/dports/science/openbabel/openbabel-3.1.1/scripts/perl/ |
H A D | OpenBabel.pm | 7 package Chemistry::OpenBabel; 10 package Chemistry::OpenBabelc; 11 bootstrap Chemistry::OpenBabel; 12 package Chemistry::OpenBabel; 17 package Chemistry::OpenBabel; 50 package Chemistry::OpenBabel; 79 *dot = *Chemistry::OpenBabelc::dot; 6123 package Chemistry::OpenBabel; 6308 *A = *Chemistry::OpenBabelc::A; 6309 *C = *Chemistry::OpenBabelc::C; [all …]
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/dports/science/p5-PerlMol/PerlMol-0.3500/ |
H A D | Changes | 7 Chemistry-File-VRML 0.10 8 Chemistry-3DBuilder 0.10 12 Chemistry-Mol 0.35 22 Chemistry-Mok 0.25 177 Chemistry-Mol 0.23 178 Chemistry-MacroMol 0.05 179 Chemistry-InternalCoords 0.11 180 Chemistry-File-MDLMol 0.15 181 Chemistry-File-SMILES 0.33 182 Chemistry-File-PDB 0.10 [all …]
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H A D | MANIFEST | 41 inc/BUNDLES/Chemistry-3DBuilder-0.10/lib/Chemistry/3DBuilder.pm 111 inc/BUNDLES/Chemistry-File-SLN-0.11/lib/Chemistry/File/SLN.pm 112 inc/BUNDLES/Chemistry-File-SLN-0.11/lib/Chemistry/File/SLN/Parser.pm 213 inc/BUNDLES/Chemistry-File-VRML-0.10/lib/Chemistry/File/VRML.pm 234 inc/BUNDLES/Chemistry-FormulaPattern-0.10/lib/Chemistry/FormulaPattern.pm 268 inc/BUNDLES/Chemistry-Isotope-0.11/lib/Chemistry/Isotope.pm 284 inc/BUNDLES/Chemistry-MidasPattern-0.11/lib/Chemistry/MidasPattern.pm 319 inc/BUNDLES/Chemistry-Mok-0.25/lib/Chemistry/Mok.pm 396 inc/BUNDLES/Chemistry-Reaction-0.02/lib/Chemistry/Reaction.pm 407 inc/BUNDLES/Chemistry-Ring-0.19/lib/Chemistry/Ring.pm [all …]
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H A D | README | 21 Chemistry-File-VRML 0.10 22 Chemistry-3DBuilder 0.10 25 Chemistry-Mol 0.35 26 Chemistry-Mok 0.25 27 Chemistry-File-SMILES 0.44 28 Chemistry-File-SMARTS 0.22 29 Chemistry-File-PDB 0.21 30 Chemistry-Pattern 0.26 31 Chemistry-MidasPattern 0.11 32 Chemistry-File-MDLMol 0.20 [all …]
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/ |
H A D | BUNDLES.yml | 1 Chemistry::3DBuilder: 'inc/BUNDLES/Chemistry-3DBuilder-0.10' 2 Chemistry::Bond::Find: 'inc/BUNDLES/Chemistry-Bond-Find-0.21' 3 Chemistry::Canonicalize: 'inc/BUNDLES/Chemistry-Canonicalize-0.10' 4 Chemistry::File::MDLMol: 'inc/BUNDLES/Chemistry-File-MDLMol-0.20' 5 Chemistry::File::Mopac: 'inc/BUNDLES/Chemistry-File-Mopac-0.15' 6 Chemistry::File::PDB: 'inc/BUNDLES/Chemistry-File-PDB-0.21' 7 Chemistry::File::SLN: 'inc/BUNDLES/Chemistry-File-SLN-0.11' 14 Chemistry::Isotope: 'inc/BUNDLES/Chemistry-Isotope-0.11' 17 Chemistry::Mok: 'inc/BUNDLES/Chemistry-Mok-0.25' 18 Chemistry::Mol: 'inc/BUNDLES/Chemistry-Mol-0.35' [all …]
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/dports/science/mpqc/mpqc-2.3.1/src/lib/chemistry/cca/ |
H A D | MPQC_IntegralEvaluatorFactory_Impl.hh | 118 Chemistry::Molecule molecule_; 194 ::Chemistry::QC::GaussianBasis::Molecular 204 /* in */ ::Chemistry::Molecule mol 214 ::Chemistry::Molecule 238 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 243 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs2 258 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 278 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 298 ::Chemistry::QC::GaussianBasis::IntegralEvaluator3 320 ::Chemistry::QC::GaussianBasis::IntegralEvaluator4 [all …]
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H A D | MPQC_IntegralEvaluatorFactory_Impl.cc | 17 using namespace Chemistry::QC; 153 ::Chemistry::QC::GaussianBasis::Molecular 169 /* in */ ::Chemistry::Molecule mol ) in set_molecule() 181 ::Chemistry::Molecule 213 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 217 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, in get_integral_evaluator2() 240 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 262 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 284 ::Chemistry::QC::GaussianBasis::IntegralEvaluator3 313 ::Chemistry::QC::GaussianBasis::IntegralEvaluator4 [all …]
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/cca/Chemistry/server/cxx/ |
H A D | NWChem_Chemistry_QC_IntEvalFactory_Impl.hh | 128 ::Chemistry::QC::GaussianBasis::CompositeIntegralDescr 162 ::Chemistry::QC::GaussianBasis::IntegralEvaluator1 165 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1 177 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 180 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, 181 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs2 193 ::Chemistry::QC::GaussianBasis::IntegralEvaluator3 196 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, 198 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs3 210 ::Chemistry::QC::GaussianBasis::IntegralEvaluator4 [all …]
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H A D | NWChem_Chemistry_QC_IntEvalFactory_Impl.cc | 60 ::Chemistry::QC::GaussianBasis::CompositeIntegralDescr 105 ::Chemistry::QC::GaussianBasis::IntegralEvaluator1 122 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 125 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, in get_evaluator2() 140 ::Chemistry::QC::GaussianBasis::IntegralEvaluator3 143 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, in get_evaluator3() 144 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs2, in get_evaluator3() 159 ::Chemistry::QC::GaussianBasis::IntegralEvaluator4 162 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, in get_evaluator4() 163 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs2, in get_evaluator4() [all …]
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/cca/Chemistry/server/cxx/ |
H A D | NWChem_Chemistry_QC_IntEvalFactory_Impl.cc | 60 ::Chemistry::QC::GaussianBasis::CompositeIntegralDescr 105 ::Chemistry::QC::GaussianBasis::IntegralEvaluator1 122 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 125 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, in get_evaluator2() 140 ::Chemistry::QC::GaussianBasis::IntegralEvaluator3 143 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, in get_evaluator3() 144 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs2, in get_evaluator3() 159 ::Chemistry::QC::GaussianBasis::IntegralEvaluator4 162 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, in get_evaluator4() 163 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs2, in get_evaluator4() [all …]
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H A D | NWChem_Chemistry_QC_IntEvalFactory_Impl.hh | 128 ::Chemistry::QC::GaussianBasis::CompositeIntegralDescr 162 ::Chemistry::QC::GaussianBasis::IntegralEvaluator1 165 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1 177 ::Chemistry::QC::GaussianBasis::IntegralEvaluator2 180 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, 181 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs2 193 ::Chemistry::QC::GaussianBasis::IntegralEvaluator3 196 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs1, 198 /* in */ ::Chemistry::QC::GaussianBasis::Molecular bs3 210 ::Chemistry::QC::GaussianBasis::IntegralEvaluator4 [all …]
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-MDLMol-0.20/t/ |
H A D | pattern.t | 4 use Chemistry::File::MDLMol; 6 if (eval "use Chemistry::Pattern; use Chemistry::Ring; 1") { 9 ok(1, "loaded Chemistry::Pattern"); 11 plan skip_all => 'Chemistry::Pattern or Chemistry::Ring not installed'; 14 #$Chemistry::File::MDLMol::DEBUG = 1; 15 my $patt = Chemistry::Pattern->read('t/query.mol'); 16 isa_ok ($patt, 'Chemistry::Pattern'); 24 #$Chemistry::Pattern::DEBUG=1; 27 my $mol = Chemistry::Mol->read($file->{name}); 28 Chemistry::Ring::aromatize_mol($mol);
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/ |
H A D | Changes | 1 Revision history for Perl extension Chemistry::Mol. 27 - New Chemistry::File interface 31 - Added support for Chemistry::Isotope 32 - Extended the Chemistry::Obj::attr method 51 - Added the Chemistry::File::Dumper module. 76 - New methods for Chemistry::Bond: delete 77 - Chemistry::Mol can export read_mol 82 - New methods for Chemistry::Atom: mass 83 - New module: Chemistry::File::Formula 87 - New methods for Chemistry::Obj: del_attr [all …]
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/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/t/ |
H A D | File.t | 9 use_ok('Chemistry::File'); 14 my $f = Chemistry::File->new; 15 isa_ok($f, "Chemistry::File"); 17 require Chemistry::File::Dumper; 22 isa_ok($file, "Chemistry::File::Dumper"); 25 isa_ok($mol, "Chemistry::Mol", 'read file'); 42 use base qw(Chemistry::File); 92 # Chemistry::Mol->file 93 $file = Chemistry::Mol->file($fname); 94 isa_ok($file, "Chemistry::File::Dumper"); [all …]
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H A D | Mol.t | 4 use_ok('Chemistry::Mol'); 8 my $mol = Chemistry::Mol->new; 9 isa_ok($mol, 'Chemistry::Mol', '$mol'); 10 isa_ok($mol, 'Chemistry::Obj', '$mol'); 12 isa_ok($atom, 'Chemistry::Atom', '$atom'); 13 isa_ok($atom, 'Chemistry::Obj', '$atom'); 15 my $bond = Chemistry::Bond->new(atoms => [$atom, $atom2], type => '='); 16 isa_ok($bond, 'Chemistry::Bond', '$bond'); 17 isa_ok($bond, 'Chemistry::Obj', '$bond'); 33 $mol = Chemistry::Mol->new; [all …]
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H A D | geom.t | 6 use Chemistry::File::Dumper; 12 my $mol = Chemistry::Mol->read("t/mol.pl"); 13 isa_ok( $mol, 'Chemistry::Mol' ); 20 is_float( Chemistry::Atom::angle_deg(@a), 110.7, 0.1, "angle" ); 24 is_float( Chemistry::Atom::dihedral_deg(@a), -85.6, 0.1, "dihedral" ); 33 is( Chemistry::Atom::angle($v0, $v1, $v0), 0, "zero angle" ); 34 is( Chemistry::Atom::angle($v0, $v0, $v0), 0, "bad angle" ); 35 is( Chemistry::Atom::angle($v0, $v0, $v1), 0, "bad angle" ); 36 is_float( Chemistry::Atom::angle_deg($v0, $v1, $v2), 180, 0.1, "linear angle" ); 37 is( Chemistry::Atom::dihedral($v0, $v0, $v0, $v0), 0, "bad dihedral" ); [all …]
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/t/ |
H A D | File.t | 9 use_ok('Chemistry::File'); 14 my $f = Chemistry::File->new; 15 isa_ok($f, "Chemistry::File"); 17 require Chemistry::File::Dumper; 22 isa_ok($file, "Chemistry::File::Dumper"); 25 isa_ok($mol, "Chemistry::Mol", 'read file'); 42 use base qw(Chemistry::File); 92 # Chemistry::Mol->file 93 $file = Chemistry::Mol->file($fname); 94 isa_ok($file, "Chemistry::File::Dumper"); [all …]
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H A D | Mol.t | 4 use_ok('Chemistry::Mol'); 8 my $mol = Chemistry::Mol->new; 9 isa_ok($mol, 'Chemistry::Mol', '$mol'); 10 isa_ok($mol, 'Chemistry::Obj', '$mol'); 12 isa_ok($atom, 'Chemistry::Atom', '$atom'); 13 isa_ok($atom, 'Chemistry::Obj', '$atom'); 15 my $bond = Chemistry::Bond->new(atoms => [$atom, $atom2], type => '='); 16 isa_ok($bond, 'Chemistry::Bond', '$bond'); 17 isa_ok($bond, 'Chemistry::Obj', '$bond'); 33 $mol = Chemistry::Mol->new; [all …]
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H A D | geom.t | 6 use Chemistry::File::Dumper; 12 my $mol = Chemistry::Mol->read("t/mol.pl"); 13 isa_ok( $mol, 'Chemistry::Mol' ); 20 is_float( Chemistry::Atom::angle_deg(@a), 110.7, 0.1, "angle" ); 24 is_float( Chemistry::Atom::dihedral_deg(@a), -85.6, 0.1, "dihedral" ); 33 is( Chemistry::Atom::angle($v0, $v1, $v0), 0, "zero angle" ); 34 is( Chemistry::Atom::angle($v0, $v0, $v0), 0, "bad angle" ); 35 is( Chemistry::Atom::angle($v0, $v0, $v1), 0, "bad angle" ); 36 is_float( Chemistry::Atom::angle_deg($v0, $v1, $v2), 180, 0.1, "linear angle" ); 37 is( Chemistry::Atom::dihedral($v0, $v0, $v0, $v0), 0, "bad dihedral" ); [all …]
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/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/ |
H A D | Changes | 1 Revision history for Perl extension Chemistry::Mol. 51 - New Chemistry::File interface 55 - Added support for Chemistry::Isotope 56 - Extended the Chemistry::Obj::attr method 75 - Added the Chemistry::File::Dumper module. 100 - New methods for Chemistry::Bond: delete 101 - Chemistry::Mol can export read_mol 106 - New methods for Chemistry::Atom: mass 107 - New module: Chemistry::File::Formula 111 - New methods for Chemistry::Obj: del_attr [all …]
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-3DBuilder-0.10/t/ |
H A D | builder.t | 6 use Chemistry::3DBuilder qw(build_3d); 7 use Chemistry::File::SMILES; 8 use Chemistry::File::SMARTS; 9 use Chemistry::Pattern; 10 use Chemistry::Atom qw(angle_deg dihedral_deg distance); 24 patt => Chemistry::Pattern->parse('CC', format => 'smarts'), 47 patt => Chemistry::Pattern->parse('*[*X4,NX3,OX2,OX3]*', 66 patt => Chemistry::Pattern->parse('*[CX4][CX4]*', 73 patt => Chemistry::Pattern->parse('*C=C*', 87 patt => Chemistry::Pattern->parse('*C(=C)*', [all …]
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/dports/science/p5-Chemistry-3DBuilder/Chemistry-3DBuilder-0.10/t/ |
H A D | builder.t | 6 use Chemistry::3DBuilder qw(build_3d); 7 use Chemistry::File::SMILES; 8 use Chemistry::File::SMARTS; 9 use Chemistry::Pattern; 10 use Chemistry::Atom qw(angle_deg dihedral_deg distance); 24 patt => Chemistry::Pattern->parse('CC', format => 'smarts'), 47 patt => Chemistry::Pattern->parse('*[*X4,NX3,OX2,OX3]*', 66 patt => Chemistry::Pattern->parse('*[CX4][CX4]*', 73 patt => Chemistry::Pattern->parse('*C=C*', 87 patt => Chemistry::Pattern->parse('*C(=C)*', [all …]
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/dports/science/p5-Chemistry-3DBuilder/Chemistry-3DBuilder-0.10/ |
H A D | META.yml | 3 name: Chemistry-3DBuilder 5 version_from: lib/Chemistry/3DBuilder.pm 8 Chemistry::File::SMARTS: 0.21 9 Chemistry::File::SMILES: 0.43 10 Chemistry::InternalCoords: 0.18 11 Chemistry::Mol: 0.33 12 Chemistry::Pattern: 0.25 13 Chemistry::Ring: 0.18
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-3DBuilder-0.10/ |
H A D | META.yml | 3 name: Chemistry-3DBuilder 5 version_from: lib/Chemistry/3DBuilder.pm 8 Chemistry::File::SMARTS: 0.21 9 Chemistry::File::SMILES: 0.43 10 Chemistry::InternalCoords: 0.18 11 Chemistry::Mol: 0.33 12 Chemistry::Pattern: 0.25 13 Chemistry::Ring: 0.18
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/dports/science/p5-Chemistry-Mok/Chemistry-Mok-0.25/ |
H A D | META.yml | 3 name: Chemistry-Mok 5 version_from: lib/Chemistry/Mok.pm 8 Chemistry::3DBuilder: 0.1 9 Chemistry::Bond::Find: 0.21 10 Chemistry::File::SMARTS: 0.11 11 Chemistry::Isotope: 0.1 12 Chemistry::Mol: 0.3 13 Chemistry::Pattern: 0.21
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