GeometricalCalculations
Quick summary of what the module does.
Perhaps a little code snippet.
use GeometricalCalculations; my $foo = GeometricalCalculations->new(); ...
A list of functions that can be exported. You can delete this section if you don't export anything, such as for a purely object-oriented module.
subroutine to calculate delta, theta, and rho angles for an smotif Input 1: $lvec - vector between the anchor points of the bracing secondary structures Input 2: $e1 - axis vector for 1st secondary structure Input 3: $e2 - axis vector for 2nd secondary structure
subroutine to check if pdb file exists in the PDB flat-file database
subroutine to get a reading file handle for a file. input: file path name to the file
exist_pdb_code_on_obsoletes input : pdb_code (4fab) return : full path name
check if a four-letters pdb code exist in uncompressed PDB folder it will return the full path name if a match is found. Return undef if not file was found input : pdb_code (4fab) return : full path name
check if a four-letters pdb code exist in user defined alternate PDB folder it will return the full path name if a match is found. Return undef if not file was found input : pdb_code (4fab) return : full path name
die if not match found
subroutine to read PDB file and obtain coordinates of backbone atoms. Input 1: @$data - smotif info (pdb ID, chain ID, start residue, ss1 length, ss2 length, loop length) Input/Output 2: @$landmarks - output array with smotif landmarks (0, loop start, ss2 start, ss2 end) Input 3: $string - backbone atom (CA, CB, C, N, or O) Input/Output 4: $seq - smotif sequence $VAR1 = [ '/usr/local/databases/pdb//uncompressed/pdb2kl8.ent.gz', 'A', 2, 7, 17, 3, 0, 'EH' ];
translate subroutine to convert from 3-letter codes to 1-letter codes
subroutine to convert from 1-letter codes to 3-letter codes
subroutine to find the centre of mass of a set of points, presented in 3 vectors
subroutine to find the centre of mass of a set of points, presented as a single vector
subroutine to calculate the principal axis of a set of points (corresponds to the principal eigenvector for the moment matrix)
subroutine to find the axis vector of a secondary structure, using at least 4 residues for a helix or 2 for a strand Input 1: Type of secondary structure (H=Helix, E=strand) Input 2: Option to indicate whether the secondary structure is the first (1) or second (2) part of the smotif Input 3: Initial residue number of the secondary structure Input 4: Final residue number of the secondar structure Input 5-7: Vectors containing the coordinates of C-alpha atoms, N atoms, and C atoms of the smotif
subroutine to calculate the matrix of moments from a set of backbone coordinates Input 1: Secondary structure type Input 2: Number of backbone atoms; Input 3: 3-D vector containing the coordinates of C-alpha, N, and C-atoms
subroutine to calculate the eigenvector of a 3x3 matrix for a given eigenvalue Input 1: Eigenvalue Input 2: 3x3 matrix
subroutine to project a point onto an axis, given a point on the line Input 1: Cooridnates of the point Input 2: Vector representing the axis Input 3: A point on the line
subroutine to find the determinant of a 3x3 matrix
subroutine to find the eigenvalues (ordered) of a 3x3 matrix
subroutine to multiply two matrices Input 1: Matrix 1 Input 2: Matrix 2 Input 3: Number of rows in matrix 1 Input 4: Number of columns in matrix 1, also the number of rows in matrix 2 Input 5: Numer of columns in matrix 2
subroutine to multiply a vector by a matrix Input 1: Matrix Input 2: Vector Input 3: Number of rows in the matrix Input 4: Number of columns in the matrix, also the number of elements in the vector
subroutine to find the outer product of two vectors of the same length Input 1: Vector 1 Input 2: Vector 2 Input 3: Dimension of vector 1, also dimension of vector 2
subroutine to find the roots of a cubic equation of the form x^3+ax^2+bx+cx=0
subroutine to rotate a point (pt) around an axis (vec) by a given angle (ang)
subroutine to rotate a point (pt) such that one axis (u) aligns with another (v)
subroutine to find the cross product of two 3-d vectors Input 1: Concatenated vector whose first three elements represent vector 1 and whose last three represent vector 2
subroutine to find the dot product of two vectors Input 1: Concatenated vector whose first half represents vector 1 and whose second half represents vector 2
subroutine to return the unit vector corresponding to a given vector
subroutine to return the 2-norm of a given vector
subroutine to add two vectors Input 1: Scalar factor to multiply the second vector Input 2: Concatenated vector whose first half represents the first vector and whose second half represents the second vector
subroutine to find the maximum of an array
subroutine to find the minimum of an array
subroutine to Fbin a value from 0-40 using a given binsize
subroutine to bin a value using a given bin size
subroutine to find the Pearson correlation coefficient between two data sets
subroutine to find the RMSD between two sets of points, using the method described by Theobald Input 1: Number of points to consider Input 2: Vector with the first set of coordinates Input 3: Vector with the second set of coordinates
subroutine to superpose one set of points onto another Input 1: Number of points to superpose Input 2: Vector of points to be used as the superposition template Input 3: Vector of points to be aligned and superposed Input 4: Vector of extra points to be superposed (not aligned, since they are "carried along")
subroutine to calculate the dihedral angle generated by four atoms
subroutine to calculate the coordinates of a beta-carbon, given statistically observed tetrahedral geometry###### Input 1: C-alpha coordinates Input 2: C coordinates Input 3: N coordinates
subroutine to distribute points evenly on a sphere Input 1: Number of points to distribute Input 2: Radius of sphere
subroutine to find the square of the 2-norm of a vector
Fiserlab Members , <andras at fiserlab.org>
<andras at fiserlab.org>
Please report any bugs or feature requests to bug-. at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=.. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
bug-. at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc GeometricalCalculations
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http://annocpan.org/dist/.
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Copyright 2015 Fiserlab Members .
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To install SmotifCS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm SmotifCS
CPAN shell
perl -MCPAN -e shell install SmotifCS
For more information on module installation, please visit the detailed CPAN module installation guide.