Syntax: gen_seq

Here we briefly describe the general usage and logic behind the program. The command line input to gen_seq are strings, which define macros. Macros are graphs and represent fragments of residue graphs. Multiple macros can then be combined to form the residue graph of interest. For example, one macro can describe a linear fragment and another one a branched fragment. Combining them gives a residue graph describing a Janus-like particle. Macros are defined as strings, with the following syntax:

<macro_name>:<#blocks>:<#branches>:<residues>

The <Macro_name> field is an arbitrary name of that macro, the <#blocks> field should be the number of residues for linear graphs and the number of generations for branched polymers. Consequently, <#branches> is the degree of branching of that polymer. Only regular branching is supported. The <residues> field can be used to define what the residue composition is within that macro using the following syntax:

<residue_name-probability, other_residue_name-porbability>

The residue name can be any string and the probability is the probability of having that residue anywhere in the chain that is described by the macro. Let us consider some examples for making macros. To generate a linear chain of 10 monomers PEO one would use A:10:1:PEO-1.0. Note that now the macro is called A. If we want instead to have a random distribution of PS and PEO with equal probabilities we would use A:10:1:PEO-0.5,PS-0.5. In that case, PS and PEO are randomly distributed along the graph with equal probability. In contrast, if we want to generate a polymer that is tree-like and consists of poly(propylene imine) (PPI) residues, we would use A:4:2:PPI-1.0. Once the macros are defined they can be combined to form a residue graph. To do so first the macros that are to be used have to be enumerated using the –seq flag. This specifies the order of the macros in the final graph. Subsequently, the connections between the macros have to be defined using the -connects flag and the following syntax:

<seq_position_macro_A>,<seq_position_macro_B>-<connect_residueA>,<connect_residueB>

In this syntax, <seq_position> is the position index of the macro provided to the –seq flag, and <connect_residue> is the residue ID of the residue that forms the connection between macros A and B, respectively. In addition to these basic functionalities, the program also allows to attach tags to each residue in the sequence with the -label option. In this way, for example, nodes can be labeled with their chirality/tacticity. There is also the possibility to modify end-groups. Both options are described in more detail in the help menu of the program. As polyply parses networkx-style json files, users can write their own protocols for making residue graphs or edit them manually as well.