HackaMol
view release on metacpan or search on metacpan
"Capture::Tiny" : "0.46",
"Cwd" : "3.6",
"HTTP::Tiny" : "0.070",
"JSON::XS" : "3.04",
"List::MoreUtils" : "0.428",
"MCE" : "1.83",
"Math::Vector::Real" : "0.18",
"Math::Vector::Real::Random" : "0.03",
"Math::Vector::Real::XS" : "0.10",
"Math::Vector::Real::kdTree" : "0.15",
"Modern::Perl" : "1.20",
"Moose" : "2.20",
"MooseX::StrictConstructor" : "0.21",
"MooseX::Types::Path::Tiny" : "0.012",
"Path::Tiny" : "0.104",
"Test::Dir" : "0.0",
"Test::Fatal" : "0.014",
"Test::Moose" : "2.20",
"Test::More" : "1.3",
"Test::Output" : "1.03",
"Test::Warn" : "0.30",
Capture::Tiny: '0.46'
Cwd: '3.6'
HTTP::Tiny: '0.070'
JSON::XS: '3.04'
List::MoreUtils: '0.428'
MCE: '1.83'
Math::Vector::Real: '0.18'
Math::Vector::Real::Random: '0.03'
Math::Vector::Real::XS: '0.10'
Math::Vector::Real::kdTree: '0.15'
Modern::Perl: '1.20'
Moose: '2.20'
MooseX::StrictConstructor: '0.21'
MooseX::Types::Path::Tiny: '0.012'
Path::Tiny: '0.104'
Test::Dir: '0.0'
Test::Fatal: '0.014'
Test::Moose: '2.20'
Test::More: '1.3'
Test::Output: '1.03'
Test::Warn: '0.30'
Makefile.PL view on Meta::CPAN
"Capture::Tiny" => "0.46",
"Cwd" => "3.6",
"HTTP::Tiny" => "0.070",
"JSON::XS" => "3.04",
"List::MoreUtils" => "0.428",
"MCE" => "1.83",
"Math::Vector::Real" => "0.18",
"Math::Vector::Real::Random" => "0.03",
"Math::Vector::Real::XS" => "0.10",
"Math::Vector::Real::kdTree" => "0.15",
"Modern::Perl" => "1.20",
"Moose" => "2.20",
"MooseX::StrictConstructor" => "0.21",
"MooseX::Types::Path::Tiny" => "0.012",
"Path::Tiny" => "0.104",
"Test::Dir" => "0.0",
"Test::Fatal" => "0.014",
"Test::Moose" => "2.20",
"Test::More" => "1.3",
"Test::Output" => "1.03",
"Test::Warn" => "0.30",
Makefile.PL view on Meta::CPAN
"Capture::Tiny" => "0.46",
"Cwd" => "3.6",
"HTTP::Tiny" => "0.070",
"JSON::XS" => "3.04",
"List::MoreUtils" => "0.428",
"MCE" => "1.83",
"Math::Vector::Real" => "0.18",
"Math::Vector::Real::Random" => "0.03",
"Math::Vector::Real::XS" => "0.10",
"Math::Vector::Real::kdTree" => "0.15",
"Modern::Perl" => "1.20",
"Moose" => "2.20",
"MooseX::StrictConstructor" => "0.21",
"MooseX::Types::Path::Tiny" => "0.012",
"Path::Tiny" => "0.104",
"Test::Dir" => "0.0",
"Test::Fatal" => "0.014",
"Test::Moose" => "2.20",
"Test::More" => "1.3",
"Test::Output" => "1.03",
"Test::Warn" => "0.30",
[@Basic]
[@Git]
[PodWeaver]
[PkgVersion]
[NextRelease]
[GithubMeta]
[Git::NextVersion]
[MetaJSON]
[MinimumPerlFast]
[Prereqs]
Modern::Perl = 1.20 ;
MooseX::StrictConstructor = 0.21 ;
Math::Vector::Real = 0.18 ;
Math::Vector::Real::XS = 0.10 ;
Math::Vector::Real::Random = 0.03 ;
Math::Vector::Real::kdTree = 0.15 ;
Moose = 2.20 ;
MCE = 1.83 ;
JSON::XS = 3.04 ;
YAML::XS = 0.69 ;
MooseX::Types::Path::Tiny = 0.012 ;
examples/Analysis/BackBone_Dihedrals.pl view on Meta::CPAN
#!/usr/bin/env perl
# DMR: update 04-10-2014
# print out backbone dihedrals for each model in an NMR ensemble
use Modern::Perl;
use HackaMol;
use Time::HiRes qw(time);
my $t1 = time;
my $hack = HackaMol->new( name => "hackitup" );
my $mol = $hack->read_file_mol("t/lib/2LL5_mod123.pdb");
#backbone
examples/Analysis/Bfact.pl view on Meta::CPAN
use Modern::Perl;
use HackaMol;
use List::Util qw(sum0);
my $mol = HackaMol->new->pdbid_mol('2cba');
my %select = (
"protein" => ['protein'],
"water" => ['water'],
"HETATM" => ['record_name HETATM'],
"not_water/protein", ['record_name HETATM','.not. water']
);
examples/Analysis/mol_maxdist.pl view on Meta::CPAN
# Demian Riccardi May 23, 2014
# Quickly find the maximum distance in a molecule
#
use Modern::Perl;
use Math::Vector::Real::Farthest;
use HackaMol;
use Time::HiRes qw(time);
my $hack = HackaMol->new(
hush_read => 1,
data => "/lustre/pdbqts/NCI_diversitySet2/pdbqt"
);
my @pdbqts = $hack->data->children(qr/\.pdbqt/);
examples/BFP/2cba.pl view on Meta::CPAN
use Modern::Perl;
use HackaMol;
my $mol_2cba = HackaMol->new()->pdbid_mol('2cba');
my $CA_group = $mol_2cba->select_group('name CA');
$CA_group->calc_bfps;
foreach my $at ($CA_group->all_atoms){
printf("%4i %5.2f %5.2f\n", $at->resid, $at->bfact, $at->bfp );
}
examples/Benchmarks/Atom-MVR-timer.pl view on Meta::CPAN
#!/usr/bin/env perl
#
use Modern::Perl;
use Math::Vector::Real;
use Time::HiRes qw(time);
use Benchmark qw(cmpthese);
use Scalar::Util qw(refaddr);
use HackaMol::Atom;
my $natoms = 100000;
print
"Atom-timer will time the construction of an array of $natoms atoms to give idea about speed\n";
examples/Benchmarks/MVR.pl view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use Math::Vector::Real;
use Math::VectorReal;
use Time::HiRes qw(time);
use Benchmark qw(cmpthese);
my $v1aa = V( 1.1, 2.0, 3.1 );
my $v2aa = V( 2.1, 3.0, 1.1 );
my $dvaa = $v2aa - $v1aa;
my $distaa = sqrt( $dvaa * $dvaa );
examples/Benchmarks/Mem.pl view on Meta::CPAN
use Modern::Perl;
use Devel::Size;
use HackaMol;
use Math::Vector::Real;
use Time::HiRes qw(time);
my $t1 = time;
my @atoms = map {HackaMol::Atom->new(Z=>'1', coords=>[V(rand,rand,rand)])} 0 .. 100000;
my $t2 = time;
printf ("Time: %.3f\n", $t2-$t1);
examples/Capsid/capsid.pl view on Meta::CPAN
######################################################################
# capsid.pl
#
# generate all coordinates for a viral capsid (1QGT)
#
######################################################################
use Modern::Perl;
use HackaMol;
use Math::Vector::Real;
my $pdbid = '1QGT';
my $mol = HackaMol->new()->pdbid_mol($pdbid);
my @symops = <DATA>;
my %sym_op = (); # a hash to store all symmetry operations
examples/Cofactor/feheme.pl view on Meta::CPAN
#!/usr/bin/env perl
#
# DMR 4-15-2014
# simple script to help get started analyzing cofactors/metals in proteins
#
# wget http://pdb.org/pdb/files/1C7D.pdb
#
# run:
# perl feheme.pl 1C7D.pdb
#
use Modern::Perl;
use HackaMol;
use Statistics::Descriptive;
my $hack = HackaMol->new ;
# load all atoms into an array
my @atoms = $hack->read_file_atoms(shift);
#pull out iron atoms
my @Fes = grep {$_->symbol eq "Fe"} @atoms;
examples/GSSG/GSSG_3DK4.pl view on Meta::CPAN
#!/usr/bin/env perl
# This script will:
# 1. pull down pdbid 3DK4 from the PDB
# 2. extract the GSSG
# 3. write out a new pdb containing only the GSSG
#
# pubchem id can also be used to fetch
# @ids = qw/65359/;
#
use Modern::Perl;
use HackaMol;
my $hack = HackaMol->new(scratch=>'structures');
$hack->scratch->mkpath unless $hack->scratch->exists;
unless ( -e "structures/3DK4.pdb" ){
system("wget http://pdb.org/pdb/files/3DK4.pdb");
system("mv 3DK4.pdb structures/3DK4.pdb");
}
examples/GSSG/GSSG_GSHgSG.pl view on Meta::CPAN
#!/usr/bin/env perl
# Demian Riccardi, May 27, 2014
#
# This script will add an Hg across the disulfide in GSSG
#
# use GSSG_3DK4.pl first to set up
use Modern::Perl;
use HackaMol;
my $hack = new HackaMol;
my @atoms = $hack->read_file_atoms("structures/GSSG.pdb");
my ($ss) = $hack->find_disulfide_bonds( @atoms );
my $mol = HackaMol::Molecule->new( atoms => [@atoms] );
my $bl = $ss->bond_length;
examples/GSSG/GSSG_rotate.pl view on Meta::CPAN
#!/usr/bin/env perl
# Demian Riccardi, May 27, 2014
#
# This script will rotate atoms about the disulfide bond in GSSG
#
# use GSSG_3DK4.pl first to set up
use Modern::Perl;
use HackaMol;
my $tang = shift || 90;
my $hack = new HackaMol;
my @atoms = $hack->read_file_atoms("structures/GSSG.pdb");
my ($dihe) = $hack->build_dihedrals( @atoms[ 13, 14, 34, 33 ] );
my $mol = HackaMol::Molecule->new( atoms => [@atoms] );
examples/MCE/carve_around_ss_mce.pl view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use HackaMol;
use MCE;
my @pdbs = glob("pdbs/*.pdb");
my $MAX_PROCESSES = 8;
my $mce = MCE->new(
max_workers => $MAX_PROCESSES,
examples/MCE/heavy_mvr.pl view on Meta::CPAN
#!/usr/bin/env perl
# repetitive calculation of the average vector length for a sphere
# of random vectors shows capabilities of using MCE to use multiple cores.
use Modern::Perl;
use Math::Vector::Real;
use Math::Vector::Real::Random;
use MCE::Map; #carry out the map using the many core engine
use Time::HiRes qw(time);
my $t1 = time;
my @avg = mce_map {
my @mvrs = &gen_mvr_sphere;
my $sum = 0;
$sum += abs($_) foreach @mvrs;
examples/MolAdjust/readpdb_select_write.pl view on Meta::CPAN
# perl readpdb_select_write.pl some.pdb
#
# reads pdb (via shift of @ARGV)
# prints a selection to STDOUT
#
# useful for overlaying visualizations with general selections in VMD
# or whatever. All accomplished without creating any variables to show
# some object method chaining.
#
use Modern::Perl;
use HackaMol;
HackaMol::Molecule -> new (
atoms=>[
grep {
$_->name eq "N" or
$_->name eq "O" or
$_->name eq "C" or
$_->name eq "CA" or
$_->bfact > 0.25
examples/MolAdjust/strip_tip_rename_his.pl view on Meta::CPAN
#!/usr/bin/env perl
# Demian Riccardi February 20, 2014
#
# strips out TIP from pdb and renames HIS residues
# pdb adjustments needed to submit pdb generated from charmm simulation
# to COACH: http://zhanglab.ccmb.med.umich.edu/COACH/
#
use Modern::Perl;
use HackaMol;
my $hack = HackaMol->new(name=>"hackitup");
my @atoms = map {
$_->resname('HIS') if $_->resname =~ /HSD|HSE|HSP/;
$_;
}
grep {
$_->resname !~ /TIP|CLA/
} $hack->read_file_atoms(shift);
examples/MolFun/Maximum_distance.pl view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use Math::Vector::Real::Farthest;
use HackaMol;
my $hack = HackaMol->new(data=>"local_pdbs");
my @pdbs = $hack -> data -> children ( qr/\.pdb/ );
foreach my $pdb ( @pdbs ){
my @xyzs = map{$_->xyz} $hack->read_file_atoms($pdbqt);
examples/MolFun/Orbit_Protein.pl view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use HackaMol;
use Math::Vector::Real;
my $hack = HackaMol->new( name => 'hackitup' );
my @atoms1 = $hack->read_file_atoms("t/lib/1L2Y.pdb");
my $mol1 = HackaMol::Molecule->new( name => 'trp-cage', atoms => [@atoms1] );
my @atoms2 = $hack->read_file_atoms("t/lib/2cba.pdb");
my $mol2 = HackaMol::Molecule->new( name => 'CAII', atoms => [@atoms2] );
examples/MolFun/bin_expand.pl view on Meta::CPAN
#!/usr/bin/env perl
# Demian Riccardi August, 22, 2013
#
use Modern::Perl;
use HackaMol;
use Math::Vector::Real;
my $t1 = time;
my $angle = shift;
$angle = 180 unless ( defined($angle) );
my $hack = HackaMol->new( name => "hackitup" );
my @atoms = $hack->read_file_atoms("t/lib/1L2Y.pdb");
examples/MolFun/graphene_roll.pl view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use HackaMol;
use Math::Vector::Real;
use Time::HiRes qw(time);
my $t1 = time;
my $l = 1.42;
my $hack = HackaMol->new(name => "hackitup");
my $a1 = V( 0, $l*sqrt(3), 0);
examples/MolFun/loadPDB_transrot.pl view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use HackaMol;
use Math::Vector::Real;
my $hack = HackaMol->new( name => "hackitup" );
my @atoms = $hack->read_file_atoms("t/lib/1L2Y_mod123.pdb");
my $mol = HackaMol::Molecule->new( name => 'trp-cage', atoms => [@atoms] );
$mol->print_xyz;
examples/MolFun/spinning_ball.pl view on Meta::CPAN
#!/usr/bin/env perl
# Demian Riccardi
# This script loads 1L2Y.pdb and then generates xyz coordinates for the molecule spinning across the screen
# to run:
# perl spinning_ball.pl > spinning_ball.xyz
#
# then load into your favorite GUI. I use VMD
use Modern::Perl;
use HackaMol;
use Math::Vector::Real;
my $bld = HackaMol->new( name => "build" );
my $mol = $bld->pdbid_mol('1l2y');
$mol->translate( -$mol->COM );
$mol->translate( V( 90, 0, 0 ) );
foreach ( 1 .. 360 ) {
examples/MolFun/unfoldBB_mol.pl view on Meta::CPAN
#!/usr/bin/env perl
# Demian Riccardi 2013/09/16
#
# Description
# grep out the backbone atoms and rotate the dihedrals to the angle read in
# adding the sidechains shouldn't be too difficult. Just have to identify which
# atoms are moving
use Modern::Perl;
use HackaMol;
use Time::HiRes qw(time);
my $t1 = time;
my $angle = shift;
$angle = 180 unless ( defined($angle) );
my $hack = HackaMol->new( name => "hackitup" );
my @all_atoms = $hack->read_file_atoms("t/lib/1L2Y.pdb");
examples/MolFun/unfoldBB_movie.pl view on Meta::CPAN
#!/usr/bin/env perl
# Demian Riccardi 2013/09/16
#
# Description
# grep out the backbone atoms and rotate the dihedrals by increment until
# they are close to 180 degrees
use Modern::Perl;
use HackaMol;
use Time::HiRes qw(time);
my $t1 = time;
my $angle = shift;
$angle = 180 unless ( defined($angle) );
my $hack = HackaMol->new( name => "hackitup" );
#my @all_atoms = $hack->read_file_atoms("t/lib/2cba.pdb");
examples/MolReadPrintWrite/pdbqt_pdb.pl view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use HackaMol;
my $bldr = HackaMol->new( name => "builder", hush_read=>1 );
my @atoms = $bldr->read_file_atoms("t/lib/test.pdbqt");
# all coordinates from NMR ensemble are loaded into atoms
my $mol = HackaMol::Molecule->new(
name => 'somedrug',
atoms => [@atoms]
);
examples/MolReadPrintWrite/print_ts.pl view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use HackaMol;
my $hack = HackaMol->new( name => "hackitup" );
my $mol = $hack->read_file_mol("1L2Y.pdb"); #download from pdb.org
$mol->print_pdb_ts([3 .. 15],'print_ts_test.pdb');
( run in 0.469 second using v1.01-cache-2.11-cpan-4d50c553e7e )