Sort PolyTop dependencies for non-GUI environments

polytop_examples/dendrimer_ethylamine.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 # Construction of an ethylamine dendrimer
 
 # Import required Classes from PolyTop

polytop_examples/linear_PEI.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 # Construction of a simple linear homopolymer of PEI
 
 # This polymer will be 20 monomers long and constructed by joining Atom N71 to

polytop_examples/star_PEG.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 # Construction of a 4-arm PEG star polymer from single monomeric units
 
 # Import required Classes from PolyTop

star_polymer_validation/build_itp.py

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+# Construction of a 4-arm PEG star polymer from single monomeric units
+
+# Import required Classes from PolyTop
+from polytop.Junction import Junction
+from polytop.Monomer import Monomer
+from polytop.Visualize import Visualize
+from polytop.Polymer import Polymer
+from polytop.Topology import Topology
+
+
+# ----- Load in monomer Topologies from the extended monomer ITP files -----
+
+# Topology format is 'gromos' by default, but it is recommended to specify the
+# format for clarity and readability.
+ethanol = Topology.from_ITP("monomers/extended_ethanol.itp", format="gromos") # main arm monomer
+methane = Topology.from_ITP("monomers/extended_methane.itp", format="gromos") # terminal monomer
+neopentane = Topology.from_ITP("monomers/extended_neopentane.itp", format="gromos") # central monomer
+
+
+# ----- Create Junctions for the different Monomers to join to and from -----
+
+# Provide the bonding atom and the leaving atom, in that order, for the Junction
+# The two atoms used to create a Junction MUST have a bond between them.
+
+# Note that junctions are specified for extend() by their name attribute and
+# NOT by the variable name they are assigned to (which are instead used to pass
+# them into a Monomer object).
+
+# You will see that all of the Junctions created below have a unique name to
+# prevent randomisation or uncertainty in the extension, and thus ensure repeatability.
+
+# Create unique Junctions for the Monomers that make up each of the 4 arms of
+# the star, as well as the central Monomer and the terminal Monomers.
+
+# Junctions for the central 'neopentane' Monomer that will initiate the Polymer
+# One junction for each of the arms of the star
+j1 = Junction(neopentane.get_atom("C1"), neopentane.get_atom("O1"), name = "branch1")
+j2 = Junction(neopentane.get_atom("C3"), neopentane.get_atom("O2"), name = "branch2")
+j3 = Junction(neopentane.get_atom("C4"), neopentane.get_atom("O3"), name = "branch3")
+j4 = Junction(neopentane.get_atom("C5"), neopentane.get_atom("O4"), name = "branch4")
+
+# Junctions for each of the ethanol 'arm' Monomers
+# The 'oxy*' Junctions will join to one of the central 'neopentane' Monomer
+# Junctions (branch*), while the 'carb*'Junctions will join to an incoming
+# ethanol Monomer to extend that arm further. Such that branch1 Junction joins
+# to oxy1 Junction, and the carb1 Junction of the same Monomer will join to
+# another incoming Monomer's oxy1 Junction.
+oxy_j1 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy1")
+carb_j1 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb1")
+oxy_j2 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy2")
+carb_j2 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb2")
+oxy_j3 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy3")
+carb_j3 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb3")
+oxy_j4 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy4")
+carb_j4 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb4")
+
+# Junctions for the 'terminal' Monomer that will terminate the Polymer's arms
+# Note how only 1 Junction is created for the terminal Monomer, as this will
+# act to cap the Polymer and prevent further extension as there will be no
+# remaining Junctions.
+# The 'term' Junction will join to the final 'ethanol' Monomer Junction (carb*)
+term_j = Junction(methane.get_atom("C1"), methane.get_atom("O1"), name = "term")
+
+
+# ----- Create Monomers from their Topologies and any specified Junctions -----
+
+# Note that a unique Monomer has been created for each of the 4 arms with
+# different Junctions, which ensures that only Monomers of the same type are
+# joined to create the same arm, which means that all 4 arms will be the same
+# desired length.
+# If all Monomers had Junctions with the same names the polymerisation would be
+# random and each of the arms would be different lengths. The lengths of each
+# branch would also vary each time you built the Polymer, which is terrible for
+# scientific replicability!
+e1 = Monomer(ethanol, [oxy_j1, carb_j1])
+e2 = Monomer(ethanol, [oxy_j2, carb_j2])
+e3 = Monomer(ethanol, [oxy_j3, carb_j3])
+e4 = Monomer(ethanol, [oxy_j4, carb_j4])
+
+central = Monomer(neopentane, [j1, j2, j3, j4])
+
+terminal = Monomer(methane, [term_j]) # only needs one junction to join to the ends of each arm
+
+
+# ----- Start the Polymer with one Monomer -----
+
+# Only a Polymer object has access to the 'extend()' and 'extra_bond()'
+# functions needed to join monomers together, so the first Monomer object must
+# be converted to a Polymer object to build from.
+# Since the polymer will be built starting from the 'central' Monomer and
+# radiating outwards, the 'central' Monomer will be used to start the Polymer.
+four_polymer = Polymer(central)
+
+
+# ----- Extending the Polymer to reach the desired structure -----
+
+# The extend() function joins an incoming Monomer object to the Polymer object
+# that is invoking the method (in this case 'four_polymer').
+# The argument 'from_junction_name' specifies which Junction (by its name) in
+# the Polymer will form a new bond to the incoming Monomer, while the argument
+# 'to_junction_name' is the Junction in the incoming Monomer that will form a
+# bond to the Polymer. Such that the Polymer Junction's 'monomer atom' will
+# join to the Monomer Junction's 'monomer atom' and both of their 'leaving atoms'
+# will be discarded.
+# To ensure that you generate a valid topology, the two Junctions you join
+# should have corresponding atoms and the same bond, angle and dihedral
+# parameters, which will be ensured by using an appropriately extended topology
+# and defining Junctions correctly.
+
+# attach three ethanols to each of the four junctions (branch1-branch4) of the
+# central monomer, by extending each arm by 1 ethanol at a time. Extend from
+# carb* or branch* Junctions to the matching numbered oxy* Junctions, and then
+# finally from a carb* Junction to a "term" Junction.
+four_polymer.extend(e1, from_junction_name="branch1", to_junction_name="oxy1")
+four_polymer.extend(e2, from_junction_name="branch2", to_junction_name="oxy2")
+four_polymer.extend(e3, from_junction_name="branch3", to_junction_name="oxy3")
+four_polymer.extend(e4, from_junction_name="branch4", to_junction_name="oxy4")
+
+four_polymer.extend(e1, from_junction_name="carb1", to_junction_name="oxy1")
+four_polymer.extend(e2, from_junction_name="carb2", to_junction_name="oxy2")
+four_polymer.extend(e3, from_junction_name="carb3", to_junction_name="oxy3")
+four_polymer.extend(e4, from_junction_name="carb4", to_junction_name="oxy4")
+
+four_polymer.extend(e1, from_junction_name="carb1", to_junction_name="oxy1")
+four_polymer.extend(e2, from_junction_name="carb2", to_junction_name="oxy2")
+four_polymer.extend(e3, from_junction_name="carb3", to_junction_name="oxy3")
+four_polymer.extend(e4, from_junction_name="carb4", to_junction_name="oxy4")
+
+four_polymer.extend(terminal, from_junction_name="carb1", to_junction_name="term")
+four_polymer.extend(terminal, from_junction_name="carb2", to_junction_name="term")
+four_polymer.extend(terminal, from_junction_name="carb3", to_junction_name="term")
+four_polymer.extend(terminal, from_junction_name="carb4", to_junction_name="term")
+
+# Optionally (but recommended), check the netcharge of the monomers is
+# preserved and give it a descriptive name
+print(f"netcharge = {four_polymer.topology.netcharge}")
+four_polymer.topology.title = "four arm star polymer" # rename your ITP header and image name
+
+
+# ----- Save the polymer dendrimer to an itp file -----
+
+# Optionally, use Visualize to generate an image of the structure with RDKit
+# for an easy visual structure check
+four_polymer.save_to_file('polymers/star_polymer.json') # optional, text dump in a dictionary format
+four_polymer.topology.to_ITP('polymers/star_polymer.itp') # write the itp to be used for simulation
+Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('polymers/star_polymer.png',(400,300)) # optional, visualize the structure in 2D