Module Protein.Abstract

module Abstract: sig  end

Contains the lightweight, live internal representation of an abstract protein. This representation should not be confused with genetic representations of proteins, which are not live data structures. This representation is used to feed the protein compiler, to output graphical representations of the protein, for some genetic manipulations, etc.

The module contains functions to create abstract proteins and, conversely, to deconstruct them in order to probe their structure.

type t

An abstract protein.

type d

An opaque handle to a domain within an abstract protein.

type interf

An opaque handle to an (arbitrary) interface of an abstract protein.

type interf_direction =

`\|`	`Acceptor`	`(*`	`or input interface`	`*)`
`\|`	`Expressor`	`(*`	`of output interface`	`*)`

The direction of an interface.

type interf_type =

`\|`	`IFBool`	`(*`	`Boolean-valued`	`*)`
`\|`	`IFInt`	`(*`	`Integer-valued`	`*)`
`\|`	`IFString`	`(*`	`String-valued`	`*)`
`\|`	`IFMatcher`	`(*`	`Matcher-valued`	`*)`

The type of an interface.

type conn_value =

`\|`	`C_Bool of bool`
`\|`	`C_Int of int`
`\|`	`C_String of string`
`\|`	`C_Matcher of Ligand.Matcher.matcher`

The possible values of a connection.

type interf_character = interf_direction * interf_type

Combines the type and the direction of an arbitrary protein interface. One can obtain the character of any particular interface by calling get_interf_character.

module type DOMDEF = sig  end

Contains the model which defines the essential characteristics of each module flavor.

module SLBD: sig  end

Characteristics of the abstract Simple Ligand Binding Domain.

module BMD: sig  end

Characteristics of the abstract Boolean Multiplexor Domain.

module LID: sig  end

Characteristics of the abstract Logical Integration Domain.

module PDMatcher: sig  end

Characteristics of the abstract Matcher Pseudo-Domain.

module LBDR: sig  end

Characteristics of the abstract Ligand Binding Domain with Remapping.

module LBDE: sig  end

Characteristics of the abstract Ligand Binding Domain with Extraction.

val make : unit -> t

make () returns a new abstract protein which does not contain any domain or any connection. Use add_domain and add_???_connection below to gradually construct the domain in a safe manner.

type domaincons =

`\|`	`D_SLBD of SLBD.cons`	`(*`	`Simple Ligand Binding Domain`	`*)`
`\|`	`D_PDMatcher of PDMatcher.cons`	`(*`	`Matcher Pseudo-Domain`	`*)`
`\|`	`D_BMD of BMD.cons`	`(*`	`Boolean Multiplexor Domain`	`*)`
`\|`	`D_LID of LID.cons`	`(*`	`Logical Integration Domain`	`*)`
`\|`	`D_LBDR of LBDR.cons`	`(*`	`Ligand Binding Domain with Remapping`	`*)`
`\|`	`D_LBDE of LBDE.cons`	`(*`	`Ligand Binding Domain with Extraction`	`*)`

A domain constructor.

val add_domain : domaincons -> t -> d

add_domain d p adds a new domain defined by the constructor d to the protein p, and returns an opaque handle to the new domain which may be used to extract interfaces.

exception Wrong_domain_type

Raised by get_interf below when the interface which is asked for is not an interface of the parameter domain.

type interfid =

`\|`	`I_SLBD of SLBD.interfid`
`\|`	`I_PDMatcher of PDMatcher.interfid`
`\|`	`I_BMD of BMD.interfid`
`\|`	`I_LID of LID.interfid`
`\|`	`I_LBDR of LBDR.interfid`
`\|`	`I_LBDE of LBDE.interfid`

A synthetic type to capture all the possible interface identifiers across all domain flavors.

val get_interf : d -> interfid -> interf

Use get_interf dp id to obtain an opaque handle to the interface identified by id of the domain referenced by dp. dp should be a return value from the add_domain function. get_interf will raise Wrong_domain_type if the interface which is asked for is not an interface of the domain passed as parameter.

exception Interface_already_set

Raised by add_connection below.

exception Wrong_type

Raised by add_connection below.

exception Wrong_direction

Raised by add_connection below.

exception Different_proteins

val add_connection : interf ->
       interf -> conn_value -> unit

add_connection i1 i2 v adds a new connection between the two interfaces i1 and i2, which have been previously obtained using the get_interf function above. If either interface has already been set, Interface_already_set is raised. If the types of the two interfaces are not equal, or do not equal the type of the value v, then Wrong_type is raised. i1 should be an expressor interface, and i2 an acceptor interface, otherwise Wrong_direction is raised. Finally, both interfaces should be part of domains which have been added to the same protein, otherwise Different_proteins is raised.