# distance definition\n%(cvname)s_p0 = %(p0_atomsel)s;\n%(cvname)s_p1 = %(p1_atomsel)s;\n%(cvname)s = dist(%(cvname)s_p0, %(cvname)s_p1);\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n', 'cvdist_grp_template': '\n# distance definition for group of atoms\n%(cvname)s_g0 = center_of_mass ( %(p0_atomsel)s );\n%(cvname)s_g1 = center_of_mass ( %(p1_atomsel)s );\n%(cvname)s = norm(min_image(%(cvname)s_g0 - %(cvname)s_g1));\nprint ("%(cvname)s", %(cvname)s);\n# the width for %(cvname)s will be set to: %(width)s\n', 'cvdist_wall_template': '\n# the upper bound, wall params for %(cvname)s are: width is 0.2;\n# location at %(wall)f; hight is 1000\n%(cvname)s_wall = 1000 / (1 + exp(( %(wall)f - %(cvname)s) / 0.2) );\n', 'cvdist_floor_template': "\n# lower bound wall or 'floor' params for %(cvname)s are: width is 0.2;\n# location at %(floor)f; # hight is 1000\n%(cvname)s_floor = 1000 / (1 + exp((%(cvname)s - %(floor)f) / 0.2) );\n\n", '__init__': <function CVDist.__init__>, 'getMExpr': <function CVDist.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVAngle(p0, p1, p2, width, wall, floor)

Bases: schrodinger.application.desmond.meta.CV

A class to define angle collective variable. Note that due to numerical instability, cosine of the angle is used instead of radian.

cvangle_template = '\n# angle definition\n%(cvname)s_p0 = %(p0_atomsel)s;\n%(cvname)s_p1 = %(p1_atomsel)s;\n%(cvname)s_p2 = %(p2_atomsel)s;\n%(cvname)s = angle_gid(%(cvname)s_p0, %(cvname)s_p1, %(cvname)s_p2);\nprint ("%(cvname)s", acos(%(cvname)s) );\n# the width for %(cvname)s will be set to: %(width)s\n'

cvangle_grp_template = '\n# angle definition for group of atoms\n%(cvname)s_g0 = center_of_mass ( %(p0_atomsel)s );\n%(cvname)s_g1 = center_of_mass ( %(p1_atomsel)s );\n%(cvname)s_g2 = center_of_mass ( %(p2_atomsel)s );\n%(cvname)s_v0 = min_image(%(cvname)s_g0 - %(cvname)s_g1);\n%(cvname)s_v1 = min_image(%(cvname)s_g2 - %(cvname)s_g1);\n%(cvname)s = angle(%(cvname)s_v0, %(cvname)s_v1);\nprint ("%(cvname)s", acos(%(cvname)s) );\n# the width for %(cvname)s will be set to: %(width)s\n '

cvangle_wall_template = '\n# the upper bound, wall params for %(cvname)s are: width is 0.57 degree;\n# location at %(wall)f; hight is 1000\n%(cvname)s_wall = 1000 / (1 + exp(( %(wall)f - acos(%(cvname)s))/0.05) );\n'

cvangle_floor_template = "\n# lower bound wall or 'floor' params for %(cvname)s are: width is 0.57 degree;\n# location at %(floor)f; # hight is 1000\n%(cvname)s_floor = 1000/(1 + (exp((acos(%(cvname)s)- %(floor)f)/0.05)) );\n"

__init__(p0, p1, p2, width, wall, floor)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n A class to define angle collective variable.\n Note that due to numerical instability, cosine of the angle is used\n instead of radian.\n ', 'cvangle_template': '\n# angle definition\n%(cvname)s_p0 = %(p0_atomsel)s;\n%(cvname)s_p1 = %(p1_atomsel)s;\n%(cvname)s_p2 = %(p2_atomsel)s;\n%(cvname)s = angle_gid(%(cvname)s_p0, %(cvname)s_p1, %(cvname)s_p2);\nprint ("%(cvname)s", acos(%(cvname)s) );\n# the width for %(cvname)s will be set to: %(width)s\n', 'cvangle_grp_template': '\n# angle definition for group of atoms\n%(cvname)s_g0 = center_of_mass ( %(p0_atomsel)s );\n%(cvname)s_g1 = center_of_mass ( %(p1_atomsel)s );\n%(cvname)s_g2 = center_of_mass ( %(p2_atomsel)s );\n%(cvname)s_v0 = min_image(%(cvname)s_g0 - %(cvname)s_g1);\n%(cvname)s_v1 = min_image(%(cvname)s_g2 - %(cvname)s_g1);\n%(cvname)s = angle(%(cvname)s_v0, %(cvname)s_v1);\nprint ("%(cvname)s", acos(%(cvname)s) );\n# the width for %(cvname)s will be set to: %(width)s\n ', 'cvangle_wall_template': '\n# the upper bound, wall params for %(cvname)s are: width is 0.57 degree;\n# location at %(wall)f; hight is 1000\n%(cvname)s_wall = 1000 / (1 + exp(( %(wall)f - acos(%(cvname)s))/0.05) );\n', 'cvangle_floor_template': "\n# lower bound wall or 'floor' params for %(cvname)s are: width is 0.57 degree;\n# location at %(floor)f; # hight is 1000\n%(cvname)s_floor = 1000/(1 + (exp((acos(%(cvname)s)- %(floor)f)/0.05)) );\n", '__init__': <function CVAngle.__init__>, 'getMExpr': <function CVAngle.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CVDihedral(p0, p1, p2, p3, width, wall, floor)

Bases: schrodinger.application.desmond.meta.CV

A class to define dihedral collective variable. Note that this collective variable is a two dimensional one. The first element is the cosine of the dihedral, and the second element is the sine of the dihedral angle.

cvdihedral_template = '\n# dihedral definition\n%(cvname)s_p0 = %(p0_atomsel)s;\n%(cvname)s_p1 = %(p1_atomsel)s;\n%(cvname)s_p2 = %(p2_atomsel)s;\n%(cvname)s_p3 = %(p3_atomsel)s;\n%(cvname)s = dihedral_gid(%(cvname)s_p0, %(cvname)s_p1, %(cvname)s_p2, %(cvname)s_p3);\nprint ("%(cvname)s", atan2(%(cvname)s));\n# the width for %(cvname)s will be set to: %(width)s\n'

cvdihedral_grp_template = '\n# dihedral definition for group of atoms\n%(cvname)s_g0 = center_of_mass ( %(p0_atomsel)s);\n%(cvname)s_g1 = center_of_mass ( %(p1_atomsel)s);\n%(cvname)s_g2 = center_of_mass ( %(p2_atomsel)s);\n%(cvname)s_g3 = center_of_mass ( %(p3_atomsel)s);\n\n%(cvname)s_v0 = min_image(%(cvname)s_g1 - %(cvname)s_g0);\n%(cvname)s_v1 = min_image(%(cvname)s_g2 - %(cvname)s_g1);\n%(cvname)s_v2 = min_image(%(cvname)s_g3 - %(cvname)s_g2);\n\n%(cvname)s = dihedral(%(cvname)s_v0, %(cvname)s_v1, %(cvname)s_v2);\nprint ("%(cvname)s", atan2(%(cvname)s[1],%(cvname)s[0]));\n# the width for %(cvname)s will be set to: %(width)s\n'

__init__(p0, p1, p2, p3, width, wall, floor)

Initialize self. See help(type(self)) for accurate signature.

getMExpr(model, cvname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': '\n A class to define dihedral collective variable.\n Note that this collective variable is a two dimensional one.\n The first element is the cosine of the dihedral,\n and the second element is the sine of the dihedral angle.\n ', 'cvdihedral_template': '\n# dihedral definition\n%(cvname)s_p0 = %(p0_atomsel)s;\n%(cvname)s_p1 = %(p1_atomsel)s;\n%(cvname)s_p2 = %(p2_atomsel)s;\n%(cvname)s_p3 = %(p3_atomsel)s;\n%(cvname)s = dihedral_gid(%(cvname)s_p0, %(cvname)s_p1, %(cvname)s_p2, %(cvname)s_p3);\nprint ("%(cvname)s", atan2(%(cvname)s));\n# the width for %(cvname)s will be set to: %(width)s\n', 'cvdihedral_grp_template': '\n# dihedral definition for group of atoms\n%(cvname)s_g0 = center_of_mass ( %(p0_atomsel)s);\n%(cvname)s_g1 = center_of_mass ( %(p1_atomsel)s);\n%(cvname)s_g2 = center_of_mass ( %(p2_atomsel)s);\n%(cvname)s_g3 = center_of_mass ( %(p3_atomsel)s);\n\n%(cvname)s_v0 = min_image(%(cvname)s_g1 - %(cvname)s_g0);\n%(cvname)s_v1 = min_image(%(cvname)s_g2 - %(cvname)s_g1);\n%(cvname)s_v2 = min_image(%(cvname)s_g3 - %(cvname)s_g2);\n\n%(cvname)s = dihedral(%(cvname)s_v0, %(cvname)s_v1, %(cvname)s_v2);\nprint ("%(cvname)s", atan2(%(cvname)s[1],%(cvname)s[0]));\n# the width for %(cvname)s will be set to: %(width)s\n', '__init__': <function CVDihedral.__init__>, 'getMExpr': <function CVDihedral.getMExpr>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.meta.CmsModel(model)

Bases: object

__init__(model)

Initialize self. See help(type(self)) for accurate signature.

atid2atomsel(atid)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__init__': <function CmsModel.__init__>, 'atid2atomsel': <function CmsModel.atid2atomsel>, '__dict__': <attribute '__dict__' of 'CmsModel' objects>, '__weakref__': <attribute '__weakref__' of 'CmsModel' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.desmond.meta.list2str(l)

class schrodinger.application.desmond.meta.Meta

Bases: object

declare_template = '\ndeclare_meta(\n dimension = %(dimension)d,\n cutoff = %(cutoff)f,\n first = %(first)f,\n interval = %(interval)f,\n name = "%(meta_name)s",\n initial = "");\n\ndeclare_output(\n name = "%(output_name)s",\n first = %(first)f,\n interval= %(interval)f);\n'

meta_template = '\n# height used for this run is: %(height)f\nmeta(0, %(height_width)s,\n %(cv)s);\n'

meta_well_tempered_template = '\n# height used for this run is: %(height)f, sampling temperature kT is: %(kTemp)f.\nmeta(0,\n array( %(height)f * exp( meta(0, %(height_width)s, %(cv)s )/(-1.0 * %(kTemp)f) ), %(width)s ),\n %(cv)s);\n'

__init__()

Initialize self. See help(type(self)) for accurate signature.

generateCfg(model=None)

addCV(cv)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', 'declare_template': '\ndeclare_meta(\n dimension = %(dimension)d,\n cutoff = %(cutoff)f,\n first = %(first)f,\n interval = %(interval)f,\n name = "%(meta_name)s",\n initial = "");\n\ndeclare_output(\n name = "%(output_name)s",\n first = %(first)f,\n interval= %(interval)f);\n', 'meta_template': '\n# height used for this run is: %(height)f\nmeta(0, %(height_width)s,\n %(cv)s);\n', 'meta_well_tempered_template': '\n# height used for this run is: %(height)f, sampling temperature kT is: %(kTemp)f.\nmeta(0,\n array( %(height)f * exp( meta(0, %(height_width)s, %(cv)s )/(-1.0 * %(kTemp)f) ), %(width)s ),\n %(cv)s);\n', '__init__': <function Meta.__init__>, 'generateCfg': <function Meta.generateCfg>, '_getMExpr': <function Meta._getMExpr>, 'addCV': <function Meta.addCV>, '__dict__': <attribute '__dict__' of 'Meta' objects>, '__weakref__': <attribute '__weakref__' of 'Meta' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.desmond.meta.parse_meta(m, model)

schrodinger.application.desmond.meta.generate_meta_cfg(meta_def, model)

Generate part of the config file for metadynamics simulation :param meta_def: The content of definition file for collective variables. :param model: topology file. :type meta_def: sea.Sea object :type model: cms.Cms object :return a string. Exception will be raised if encounting any errors.

schrodinger.application.desmond.meta.get_meta_cfg_filename(meta_def)

Returns the name of the kerseq and cvseq files given a metadynamics definition file :param meta_def: The content of definition file for collective variables. :param model: topology file.

class schrodinger.application.desmond.meta.MetaDynamicsAnalysis(data_fname, inp_fname=None, key=None)

Bases: object

Analysis tools for Desmond’s metadynamics jobs. The class can be used and run from the command-line or as a module.

__init__(data_fname, inp_fname=None, key=None)

Initialize self. See help(type(self)) for accurate signature.

evaluate(x)

computeFES(out_fname='', units='degrees', progress_callback=None)

This function figures out the grid from the ranges and the bins given the cfg. For each gaussian, add it to the previous gaussian sum for each grid point.

static convertDataToPlot(bins, data)

Converts data, usually read in from an exported plot result, to structures usable by the plot.

Parameters:

• bins (list or tuple) – The FES shape
• data – List of lists containing cv and FES values

Returns:

list of x and y values

Returns:

array of FES

static convertPlotToData(bins, edges, FES)

Takes data used to plot FES values and converts it to a list of lists for exporting purposes.

Parameters:

• bins (list or tuple) – The FES shape
• edges (List of lists) – The x and y values for the plot
• FES (numpy.array) – The FES values for the plot

Returns:

List of lists containing cv and FES values

static writeFES(fname, data, fes_shape, cvs, units)

Write out the free energy distribution in a common way. The GUI utilizing this class needs to write out data from self.computeFES

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.meta', '__doc__': "\n Analysis tools for Desmond's metadynamics jobs. The class can be used\n and run from the command-line or as a module.\n ", '__init__': <function MetaDynamicsAnalysis.__init__>, '_parseInp': <function MetaDynamicsAnalysis._parseInp>, '_getInp': <function MetaDynamicsAnalysis._getInp>, '_parseData': <function MetaDynamicsAnalysis._parseData>, 'evaluate': <function MetaDynamicsAnalysis.evaluate>, 'computeFES': <function MetaDynamicsAnalysis.computeFES>, 'convertDataToPlot': <staticmethod object>, 'convertPlotToData': <staticmethod object>, 'writeFES': <staticmethod object>, '__dict__': <attribute '__dict__' of 'MetaDynamicsAnalysis' objects>, '__weakref__': <attribute '__weakref__' of 'MetaDynamicsAnalysis' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.meta'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.desmond.meta.read_meta_cfg(config, model)

Read config file for metadynamics simulation :param meta_def: The content of definition file for collective variables. :param model: topology file. :type meta_def: string :type model: cms.Cms object :return a Meta

schrodinger.application.desmond.meta.get_distance(model, atom_list)

Check distance of the two groups of atoms defined in the atom list :param model: topology file :type model: cms.Cms object :param atom_list: atom list :type atom_list: list

schrodinger.application.desmond.meta.get_local_symmetry(st, atom_list)