Package schrodinger :: Package application :: Package desmond :: Module meta :: Class CVDist

Class CVDist

CV --+
     |
    CVDist

distance collective variable

Instance Methods

[hide private]

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

getMExpr(self, model, cvname)

Class Variables

[hide private]

cvdist_template = '\n# distance definition\n%(cvname)s_p0 = %(...

cvdist_grp_template = '\n# distance definition for group of at...

cvdist_wall_template = '\n# the upper bound, wall params for %...

cvdist_floor_template = '\n# lower bound wall or \'floor\' par...

Method Details

[hide private]

init(self, p0, p1, width, wall, floor)
(Constructor)

Overrides: CV.__init__

getMExpr(self, model, cvname)

Overrides: CV.getMExpr

Class Variable Details

[hide private]

cvdist_template

Value:

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

cvdist_grp_template

Value:

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

cvdist_wall_template

Value:

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

cvdist_floor_template

Value:

'''
# lower bound wall or \'floor\' params for %(cvname)s are: width is 0.
2;
# location at %(floor)f; # hight is 1000
%(cvname)s_floor = 1000 / (1 + exp((%(cvname)s - %(floor)f) / 0.2) );

'''

Class CVDist

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

getMExpr(self, model, cvname)

cvdist_template

cvdist_grp_template

cvdist_wall_template

cvdist_floor_template

init(self, p0, p1, width, wall, floor)
(Constructor)