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NAME
TetraSeqGen (ver.
0.2)
- Compute the folded tetrahedron sequence from the
U/D sequence (i.e., variation of the gradient) specified in the ".tsg"
file.

It also computes a correspondence table between 5-tile code sequences and U/D sequences of any length (the "-t" option).

Moreover, it could compute the ".pdb" and ".udcode" files of all the folded tetrahedron sequences of a given length (the "-a" option).

ABOUT ver. 0.2: Bug fix for the "-t" option.

It also computes a correspondence table between 5-tile code sequences and U/D sequences of any length (the "-t" option).

Moreover, it could compute the ".pdb" and ".udcode" files of all the folded tetrahedron sequences of a given length (the "-a" option).

ABOUT ver. 0.2: Bug fix for the "-t" option.

DOWNLOADS (Free for academic use)

SYNOPSIS

(1) TetraSeqGen [-w width] [-d
distance] [-e length] U/D-seq_file.tsg

(2) TetraSeqGen [-w width] [-l length] -t 5-tile_code_to_U/D-seq.tbl

(3) TetraSeqGen [-w width] [-l length] -a

(4) TetraSeqGen -h

Examples:

(2) TetraSeqGen [-w width] [-l length] -t 5-tile_code_to_U/D-seq.tbl

(3) TetraSeqGen [-w width] [-l length] -a

(4) TetraSeqGen -h

Examples:

% TetraSeqGen xxx.tsg

(Compute folded tetrshedron sequences from the U/D sequence, where five successive tetrahedons form a block and the distance between successive block is 3.8 angstrom. In other words, they form a polygonal chain consisted of 3.8 angstrom line segments.)

% TetraSeqGen -d 0.0 xxx.tsg

(Compute folded tetrshedron sequences from the U/D sequence, where no translation is allowed.)

% TetraSeqGen -l 7 -t xxx.tbl

(Computes a correspondence table between 5-tile code sequences of length 7 and U/D sequences of length 5*7, using the given table, where 5 successive tetrahedons form a block and the distance between successive block is 3.8 angstrom.)

% TetraSeqGen -w 3 -l 7 -a

(Compute all the folded tetrahedron sequences of length 3*7, where 3 successive tetrahedons form a block and the distance between successive block is 3.8 angstrom. In this case, the amount of the output file is about 3GB.)

(Compute folded tetrshedron sequences from the U/D sequence, where five successive tetrahedons form a block and the distance between successive block is 3.8 angstrom. In other words, they form a polygonal chain consisted of 3.8 angstrom line segments.)

% TetraSeqGen -d 0.0 xxx.tsg

(Compute folded tetrshedron sequences from the U/D sequence, where no translation is allowed.)

% TetraSeqGen -l 7 -t xxx.tbl

(Computes a correspondence table between 5-tile code sequences of length 7 and U/D sequences of length 5*7, using the given table, where 5 successive tetrahedons form a block and the distance between successive block is 3.8 angstrom.)

% TetraSeqGen -w 3 -l 7 -a

(Compute all the folded tetrahedron sequences of length 3*7, where 3 successive tetrahedons form a block and the distance between successive block is 3.8 angstrom. In this case, the amount of the output file is about 3GB.)

INPUT

(1) A file which
specifies a U/D sequence (".tsg" file). U/D sequences could be
represented by the one letter representations:

If width=3, then 0 for DDD, 1 for DDU, ..., 7 for UUU.

If width=5, then 0 for DDDDD, ..., 9 for DUDDU, A for DUDUD, ...

(2) A correspondence table between 5-tile codes and U/D-valued sequences (".tbl" file). U/D sequences are represented by the one letter representation. (example)

(3) None

If width=3, then 0 for DDD, 1 for DDU, ..., 7 for UUU.

If width=5, then 0 for DDDDD, ..., 9 for DUDDU, A for DUDUD, ...

(2) A correspondence table between 5-tile codes and U/D-valued sequences (".tbl" file). U/D sequences are represented by the one letter representation. (example)

(3) None

OUTPUT

(1) Two types of
folded tetrahedron sequences whose variation of the gradient is equal
to the U/D-sequence given in the "xxx.tsg" file:

xxxXZY.pdb, xxxXZYg.udcode,

xxxZXY.pdb, xxxZXYg.udcode

(To distinguish the ".udcode" from the output file of "ProteinEnocder", "g.udcode" is appended to "xxx".)

(2) The correspondence table between 5-tile code sequences and U/D sequences of the given length:

xxx_corres.tbl (example)

(3) The ".pdb" and ".udcode" files of all the folded tetrahedron sequences of the given length, which are organized into the follwoing directories under the current directory (examples: ".pdb" file, "udcode" file):

XZY00/, XZY01/, ..., XZY17/, ZXY00/, ZXY01/, ..., ZXY17/

In the follwing examples, click the images to view larger images.

DESCRIPTION

xxxXZY.pdb, xxxXZYg.udcode,

xxxZXY.pdb, xxxZXYg.udcode

(To distinguish the ".udcode" from the output file of "ProteinEnocder", "g.udcode" is appended to "xxx".)

(2) The correspondence table between 5-tile code sequences and U/D sequences of the given length:

xxx_corres.tbl (example)

(3) The ".pdb" and ".udcode" files of all the folded tetrahedron sequences of the given length, which are organized into the follwoing directories under the current directory (examples: ".pdb" file, "udcode" file):

XZY00/, XZY01/, ..., XZY17/, ZXY00/, ZXY01/, ..., ZXY17/

In the follwing examples, click the images to view larger images.

Input file | Option |
Result (XZY) | Output file |

Example 1: | .tsg (U/D=0F1111100) |
None | XZY.pdb XZYg.udcode ZXY.pdb ZXY.udcode |

Example 2: | .tsg (U/D=0F1111100) |
-d 0.0 | XZY.pdb XZYg.udcode ZXY.pdb ZXY.udcode |

Example 3: | .tsg (U/D=00341020...) |
-w 3 | XZY.pdb XZYg.udcode ZXY.pdb ZXY.udcode |

DESCRIPTION

TetraSeqGen reads a ".tsg"
file and computes the ".pdb" and ".udcode" files of two types of folded
tetrahedron sequences from a given U/D sequence, one starts from
tetrahedron 0[xzy] and the other starts from 0[zxy].

Using "ProteinViwer" (ver. 0.4 or later), one could view the tetrahedron sequences interactively. One could compute the 5-tile code of the folded tetrahedron sequences by feeding the ".pdb" files to "Proteinencoder."

By dafault, translation is allowed during the fildong process, where five successive tetrahedrons form a block and the distance between successive block is 3.8 angstrom. In other words, by connecting the blocks, one would obtain a polygonal chain consisted of 3.8 angstrom line segments.

One could specifiy the length of the segment, using the "-d" option, and the size of a tetrahedron block, using the "-w" option.

TetraSeqGen also reads a ".tbl" file, which specifies a correspondence between 5-tile codes and U/D sequences, and computes a correspondence table between 5-tile code sequences and U/D sequences of any length based on the correspondence given in the ".tbl" file (the "-t" option).

TetraSeqGen also could compute the ".pdb" and ".udcode" files of all the folded tetrahedron sequences of a given length (the "-a" option). The files are organized into a file hierarchy under the current directory.

The following options are available:

Using "ProteinViwer" (ver. 0.4 or later), one could view the tetrahedron sequences interactively. One could compute the 5-tile code of the folded tetrahedron sequences by feeding the ".pdb" files to "Proteinencoder."

By dafault, translation is allowed during the fildong process, where five successive tetrahedrons form a block and the distance between successive block is 3.8 angstrom. In other words, by connecting the blocks, one would obtain a polygonal chain consisted of 3.8 angstrom line segments.

One could specifiy the length of the segment, using the "-d" option, and the size of a tetrahedron block, using the "-w" option.

TetraSeqGen also reads a ".tbl" file, which specifies a correspondence between 5-tile codes and U/D sequences, and computes a correspondence table between 5-tile code sequences and U/D sequences of any length based on the correspondence given in the ".tbl" file (the "-t" option).

TetraSeqGen also could compute the ".pdb" and ".udcode" files of all the folded tetrahedron sequences of a given length (the "-a" option). The files are organized into a file hierarchy under the current directory.

The following options are available:

-w width (int type)

By default, thetrahedron
sequences are decomposed into blocks of successive five tetrahedrons.
If -w is specified, they are decomposed into blocks of "width"
tetrahedrons.

-d distance (float
type)

By default, translation is
allowed during the folding process, and the distance between successive
block is kept 3.8 angstrom. (Note that 3.8 angstrom is the
average distance between successive CA atoms on protein backbones.) If
-r is specified, the distance is set to "distance". If "0.0"
is specified as the "distance", no translation is performed
during the folding process.

-e length (float type)

By default, the length of
the short edges of a tetrahedrons is about 2.058 angstrom. If -e is
specified, the length is set to "distance". Using the option,
one could adjust the size ratio of a tetrahedron to the
polygonal chain.

-l length
(int type)

By default, five
tetrahedron-blocks are computed, where each block corresponds to a
5-tile code. (In other words, polygonal chains of five vertices are
computed.) Each block consists of successive "width" tetrahedrons which
is specified by the "-w" option. If -l is specified, "length"
tetrahedron-blocks are computed. (That is, polygonal chains of "length"
vertices.) Note that the length of the U/D sequence is equal
to "length"*"width".

-t xxx.tbl (table
name)

If the "-t" option is
specified, the
correspondence table between 5-tile code sequences and U/D sequences of
the given length is computed based on the specified table, "xxx.tbl".
The length of the U/D sequence is equal to "length"*"width".

-a

If the "-a" option is
specified, the
".pdb" and ".udcode" files of all the folded tetrahedron
sequences of a given length are computed. The length of the U/D
sequence is equal to "length"*"width". (If "-w 3 -l 7" is specified,
the amount of the output file is about 3GB.)

-h

If the "-h" option is
specified, synopsis is shown.