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‎man/man1/aflock.1

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.\" man page template. See intro.l for more stuff to use
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.\" see mdoc for list of valid commands
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.\" Convert with groff:
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.\" groff -m man -T xhtml aflock.1 > aflock.html
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.Dd May 20, 2019
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.Dt AFLOCK 1
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.Sh NAME
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.Nm aflock
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.Nd the contact assigner in chromflock.
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.Sh SYNOPSIS
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.Sy aflock
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.Op Fl A Fl Fl aFile Ar fname
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.Op Fl l Fl Fl low Ar th
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.Op Fl h Fl Fl high Ar th
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.Op Fl n Fl Fl nStruct Ar N
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.Op Fl R Fl Fl radius Ar R
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.Op Fl Q Fl Fl vq Ar q
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.Op Fl m Fl Fl mArgs Ar args
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.Op Fl I Fl Fl init
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.Op Fl F Fl Fl final
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.Op Fl U Fl Fl update
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.Op Fl B Fl Fl blockupdate
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.Op Fl S Fl Fl score
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.Op Fl Fl rpos Ar fname
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.Op Fl Fl prpos Ar fname
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.Ys
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.Sh DESCRIPTION
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.Nm aflock
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is to be used before, between and after
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.Nm mflock
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is used. Typically in a script generated by
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.Nm chromflock.
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.Nm aflock
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can be used to initialize
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.Ar N
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new structures (or actually their W matrices), it can also be used to
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update the W matrices by moving contacts between them, or to add more contacts to them.
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.Pp
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The contact probability matix, passed as the
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.Ar aFile
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is supposed to be a [NxN] symmetric matrix stored linearly and encoded as 'double'.
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Since the A matrix should be symmetric either row or column order will work.
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.Pp
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If the same radial preference is to be enforced for all structures, this can be passed directly as an argument to
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.Nm mflock
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(use the -mArgs argument).
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To assign a radial preference with some probability to each structure, use the --rpos and --prpos pair of arguments.
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That will generate a separate file with radial constrains for each structure which is updated in the same way as W by
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.Nm aflock.
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.Pp
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.Sh MODES
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There are three modes, in initialization mode (
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.Fl --init
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), the entries (m,n) where A_mn=1 are assigned to all W matrices.
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In update mode, (
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.Fl --update
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) the contact maps, W, are updated with more contacts, or the contacts are re-distributed among them.
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The finalization mode (
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.Fl --final
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) is used to creates some summary statistics.
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.Sh OPTIONS
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.\" Begin list, ends with .El
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.Bl -tag -width Fl
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.It Fl A Ar file , Fl Fl aFile Ar file
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Specifies a file that contains the contact probability matrix.
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.It Fl Q, Fl Fl vq Ar q
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Sets the volume quotient,
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.Ar q
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of the beads, i.e. how large the volume of all beads should be in contrast to the volume of the nucleus.
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By specifying a volume quotient, the bead radius will be set and hence it is not possible to use -Q and -R simultaneously.
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.It Fl l Ar th, Fl Fl low th
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Sets the lower threshold to use, i.e., the lowest values of A to use.
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.It Fl h Ar th, Fl Fl high th
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Sets the lower threshold to use, i.e., the highest values of A to use.
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.It Fl R Ar r0, Fl Fl radius Ar r0
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Sets the radius of all beads to
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Ar r0
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(they can't be set individually). Probably you would like to use
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.Fl Q
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instead.
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.It Fl m Ar args, Fl Fl mArgs Ar args
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Set the arguments to be used by mflock, these will be passed over to the file named mflock_jobs that will be created.
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.It Fl I, Fl Fl init
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Set the mode to initialization.
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.It Fl U, Fl Fl update
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Set the mode to update.
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.It Fl B, Fl Fl blockupdate
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Set the mode to update, and blocks failed contacts be assigned again.
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.It Fl F, Fl Fl final
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Set the mode to finialization.
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.It Fl h, Fl Fl help
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Show a brief help message.
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.It Fl Fl rpos Ar fname
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Specifies a file that contains the radial preferences for each bead. The file should be encoded as double.
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Only to be used together with --prpos.
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.It Fl Fl prpos Ar fname
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Specifies a file that contains the probability or proportion of structures that should have each radial constraint.
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The file should be encoded as double. Only to be used with --rpos.
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.El
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.Sh EXAMPLES
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See the script `/util/chromflock_gen`.
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.Ss Basic usage:
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Initialize 10,000 structures using the contact probability matrix in A.double and give the beads a total volume that is 20% of the nuclei.
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.Pp
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$ aflock --init --aFile A.double --nStruct 10000 --vq 0.02
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.Sh SEE ALSO
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chromflock, mflock

‎man/man1/chromflock.1

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.\" man page template. See intro.l for more stuff to use
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.TH CHROMFLOCK 1
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.SH NAME
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chromflock -- Initialize a script for running chromflock in the current directory.
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.SH DESCRIPTION
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Chromflock is used as the first step in generating an ensemble of structures. The purpose is to initiate a configuration file with default settings in the current directory.
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.PP
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.SH EXAMPLE
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.SS Basic usage:
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.PP
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Replace nvim with something else if it isn't your favourite editor.
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.RS
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.nf
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.B $ mkdir 10000structures
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.B $ cd 10000structures
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.B $ # create chromflock_gen
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.B $ chromflock
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.B $ # edit settings and point to correct A-file and possible G-file.
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.B $ nvim chromflock_gen
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.B # Generate a (linear) batch script with everything to be run
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.B $ ./chromflock_gen
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.B # Run everything:
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.B $ ./chromflock_run
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.fi
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.RE
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.PP
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.SS TIPS
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.PP
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.RS
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Use screen or some other program to run chromflock in the background.
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This allows you to log out from a (remote) computer while chromflock is still running.
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.PP
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chromflock_run outputs some progress information to status.txt while running.
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.RE
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.SH SEE ALSO
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mflock, aflock

‎man/man1/mflock.1

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.\" man page template. See intro.l for more stuff to use
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.Dd May 21, 2019
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.Dt MFLOCK 1
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.Sh NAME
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.Nm mflock
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.Nd the molecular dynamics optimizer in chromflock.
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.Sh SYNOPSIS
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.Sy mflock
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.Op Fl w Fl Fl wFile Ar wFile
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.Op Fl L Fl Fl lFile Ar lFile
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.Op Fl x Fl Fl xFile Ar xfile
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.OP Fl o Fl Fl outFolder Ar folder
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.Op Fl e Fl Fl errstop Ar X
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.Op Fl g Fl Fl gradstop Ar X
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.Op Fl l Fl Fl linestop Ar X
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.Op Fl n Fl Fl maxiter Ar X
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.Op Fl t Fl Fl maxtime Ar X
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.Op Fl s Fl Fl seed Ar seed
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.Op Fl r Fl Fl rFile Ar rfile
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.Op Fl V Fl Fl kVol Ar kVol
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.Op Fl I Fl Fl kInt Ar kInt
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.Op Fl S Fl Fl kSph Ar kSph
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.Op Fl G Fl Fl kRad Ar kRad
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.Op Fl R Fl Fl radius Ar r0
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.Op Fl v Fl Fl verbose Ar level
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.Op Fl o Fl Fl oFolder Ar ofolder
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.Op Fl D Fl Fl dynamic
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.Op Fl z Fl Fl cmmz
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.Op Fl D Fl Fl dynamic
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.Ys
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.Sh DESCRIPTION
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mflock uses molecular dynamics to find a 3D structure based on a contact indication matrix
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W.
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For a complete description on how it is implemented, please see the documentation under 'doc/' in the source directory.
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In short: Verlet integration is used to update the positions of the beads which are under influence of a set of forces:
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a) Volume exclusion (beads should not overlap), controlled by
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.Ar kVol
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b) Spherical containment, that keeps the beads in the unit sphere, controlled by
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.Ar kSph
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c) Interaction forces that keeps beads with indicated contacts to be close to each others, controlled by
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.Ar kInt
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d) Possibly also a radial preference per bead, controlled by
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.Ar kRad
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By design all beads have to have the same size and the geometry is always in the unit sphere (radius=1).
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.Sh wFile
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The wFile contains
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W, a [NxN] size symmetric matrix stored linearly and encoded as 'uint8'.
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.Sh xFile
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The xFile contains 3D coordinates
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.Ar X
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that the molecular dynamics will start from. If not passed, beads will be placed randomly within the domain.
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Note that the parser is primitive and might fail if the xFile is edited without care.
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It reads comma separated values and does not accept headers, comments, etc.
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.Sh oFolder
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An output folder called 'cf_%05d/' will be created if no oFolder is specified.
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.Sh OPTIONS
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.Bl -tag -width Fl
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.It Fl w Fl Fl wFile Ar file
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Specifies the contact indicator matrix to be used where 1=contact, and 0=non contact. A force of kInt will be placed between beads that are in contact.
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.It Fl L Fl Fl lFile Ar file
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Specify a file with labels (chromosome) for the beads.
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.It Fl x Fl Fl xFile Ar file
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Specify a file with coordinates for the beads.
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.It Fl s Fl Fl seed Ar x
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Set a seed for the random number generator. If not time(NULL)*getpid() will be used.
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.It Fl r Fl Fl rFile Ar file
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Specify a file with radial information to be used with kRad
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.It Fl e Fl Fl errstop Ar x
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Set a stop condition on the error.
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.It Fl g Fl Fl gstop Ar x
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Set a condition for stopping on the gradient magnitude.
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.It Fl l Fl Fl ltol Ar x
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Set the line tolerance (only for Quasi-Newton)
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.It Fl n Fl Fl maxiter Ar n
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Set the number of iterations to be used.
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.It Fl t Fl Fl maxtime Ar t
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Limit the simulations in time
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.It Fl V Fl Fl kVol Ar k
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Set the volume exclusion force
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.It Fl I Fl Fl kInt Ar k
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Set the interaction force.
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.It Fl S Fl Fl kSph Ar k
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Set the force used to keep the beads in the domain.
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.It Fl G Fl Fl kRad Ar k
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Set the force for the radial guidance of the beads.
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.It Fl R Fl Fl radius Ar r0
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Set the bead radius.
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.It Fl v Fl Fl verbose Ar level
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Set verbosity level
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.It Fl o Fl Fl oFolder
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specify output folder
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.It Fl z Fl Fl cmmz
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Write compressed chimera files.
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.It Fl D Fl Fl dynamic
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Enable molecular dynamics (will be default in the future). If not a Quasi-Newton optimizer is used.
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.It Fl c Fl Fl compress
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Use chromosome compression.
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.It Fl a Fl Fl live
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Pops up a renderer that shows the beads during the simulation. Requires that mflock is compiled with SDL2.
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.It Fl h Fl Fl help
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Show a brief help message.
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.El
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.Sh EXAMPLES
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See the script `/util/chromflock_run`.
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.Ss Basic usage:
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Assume that you want to discard sequences in sequences.fa that are also in Chr1, then run:
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.Pp
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$ mflock --wFile ../W.uint8 --lFile ../L.uint8
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.Sh SEE ALSO
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chromflock, aflock

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