&sortAtoms
Summary:
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@atoms = &sortAtoms( \@atoms );
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Some of the returned statistics are only meaningful for
NMR NOE volumes (i.e.: q^6 );
Supported statistics:
Root Mean Square (rms):
R-factor (r):
Q-factor (q):
Q^(1/6)-factor (q6):
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&normHash
Summary:
%normed_hash1 = &normHash( \%hash1, \%hash2 );
or
%normed_hash1 = &normHash( \%hash1, \%hash2, \%ref_hash );
Normalize all values in a 2D hash1 to those in 2D hash2 by
summing all common values and calculating a normalization factor.
This normalization factor is then multiplied to each element in hash1
and returned. If a 2D ref_hash is supplied, the summing process will
only use those atom pairs (for instance, if you only want to use an
H5-H6 pair)
&calcAngle
Summary:
$angle = &calcAngle( $Ax, $Ay, $Az, $Bx, $By, $Bz );
Calculate the angle between two vectors, $Ax, $Ay, $Az,
$Bx, $By, $Bz. Only use this to calculate a few angles!!!
If you need many, it is much faster to use Beta_Hash
(which calls the C++ programs!)
&calcStats
Summary:
Calculates the standard deviation, average, or sum of a input
list of numbers
$sd = &calcSDev( \@numbers, "sd" );
or
( $sd, $avg, $sum ) = &calcSDev( \@numbers, "sd", "avg", "sum" );
Calculates the standard deviation of a input list of numbers.
Also returns the average value and sum of all input numbers, if
you want them.
@list = ( 12, 10, 11.2, 4.5, 14, 10.01 );
$sd = &calcStats( \@list, "sd" );
print "sd=$sd\n";
returns
sd=3.20008593634608
&calcStats1d
Summary:
( $rms, $r, $q, $q6 ) = &calcStats1D( \%hash1, \%hash2 );
or
( $rms, $r, $q, $q6 ) = &calcStats1D( \%hash1, \%hash2, \%ref );
See &calcStats_2D below for a description.
&calcStats2d
Summary:
( $rms, $r, $q, $q6 ) = &calcStats2D( \%hash1, \%hash2 );
or
( $rms, $r, $q, $q6 ) = &calcStats2D( \%hash1, \%hash2, \%ref );
Calculates pairwise statistical analysis
between the values of %hash1 and %hash2. Optionally, if
%ref is supplied, the analysis between %hash1 and %hash2
will be restricted only to the atom pairs found in %ref,
this can be used to examine the statistics of a particular
nucleotide, for instance.
&calcIsotope
Summary:
$I = &Get_Isotope( "A 3 CYT H1'" );
Returns the isotope number of the supplied atom.
&calcNmrActive
Summary:
Determine which nuclei in %YarmModel{xyz_pdb} are NMR active
%xyz_nmr = &calcNmrActive( \%YarmModel );
&calcSubset
Summary:
%vol_keys = &calcSubset($i_identifier, $j_identifier, \%vol_exp_hash );
Makes a new 2D hash from vol_exp with identifiers specified by
$i_identifier and $j_identifier
&calcFixed_Rij
Summary:
$fixed_rij = &calcFixed_Rij( $atom_i, $atom_j );