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/dports/science/openbabel/openbabel-3.1.1/scripts/perl/
H A DOpenBabel.pm7 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 …]
/dports/science/p5-PerlMol/PerlMol-0.3500/
H A DChanges7 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 …]
H A DMANIFEST41 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 …]
H A DREADME21 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 …]
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/
H A DBUNDLES.yml1 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 …]
/dports/science/mpqc/mpqc-2.3.1/src/lib/chemistry/cca/
H A DMPQC_IntegralEvaluatorFactory_Impl.hh118 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 …]
H A DMPQC_IntegralEvaluatorFactory_Impl.cc17 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 …]
/dports/science/nwchem-data/nwchem-7.0.2-release/src/cca/Chemistry/server/cxx/
H A DNWChem_Chemistry_QC_IntEvalFactory_Impl.hh128 ::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 …]
H A DNWChem_Chemistry_QC_IntEvalFactory_Impl.cc60 ::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 …]
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/cca/Chemistry/server/cxx/
H A DNWChem_Chemistry_QC_IntEvalFactory_Impl.cc60 ::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 …]
H A DNWChem_Chemistry_QC_IntEvalFactory_Impl.hh128 ::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 …]
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-MDLMol-0.20/t/
H A Dpattern.t4 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);
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/
H A DChanges1 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 …]
/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/t/
H A DFile.t9 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 …]
H A DMol.t4 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 …]
H A Dgeom.t6 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 …]
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/t/
H A DFile.t9 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 …]
H A DMol.t4 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 …]
H A Dgeom.t6 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 …]
/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/
H A DChanges1 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 …]
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-3DBuilder-0.10/t/
H A Dbuilder.t6 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 …]
/dports/science/p5-Chemistry-3DBuilder/Chemistry-3DBuilder-0.10/t/
H A Dbuilder.t6 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 …]
/dports/science/p5-Chemistry-3DBuilder/Chemistry-3DBuilder-0.10/
H A DMETA.yml3 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
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-3DBuilder-0.10/
H A DMETA.yml3 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
/dports/science/p5-Chemistry-Mok/Chemistry-Mok-0.25/
H A DMETA.yml3 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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