---
name: "FreeContact"
section: "3pm"
platform: "linux"
package: "libfreecontact-perl"
version: "0.08-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/FreeContact"
---

# FreeContact(3pm)

fast protein contact predictor

## NAME

FreeContact - fast protein contact predictor

## SYNOPSIS

```
  use FreeContact;
  open(EXAMPLE, '<', '/usr/share/doc/libfreecontact-perl/examples/demo_1000.aln') || confess($!);
  my @aln = <EXAMPLE>; chomp(@aln); close(EXAMPLE);
  my $contacts = FreeContact::Predictor->new()->run(ali => \@aln);
  my $predictor = FreeContact::Predictor->new();
  my %parset = FreeContact::get_ps_evfold();
  my $contacts = $predictor->run(ali => \@aln, %parset, num_threads => 1);
  my $predictor = FreeContact::Predictor->new();
  my($aliw, $wtot) = $predictor->get_seq_weights(ali => \@aln, num_threads => 1);
  my $contacts = $predictor->run_with_seq_weights(ali => \@aln, aliw => $aliw, wtot => $wtot, num_threads => 1);
```

## DESCRIPTION

FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011). FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 10-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

[**jackhmmer**(1)](/jackhmmer/1.md) from the hmmer package, or [**hhblits**(1)](/hhblits/1.md) from hhsuite can be used to generate the alignments, for example.

## FreeContact

### EXPORT\_OK

- **get\_ps\_evfold()**

  Get parameters for EVfold-mfDCA operating mode.

- **get\_ps\_psicov()**

  Get parameters for PSICOV 'improved results' operating mode.

- **get\_ps\_psicov\_sd()**

  Get parameters for PSICOV 'sensible default' operating mode. This is much faster than 'improved results' for a slight loss of precision.

  These **get\_ps\_()** functions return a hash of arguments (clustpc =\> *num*,...,rho =\> *num*) that can be used with **get\_seq\_weights()**, **run()** or **run\_with\_seq\_weights()**. The arguments correspond to the published parametrization of the respective method.

## FreeContact::Predictor

### Constructor

- new( dbg =\> bool )

  Creates an "FreeContact::Predictor".

### Methods

- **get\_seq\_weights()**

  Defaults for the arguments are obtained with **get\_ps\_evfold()**.

- run(ali =\> *\[\]*, clustpc =\> dbl, density =\> dbl, gapth =\> dbl, mincontsep =\> uint, pseudocnt =\> dbl, pscnt\_weight =\> dbl, estimate\_ivcov =\> bool, shrink\_lambda =\> dbl, cov20 =\> bool, apply\_gapth =\> bool, rho =\> dbl, \[veczw =\> bool\], \[num\_threads =\> int\], \[icme\_timeout =\> int\], \[timing =\> *{}*\])

  Defaults for the arguments are obtained with **get\_ps\_evfold()**.

  - ali

    Reference to array holding alignment rows as strings. The first row must hold the query, with no gaps.

  - clustpc

    BLOSUM-style clustering similarity threshold \[0-1\].

  - icme\_timeout

    Inverse covariance matrix estimation timeout in seconds. Default: 1800.

    The estimation sometimes gets stuck. If the timeout is reached, the **run()** method dies with "Caught FreeContact timeout exception: ...". You can catch this exception and handle it as needed, e.g. by setting a higher **rho** value.

  - num\_threads

    Number of OpenMP threads to use. If unset, all CPUs are used.

  - timing

    If given, this hash reference is filled with data containing wall clock timing results in seconds:

    ```
      {
        num_threads =>  NUM,
        seqw =>         NUM,
        pairfreq =>     NUM,
        shrink =>       NUM,
        inv =>          NUM,
        all =>          NUM
      }
    ```

  **run()** returns a hash reference of contact prediction results:

  ```
    {
      fro => [  # identifier of scoring scheme
        [
          I,    # 0-based index of amino acid i
          J,    # 0-based index of amino acid j
          SCORE # contact score
        ], ...
      ],
      MI => ...,
      l1norm => ...
    }
  ```

  Use 'fro' scores with EVfold.

## AUTHOR

Laszlo Kajan, \<lkajan@rostlab.org\>

## COPYRIGHT AND LICENSE

Copyright (C) 2013 by Laszlo Kajan

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.1 or, at your option, any later version of Perl 5 you may have available.