From 1079630d04a3ce7c010002d5717fcf5a9b130331 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 18 Feb 2025 11:03:10 +1000 Subject: [PATCH 1/6] Create README.md for PolyTop examples to guide users through the tutorial scripts --- polytop_examples/README.md | 69 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 polytop_examples/README.md diff --git a/polytop_examples/README.md b/polytop_examples/README.md new file mode 100644 index 0000000..4b37f61 --- /dev/null +++ b/polytop_examples/README.md @@ -0,0 +1,69 @@ +# PolyTop example scripts + +This folder contains a handful of example scripts demonstrating the use of +*PolyTop*. All the files you need to run these examples are contained within +this folder. + +For detailed documentation of all *PolyTop* methods, please refer to the +[PolyConstruct ReadTheDocs](https://polyconstruct.readthedocs.io/en/latest/index.html). + +These tutorials are not intended as a primer on polymer design or +stereochemistry. It is assumed that the reader is familiar with polymer +chemistry and common types of copolymers. + +## Tutorial 01: Building a linear polyethyleneimine polymer topology using PolyTop + +The first tutorial is an example of how to make a linear 20 unit +polyethyleneimine chain using *PolyTop*. It is contained in the file +`linear_PEI.py`. + +This tutorial showcases several approaches, including: +* loading in itp files to create Topology objects +* defining appropriate Junctions for polymer extension +* creating Monomer objects from a Topology and list of Junctions +* building a polymer chain with `extend()` +* saving the polymer to an itp file + +This tutorial is all contained in a single script, with detailed comments +discussing the strategies used and the reasoning behind them or another method. +You are encouraged to view the topologies generated by this script, and others +you develop, to understand how the monomers are connected. + +## Tutorial 02: Building an ethlyamine dendrimer polymer topology using PolyTop + +The second tutorial shows strategies for making a more complex polymer with +levels of branching building outwards from a central monomer. It is contained +in the file `dendrimer_ethylamine.py`. + +This tutorial showcases several approaches, including: +* breaking down a polymer structure into the monomers required to build it +* loading in itp files to create Topology objects +* defining appropriate, distinct Junctions for precise polymer extension +* creating Monomer objects from a Topology and list of Junctions +* building a polymer chain with `extend()` +* saving the polymer to an itp file + +This tutorial is all contained in a single script, with detailed comments +discussing the strategies used and the reasoning behind them or another method. +You are encouraged to view the topologies generated by this script, and others +you develop, to understand how the monomers are connected. + +## Tutorial 03: Building a 4-arm PEG star polymer topology using PolyTop + +The third tutorial shows strategies for making another complex polymer with +long linear arms branching out from a central monomer. It is contained +in the file `star_PEG.py`. + +This tutorial showcases several approaches, including: +* breaking down a polymer structure into the monomers required to build it +* discussing different approaches to create the same polymer structure +* loading in itp files to create Topology objects +* defining appropriate, distinct Junctions for precise polymer extension +* creating Monomer objects from a Topology and list of Junctions +* building a polymer chain with `extend()` +* saving the polymer to an itp file + +This tutorial is all contained in a single script, with detailed comments +discussing the strategies used and the reasoning behind them or another method. +You are encouraged to view the topologies generated by this script, and others +you develop, to understand how the monomers are connected. From bc3a7f21eae0b8fac9db484fae1e25433279ee23 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 18 Feb 2025 11:13:38 +1000 Subject: [PATCH 2/6] Beef up comments for linear_PEI.py example script --- polytop_examples/linear_PEI.py | 70 +++++++++++++++++++++++++++------- 1 file changed, 56 insertions(+), 14 deletions(-) diff --git a/polytop_examples/linear_PEI.py b/polytop_examples/linear_PEI.py index 1943729..1854293 100644 --- a/polytop_examples/linear_PEI.py +++ b/polytop_examples/linear_PEI.py @@ -1,33 +1,75 @@ # Construction of a simple linear homopolymer of PEI -# Import required classes from PolyTop +# This polymer will be 20 monomers long and constructed by joining Atom C51 to +# N7, and discarding the atoms C62 and C6 (and any other atoms, such as +# hydrogens, connected to them but not the rest of the polymer). + +# 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 Topology from ITP file -top = Topology.from_ITP("data/pei.itp") -# Create a Junction to join 'to' and another to join 'from'. -# Provide the bonding atom and the leaving atom, in that order, for the -# Junction - they must have a bond between them. +# ----- Load in the monomer Topology from the extended PEI monomer ITP file ----- + +# Topology format is 'gromos' by default, but it is recommended to specify the +# format for clarity and readability. +top = Topology.from_ITP("data/pei.itp", format="gromos") + + +# ----- Create a Junction to join 'to' and another to join '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 (in +# this example 'to' and 'from', and NOT by the variable name they are assigned +# to 'to_j' and 'from_j', which are used to pass them into a Monomer object) to_j = Junction(top.get_atom("C51"), top.get_atom("C62"), name = "to") from_j = Junction(top.get_atom("N7"), top.get_atom("C6"), name = "from") -# Create a Monomer from the Topology and a list of the Junctions + +# ----- Create a Monomer from the Topology and a list of the Junctions ----- + +# Note that you could also create an 'initial' Monomer with the 'from_j' +# Junction only and a 'terminal' Monomer with the 'to_j' only, but this is not +# necessary, as any Junctions which are not extended to or from with extend() +# will not lose their leaving atoms. However, this is a beneficial approach for +# more complex polymers, such as with branching, to prevent ambiguity during +# extension. For examples of this, see tutorial scripts in +# `dendrimer_ethlyamine.py` or `star_PEG.py` monomer = Monomer(top, [to_j, from_j]) -# Start the Polymer with one Monomer +# ----- 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. polymer = Polymer(monomer) -# Extend the Polymer to the desired length (in this case 20) + +# ----- Extend the Polymer to the desired length (in this case 20) ----- + +# The extend() function joins an incoming Monomer object (in this case 'monomer') +# to the Polymer object that is invoking the method (in this case '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. for i in range(19): polymer.extend(monomer, from_junction_name="from", to_junction_name="to") -# Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check -polymer.topology.title = "pei polymer" # renames the ITP header and image -polymer.save_to_file('data/pei_linear_polymer.json') # text dump -polymer.topology.to_ITP('data/pei_linear_polymer.itp') -Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/pei_linear_polymer.png',(400,300)) \ No newline at end of file +# ----- Save the polymer to an itp file ----- +# Optionally, use Visualize to generate an image of the structure with RDKit +# for an easy visual structure check +polymer.topology.title = "pei polymer" # optional but good for identifying files, renames the ITP header and image +polymer.save_to_file('data/pei_linear_polymer.json') # optional, text dump in a dictionary format +polymer.topology.to_ITP('data/pei_linear_polymer.itp') # write the itp to be used for simulation +Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/pei_linear_polymer.png',(400,300)) # optional, visualize the structure in 2Da \ No newline at end of file From 6a9167b2b009971012f97ad284d2df6918142580 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 18 Feb 2025 11:41:56 +1000 Subject: [PATCH 3/6] Beef up comments for dendrimer_ethylanime.py example script --- polytop_examples/dendrimer_ethylamine.py | 104 ++++++++++++++++++----- 1 file changed, 85 insertions(+), 19 deletions(-) diff --git a/polytop_examples/dendrimer_ethylamine.py b/polytop_examples/dendrimer_ethylamine.py index 247f465..c343a28 100644 --- a/polytop_examples/dendrimer_ethylamine.py +++ b/polytop_examples/dendrimer_ethylamine.py @@ -1,32 +1,66 @@ # Construction of an ethylamine dendrimer -# import required classes from PolyTop +# 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 ITP files -core_mono = Topology.from_ITP("data/dendrimer_core.itp") -bifurcating_mono = Topology.from_ITP("data/dendrimer_bifurcating.itp") -terminal_mono = Topology.from_ITP("data/dendrimer_terminal.itp") -# create junctions for different 'levels' of monomers, depending on what level of branching they exist at in the dendrimer -# junctions are created with the bonding atom and then the leaving atom specified, in that order, and should be given a unique name +# ----- 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. +core_mono = Topology.from_ITP("data/dendrimer_core.itp", format="gromos") +bifurcating_mono = Topology.from_ITP("data/dendrimer_bifurcating.itp", format="gromos") +terminal_mono = Topology.from_ITP("data/dendrimer_terminal.itp", format="gromos") + + +# ----- 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 (in +# this example 'to' and 'from', and NOT by the variable name they are assigned +# to 'to_j' and 'from_j', which are 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 junctions for different 'levels' of monomers, depending on what level +# of branching they exist at in the dendrimer (e.g. central, first branching +# level, second branching level or terminal) + +# Junctions for the 'central' Monomer that will initiate the Polymer +# One junction for each of the branches radiating out central1 = Junction(core_mono.get_atom("N2"), core_mono.get_atom("C9"), name="C1") central2 = Junction(core_mono.get_atom("N2"), core_mono.get_atom("C7"), name="C2") central3 = Junction(core_mono.get_atom("N1"), core_mono.get_atom("C2"), name="C3") central4 = Junction(core_mono.get_atom("N1"), core_mono.get_atom("C3"), name="C4") +# Junctions for the first level of branching with a 'bifurcating' Monomer +# The 'to' Junction will join to one of the 'central' Monomer Junctions, while +# the 'from1' and 'from2' Junctions will join to incoming second level of branching Monomers b1 = Junction(bifurcating_mono.get_atom("C6"), bifurcating_mono.get_atom("N2"), name = "to") b2a = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C2"), name = "from1") b2b = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C3"), name = "from2") +# Junctions for the second level of branching with a 'bifurcating' Monomer +# The 'to2' Junction will join to one of the first level branching 'bifurcating' +# Monomer Junctions (i.e. from1 or from2), while the 'from12' and 'from22' +# Junctions will join to incoming terminal Monomers c1 = Junction(bifurcating_mono.get_atom("C6"), bifurcating_mono.get_atom("N2"), name = "to2") c2a = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C2"), name = "from12") c2b = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C3"), name = "from22") +# Junctions for the 'terminal' Monomer that will terminate the Polymer +# 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 one of the second level branching 'bifurcating' +# Monomer Junctions (i.e. from12 or from22) t = Junction(terminal_mono.get_atom("C1"), terminal_mono.get_atom("N1"), name = "term") # create monomers from their topologies and any specified junctions @@ -38,19 +72,45 @@ bifur2 = Monomer(bifurcating_mono, [c1, c2a, c2b]) cap = Monomer(terminal_mono, [t]) -# start the polymer with the central monomer +# ----- 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. polymer = Polymer(central) -# extend first layer of dendrimer + +# ----- 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 '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. + +# Extend first layer of dendrimer polymer.extend(bifur1, from_junction_name="C1", to_junction_name="to") polymer.extend(bifur1, from_junction_name="C2", to_junction_name="to") polymer.extend(bifur1, from_junction_name="C3", to_junction_name="to") polymer.extend(bifur1, from_junction_name="C4", to_junction_name="to") -# extend second layer of dendrimer -# note how the first and second 'layers' have different monomers with different -# Junction names to ensure the correct structure is always formed. Junction and -# Monomer name ambiguity WILL cause formation of random, unreplicatable polymer topologies +# Extend second layer of dendrimer +# Note how the first and second levels of branching have different Monomers +# with different Junction names to ensure the correct structure is always +# formed. Junction and Monomer name ambiguity or redundancy *WILL* cause +# formation of random, unreplicatable polymer topologies. +# These extends could be completed within a for loop to reduce the amount of +# code, but have been expanded for this example to make sure that all commands +# are clear and explicit. polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") polymer.extend(bifur2, from_junction_name="from2", to_junction_name="to2") polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") @@ -60,7 +120,9 @@ polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") polymer.extend(bifur2, from_junction_name="from2", to_junction_name="to2") -# finish polymer by extending on the capping monomer +# Finish polymer by extending on the capping monomer +# Note how each level of extension radiating outward from the central Monomer +# has double the number of extend() calls as the branching doubles each layer. polymer.extend(cap, from_junction_name="from12", to_junction_name="term") polymer.extend(cap, from_junction_name="from22", to_junction_name="term") polymer.extend(cap, from_junction_name="from12", to_junction_name="term") @@ -78,10 +140,14 @@ polymer.extend(cap, from_junction_name="from12", to_junction_name="term") polymer.extend(cap, from_junction_name="from22", to_junction_name="term") -# check netcharge of the monomers is preserved (in this case, close to 0) +# Optionally (but recommended), check the netcharge of the monomers is +# preserved (in this case, close to 0) print(polymer.topology.netcharge) -# save the dendrimer to a file and visualise the structure with RDKit for an easy visual structure check -polymer.save_to_file('data/ethylamine_dendrimer.json') # text dump -polymer.topology.to_ITP('data/ethylamine_dendrimer.itp') -Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/ethylamine_dendrimer.png',(400,300)) \ No newline at end of file +# ----- 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 +polymer.save_to_file('data/ethylamine_dendrimer.json') # optional, text dump in a dictionary format +polymer.topology.to_ITP('data/ethylamine_dendrimer.itp') # write the itp to be used for simulation +Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/ethylamine_dendrimer.png',(400,300)) # optional, visualize the structure in 2D \ No newline at end of file From 682c92eb6870019b3377a612889d750eae4e5d88 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 18 Feb 2025 12:30:40 +1000 Subject: [PATCH 4/6] Beef up comments for star_PEG.py example script --- polytop_examples/star_PEG.py | 113 ++++++++++++++++++++++++++++------- 1 file changed, 93 insertions(+), 20 deletions(-) diff --git a/polytop_examples/star_PEG.py b/polytop_examples/star_PEG.py index f93df60..86ed8d7 100644 --- a/polytop_examples/star_PEG.py +++ b/polytop_examples/star_PEG.py @@ -1,18 +1,50 @@ # Construction of a 4-arm PEG star polymer from single monomeric units -# import required classes from PolyTop +# 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 ITP files -ethanol = Topology.from_ITP("data/extended_ethanol.itp") # main arm monomer -methane = Topology.from_ITP("data/extended_methane.itp") # terminal monomer -neopentane = Topology.from_ITP("data/extended_neopentane.itp") # central monomer -# create junctions for each monomer with the bonding atom and then the leaving atom specified, in that order, with a unique name +# ----- 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("data/extended_ethanol.itp", format="gromos") # main arm monomer +methane = Topology.from_ITP("data/extended_methane.itp", format="gromos") # terminal monomer +neopentane = Topology.from_ITP("data/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") @@ -22,14 +54,24 @@ 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") -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 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 + +# ----- 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]) @@ -39,10 +81,36 @@ terminal = Monomer(methane, [term_j]) # only needs one junction to join to the ends of each arm -# start the polymer with the central monomer + +# ----- 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) -# attach three ethanols to each of the four junctions (j1-j4) of the central monomer + +# ----- 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") @@ -63,11 +131,16 @@ four_polymer.extend(terminal, from_junction_name="carb3", to_junction_name="term") four_polymer.extend(terminal, from_junction_name="carb4", to_junction_name="term") -# check polymer charge and give it a descriptive name +# 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 - overlapped monomers" # rename your ITP header and image name +four_polymer.topology.title = "four arm star polymer" # rename your ITP header and image name + + +# ----- Save the polymer dendrimer to an itp file ----- -# save the polymer to a file and visualise the structure with RDKit for an easy visual structure check -four_polymer.save_to_file('data/four_arm_star_overlapped_monomers.json') # text dump -four_polymer.topology.to_ITP('data/four_arm_star_overlapped_monomers.itp') -Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('data/four_arm_star_overlapped_monomers.png',(400,300)) \ No newline at end of file +# Optionally, use Visualize to generate an image of the structure with RDKit +# for an easy visual structure check +four_polymer.save_to_file('data/four_arm_star.json') # optional, text dump in a dictionary format +four_polymer.topology.to_ITP('data/four_arm_star.itp') # write the itp to be used for simulation +Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('data/four_arm_star.png',(400,300)) # optional, visualize the structure in 2D \ No newline at end of file From 8508778516977cc665730155ae4d26700e57032b Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 18 Feb 2025 12:32:43 +1000 Subject: [PATCH 5/6] Update method used to join monomers to make PEI polymer to ensure it is correct, correct some typos in script comments and update output files as required --- ...rlapped_monomers.itp => four_arm_star.itp} | 354 ++++---- ...apped_monomers.json => four_arm_star.json} | 2 +- polytop_examples/data/four_arm_star.png | Bin 0 -> 13685 bytes .../four_arm_star_overlapped_monomers.png | Bin 16291 -> 0 bytes polytop_examples/data/pei_linear_polymer.itp | 857 ++++++------------ polytop_examples/data/pei_linear_polymer.json | 2 +- polytop_examples/data/pei_linear_polymer.png | Bin 12032 -> 10073 bytes polytop_examples/dendrimer_ethylamine.py | 19 +- polytop_examples/linear_PEI.py | 7 +- 9 files changed, 480 insertions(+), 761 deletions(-) rename polytop_examples/data/{four_arm_star_overlapped_monomers.itp => four_arm_star.itp} (99%) rename polytop_examples/data/{four_arm_star_overlapped_monomers.json => four_arm_star.json} (63%) create mode 100644 polytop_examples/data/four_arm_star.png delete mode 100644 polytop_examples/data/four_arm_star_overlapped_monomers.png diff --git a/polytop_examples/data/four_arm_star_overlapped_monomers.itp b/polytop_examples/data/four_arm_star.itp similarity index 99% rename from polytop_examples/data/four_arm_star_overlapped_monomers.itp rename to polytop_examples/data/four_arm_star.itp index 0ed2e6e..4fa0280 100644 --- a/polytop_examples/data/four_arm_star_overlapped_monomers.itp +++ b/polytop_examples/data/four_arm_star.itp @@ -1,5 +1,5 @@ ;----------------------------TITLE ----------------------------------------------------------------------------------------- -; four arm star polymer - overlapped monomers +; four arm star polymer ; ;----------------------------TITLE ----------------------------------------------------------------------------------------- ; Pentaerythritol @@ -182,46 +182,46 @@ [ bonds ] 1 3 2 0.1090 1.2300e+07 - 1 2 2 0.1090 1.2300e+07 1 41 2 0.1430 8.1800e+06 1 4 2 0.1540 4.0057e+06 - 4 11 2 0.1540 4.0057e+06 + 1 2 2 0.1090 1.2300e+07 4 5 2 0.1540 4.0057e+06 4 8 2 0.1540 4.0057e+06 - 5 6 2 0.1090 1.2300e+07 + 4 11 2 0.1540 4.0057e+06 5 20 2 0.1430 8.1800e+06 5 7 2 0.1090 1.2300e+07 - 8 27 2 0.1430 8.1800e+06 + 5 6 2 0.1090 1.2300e+07 8 10 2 0.1090 1.2300e+07 + 8 27 2 0.1430 8.1800e+06 8 9 2 0.1090 1.2300e+07 - 11 34 2 0.1430 8.1800e+06 - 11 13 2 0.1090 1.2300e+07 11 12 2 0.1090 1.2300e+07 + 11 13 2 0.1090 1.2300e+07 + 11 34 2 0.1430 8.1800e+06 + 14 15 2 0.1090 1.2300e+07 14 16 2 0.1090 1.2300e+07 14 17 2 0.1530 7.1500e+06 14 48 2 0.1430 8.1800e+06 - 14 15 2 0.1090 1.2300e+07 + 17 20 2 0.1430 8.1800e+06 17 18 2 0.1090 1.2300e+07 17 19 2 0.1090 1.2300e+07 - 17 20 2 0.1430 8.1800e+06 - 21 55 2 0.1430 8.1800e+06 21 23 2 0.1090 1.2300e+07 21 24 2 0.1530 7.1500e+06 + 21 55 2 0.1430 8.1800e+06 21 22 2 0.1090 1.2300e+07 + 24 26 2 0.1090 1.2300e+07 24 27 2 0.1430 8.1800e+06 24 25 2 0.1090 1.2300e+07 - 24 26 2 0.1090 1.2300e+07 - 28 30 2 0.1090 1.2300e+07 - 28 29 2 0.1090 1.2300e+07 28 31 2 0.1530 7.1500e+06 + 28 29 2 0.1090 1.2300e+07 + 28 30 2 0.1090 1.2300e+07 28 62 2 0.1430 8.1800e+06 31 34 2 0.1430 8.1800e+06 31 33 2 0.1090 1.2300e+07 31 32 2 0.1090 1.2300e+07 - 35 69 2 0.1430 8.1800e+06 - 35 38 2 0.1530 7.1500e+06 35 37 2 0.1090 1.2300e+07 35 36 2 0.1090 1.2300e+07 + 35 69 2 0.1430 8.1800e+06 + 35 38 2 0.1530 7.1500e+06 38 40 2 0.1090 1.2300e+07 38 41 2 0.1430 8.1800e+06 38 39 2 0.1090 1.2300e+07 @@ -229,30 +229,30 @@ 42 44 2 0.1090 1.2300e+07 42 45 2 0.1530 7.1500e+06 42 76 2 0.1430 8.1800e+06 + 45 48 2 0.1430 8.1800e+06 45 46 2 0.1090 1.2300e+07 45 47 2 0.1090 1.2300e+07 - 45 48 2 0.1430 8.1800e+06 49 52 2 0.1530 7.1500e+06 + 49 51 2 0.1090 1.2300e+07 49 50 2 0.1090 1.2300e+07 49 83 2 0.1430 8.1800e+06 - 49 51 2 0.1090 1.2300e+07 52 53 2 0.1090 1.2300e+07 52 55 2 0.1430 8.1800e+06 52 54 2 0.1090 1.2300e+07 + 56 90 2 0.1430 8.1800e+06 56 58 2 0.1090 1.2300e+07 56 59 2 0.1530 7.1500e+06 56 57 2 0.1090 1.2300e+07 - 56 90 2 0.1430 8.1800e+06 + 59 60 2 0.1090 1.2300e+07 59 61 2 0.1090 1.2300e+07 59 62 2 0.1430 8.1800e+06 - 59 60 2 0.1090 1.2300e+07 + 63 97 2 0.1430 8.1800e+06 63 65 2 0.1090 1.2300e+07 63 66 2 0.1530 7.1500e+06 63 64 2 0.1090 1.2300e+07 - 63 97 2 0.1430 8.1800e+06 - 66 67 2 0.1090 1.2300e+07 66 68 2 0.1090 1.2300e+07 66 69 2 0.1430 8.1800e+06 + 66 67 2 0.1090 1.2300e+07 70 71 2 0.1090 1.2300e+07 70 72 2 0.1090 1.2300e+07 70 98 2 0.1430 8.1800e+06 @@ -260,356 +260,356 @@ 73 76 2 0.1430 8.1800e+06 73 74 2 0.1090 1.2300e+07 73 75 2 0.1090 1.2300e+07 + 77 102 2 0.1430 8.1800e+06 77 79 2 0.1090 1.2300e+07 77 80 2 0.1530 7.1500e+06 77 78 2 0.1090 1.2300e+07 - 77 102 2 0.1430 8.1800e+06 - 80 81 2 0.1090 1.2300e+07 80 82 2 0.1090 1.2300e+07 80 83 2 0.1430 8.1800e+06 + 80 81 2 0.1090 1.2300e+07 + 84 106 2 0.1430 8.1800e+06 + 84 85 2 0.1090 1.2300e+07 84 86 2 0.1090 1.2300e+07 84 87 2 0.1530 7.1500e+06 - 84 85 2 0.1090 1.2300e+07 - 84 106 2 0.1430 8.1800e+06 + 87 89 2 0.1090 1.2300e+07 87 90 2 0.1430 8.1800e+06 87 88 2 0.1090 1.2300e+07 - 87 89 2 0.1090 1.2300e+07 91 94 2 0.1530 7.1500e+06 - 91 93 2 0.1090 1.2300e+07 91 110 2 0.1430 8.1800e+06 91 92 2 0.1090 1.2300e+07 - 94 97 2 0.1430 8.1800e+06 + 91 93 2 0.1090 1.2300e+07 94 96 2 0.1090 1.2300e+07 94 95 2 0.1090 1.2300e+07 + 94 97 2 0.1430 8.1800e+06 98 99 2 0.1090 1.2300e+07 98 101 2 0.1090 1.2300e+07 98 100 2 0.1090 1.2300e+07 102 104 2 0.1090 1.2300e+07 102 103 2 0.1090 1.2300e+07 102 105 2 0.1090 1.2300e+07 - 106 109 2 0.1090 1.2300e+07 106 107 2 0.1090 1.2300e+07 + 106 109 2 0.1090 1.2300e+07 106 108 2 0.1090 1.2300e+07 + 110 113 2 0.1090 1.2300e+07 110 111 2 0.1090 1.2300e+07 110 112 2 0.1090 1.2300e+07 - 110 113 2 0.1090 1.2300e+07 [ pairs ] - 1 13 1 - 1 9 1 1 12 1 - 1 7 1 - 1 10 1 + 1 13 1 1 6 1 + 1 10 1 + 1 7 1 + 1 9 1 + 2 8 1 2 5 1 2 11 1 - 2 8 1 - 3 8 1 - 3 5 1 3 11 1 - 5 10 1 + 3 5 1 + 3 8 1 5 9 1 5 12 1 + 5 10 1 5 13 1 - 6 11 1 6 8 1 - 7 11 1 + 6 11 1 7 8 1 - 8 13 1 + 7 11 1 8 12 1 + 8 13 1 9 11 1 10 11 1 15 18 1 - 15 19 1 15 20 1 + 15 19 1 16 18 1 16 20 1 16 19 1 22 26 1 - 22 25 1 22 27 1 - 23 25 1 + 22 25 1 23 26 1 23 27 1 - 29 33 1 - 29 32 1 + 23 25 1 29 34 1 - 30 34 1 - 30 32 1 + 29 32 1 + 29 33 1 30 33 1 - 36 41 1 + 30 32 1 + 30 34 1 36 40 1 + 36 41 1 36 39 1 37 40 1 - 37 41 1 37 39 1 + 37 41 1 + 43 47 1 43 46 1 43 48 1 - 43 47 1 - 44 48 1 44 46 1 44 47 1 - 50 54 1 - 50 53 1 + 44 48 1 50 55 1 - 51 53 1 + 50 53 1 + 50 54 1 51 54 1 51 55 1 - 57 62 1 - 57 60 1 + 51 53 1 57 61 1 - 58 60 1 + 57 60 1 + 57 62 1 58 61 1 58 62 1 + 58 60 1 + 64 68 1 64 67 1 64 69 1 - 64 68 1 + 65 67 1 65 68 1 65 69 1 - 65 67 1 - 71 74 1 - 71 76 1 71 75 1 - 72 74 1 + 71 76 1 + 71 74 1 72 76 1 72 75 1 - 78 83 1 + 72 74 1 78 81 1 78 82 1 - 79 83 1 - 79 81 1 + 78 83 1 79 82 1 - 85 90 1 + 79 81 1 + 79 83 1 85 88 1 85 89 1 + 85 90 1 86 89 1 - 86 90 1 86 88 1 - 92 97 1 + 86 90 1 92 95 1 + 92 97 1 92 96 1 93 97 1 93 95 1 93 96 1 [ angles ] - 3 1 41 2 109.6000 4.5000e+02 - 3 1 4 2 109.5000 4.4800e+02 2 1 3 2 107.5700 4.8400e+02 - 2 1 41 2 109.6000 4.5000e+02 - 2 1 4 2 109.5000 4.4800e+02 + 3 1 4 2 109.5000 4.4800e+02 + 3 1 41 2 109.6000 4.5000e+02 1 41 38 2 109.5000 4.5000e+02 + 2 1 41 2 109.6000 4.5000e+02 4 1 41 2 115.0000 6.1000e+02 - 1 4 8 2 109.5000 5.2000e+02 - 1 4 11 2 109.5000 5.2000e+02 1 4 5 2 109.5000 5.2000e+02 - 4 11 12 2 109.5000 4.4800e+02 + 2 1 4 2 109.5000 4.4800e+02 + 1 4 11 2 109.5000 5.2000e+02 + 1 4 8 2 109.5000 5.2000e+02 + 5 4 8 2 109.5000 5.2000e+02 5 4 11 2 109.5000 5.2000e+02 - 8 4 11 2 109.5000 5.2000e+02 - 4 11 34 2 115.0000 6.1000e+02 - 4 11 13 2 109.5000 4.4800e+02 + 4 5 6 2 109.5000 4.4800e+02 4 5 20 2 115.0000 6.1000e+02 4 5 7 2 109.5000 4.4800e+02 - 4 5 6 2 109.5000 4.4800e+02 - 5 4 8 2 109.5000 5.2000e+02 + 8 4 11 2 109.5000 5.2000e+02 4 8 10 2 109.5000 4.4800e+02 4 8 27 2 115.0000 6.1000e+02 4 8 9 2 109.5000 4.4800e+02 - 6 5 7 2 107.5700 4.8400e+02 + 4 11 13 2 109.5000 4.4800e+02 + 4 11 12 2 109.5000 4.4800e+02 + 4 11 34 2 115.0000 6.1000e+02 + 7 5 20 2 109.6000 4.5000e+02 6 5 20 2 109.6000 4.5000e+02 5 20 17 2 109.5000 4.5000e+02 - 7 5 20 2 109.6000 4.5000e+02 - 8 27 24 2 109.5000 4.5000e+02 + 6 5 7 2 107.5700 4.8400e+02 + 9 8 10 2 107.5700 4.8400e+02 10 8 27 2 109.6000 4.5000e+02 + 8 27 24 2 109.5000 4.5000e+02 9 8 27 2 109.6000 4.5000e+02 - 9 8 10 2 107.5700 4.8400e+02 + 12 11 13 2 107.5700 4.8400e+02 12 11 34 2 109.6000 4.5000e+02 13 11 34 2 109.6000 4.5000e+02 11 34 31 2 109.5000 4.5000e+02 - 12 11 13 2 107.5700 4.8400e+02 - 16 14 48 2 111.0000 5.3000e+02 - 16 14 17 2 110.3000 5.2400e+02 15 14 16 2 107.6000 5.0700e+02 15 14 17 2 110.3000 5.2400e+02 + 15 14 48 2 111.0000 5.3000e+02 + 16 14 48 2 111.0000 5.3000e+02 + 16 14 17 2 110.3000 5.2400e+02 + 17 14 48 2 109.5000 5.2000e+02 14 17 18 2 109.6000 4.5000e+02 - 14 17 20 2 111.0000 5.3000e+02 14 17 19 2 109.6000 4.5000e+02 - 17 14 48 2 109.5000 5.2000e+02 - 15 14 48 2 111.0000 5.3000e+02 + 14 17 20 2 111.0000 5.3000e+02 14 48 45 2 109.5000 4.5000e+02 - 18 17 19 2 108.0000 4.6500e+02 18 17 20 2 111.0000 5.3000e+02 19 17 20 2 111.0000 5.3000e+02 - 24 21 55 2 109.5000 5.2000e+02 - 22 21 55 2 111.0000 5.3000e+02 - 23 21 55 2 111.0000 5.3000e+02 - 21 55 52 2 109.5000 4.5000e+02 + 18 17 19 2 108.0000 4.6500e+02 22 21 23 2 107.6000 5.0700e+02 23 21 24 2 110.3000 5.2400e+02 - 21 24 26 2 109.6000 4.5000e+02 + 23 21 55 2 111.0000 5.3000e+02 + 24 21 55 2 109.5000 5.2000e+02 21 24 25 2 109.6000 4.5000e+02 - 22 21 24 2 110.3000 5.2400e+02 + 21 24 26 2 109.6000 4.5000e+02 21 24 27 2 111.0000 5.3000e+02 - 25 24 27 2 111.0000 5.3000e+02 - 26 24 27 2 111.0000 5.3000e+02 + 22 21 24 2 110.3000 5.2400e+02 + 21 55 52 2 109.5000 4.5000e+02 + 22 21 55 2 111.0000 5.3000e+02 25 24 26 2 108.0000 4.6500e+02 - 29 28 30 2 107.6000 5.0700e+02 - 30 28 31 2 110.3000 5.2400e+02 - 30 28 62 2 111.0000 5.3000e+02 - 29 28 62 2 111.0000 5.3000e+02 + 26 24 27 2 111.0000 5.3000e+02 + 25 24 27 2 111.0000 5.3000e+02 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- 70 73 76 2 111.0000 5.3000e+02 70 73 75 2 109.6000 4.5000e+02 + 70 73 76 2 111.0000 5.3000e+02 70 73 74 2 109.6000 4.5000e+02 - 74 73 76 2 111.0000 5.3000e+02 75 73 76 2 111.0000 5.3000e+02 + 74 73 76 2 111.0000 5.3000e+02 74 73 75 2 108.0000 4.6500e+02 - 78 77 79 2 107.6000 5.0700e+02 + 78 77 102 2 111.0000 5.3000e+02 79 77 102 2 111.0000 5.3000e+02 + 77 102 104 2 106.7500 5.0300e+02 + 80 77 102 2 109.5000 5.2000e+02 + 77 102 103 2 106.7500 5.0300e+02 + 77 102 105 2 106.7500 5.0300e+02 + 78 77 79 2 107.6000 5.0700e+02 79 77 80 2 110.3000 5.2400e+02 - 77 80 83 2 111.0000 5.3000e+02 - 77 80 82 2 109.6000 4.5000e+02 77 80 81 2 109.6000 4.5000e+02 + 77 80 82 2 109.6000 4.5000e+02 + 77 80 83 2 111.0000 5.3000e+02 78 77 80 2 110.3000 5.2400e+02 - 80 77 102 2 109.5000 5.2000e+02 - 78 77 102 2 111.0000 5.3000e+02 - 77 102 105 2 106.7500 5.0300e+02 - 77 102 103 2 106.7500 5.0300e+02 - 77 102 104 2 106.7500 5.0300e+02 - 81 80 83 2 111.0000 5.3000e+02 - 81 80 82 2 108.0000 4.6500e+02 82 80 83 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23, "pair_type": 1}, {"atom_a": 2, "atom_b": 23, "pair_type": 1}, {"atom_a": 2, "atom_b": 16, "pair_type": 1}, {"atom_a": 2, "atom_b": 30, "pair_type": 1}, {"atom_a": 4, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 4, "pair_type": 1}, {"atom_a": 4, "atom_b": 23, "pair_type": 1}, {"atom_a": 37, "atom_b": 5, "pair_type": 1}, {"atom_a": 5, "atom_b": 30, "pair_type": 1}, {"atom_a": 5, "atom_b": 23, "pair_type": 1}, {"atom_a": 6, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 6, "pair_type": 1}, {"atom_a": 16, "atom_b": 6, "pair_type": 1}, {"atom_a": 7, "atom_b": 30, "pair_type": 1}, {"atom_a": 16, "atom_b": 7, "pair_type": 1}, {"atom_a": 37, "atom_b": 7, "pair_type": 1}, {"atom_a": 16, "atom_b": 8, "pair_type": 1}, {"atom_a": 23, "atom_b": 8, "pair_type": 1}, {"atom_a": 37, "atom_b": 8, "pair_type": 1}, {"atom_a": 37, "atom_b": 9, "pair_type": 1}, {"atom_a": 16, "atom_b": 9, "pair_type": 1}, {"atom_a": 23, "atom_b": 9, "pair_type": 1}, {"atom_a": 10, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 14, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 11, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 14, "pair_type": 1}, {"atom_a": 17, "atom_b": 21, "pair_type": 1}, {"atom_a": 17, "atom_b": 20, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 18, "atom_b": 21, "pair_type": 1}, {"atom_a": 18, "atom_b": 22, "pair_type": 1}, {"atom_a": 24, "atom_b": 28, "pair_type": 1}, {"atom_a": 24, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 25, "atom_b": 29, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 25, "atom_b": 28, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 31, "atom_b": 35, "pair_type": 1}, {"atom_a": 31, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 35, "pair_type": 1}, {"atom_a": 32, "atom_b": 36, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 38, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 38, "atom_b": 42, "pair_type": 1}, {"atom_a": 39, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 39, "atom_b": 42, "pair_type": 1}, {"atom_a": 45, "atom_b": 49, "pair_type": 1}, {"atom_a": 45, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 46, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 50, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 52, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 53, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 57, "pair_type": 1}, {"atom_a": 59, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 59, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 66, "atom_b": 69, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 66, "atom_b": 70, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 67, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 70, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 73, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 77, "pair_type": 1}, {"atom_a": 74, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 74, "atom_b": 77, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 80, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 89, "atom_b": 94, "pair_type": 1}, {"atom_a": 89, "atom_b": 92, "pair_type": 1}, {"atom_a": 89, "atom_b": 93, "pair_type": 1}, {"atom_a": 90, "atom_b": 94, "pair_type": 1}, {"atom_a": 90, "atom_b": 92, "pair_type": 1}, {"atom_a": 90, "atom_b": 93, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Pentaerythritol", ";", "; This file was generated at 13:37 on 2024-11-22 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 8WDY", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 39051", "; ATB Topology Hash: 07f0b", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "8WDY", "nrexcl": 3}}, "junctions": []} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H10", "charge_group_num": 4, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H11", "charge_group_num": 5, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "C", "residue_id": 1, "residue_name": "8WDY", "atom_name": "C2", "charge_group_num": 6, "partial_charge": -0.014500000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H2", "charge_group_num": 8, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H3", "charge_group_num": 9, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H4", "charge_group_num": 13, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H5", "charge_group_num": 14, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H7", "charge_group_num": 18, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H8", "charge_group_num": 19, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.0063333333333333375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.0063333333333333375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "CPos", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, 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1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 24, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 28, "pair_type": 1}, {"atom_a": 25, "atom_b": 28, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 25, "atom_b": 29, "pair_type": 1}, {"atom_a": 31, "atom_b": 35, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 31, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 35, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 36, "pair_type": 1}, {"atom_a": 38, "atom_b": 42, "pair_type": 1}, {"atom_a": 38, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 39, "atom_b": 42, "pair_type": 1}, {"atom_a": 39, "atom_b": 43, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 45, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 52, "atom_b": 56, "pair_type": 1}, {"atom_a": 52, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 59, "atom_b": 63, "pair_type": 1}, {"atom_a": 59, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 60, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 64, "pair_type": 1}, {"atom_a": 66, "atom_b": 70, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 66, "atom_b": 69, "pair_type": 1}, {"atom_a": 67, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 70, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 73, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 77, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 77, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 74, "atom_b": 78, "pair_type": 1}, {"atom_a": 80, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 84, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 89, "atom_b": 92, "pair_type": 1}, {"atom_a": 89, "atom_b": 94, "pair_type": 1}, {"atom_a": 89, "atom_b": 93, "pair_type": 1}, {"atom_a": 90, "atom_b": 94, "pair_type": 1}, {"atom_a": 90, "atom_b": 92, "pair_type": 1}, {"atom_a": 90, "atom_b": 93, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Pentaerythritol", ";", "; This file was generated at 13:37 on 2024-11-22 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 8WDY", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 39051", "; ATB Topology Hash: 07f0b", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "8WDY", "nrexcl": 3}}, "junctions": []} \ No newline at end of file diff --git a/polytop_examples/data/four_arm_star.png b/polytop_examples/data/four_arm_star.png new file mode 100644 index 0000000000000000000000000000000000000000..f5beba208d400fbb0ca5c99880b5e158bd2466a3 GIT binary patch literal 13685 zcmbt*bx>8&_wS`Ijda5W0qHI&y@WJKTrS<664Kou0wUca0us_lN=PVO0@5NKqIAE_ zcfK?4{qdW5Gw)r-;c)Ibd!MuSTA%exD$nE~clSR9?IkG?2qQ#E?x~JX&iEt!k3JP9zl-6`|DeSV6XcJpryDE=-6|@B>*!M>-KWo??fPIkA%nD$9)12OAwGU(dAXo}E)1ylZ{QMy+ ztIKjn`-cyGhcBlbytK54A)lL@$;iku+trV-$oX08-YTz;7d=Z!N$F3ZDPbtOy}ga6 z;0-!k^kxV+d4lrySUbDAx;k;J)zQXqadELhWtv|# 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0.229302 14.0270 - 17 NOpt 3 LHCU N71 17 -0.669698 14.0067 - 18 HS14 3 LHCU H72 18 0.320302 1.0080 - 19 CH2 3 LHCU C61 19 0.226302 14.0270 - 20 CH2 3 LHCU C5 20 0.241302 14.0270 - 21 NOpt 3 LHCU N7 21 -0.682698 14.0067 - 22 HS14 3 LHCU H21 22 0.334302 1.0080 - 23 CH2 4 LHCU C51 23 0.229420 14.0270 - 24 NOpt 4 LHCU N71 24 -0.669580 14.0067 - 25 HS14 4 LHCU H72 25 0.320420 1.0080 - 26 CH2 4 LHCU C61 26 0.226420 14.0270 - 27 CH2 4 LHCU C5 27 0.241420 14.0270 - 28 NOpt 4 LHCU N7 28 -0.682580 14.0067 - 29 HS14 4 LHCU H21 29 0.334420 1.0080 - 30 CH2 5 LHCU C51 30 0.229428 14.0270 - 31 NOpt 5 LHCU N71 31 -0.669572 14.0067 - 32 HS14 5 LHCU H72 32 0.320428 1.0080 - 33 CH2 5 LHCU C61 33 0.226428 14.0270 - 34 CH2 5 LHCU C5 34 0.241428 14.0270 - 35 NOpt 5 LHCU N7 35 -0.682572 14.0067 - 36 HS14 5 LHCU H21 36 0.334428 1.0080 - 37 CH2 6 LHCU C51 37 0.229429 14.0270 - 38 NOpt 6 LHCU N71 38 -0.669571 14.0067 - 39 HS14 6 LHCU H72 39 0.320429 1.0080 - 40 CH2 6 LHCU C61 40 0.226429 14.0270 - 41 CH2 6 LHCU C5 41 0.241429 14.0270 - 42 NOpt 6 LHCU N7 42 -0.682571 14.0067 - 43 HS14 6 LHCU H21 43 0.334429 1.0080 - 44 CH2 7 LHCU C51 44 0.229429 14.0270 - 45 NOpt 7 LHCU N71 45 -0.669571 14.0067 - 46 HS14 7 LHCU H72 46 0.320429 1.0080 - 47 CH2 7 LHCU C61 47 0.226429 14.0270 - 48 CH2 7 LHCU C5 48 0.241429 14.0270 - 49 NOpt 7 LHCU N7 49 -0.682571 14.0067 - 50 HS14 7 LHCU H21 50 0.334429 1.0080 - 51 CH2 8 LHCU C51 51 0.229429 14.0270 - 52 NOpt 8 LHCU N71 52 -0.669571 14.0067 - 53 HS14 8 LHCU H72 53 0.320429 1.0080 - 54 CH2 8 LHCU C61 54 0.226429 14.0270 - 55 CH2 8 LHCU C5 55 0.241429 14.0270 - 56 NOpt 8 LHCU N7 56 -0.682571 14.0067 - 57 HS14 8 LHCU H21 57 0.334429 1.0080 - 58 CH2 9 LHCU C51 58 0.229429 14.0270 - 59 NOpt 9 LHCU N71 59 -0.669571 14.0067 - 60 HS14 9 LHCU H72 60 0.320429 1.0080 - 61 CH2 9 LHCU C61 61 0.226429 14.0270 - 62 CH2 9 LHCU C5 62 0.241429 14.0270 - 63 NOpt 9 LHCU N7 63 -0.682571 14.0067 - 64 HS14 9 LHCU H21 64 0.334429 1.0080 - 65 CH2 10 LHCU C51 65 0.229429 14.0270 - 66 NOpt 10 LHCU N71 66 -0.669571 14.0067 - 67 HS14 10 LHCU H72 67 0.320429 1.0080 - 68 CH2 10 LHCU C61 68 0.226429 14.0270 - 69 CH2 10 LHCU C5 69 0.241429 14.0270 - 70 NOpt 10 LHCU N7 70 -0.682571 14.0067 - 71 HS14 10 LHCU H21 71 0.334429 1.0080 - 72 CH2 11 LHCU C51 72 0.229429 14.0270 - 73 NOpt 11 LHCU N71 73 -0.669571 14.0067 - 74 HS14 11 LHCU H72 74 0.320429 1.0080 - 75 CH2 11 LHCU C61 75 0.226429 14.0270 - 76 CH2 11 LHCU C5 76 0.241429 14.0270 - 77 NOpt 11 LHCU N7 77 -0.682571 14.0067 - 78 HS14 11 LHCU H21 78 0.334429 1.0080 - 79 CH2 12 LHCU C51 79 0.229429 14.0270 - 80 NOpt 12 LHCU N71 80 -0.669571 14.0067 - 81 HS14 12 LHCU H72 81 0.320429 1.0080 - 82 CH2 12 LHCU C61 82 0.226429 14.0270 - 83 CH2 12 LHCU C5 83 0.241429 14.0270 - 84 NOpt 12 LHCU N7 84 -0.682571 14.0067 - 85 HS14 12 LHCU H21 85 0.334429 1.0080 - 86 CH2 13 LHCU C51 86 0.229429 14.0270 - 87 NOpt 13 LHCU N71 87 -0.669571 14.0067 - 88 HS14 13 LHCU H72 88 0.320429 1.0080 - 89 CH2 13 LHCU C61 89 0.226429 14.0270 - 90 CH2 13 LHCU C5 90 0.241429 14.0270 - 91 NOpt 13 LHCU N7 91 -0.682571 14.0067 - 92 HS14 13 LHCU H21 92 0.334429 1.0080 - 93 CH2 14 LHCU C51 93 0.229429 14.0270 - 94 NOpt 14 LHCU N71 94 -0.669571 14.0067 - 95 HS14 14 LHCU H72 95 0.320429 1.0080 - 96 CH2 14 LHCU C61 96 0.226429 14.0270 - 97 CH2 14 LHCU C5 97 0.241429 14.0270 - 98 NOpt 14 LHCU N7 98 -0.682571 14.0067 - 99 HS14 14 LHCU H21 99 0.334429 1.0080 - 100 CH2 15 LHCU C51 100 0.229429 14.0270 - 101 NOpt 15 LHCU N71 101 -0.669571 14.0067 - 102 HS14 15 LHCU H72 102 0.320429 1.0080 - 103 CH2 15 LHCU C61 103 0.226429 14.0270 - 104 CH2 15 LHCU C5 104 0.241429 14.0270 - 105 NOpt 15 LHCU N7 105 -0.682571 14.0067 - 106 HS14 15 LHCU H21 106 0.334429 1.0080 - 107 CH2 16 LHCU C51 107 0.229429 14.0270 - 108 NOpt 16 LHCU N71 108 -0.669571 14.0067 - 109 HS14 16 LHCU H72 109 0.320429 1.0080 - 110 CH2 16 LHCU C61 110 0.226429 14.0270 - 111 CH2 16 LHCU C5 111 0.241429 14.0270 - 112 NOpt 16 LHCU N7 112 -0.682571 14.0067 - 113 HS14 16 LHCU H21 113 0.334429 1.0080 - 114 CH2 17 LHCU C51 114 0.229429 14.0270 - 115 NOpt 17 LHCU N71 115 -0.669571 14.0067 - 116 HS14 17 LHCU H72 116 0.320429 1.0080 - 117 CH2 17 LHCU C61 117 0.226429 14.0270 - 118 CH2 17 LHCU C5 118 0.241429 14.0270 - 119 NOpt 17 LHCU N7 119 -0.682571 14.0067 - 120 HS14 17 LHCU H21 120 0.334429 1.0080 - 121 CH2 18 LHCU C51 121 0.229429 14.0270 - 122 NOpt 18 LHCU N71 122 -0.669571 14.0067 - 123 HS14 18 LHCU H72 123 0.320429 1.0080 - 124 CH2 18 LHCU C61 124 0.226429 14.0270 - 125 CH2 18 LHCU C5 125 0.241429 14.0270 - 126 NOpt 18 LHCU N7 126 -0.682571 14.0067 - 127 HS14 18 LHCU H21 127 0.334429 1.0080 - 128 CH2 19 LHCU C51 128 0.229429 14.0270 - 129 NOpt 19 LHCU N71 129 -0.669571 14.0067 - 130 HS14 19 LHCU H72 130 0.320429 1.0080 - 131 CH2 19 LHCU C61 131 0.226429 14.0270 - 132 CH2 19 LHCU C5 132 0.241429 14.0270 - 133 NOpt 19 LHCU N7 133 -0.682571 14.0067 - 134 HS14 19 LHCU H21 134 0.334429 1.0080 - 135 CH2 20 LHCU C51 135 0.215214 14.0270 - 136 NOpt 20 LHCU N71 136 -0.683786 14.0067 - 137 HS14 20 LHCU H72 137 0.306214 1.0080 - 138 CH2 20 LHCU C61 138 0.212214 14.0270 - 139 CH2 20 LHCU C5 139 0.227214 14.0270 - 140 NOpt 20 LHCU N7 140 -0.696786 14.0067 - 141 HS14 20 LHCU H21 141 0.320214 1.0080 - 142 CH3 20 LHCU C6 142 0.212214 15.0350 + 1 CH3 1 LHCU C62 1 0.000615 15.0350 + 2 CH2 1 LHCU C51 2 0.200615 14.0270 + 3 NOpt 1 LHCU N71 3 -0.698385 14.0067 + 4 HS14 1 LHCU H72 4 0.291615 1.0080 + 5 CH2 1 LHCU C61 5 0.197615 14.0270 + 6 CH2 1 LHCU C5 6 0.212615 14.0270 + 7 NOpt 2 LHCU N71 7 -0.698944 14.0067 + 8 HS14 2 LHCU H72 8 0.291056 1.0080 + 9 CH2 2 LHCU C61 9 0.197056 14.0270 + 10 CH2 2 LHCU C5 10 0.212056 14.0270 + 11 NOpt 3 LHCU N71 11 -0.699167 14.0067 + 12 HS14 3 LHCU H72 12 0.290833 1.0080 + 13 CH2 3 LHCU C61 13 0.196833 14.0270 + 14 CH2 3 LHCU C5 14 0.211833 14.0270 + 15 NOpt 4 LHCU N71 15 -0.699227 14.0067 + 16 HS14 4 LHCU H72 16 0.290773 1.0080 + 17 CH2 4 LHCU C61 17 0.196773 14.0270 + 18 CH2 4 LHCU C5 18 0.211773 14.0270 + 19 NOpt 5 LHCU N71 19 -0.699244 14.0067 + 20 HS14 5 LHCU H72 20 0.290756 1.0080 + 21 CH2 5 LHCU C61 21 0.196756 14.0270 + 22 CH2 5 LHCU C5 22 0.211756 14.0270 + 23 NOpt 6 LHCU N71 23 -0.699248 14.0067 + 24 HS14 6 LHCU H72 24 0.290752 1.0080 + 25 CH2 6 LHCU C61 25 0.196752 14.0270 + 26 CH2 6 LHCU C5 26 0.211752 14.0270 + 27 NOpt 7 LHCU N71 27 -0.699250 14.0067 + 28 HS14 7 LHCU H72 28 0.290750 1.0080 + 29 CH2 7 LHCU C61 29 0.196750 14.0270 + 30 CH2 7 LHCU C5 30 0.211750 14.0270 + 31 NOpt 8 LHCU N71 31 -0.699250 14.0067 + 32 HS14 8 LHCU H72 32 0.290750 1.0080 + 33 CH2 8 LHCU C61 33 0.196750 14.0270 + 34 CH2 8 LHCU C5 34 0.211750 14.0270 + 35 NOpt 9 LHCU N71 35 -0.699250 14.0067 + 36 HS14 9 LHCU H72 36 0.290750 1.0080 + 37 CH2 9 LHCU C61 37 0.196750 14.0270 + 38 CH2 9 LHCU C5 38 0.211750 14.0270 + 39 NOpt 10 LHCU N71 39 -0.699250 14.0067 + 40 HS14 10 LHCU H72 40 0.290750 1.0080 + 41 CH2 10 LHCU C61 41 0.196750 14.0270 + 42 CH2 10 LHCU C5 42 0.211750 14.0270 + 43 NOpt 11 LHCU N71 43 -0.699250 14.0067 + 44 HS14 11 LHCU H72 44 0.290750 1.0080 + 45 CH2 11 LHCU C61 45 0.196750 14.0270 + 46 CH2 11 LHCU C5 46 0.211750 14.0270 + 47 NOpt 12 LHCU N71 47 -0.699250 14.0067 + 48 HS14 12 LHCU H72 48 0.290750 1.0080 + 49 CH2 12 LHCU C61 49 0.196750 14.0270 + 50 CH2 12 LHCU C5 50 0.211750 14.0270 + 51 NOpt 13 LHCU N71 51 -0.699250 14.0067 + 52 HS14 13 LHCU H72 52 0.290750 1.0080 + 53 CH2 13 LHCU C61 53 0.196750 14.0270 + 54 CH2 13 LHCU C5 54 0.211750 14.0270 + 55 NOpt 14 LHCU N71 55 -0.699250 14.0067 + 56 HS14 14 LHCU H72 56 0.290750 1.0080 + 57 CH2 14 LHCU C61 57 0.196750 14.0270 + 58 CH2 14 LHCU C5 58 0.211750 14.0270 + 59 NOpt 15 LHCU N71 59 -0.699250 14.0067 + 60 HS14 15 LHCU H72 60 0.290750 1.0080 + 61 CH2 15 LHCU C61 61 0.196750 14.0270 + 62 CH2 15 LHCU C5 62 0.211750 14.0270 + 63 NOpt 16 LHCU N71 63 -0.699250 14.0067 + 64 HS14 16 LHCU H72 64 0.290750 1.0080 + 65 CH2 16 LHCU C61 65 0.196750 14.0270 + 66 CH2 16 LHCU C5 66 0.211750 14.0270 + 67 NOpt 17 LHCU N71 67 -0.699250 14.0067 + 68 HS14 17 LHCU H72 68 0.290750 1.0080 + 69 CH2 17 LHCU C61 69 0.196750 14.0270 + 70 CH2 17 LHCU C5 70 0.211750 14.0270 + 71 NOpt 18 LHCU N71 71 -0.699250 14.0067 + 72 HS14 18 LHCU H72 72 0.290750 1.0080 + 73 CH2 18 LHCU C61 73 0.196750 14.0270 + 74 CH2 18 LHCU C5 74 0.211750 14.0270 + 75 NOpt 19 LHCU N71 75 -0.699250 14.0067 + 76 HS14 19 LHCU H72 76 0.290750 1.0080 + 77 CH2 19 LHCU C61 77 0.196750 14.0270 + 78 CH2 19 LHCU C5 78 0.211750 14.0270 + 79 NOpt 20 LHCU N71 79 -0.698625 14.0067 + 80 HS14 20 LHCU H72 80 0.291375 1.0080 + 81 CH2 20 LHCU C61 81 0.197375 14.0270 + 82 CH2 20 LHCU C5 82 0.212375 14.0270 + 83 NOpt 20 LHCU N7 83 -0.711625 14.0067 + 84 HS14 20 LHCU H21 84 0.305375 1.0080 + 85 CH3 20 LHCU C6 85 0.197375 15.0350 [ bonds ] 1 2 2 0.1530 7.1500e+06 @@ -216,265 +159,150 @@ LHCU 3 3 5 2 0.1470 8.7100e+06 5 6 2 0.1530 7.1500e+06 6 7 2 0.1470 8.7100e+06 - 7 9 2 0.1500 8.7100e+06 + 7 9 2 0.1470 8.7100e+06 7 8 2 0.1020 1.7782e+07 - 9 10 2 0.1470 8.7100e+06 - 10 12 2 0.1470 8.7100e+06 - 10 11 2 0.1020 1.7782e+07 - 12 13 2 0.1530 7.1500e+06 - 13 14 2 0.1470 8.7100e+06 - 14 16 2 0.1500 8.7100e+06 - 14 15 2 0.1020 1.7782e+07 - 16 17 2 0.1470 8.7100e+06 - 17 19 2 0.1470 8.7100e+06 - 17 18 2 0.1020 1.7782e+07 - 19 20 2 0.1530 7.1500e+06 - 20 21 2 0.1470 8.7100e+06 - 21 22 2 0.1020 1.7782e+07 - 21 23 2 0.1500 8.7100e+06 - 23 24 2 0.1470 8.7100e+06 - 24 25 2 0.1020 1.7782e+07 - 24 26 2 0.1470 8.7100e+06 - 26 27 2 0.1530 7.1500e+06 - 27 28 2 0.1470 8.7100e+06 - 28 29 2 0.1020 1.7782e+07 - 28 30 2 0.1500 8.7100e+06 + 9 10 2 0.1530 7.1500e+06 + 10 11 2 0.1470 8.7100e+06 + 11 12 2 0.1020 1.7782e+07 + 11 13 2 0.1470 8.7100e+06 + 13 14 2 0.1530 7.1500e+06 + 14 15 2 0.1470 8.7100e+06 + 15 16 2 0.1020 1.7782e+07 + 15 17 2 0.1470 8.7100e+06 + 17 18 2 0.1530 7.1500e+06 + 18 19 2 0.1470 8.7100e+06 + 19 21 2 0.1470 8.7100e+06 + 19 20 2 0.1020 1.7782e+07 + 21 22 2 0.1530 7.1500e+06 + 22 23 2 0.1470 8.7100e+06 + 23 24 2 0.1020 1.7782e+07 + 23 25 2 0.1470 8.7100e+06 + 25 26 2 0.1530 7.1500e+06 + 26 27 2 0.1470 8.7100e+06 + 27 28 2 0.1020 1.7782e+07 + 27 29 2 0.1470 8.7100e+06 + 29 30 2 0.1530 7.1500e+06 30 31 2 0.1470 8.7100e+06 - 31 32 2 0.1020 1.7782e+07 31 33 2 0.1470 8.7100e+06 + 31 32 2 0.1020 1.7782e+07 33 34 2 0.1530 7.1500e+06 34 35 2 0.1470 8.7100e+06 - 35 37 2 0.1500 8.7100e+06 + 35 37 2 0.1470 8.7100e+06 35 36 2 0.1020 1.7782e+07 - 37 38 2 0.1470 8.7100e+06 - 38 39 2 0.1020 1.7782e+07 - 38 40 2 0.1470 8.7100e+06 - 40 41 2 0.1530 7.1500e+06 - 41 42 2 0.1470 8.7100e+06 - 42 43 2 0.1020 1.7782e+07 - 42 44 2 0.1500 8.7100e+06 - 44 45 2 0.1470 8.7100e+06 - 45 46 2 0.1020 1.7782e+07 - 45 47 2 0.1470 8.7100e+06 - 47 48 2 0.1530 7.1500e+06 - 48 49 2 0.1470 8.7100e+06 - 49 51 2 0.1500 8.7100e+06 - 49 50 2 0.1020 1.7782e+07 - 51 52 2 0.1470 8.7100e+06 - 52 53 2 0.1020 1.7782e+07 - 52 54 2 0.1470 8.7100e+06 - 54 55 2 0.1530 7.1500e+06 - 55 56 2 0.1470 8.7100e+06 - 56 58 2 0.1500 8.7100e+06 - 56 57 2 0.1020 1.7782e+07 + 37 38 2 0.1530 7.1500e+06 + 38 39 2 0.1470 8.7100e+06 + 39 41 2 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0.1020 1.7782e+07 - 110 111 2 0.1530 7.1500e+06 - 111 112 2 0.1470 8.7100e+06 - 112 114 2 0.1500 8.7100e+06 - 112 113 2 0.1020 1.7782e+07 - 114 115 2 0.1470 8.7100e+06 - 115 117 2 0.1470 8.7100e+06 - 115 116 2 0.1020 1.7782e+07 - 117 118 2 0.1530 7.1500e+06 - 118 119 2 0.1470 8.7100e+06 - 119 120 2 0.1020 1.7782e+07 - 119 121 2 0.1500 8.7100e+06 - 121 122 2 0.1470 8.7100e+06 - 122 123 2 0.1020 1.7782e+07 - 122 124 2 0.1470 8.7100e+06 - 124 125 2 0.1530 7.1500e+06 - 125 126 2 0.1470 8.7100e+06 - 126 128 2 0.1500 8.7100e+06 - 126 127 2 0.1020 1.7782e+07 - 128 129 2 0.1470 8.7100e+06 - 129 130 2 0.1020 1.7782e+07 - 129 131 2 0.1470 8.7100e+06 - 131 132 2 0.1530 7.1500e+06 - 132 133 2 0.1470 8.7100e+06 - 133 135 2 0.1500 8.7100e+06 - 133 134 2 0.1020 1.7782e+07 - 135 136 2 0.1470 8.7100e+06 - 136 138 2 0.1470 8.7100e+06 - 136 137 2 0.1020 1.7782e+07 - 138 139 2 0.1530 7.1500e+06 - 139 140 2 0.1470 8.7100e+06 - 140 142 2 0.1470 8.7100e+06 - 140 141 2 0.1020 1.7782e+07 + 63 65 2 0.1470 8.7100e+06 + 65 66 2 0.1530 7.1500e+06 + 66 67 2 0.1470 8.7100e+06 + 67 68 2 0.1020 1.7782e+07 + 67 69 2 0.1470 8.7100e+06 + 69 70 2 0.1530 7.1500e+06 + 70 71 2 0.1470 8.7100e+06 + 71 72 2 0.1020 1.7782e+07 + 71 73 2 0.1470 8.7100e+06 + 73 74 2 0.1530 7.1500e+06 + 74 75 2 0.1470 8.7100e+06 + 75 76 2 0.1020 1.7782e+07 + 75 77 2 0.1470 8.7100e+06 + 77 78 2 0.1530 7.1500e+06 + 78 79 2 0.1470 8.7100e+06 + 79 81 2 0.1470 8.7100e+06 + 79 80 2 0.1020 1.7782e+07 + 81 82 2 0.1530 7.1500e+06 + 82 83 2 0.1470 8.7100e+06 + 83 85 2 0.1470 8.7100e+06 + 83 84 2 0.1020 1.7782e+07 [ pairs ] 1 4 1 1 5 1 2 6 1 - 3 7 1 4 6 1 - 5 8 1 - 9 13 1 - 10 14 1 - 11 13 1 - 12 15 1 - 16 20 1 - 17 21 1 - 18 20 1 - 19 22 1 - 23 27 1 - 24 28 1 - 25 27 1 - 26 29 1 - 30 34 1 - 31 35 1 + 8 10 1 + 12 14 1 + 16 18 1 + 20 22 1 + 24 26 1 + 28 30 1 32 34 1 - 33 36 1 - 37 41 1 - 38 42 1 - 39 41 1 - 40 43 1 - 44 48 1 - 45 49 1 - 46 48 1 - 47 50 1 - 51 55 1 - 52 56 1 - 53 55 1 - 54 57 1 - 58 62 1 - 59 63 1 + 36 38 1 + 40 42 1 + 44 46 1 + 48 50 1 + 52 54 1 + 56 58 1 60 62 1 - 61 64 1 - 65 69 1 - 66 70 1 - 67 69 1 - 68 71 1 - 72 76 1 - 73 77 1 - 74 76 1 - 75 78 1 + 64 66 1 + 68 70 1 + 72 74 1 + 76 78 1 79 83 1 - 80 84 1 - 81 83 1 - 82 85 1 - 86 90 1 - 87 91 1 - 88 90 1 - 89 92 1 - 93 97 1 - 94 98 1 - 95 97 1 - 96 99 1 - 100 104 1 - 101 105 1 - 102 104 1 - 103 106 1 - 107 111 1 - 108 112 1 - 109 111 1 - 110 113 1 - 114 118 1 - 115 119 1 - 116 118 1 - 117 120 1 - 121 125 1 - 122 126 1 - 123 125 1 - 124 127 1 - 128 132 1 - 129 133 1 - 130 132 1 - 131 134 1 - 135 139 1 - 136 140 1 - 137 139 1 - 138 142 1 - 138 141 1 + 80 82 1 + 81 85 1 + 81 84 1 [ angles ] 1 2 3 2 111.0000 5.3000e+02 - 2 3 5 2 116.0000 6.2000e+02 2 3 4 2 109.5000 4.2500e+02 + 2 3 5 2 116.0000 6.2000e+02 4 3 5 2 109.5000 4.2500e+02 3 5 6 2 111.0000 5.3000e+02 5 6 7 2 111.0000 5.3000e+02 - 6 7 8 2 109.5000 4.2500e+02 6 7 9 2 116.0000 6.2000e+02 + 6 7 8 2 109.5000 4.2500e+02 7 9 10 2 111.0000 5.3000e+02 8 7 9 2 109.5000 4.2500e+02 - 9 10 11 2 109.5000 4.2500e+02 - 9 10 12 2 116.0000 6.2000e+02 - 11 10 12 2 109.5000 4.2500e+02 - 10 12 13 2 111.0000 5.3000e+02 - 12 13 14 2 111.0000 5.3000e+02 - 13 14 16 2 116.0000 6.2000e+02 - 13 14 15 2 109.5000 4.2500e+02 - 15 14 16 2 109.5000 4.2500e+02 - 14 16 17 2 111.0000 5.3000e+02 - 16 17 18 2 109.5000 4.2500e+02 - 16 17 19 2 116.0000 6.2000e+02 - 17 19 20 2 111.0000 5.3000e+02 - 18 17 19 2 109.5000 4.2500e+02 - 19 20 21 2 111.0000 5.3000e+02 - 20 21 22 2 109.5000 4.2500e+02 - 20 21 23 2 116.0000 6.2000e+02 - 22 21 23 2 109.5000 4.2500e+02 - 21 23 24 2 111.0000 5.3000e+02 - 23 24 25 2 109.5000 4.2500e+02 - 23 24 26 2 116.0000 6.2000e+02 - 25 24 26 2 109.5000 4.2500e+02 - 24 26 27 2 111.0000 5.3000e+02 - 26 27 28 2 111.0000 5.3000e+02 - 27 28 30 2 116.0000 6.2000e+02 - 27 28 29 2 109.5000 4.2500e+02 - 29 28 30 2 109.5000 4.2500e+02 - 28 30 31 2 111.0000 5.3000e+02 + 9 10 11 2 111.0000 5.3000e+02 + 10 11 12 2 109.5000 4.2500e+02 + 10 11 13 2 116.0000 6.2000e+02 + 12 11 13 2 109.5000 4.2500e+02 + 11 13 14 2 111.0000 5.3000e+02 + 13 14 15 2 111.0000 5.3000e+02 + 14 15 16 2 109.5000 4.2500e+02 + 14 15 17 2 116.0000 6.2000e+02 + 16 15 17 2 109.5000 4.2500e+02 + 15 17 18 2 111.0000 5.3000e+02 + 17 18 19 2 111.0000 5.3000e+02 + 18 19 21 2 116.0000 6.2000e+02 + 18 19 20 2 109.5000 4.2500e+02 + 20 19 21 2 109.5000 4.2500e+02 + 19 21 22 2 111.0000 5.3000e+02 + 21 22 23 2 111.0000 5.3000e+02 + 22 23 25 2 116.0000 6.2000e+02 + 22 23 24 2 109.5000 4.2500e+02 + 24 23 25 2 109.5000 4.2500e+02 + 23 25 26 2 111.0000 5.3000e+02 + 25 26 27 2 111.0000 5.3000e+02 + 26 27 28 2 109.5000 4.2500e+02 + 26 27 29 2 116.0000 6.2000e+02 + 28 27 29 2 109.5000 4.2500e+02 + 27 29 30 2 111.0000 5.3000e+02 + 29 30 31 2 111.0000 5.3000e+02 30 31 32 2 109.5000 4.2500e+02 30 31 33 2 116.0000 6.2000e+02 32 31 33 2 109.5000 4.2500e+02 @@ -484,221 +312,108 @@ LHCU 3 34 35 36 2 109.5000 4.2500e+02 36 35 37 2 109.5000 4.2500e+02 35 37 38 2 111.0000 5.3000e+02 - 37 38 39 2 109.5000 4.2500e+02 - 37 38 40 2 116.0000 6.2000e+02 - 39 38 40 2 109.5000 4.2500e+02 - 38 40 41 2 111.0000 5.3000e+02 - 40 41 42 2 111.0000 5.3000e+02 - 41 42 44 2 116.0000 6.2000e+02 - 41 42 43 2 109.5000 4.2500e+02 - 43 42 44 2 109.5000 4.2500e+02 - 42 44 45 2 111.0000 5.3000e+02 - 44 45 47 2 116.0000 6.2000e+02 - 44 45 46 2 109.5000 4.2500e+02 - 46 45 47 2 109.5000 4.2500e+02 - 45 47 48 2 111.0000 5.3000e+02 - 47 48 49 2 111.0000 5.3000e+02 - 48 49 51 2 116.0000 6.2000e+02 - 48 49 50 2 109.5000 4.2500e+02 - 49 51 52 2 111.0000 5.3000e+02 - 50 49 51 2 109.5000 4.2500e+02 - 51 52 53 2 109.5000 4.2500e+02 - 51 52 54 2 116.0000 6.2000e+02 - 53 52 54 2 109.5000 4.2500e+02 - 52 54 55 2 111.0000 5.3000e+02 - 54 55 56 2 111.0000 5.3000e+02 - 55 56 57 2 109.5000 4.2500e+02 - 55 56 58 2 116.0000 6.2000e+02 - 56 58 59 2 111.0000 5.3000e+02 - 57 56 58 2 109.5000 4.2500e+02 - 58 59 61 2 116.0000 6.2000e+02 + 37 38 39 2 111.0000 5.3000e+02 + 38 39 41 2 116.0000 6.2000e+02 + 38 39 40 2 109.5000 4.2500e+02 + 40 39 41 2 109.5000 4.2500e+02 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"atom_c": 101, "atom_d": 103, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 100, "atom_b": 101, "atom_c": 103, "atom_d": 104, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 101, "atom_b": 103, "atom_c": 104, "atom_d": 106, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 103, "atom_b": 104, "atom_c": 106, "atom_d": 107, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 106, "atom_b": 107, "atom_c": 108, "atom_d": 110, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 107, "atom_b": 108, "atom_c": 110, "atom_d": 111, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 108, "atom_b": 110, "atom_c": 111, "atom_d": 113, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 110, "atom_b": 111, "atom_c": 113, "atom_d": 114, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 113, "atom_b": 114, "atom_c": 115, "atom_d": 117, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 114, "atom_b": 115, "atom_c": 117, "atom_d": 118, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 115, "atom_b": 117, "atom_c": 118, "atom_d": 120, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 117, "atom_b": 118, "atom_c": 120, "atom_d": 121, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 120, "atom_b": 121, "atom_c": 122, "atom_d": 124, 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"phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 131, "atom_b": 132, "atom_c": 133, "atom_d": 137, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 133, "atom_b": 137, "atom_c": 138, "atom_d": 140, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 137, "atom_b": 138, "atom_c": 140, "atom_d": 141, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 138, "atom_b": 140, "atom_c": 141, "atom_d": 142, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 140, "atom_b": 141, "atom_c": 142, "atom_d": 144, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 4, "pair_type": 1}, {"atom_a": 1, "atom_b": 5, "pair_type": 1}, {"atom_a": 2, "atom_b": 6, "pair_type": 1}, {"atom_a": 3, "atom_b": 8, "pair_type": 1}, {"atom_a": 4, "atom_b": 6, "pair_type": 1}, {"atom_a": 5, "atom_b": 7, "pair_type": 1}, {"atom_a": 9, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 12, "atom_b": 14, "pair_type": 1}, {"atom_a": 16, "atom_b": 20, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 19, "atom_b": 21, "pair_type": 1}, {"atom_a": 23, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 26, "atom_b": 28, "pair_type": 1}, {"atom_a": 30, "atom_b": 34, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 33, "atom_b": 35, "pair_type": 1}, {"atom_a": 37, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 40, "atom_b": 42, "pair_type": 1}, {"atom_a": 44, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 54, "atom_b": 56, "pair_type": 1}, {"atom_a": 58, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 61, "atom_b": 63, "pair_type": 1}, {"atom_a": 65, "atom_b": 69, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 68, "atom_b": 70, "pair_type": 1}, {"atom_a": 72, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 75, "atom_b": 77, "pair_type": 1}, {"atom_a": 79, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 82, "atom_b": 84, "pair_type": 1}, {"atom_a": 86, "atom_b": 90, "pair_type": 1}, {"atom_a": 87, "atom_b": 92, "pair_type": 1}, {"atom_a": 88, "atom_b": 90, "pair_type": 1}, {"atom_a": 89, "atom_b": 91, "pair_type": 1}, {"atom_a": 93, "atom_b": 97, "pair_type": 1}, {"atom_a": 94, "atom_b": 99, "pair_type": 1}, {"atom_a": 95, "atom_b": 97, "pair_type": 1}, {"atom_a": 96, "atom_b": 98, "pair_type": 1}, {"atom_a": 100, "atom_b": 104, "pair_type": 1}, {"atom_a": 101, "atom_b": 106, "pair_type": 1}, {"atom_a": 102, "atom_b": 104, "pair_type": 1}, {"atom_a": 103, "atom_b": 105, "pair_type": 1}, {"atom_a": 107, "atom_b": 111, "pair_type": 1}, {"atom_a": 108, "atom_b": 113, "pair_type": 1}, {"atom_a": 109, "atom_b": 111, "pair_type": 1}, {"atom_a": 110, "atom_b": 112, "pair_type": 1}, {"atom_a": 114, "atom_b": 118, "pair_type": 1}, {"atom_a": 115, "atom_b": 120, "pair_type": 1}, {"atom_a": 116, "atom_b": 118, "pair_type": 1}, {"atom_a": 117, "atom_b": 119, "pair_type": 1}, {"atom_a": 121, "atom_b": 125, "pair_type": 1}, {"atom_a": 122, "atom_b": 127, "pair_type": 1}, {"atom_a": 123, "atom_b": 125, "pair_type": 1}, {"atom_a": 124, "atom_b": 126, "pair_type": 1}, {"atom_a": 128, "atom_b": 132, "pair_type": 1}, {"atom_a": 129, "atom_b": 133, "pair_type": 1}, {"atom_a": 130, "atom_b": 132, "pair_type": 1}, {"atom_a": 131, "atom_b": 134, "pair_type": 1}, {"atom_a": 137, "atom_b": 141, "pair_type": 1}, {"atom_a": 138, "atom_b": 142, "pair_type": 1}, {"atom_a": 139, "atom_b": 141, "pair_type": 1}, {"atom_a": 140, "atom_b": 144, "pair_type": 1}, {"atom_a": 140, "atom_b": 143, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C51", "residue_atom": "C62"}, {"name": "from", "monomer_atom": "N7", "residue_atom": "C6"}]} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CH3", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C62", "charge_group_num": 1, "partial_charge": 0.0006153846153846235, "mass": 15.035, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, "partial_charge": 0.20061538461538464, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, 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"pair_type": 1}, {"atom_a": 8, "atom_b": 10, "pair_type": 1}, {"atom_a": 12, "atom_b": 14, "pair_type": 1}, {"atom_a": 16, "atom_b": 18, "pair_type": 1}, {"atom_a": 20, "atom_b": 22, "pair_type": 1}, {"atom_a": 24, "atom_b": 26, "pair_type": 1}, {"atom_a": 28, "atom_b": 30, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 36, "atom_b": 38, "pair_type": 1}, {"atom_a": 40, "atom_b": 42, "pair_type": 1}, {"atom_a": 44, "atom_b": 46, "pair_type": 1}, {"atom_a": 48, "atom_b": 50, "pair_type": 1}, {"atom_a": 52, "atom_b": 54, "pair_type": 1}, {"atom_a": 56, "atom_b": 58, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 64, "atom_b": 66, "pair_type": 1}, {"atom_a": 68, "atom_b": 70, "pair_type": 1}, {"atom_a": 72, "atom_b": 74, "pair_type": 1}, {"atom_a": 76, "atom_b": 78, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 82, "atom_b": 84, "pair_type": 1}, {"atom_a": 83, "atom_b": 87, "pair_type": 1}, {"atom_a": 83, "atom_b": 86, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "N71", "residue_atom": "C51"}, {"name": "from", "monomer_atom": "C5", "residue_atom": "N7"}]} \ No newline at end of file diff --git a/polytop_examples/data/pei_linear_polymer.png b/polytop_examples/data/pei_linear_polymer.png index c6948dd1eb3a5eb89e22e39bda8359c76a3f3879..7d9be32e2a6a23420508b26b4628fc0be1d7285f 100644 GIT binary patch literal 10073 zcmeHtWl&pPyEYY|MN4rnJh(%U0)@0RcyV`H910Y7c%WF(;skB*;2skuOfqZlJ$vo@zHYg$wZEvV$`j(z;9+555h^M`G_kNAdfFGO>%JLAb`@f%W?Zru0SoAH5kT=@iS$p$7#@d)WDFrO(4b7^_OoMDS+Y-CAIf|AndDhicG+d;{=1taDuDJcy%f2x$-+}zqLDJxns 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zYmK}K9%s4exf`WQJjnL#VJG_66sxUdT@p5x?8GH$^;2&J|sMTO5L0yP;dZ z!#o|%8gDWjtt}8kI2J))C3^WhB-m zZLMS#bn!OJdh=G`u_%8gWBHxZbIslQ3#w1EE;p6G5CY%HF(pk$6bX3Pfc?T!7l-P& z$$}*tUs3L}@dFK7>@wWc9`Xe&Ujo;ut-Umb1fP*sQi@s;Tb!LVasi+mF`Hwsk#< zU=$nASe4!KrMx_fOVs@xAU=gdC$;s)y^=bgTM=6 zB>_cYH~4+--r6FNT@!k5Eo$nc9Z@|&SX``9EGk(qFKJY}4|+Di{uR`n^JL(g6PY(< zR7xZ)18#)_JIOk&xs~G~UzsvyD=xD4^X=v~OH${dm3}p78Z-MUm#-#qln83*T~_i8{Epu1-+D0Pei=$gD`-!;wj3i K$yC0x2>V}f3gI6B diff --git a/polytop_examples/dendrimer_ethylamine.py b/polytop_examples/dendrimer_ethylamine.py index c343a28..4a0d200 100644 --- a/polytop_examples/dendrimer_ethylamine.py +++ b/polytop_examples/dendrimer_ethylamine.py @@ -1,6 +1,6 @@ # Construction of an ethylamine dendrimer -# import required Classes from PolyTop +# Import required Classes from PolyTop from polytop.Junction import Junction from polytop.Monomer import Monomer from polytop.Visualize import Visualize @@ -22,9 +22,9 @@ # 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 (in -# this example 'to' and 'from', and NOT by the variable name they are assigned -# to 'to_j' and 'from_j', which are used to pass them into a Monomer object). +# 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. @@ -63,15 +63,19 @@ # Monomer Junctions (i.e. from12 or from22) t = Junction(terminal_mono.get_atom("C1"), terminal_mono.get_atom("N1"), name = "term") -# create monomers from their topologies and any specified junctions -# note that different 'levels' of monomers have different names for their junctions. + +# ----- Create Monomers from their Topologies and any specified Junctions ----- + +# Note that different 'levels' of monomers have different names for their junctions. # This ensures that layers are added on sequentially. -# If all monomers have the same junction names the polymerisation will be random and often defaults to a linear shape! +# If all monomers have the same junction names the polymerisation will be random +# and often defaults to a linear shape! central = Monomer(core_mono, [central1, central2, central3, central4]) bifur1 = Monomer(bifurcating_mono, [b1, b2a, b2b]) bifur2 = Monomer(bifurcating_mono, [c1, c2a, c2b]) cap = Monomer(terminal_mono, [t]) + # ----- Start the Polymer with one Monomer ----- # Only a Polymer object has access to the 'extend()' and 'extra_bond()' @@ -144,6 +148,7 @@ # preserved (in this case, close to 0) print(polymer.topology.netcharge) + # ----- Save the polymer dendrimer to an itp file ----- # Optionally, use Visualize to generate an image of the structure with RDKit diff --git a/polytop_examples/linear_PEI.py b/polytop_examples/linear_PEI.py index 1854293..edef669 100644 --- a/polytop_examples/linear_PEI.py +++ b/polytop_examples/linear_PEI.py @@ -26,9 +26,8 @@ # Note that junctions are specified for extend() by their name attribute (in # this example 'to' and 'from', and NOT by the variable name they are assigned # to 'to_j' and 'from_j', which are used to pass them into a Monomer object) -to_j = Junction(top.get_atom("C51"), top.get_atom("C62"), name = "to") -from_j = Junction(top.get_atom("N7"), top.get_atom("C6"), name = "from") - +to_j = Junction(top.get_atom("N71"), top.get_atom("C51"), name = "to") +from_j = Junction(top.get_atom("C5"), top.get_atom("N7"), name = "from") # ----- Create a Monomer from the Topology and a list of the Junctions ----- @@ -72,4 +71,4 @@ polymer.topology.title = "pei polymer" # optional but good for identifying files, renames the ITP header and image polymer.save_to_file('data/pei_linear_polymer.json') # optional, text dump in a dictionary format polymer.topology.to_ITP('data/pei_linear_polymer.itp') # write the itp to be used for simulation -Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/pei_linear_polymer.png',(400,300)) # optional, visualize the structure in 2Da \ No newline at end of file +Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/pei_linear_polymer.png',(400,300)) # optional, visualize the structure in 2D \ No newline at end of file From 82bbbd51b37cb2e6dfc8c1fa2024534a9a69b873 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Tue, 18 Feb 2025 13:08:08 +1000 Subject: [PATCH 6/6] Reverse direction of PEI polymer construction so that it matches with the direction used to create a PEI polymer in the PolyConf examples --- polytop_examples/data/pei_linear_polymer.itp | 678 +++++++++--------- polytop_examples/data/pei_linear_polymer.json | 2 +- polytop_examples/data/pei_linear_polymer.png | Bin 10073 -> 10153 bytes polytop_examples/linear_PEI.py | 8 +- 4 files changed, 344 insertions(+), 344 deletions(-) diff --git a/polytop_examples/data/pei_linear_polymer.itp b/polytop_examples/data/pei_linear_polymer.itp index 2843dca..9e6bc1d 100644 --- a/polytop_examples/data/pei_linear_polymer.itp +++ b/polytop_examples/data/pei_linear_polymer.itp @@ -66,354 +66,354 @@ [ moleculetype ] LHCU 3 [ atoms ] - 1 CH3 1 LHCU C62 1 0.000615 15.0350 - 2 CH2 1 LHCU C51 2 0.200615 14.0270 - 3 NOpt 1 LHCU N71 3 -0.698385 14.0067 - 4 HS14 1 LHCU H72 4 0.291615 1.0080 - 5 CH2 1 LHCU C61 5 0.197615 14.0270 - 6 CH2 1 LHCU C5 6 0.212615 14.0270 - 7 NOpt 2 LHCU N71 7 -0.698944 14.0067 - 8 HS14 2 LHCU H72 8 0.291056 1.0080 - 9 CH2 2 LHCU C61 9 0.197056 14.0270 - 10 CH2 2 LHCU C5 10 0.212056 14.0270 - 11 NOpt 3 LHCU N71 11 -0.699167 14.0067 - 12 HS14 3 LHCU H72 12 0.290833 1.0080 - 13 CH2 3 LHCU C61 13 0.196833 14.0270 - 14 CH2 3 LHCU C5 14 0.211833 14.0270 - 15 NOpt 4 LHCU N71 15 -0.699227 14.0067 - 16 HS14 4 LHCU H72 16 0.290773 1.0080 - 17 CH2 4 LHCU C61 17 0.196773 14.0270 - 18 CH2 4 LHCU C5 18 0.211773 14.0270 - 19 NOpt 5 LHCU N71 19 -0.699244 14.0067 - 20 HS14 5 LHCU H72 20 0.290756 1.0080 - 21 CH2 5 LHCU C61 21 0.196756 14.0270 - 22 CH2 5 LHCU C5 22 0.211756 14.0270 - 23 NOpt 6 LHCU N71 23 -0.699248 14.0067 - 24 HS14 6 LHCU H72 24 0.290752 1.0080 - 25 CH2 6 LHCU C61 25 0.196752 14.0270 - 26 CH2 6 LHCU C5 26 0.211752 14.0270 - 27 NOpt 7 LHCU N71 27 -0.699250 14.0067 - 28 HS14 7 LHCU H72 28 0.290750 1.0080 - 29 CH2 7 LHCU C61 29 0.196750 14.0270 - 30 CH2 7 LHCU C5 30 0.211750 14.0270 - 31 NOpt 8 LHCU N71 31 -0.699250 14.0067 - 32 HS14 8 LHCU H72 32 0.290750 1.0080 - 33 CH2 8 LHCU C61 33 0.196750 14.0270 - 34 CH2 8 LHCU C5 34 0.211750 14.0270 - 35 NOpt 9 LHCU N71 35 -0.699250 14.0067 - 36 HS14 9 LHCU H72 36 0.290750 1.0080 - 37 CH2 9 LHCU C61 37 0.196750 14.0270 - 38 CH2 9 LHCU C5 38 0.211750 14.0270 - 39 NOpt 10 LHCU N71 39 -0.699250 14.0067 - 40 HS14 10 LHCU H72 40 0.290750 1.0080 - 41 CH2 10 LHCU C61 41 0.196750 14.0270 - 42 CH2 10 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5.9200e+00 3 + 71 64 66 67 1 180.0000 1.0000e+00 6 + 75 68 70 71 1 180.0000 1.0000e+00 6 + 72 74 75 68 1 0.0000 5.9200e+00 3 + 79 72 74 75 1 180.0000 1.0000e+00 6 + 76 78 79 72 1 0.0000 5.9200e+00 3 + 85 76 78 79 1 180.0000 1.0000e+00 6 + 82 84 85 76 1 0.0000 5.9200e+00 3 + 80 81 82 84 1 180.0000 1.0000e+00 6 + 81 82 84 85 1 180.0000 1.0000e+00 6 [ exclusions ] diff --git a/polytop_examples/data/pei_linear_polymer.json b/polytop_examples/data/pei_linear_polymer.json index 8e80840..1c1dd5b 100644 --- a/polytop_examples/data/pei_linear_polymer.json +++ b/polytop_examples/data/pei_linear_polymer.json @@ -1 +1 @@ -{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CH3", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C62", "charge_group_num": 1, "partial_charge": 0.0006153846153846235, "mass": 15.035, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, 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71, "atom_b": 73, "atom_c": 74, "atom_d": 75, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 74, "atom_b": 75, "atom_c": 77, "atom_d": 78, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 75, "atom_b": 77, "atom_c": 78, "atom_d": 81, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 78, "atom_b": 81, "atom_c": 83, "atom_d": 84, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 81, "atom_b": 83, "atom_c": 84, "atom_d": 85, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 83, "atom_b": 84, "atom_c": 85, "atom_d": 87, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 4, "pair_type": 1}, {"atom_a": 1, "atom_b": 5, "pair_type": 1}, {"atom_a": 2, "atom_b": 6, "pair_type": 1}, {"atom_a": 4, "atom_b": 6, "pair_type": 1}, {"atom_a": 8, "atom_b": 10, "pair_type": 1}, {"atom_a": 12, "atom_b": 14, "pair_type": 1}, {"atom_a": 16, "atom_b": 18, "pair_type": 1}, {"atom_a": 20, "atom_b": 22, "pair_type": 1}, {"atom_a": 24, "atom_b": 26, "pair_type": 1}, {"atom_a": 28, "atom_b": 30, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 36, "atom_b": 38, "pair_type": 1}, {"atom_a": 40, "atom_b": 42, "pair_type": 1}, {"atom_a": 44, "atom_b": 46, "pair_type": 1}, {"atom_a": 48, "atom_b": 50, "pair_type": 1}, {"atom_a": 52, "atom_b": 54, "pair_type": 1}, {"atom_a": 56, "atom_b": 58, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 64, "atom_b": 66, "pair_type": 1}, {"atom_a": 68, "atom_b": 70, "pair_type": 1}, {"atom_a": 72, "atom_b": 74, "pair_type": 1}, {"atom_a": 76, "atom_b": 78, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 82, "atom_b": 84, "pair_type": 1}, {"atom_a": 83, "atom_b": 87, "pair_type": 1}, {"atom_a": 83, "atom_b": 86, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "N71", "residue_atom": "C51"}, {"name": "from", "monomer_atom": "C5", "residue_atom": "N7"}]} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2916153846153846, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19761538461538464, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21261538461538462, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "NOpt", "residue_id": 1, "residue_name": "LHCU", "atom_name": "N7", "charge_group_num": 7, "partial_charge": -0.7113846153846153, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", "atom_name": "H21", "charge_group_num": 8, "partial_charge": 0.3056153846153846, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "CH3", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C6", "charge_group_num": 9, "partial_charge": 0.19761538461538464, "mass": 15.035, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "HS14", "residue_id": 2, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2910384615384616, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19703846153846158, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21203846153846156, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "NOpt", "residue_id": 1, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6983846153846153, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HS14", "residue_id": 3, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2908076923076923, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "CH2", "residue_id": 3, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19680769230769235, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 13, "atom_type": "CH2", "residue_id": 3, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21180769230769234, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 14, "atom_type": "NOpt", "residue_id": 2, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6989615384615383, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 15, "atom_type": "HS14", "residue_id": 4, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.29076153846153846, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 16, "atom_type": "CH2", "residue_id": 4, "residue_name": "LHCU", 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"pair_type": 1}, {"atom_a": 7, "atom_b": 9, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 15, "atom_b": 17, "pair_type": 1}, {"atom_a": 19, "atom_b": 21, "pair_type": 1}, {"atom_a": 23, "atom_b": 25, "pair_type": 1}, {"atom_a": 27, "atom_b": 29, "pair_type": 1}, {"atom_a": 31, "atom_b": 33, "pair_type": 1}, {"atom_a": 35, "atom_b": 37, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 43, "atom_b": 45, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 53, "pair_type": 1}, {"atom_a": 55, "atom_b": 57, "pair_type": 1}, {"atom_a": 59, "atom_b": 61, "pair_type": 1}, {"atom_a": 63, "atom_b": 65, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 71, "atom_b": 73, "pair_type": 1}, {"atom_a": 77, "atom_b": 79, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 82, "atom_b": 86, "pair_type": 1}, {"atom_a": 84, "atom_b": 86, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C5", "residue_atom": "N7"}, {"name": "from", "monomer_atom": "N71", "residue_atom": "C51"}]} \ No newline at end of file diff --git a/polytop_examples/data/pei_linear_polymer.png b/polytop_examples/data/pei_linear_polymer.png index 7d9be32e2a6a23420508b26b4628fc0be1d7285f..6fff54d1e1fea35b8e50a5b6679e66d55ef55454 100644 GIT binary patch literal 10153 zcmeHtWn5El+&7AdNr-@sl9KLjfzdFe8>C}^(mnnv2uL?0r5h9&JrI=c(VYWEjP81l z&+Gfm^LgIhXMMKo?ArBAw_OK&Kc7E(Tty%Bh2k;G_mmVm=R_ek z){(hxRUTPs4O!&rsCI>+Pe*>ZjG^JT)M7n)0rGw#Y48K-2e`3vy0HOMt*ugn{Lh3v 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hydrogens, connected to them but not the rest of the polymer). # Import required Classes from PolyTop @@ -26,8 +26,8 @@ # Note that junctions are specified for extend() by their name attribute (in # this example 'to' and 'from', and NOT by the variable name they are assigned # to 'to_j' and 'from_j', which are used to pass them into a Monomer object) -to_j = Junction(top.get_atom("N71"), top.get_atom("C51"), name = "to") -from_j = Junction(top.get_atom("C5"), top.get_atom("N7"), name = "from") +to_j = Junction(top.get_atom("N71"), top.get_atom("C51"), name = "from") +from_j = Junction(top.get_atom("C5"), top.get_atom("N7"), name = "to") # ----- Create a Monomer from the Topology and a list of the Junctions -----