Visualize coarse-grained systems#
On this page you can find various examples how to colorize and visualize a coarse-grained (CG) system in SAMSON.
Colorize by group names#
The example below demonstrates how to colorize groups based on their names using a color palette.
Colorize by group names#
names = ['DAPC', 'DAPS', 'DFPC', 'DFPS',
'DIPC', 'DIPS', 'DPPC', 'DPPS',
'DLPC', 'DLPS', 'DYPC', 'DYPS',
'DOPE']
# get all structural groups in the active document
indexer = SAMSON.getNodes('node.type sg')
# make the operation undoable
SAMSON.beginHolding("Colorize nodes")
for node in indexer:
if len(node.name):
# get the first part of the name (name before the ID)
name = node.name.split(' ')[0]
if name in names:
# colorize the node acording to its index in the list
# get the index of the name in the list
i = names.index(name)
# get the color 'intensity' value, which should be in the [0, 1] range
h = 1 - i / (len(names))
# get RGB color from the palette
color = SBPaletteDefaultPalette.sequentialHCLViridis.getColor(h)
# set the color of the node
node.setColor(color)
# stop holding the undoable operation
SAMSON.endHolding()
You can get a list of all structural group names (without IDs) in the document using the following code:
Get structural group names#
def get_structural_group_names():
names = set()
# get all structural groups in the active document
indexer = SAMSON.getNodes('node.type sg')
for node in indexer:
if len(node.name):
# get the first part of the name (name before the ID)
names.add(node.name.split(' ')[0])
return names
names = list(get_structural_group_names())
print(names)
Colorize coarse-grained atoms by name#
The example below demnonstrates how to colorize coarse-grained atoms by their name.
Colorize coarse-grained atoms by name#
atom_name_to_color = {
'NH3' : SBElement.getColorCPK(SBElement.Nitrogen), # the CPK color for Nitrogen
'NC3' : SBElement.getColorCPK(SBElement.N), # the CPK color for Nitrogen
'TAP' : SBElement.getColorCPK(SBElement.N), # the CPK color for Nitrogen
'PO4' : SBElement.getColorCPK(SBElement.P), # the CPK color for Phosphorus
'GL1' : SBColor.yellow,
'GL2' : SBColor.yellow,
'C1A' : SBColor.yellow,
'C2A' : SBColor.yellow,
'C3A' : SBColor.yellow,
'C4A' : SBColor.yellow,
'D1A' : SBColor.yellow,
'D2A' : SBColor.yellow,
'D3A' : SBColor.yellow,
'D4A' : SBColor.yellow,
'C1B' : SBColor.yellow,
'C2B' : SBColor.yellow,
'C3B' : SBColor.yellow,
'C4B' : SBColor.yellow,
'D1B' : SBColor.yellow,
'D2B' : SBColor.yellow,
'D3B' : SBColor.yellow,
'D4B' : SBColor.yellow,
}
atom_name_to_radius = {
'NH3' : SBQuantity.angstrom(1.5),
'NC3' : SBQuantity.angstrom(1.5),
'TAP' : SBQuantity.angstrom(1.5),
'PO4' : SBQuantity.angstrom(1.5)
}
# get all coarse-grained atoms in the active document
indexer = SAMSON.getNodes('node.type atom and atom.symbol CG')
# make the operation undoable
SAMSON.beginHolding("Colorize nodes")
for node in indexer:
if node.name in atom_name_to_color:
# set the CG color for the atom
node.setCoarseGrainedColor(atom_name_to_color[node.name])
if node.name in atom_name_to_radius:
# set the CG radius for the atom
node.setCoarseGrainedRadius(atom_name_to_radius[node.name])
# stop holding the undoable operation
SAMSON.endHolding()
Colorize coarse-grained atoms by type#
The example below demnonstrates how to colorize coarse-grained atoms by their CG type using a color palette.
Colorize coarse-grained atoms by type#
def get_coarse_grained_types(atom_indexer):
cg_types = set()
for node in atom_indexer:
if node.type == SBNode.Atom:
cg_types.add(node.getCoarseGrainedType())
return cg_types
# get all coarse-grained atoms in the active document
indexer = SAMSON.getNodes('node.type atom and atom.symbol CG')
cg_types = list(get_coarse_grained_types(atom_indexer = indexer))
print(f"Coarse-grained types in the document: {cg_types}")
# make the operation undoable
SAMSON.beginHolding("Colorize nodes")
for node in indexer:
cg_type = node.getCoarseGrainedType()
if cg_type in cg_types:
# colorize the node acording to its index in the list
# get the index of the CG type in the list
i = cg_types.index(cg_type)
# get the color 'intensity' value, which should be in the [0, 1] range
h = 1 - i / (len(cg_types))
# get RGB color from the palette
color = SBPaletteDefaultPalette.sequentialHCLViridis.getColor(h)
# set the CG color of the atom
node.setCoarseGrainedColor(color)
# stop holding the undoable operation
SAMSON.endHolding()
You can also set specific colors per CG type. For example, for Martini 2 types:
Colorize coarse-grained atoms by Martini 2 type#
# The beads types for Martini 2 and some arbitrary colors for them
cg_types = {
'C1' : SBElement.getColorCPK(SBElement.C),
'C2' : SBElement.getColorCPK(SBElement.C),
'C3' : SBElement.getColorCPK(SBElement.C),
'C4' : SBElement.getColorCPK(SBElement.C),
'C5' : SBElement.getColorCPK(SBElement.C),
'Nda' : SBColor.magenta,
'Nd' : SBColor.magenta,
'Na' : SBColor.magenta,
'N0' : SBColor.magenta,
'P1' : SBColor.green,
'P2' : SBColor.green,
'P3' : SBColor.green,
'P4' : SBColor.green,
'P5' : SBColor.green,
'Qda+' : SBColor.blue,
'Qd+' : SBColor.blue,
'Qa+' : SBColor.blue,
'Q0+' : SBColor.blue,
'Qda-' : SBColor.red,
'Qd-' : SBColor.red,
'Qa-' : SBColor.red,
'Q0-' : SBColor.red,
}
# get all coarse-grained atoms in the active document
indexer = SAMSON.getNodes('node.type atom and atom.symbol CG')
# make the operation undoable
SAMSON.beginHolding("Colorize nodes")
for node in indexer:
cg_type = node.getCoarseGrainedType()
# take the partial charge into account for Qda, Qa, Qd, Q0 types
if cg_type.startswith('Q'):
if node.partialCharge < 0: cg_type += '-'
elif node.partialCharge > 0: cg_type += '+'
if cg_type in cg_types:
# set the CG color of the atom
node.setCoarseGrainedColor(cg_types[cg_type])
# stop holding the undoable operation
SAMSON.endHolding()