/dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/t/data/ |
H A D | test.ptt | 4 15..2531 + 838 24217062 - LB001 - - hypothetical protein 6 3716..3823 - 35 24217064 - LB004 - - hypothetical protein 7 3779..3886 + 35 24217065 - LB003 - - hypothetical protein 9 4975..5085 + 36 24217067 - LB006 - - hypothetical protein 12 6083..6373 - 96 24217070 - LB009 - - hypothetical protein 21 15186..16169 + 327 24217079 - LB018 - - hypothetical protein 22 16244..16384 + 46 24217080 - LB019 - - hypothetical protein 24 17941..18075 - 44 24217082 - LB021 - - hypothetical protein 28 21008..22150 - 380 24217086 - LB025 - - hypothetical protein 32 24684..24791 - 35 24217090 - LB029 - - hypothetical protein [all …]
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/dports/misc/py-orange3-network/orange3-network-ec534c9/orangecontrib/network/networks/ |
H A D | leu_huttenhower_a_items.tab | 5 ACTN1 <=0.00 protein binding 6 ADA >0.00 protein binding 7 ADAM15 <=0.00 protein binding 8 AHR <=0.00 protein binding 11 ANXA2 <=0.00 protein binding 13 AREG <=0.00 protein binding 16 ATRX >0.00 protein binding 17 BARD1 >0.00 protein binding 20 BLK >0.00 protein binding 21 BRF1 >0.00 protein binding [all …]
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/protein/ |
H A D | empirical.bf | 1 LoadFunctionLibrary("../protein.bf"); 8 /** @module models.protein.empirical */ 192 __rate_matrix = {models.protein.dimensions,models.protein.dimensions}; 258 models.protein.empirical.default_generators = {"LG": "models.protein.LG.ModelDescription", 269 models.protein.empirical.plusF_generators = {"LG": "models.protein.LGF.ModelDescription", 279 models.protein.empirical.mleF_generators = {"LG": "models.protein.LGML.ModelDescription", 312 models.protein.LGF.ModelDescription.model_definition = models.protein.LG.ModelDescription(type); 326 … models.protein.LGML.ModelDescription.model_definition = models.protein.LG.ModelDescription(type); 357 … models.protein.JTTF.ModelDescription.model_definition = models.protein.JTT.ModelDescription(type); 526 models.protein.ABF.ModelDescription.model_definition = models.protein.AB.ModelDescription(type); [all …]
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H A D | REV.bf | 1 LoadFunctionLibrary("../protein.bf"); 6 /** @module models.protein.REV */ 9 * @name models.protein.REV.ModelDescription 13 lfunction models.protein.REV.ModelDescription(type) { 38 models.protein.REV._generateRate.p = {}; 48 …models.protein.REV.parameter_name = parameters.ApplyNameSpace(models.protein.REV.parameter_name, n… 52 …models.protein.REV._generateRate.p[utility.getGlobalValue("terms.model.rate_entry")] = models.prot… 54 return models.protein.REV._generateRate.p; 59 * @name models.protein.REV._DefineQ 98 * @name models.protein.REV.DefineQMatrix [all …]
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/dports/biology/py-biopython/biopython-1.79/Tests/UniProt/ |
H A D | gp_information.goa_yeast.28.gpi | 25 A5Z2X5 YPR010C-A UPF0495 protein YPR010C-A YP010_YEAST|YPR010C-A protein taxon:559292 db_subset=S… 26 D6VPM8 YAR023C Putative DUP240 protein YAR023C YAJ3_YEAST|YAR023C protein taxon:559292 db_subset=… 33 E9PAE4 Putative uncharacterized protein E9PAE4_YEAST protein taxon:559292 db_subset=TrEMBL 34 E9PAE7 Putative uncharacterized protein E9PAE7_YEAST protein taxon:559292 db_subset=TrEMBL 35 E9PAE8 Putative uncharacterized protein E9PAE8_YEAST protein taxon:559292 db_subset=TrEMBL 36 E9PAF1 Putative uncharacterized protein E9PAF1_YEAST protein taxon:559292 db_subset=TrEMBL 41 O13511 YAL065C Uncharacterized protein YAL065C YA065_YEAST|YAL065C protein taxon:559292 db_subset… 191 P03871 REP1 Partitioning protein REP1 REP1_YEAST|REP1|R0020C protein taxon:559292 db_subset=Swiss… 192 P03872 REP2 Partitioning protein REP2 REP2_YEAST|REP2|R0040C protein taxon:559292 db_subset=Swiss… 214 P04386 GAL4 Regulatory protein GAL4 GAL4_YEAST|GAL4|YPL248C protein taxon:559292 db_subset=Swiss-… [all …]
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H A D | goa_yeast.gaf | 3 !The set of protein accessions included in this file is based on UniProt reference proteomes, which… 13 …003674 GO_REF:0000015 ND F Putative uncharacterized protein YAL019W-A YA19A_YEAST|YAL019W-A prote… 14 …005575 GO_REF:0000015 ND C Putative uncharacterized protein YAL019W-A YA19A_YEAST|YAL019W-A prote… 363 …5 YPR010C-A GO:0003674 GO_REF:0000015 ND F UPF0495 protein YPR010C-A YP010_YEAST|YPR010C-A prote… 364 …5 YPR010C-A GO:0008150 GO_REF:0000015 ND P UPF0495 protein YPR010C-A YP010_YEAST|YPR010C-A prote… 366 …R023C GO:0003674 GO_REF:0000015 ND F Putative DUP240 protein YAR023C YAJ3_YEAST|YAR023C protein … 367 …R023C GO:0005575 GO_REF:0000015 ND C Putative DUP240 protein YAR023C YAJ3_YEAST|YAR023C protein … 371 …R023C GO:0008150 GO_REF:0000015 ND P Putative DUP240 protein YAR023C YAJ3_YEAST|YAR023C protein … 437 …L065C GO:0003674 GO_REF:0000015 ND F Uncharacterized protein YAL065C YA065_YEAST|YAL065C protein… 438 …L065C GO:0005575 GO_REF:0000015 ND C Uncharacterized protein YAL065C YA065_YEAST|YAL065C protein… [all …]
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H A D | gene_association.goa_yeast.1.gaf | 32 …000011 PMID:1493335 IMP P Vacuolar protein sorting-associated protein 9 VPS9_YEAST|YML097C|VPT9|V… 39 … GO:0000022 PMID:10465783 TAS P APC/C activator protein CDC20 CDC20_YEAST|YGL116W|CDC20|D6VU31 pr… 72 …1 PMID:1493335 IMP P Vacuolar protein sorting-associated protein 45 VPS45_YEAST|YGL095C|STT10|VPS… 77 …AC8 GO:0000011 PMID:16301533 IMP P Vacuolar protein 8 VAC8_YEAST|YEL013W|VAC8|YEB3|D3DLN6|Q549T0… 78 …VAC8 GO:0000011 PMID:8885233 IMP P Vacuolar protein 8 VAC8_YEAST|YEL013W|VAC8|YEB3|D3DLN6|Q549T0… 99 …7W GO:0000022 PMID:18194531 IMP P Uncharacterized protein YHR127W YHS7_YEAST|YHR127W|D3DL76 prot… 127 … GO:0000027 PMID:15126390 IPI P Ribosome assembly protein 3 RSA3_YEAST|YLR221C|RSA3|D6VYM1 prote… 133 … GO:0000001 PMID:17905927 IMP P Accumulates dyads protein 3 ADY3_YEAST|YDL239C|ADY3|D6VRB7 prote… 176 …11 PMID:1493335 IMP P Vacuolar protein sorting-associated protein 3 VPS3_YEAST|VPS3|YDR495C|VPT17… 179 …3335 IMP P Vacuolar protein sorting-associated protein 21 VPS21_YEAST|YOR089C|VPS12|VPS21|YOR3154… [all …]
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/dports/biology/emboss/EMBOSS-6.6.0/doc/programs/master/emboss/apps/inc/ |
H A D | extractfeat.output | 231 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… 233 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… 235 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… 237 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… 239 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… 241 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… 243 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… 245 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… 247 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… 249 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma… [all …]
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/protein/matrices/ |
H A D | mt.ibf | 3 LoadFunctionLibrary("../../protein.bf"); 13 * @name models.protein.mtMet.ModelDescription 19 …models.protein.mtMet.ModelDescription.model_definition = models.protein.empirical.ModelDescription… 20 …models.protein.mtMet.ModelDescription.model_definition [terms.model.empirical_rates] = models.prot… 32 …models.protein.mtMetF.ModelDescription.model_definition = models.protein.mtMet.ModelDescription(ty… 45 …models.protein.mtMetML.ModelDescription.model_definition = models.protein.mtMet.ModelDescription(t… 53 models.protein.mtMet.Rij = { 302 …models.protein.mtVerF.ModelDescription.model_definition = models.protein.mtVer.ModelDescription(ty… 315 …models.protein.mtVerML.ModelDescription.model_definition = models.protein.mtVer.ModelDescription(t… 326 models.protein.mtVer.Rij = { [all …]
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H A D | HIV.ibf | 3 LoadFunctionLibrary("../../protein.bf"); 15 * @name models.protein.HIVBm.ModelDescription 21 …models.protein.HIVBm.ModelDescription.model_definition = models.protein.empirical.ModelDescription… 22 …models.protein.HIVBm.ModelDescription.model_definition [terms.model.empirical_rates] = models.prot… 34 …models.protein.HIVBmF.ModelDescription.model_definition = models.protein.HIVBm.ModelDescription(ty… 47 …models.protein.HIVBmML.ModelDescription.model_definition = models.protein.HIVBm.ModelDescription(t… 56 models.protein.HIVBm.Rij = { 336 …models.protein.HIVWm.ModelDescription.model_definition = models.protein.empirical.ModelDescription… 349 …models.protein.HIVWmF.ModelDescription.model_definition = models.protein.HIVWm.ModelDescription(ty… 362 …models.protein.HIVWmML.ModelDescription.model_definition = models.protein.HIVWm.ModelDescription(t… [all …]
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H A D | JC69.ibf | 3 LoadFunctionLibrary("../../protein.bf"); 12 * @name models.protein.JC69.ModelDescription 18 …models.protein.JC69.ModelDescription.model_definition = models.protein.empirical.ModelDescription(… 19 …models.protein.JC69.ModelDescription.model_definition [terms.model.empirical_rates] = models.prote… 20 …models.protein.JC69.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.… 25 * @name models.protein.JC69F.ModelDescription 31 …models.protein.JC69F.ModelDescription.model_definition = models.protein.JC69.ModelDescription(type… 44 …models.protein.JC69ML.ModelDescription.model_definition = models.protein.JC69.ModelDescription(typ… 45 …models.protein.JC69ML.ModelDescription.model_definition [terms.model.frequency_estimator] = "frequ… 51 models.protein.JC69.Rij = { [all …]
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H A D | JTT.ibf | 3 LoadFunctionLibrary("../../protein.bf"); 12 * @name models.protein.JTT.ModelDescription 18 …models.protein.JTT.ModelDescription.model_definition = models.protein.empirical.ModelDescription(t… 19 …models.protein.JTT.ModelDescription.model_definition [terms.model.empirical_rates] = models.protei… 20 …models.protein.JTT.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.p… 25 * @name models.protein.JTTF.ModelDescription 31 … models.protein.JTTF.ModelDescription.model_definition = models.protein.JTT.ModelDescription(type); 44 …models.protein.JTTML.ModelDescription.model_definition = models.protein.JTT.ModelDescription(type); 45 …models.protein.JTTML.ModelDescription.model_definition [terms.model.frequency_estimator] = "freque… 51 models.protein.JTT.Rij = { [all …]
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H A D | LG.ibf | 3 LoadFunctionLibrary("../../protein.bf"); 12 * @name models.protein.LG.ModelDescription 18 …models.protein.LG.ModelDescription.model_definition = models.protein.empirical.ModelDescription(ty… 19 …models.protein.LG.ModelDescription.model_definition [terms.model.empirical_rates] = models.protein… 20 …models.protein.LG.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.pr… 25 * @name models.protein.LGF.ModelDescription 31 models.protein.LGF.ModelDescription.model_definition = models.protein.LG.ModelDescription(type); 44 … models.protein.LGML.ModelDescription.model_definition = models.protein.LG.ModelDescription(type); 45 …models.protein.LGML.ModelDescription.model_definition [terms.model.frequency_estimator] = "frequen… 51 models.protein.LG.Rij = { [all …]
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H A D | WAG.ibf | 3 LoadFunctionLibrary("../../protein.bf"); 12 * @name models.protein.WAG.ModelDescription 18 …models.protein.WAG.ModelDescription.model_definition = models.protein.empirical.ModelDescription(t… 19 …models.protein.WAG.ModelDescription.model_definition [terms.model.empirical_rates] = models.protei… 20 …models.protein.WAG.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.p… 25 * @name models.protein.WAGF.ModelDescription 31 … models.protein.WAGF.ModelDescription.model_definition = models.protein.WAG.ModelDescription(type); 44 …models.protein.WAGML.ModelDescription.model_definition = models.protein.WAG.ModelDescription(type); 45 …models.protein.WAGML.ModelDescription.model_definition [terms.model.frequency_estimator] = "freque… 51 models.protein.WAG.Rij = { [all …]
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H A D | gcpREV.ibf | 3 LoadFunctionLibrary("../../protein.bf"); 12 * @name models.protein.gcpREV.ModelDescription 18 …models.protein.gcpREV.ModelDescription.model_definition = models.protein.empirical.ModelDescriptio… 19 …models.protein.gcpREV.ModelDescription.model_definition [terms.model.empirical_rates] = models.pro… 20 …models.protein.gcpREV.ModelDescription.model_definition [terms.model.frequency_estimator] = "model… 25 * @name models.protein.gcpREVF.ModelDescription 31 …models.protein.gcpREVF.ModelDescription.model_definition = models.protein.gcpREV.ModelDescription(… 44 …models.protein.gcpREVML.ModelDescription.model_definition = models.protein.gcpREV.ModelDescription… 45 …models.protein.gcpREVML.ModelDescription.model_definition [terms.model.frequency_estimator] = "fre… 51 models.protein.gcpREV.Rij = { [all …]
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/dports/science/py-oddt/oddt-0.7/oddt/scoring/descriptors/ |
H A D | __init__.py | 130 self.protein = protein 163 self.protein = protein 238 self.protein = protein 260 self.protein = protein 268 out.append(self.func(mol, protein=self.protein)) 320 self.protein = protein 331 self.protein = protein 338 protein = self.protein 365 self.protein = protein 385 self.protein = protein [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/gff3writer_test_cases/ |
H A D | rw-310.entry.gff3 | 420 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus… 421 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus… 422 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus… 423 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus… 424 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus… 425 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus… 559 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR024873;locus… 560 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR024873;locus… 561 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR024873;locus… 562 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR024873;locus… [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/unit_test/data/ |
H A D | redundant_deflines.asn | 3065 title "TIGR01620 family protein [Salmonella enterica]", 3507 title "TIGR01620 family protein [Salmonella enterica]", 3632 title "TIGR01620 family protein [Salmonella enterica]", 3710 title "TIGR01620 family protein [Salmonella enterica]", 3723 title "TIGR01620 family protein [Salmonella enterica]", 3736 title "TIGR01620 family protein [Salmonella enterica]", 3749 title "TIGR01620 family protein [Salmonella enterica]", 14392 title "Membrane protein YcjF [Salmonella enterica]", 16821 title "membrane protein [Escherichia coli]", 16834 title "membrane protein [Escherichia coli]", [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/unit_test/data/ |
H A D | redundant_deflines.asn | 3065 title "TIGR01620 family protein [Salmonella enterica]", 3507 title "TIGR01620 family protein [Salmonella enterica]", 3632 title "TIGR01620 family protein [Salmonella enterica]", 3710 title "TIGR01620 family protein [Salmonella enterica]", 3723 title "TIGR01620 family protein [Salmonella enterica]", 3736 title "TIGR01620 family protein [Salmonella enterica]", 3749 title "TIGR01620 family protein [Salmonella enterica]", 14392 title "Membrane protein YcjF [Salmonella enterica]", 16821 title "membrane protein [Escherichia coli]", 16834 title "membrane protein [Escherichia coli]", [all …]
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/dports/science/py-oddt/oddt-0.7/tests/ |
H A D | test_virtualscreening.py | 202 protein.protein = True 228 vs.score('bad_sf', protein=protein) 231 vs.score('rfscore_v1', protein=protein) 233 vs.score('rfscore_v2', protein=protein) 234 vs.score('rfscore_v3', protein=protein) 235 vs.score('pleclinear', protein=protein) 238 vs.score(filenames[0], protein=protein) 243 vs.score(sum, protein=protein) 257 vs.score('nnscore', protein=protein) 258 vs.score('rfscore_v1', protein=protein) [all …]
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H A D | test_toolkit.py | 37 protein.protein = True 73 protein.addh() 79 protein.removeh() 86 protein.removeh() 105 protein.protein = True 124 protein.protein = True 130 protein.addh() 269 rec.protein = True 395 protein.protein = True 412 protein.protein = True [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/srcwriter_test_cases/ |
H A D | test.srcchk.output | 3 NP_963295.1 41614797 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ001… 4 NP_963296.1 41614798 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ003… 5 NP_963297.1 41614799 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ002… 6 NP_963298.1 41614800 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ004… 7 NP_963299.1 41614801 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ005… 8 NP_963300.1 41614802 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ007… 9 NP_963301.1 41614803 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ006… 10 NP_963302.1 41614804 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ008… 11 NP_963303.1 41614805 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ009… 12 NP_963304.1 41614806 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ010… [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/unit_test/data/ |
H A D | large.fa | 4 >gi|49902846|gb|AAH76068.1| Pax6b protein [Danio rerio] 123 >gi|18138024|emb|CAC80514.1| paired box protein [Mus musculus] 135 …PAX-6 protein [Astyanax mexicanus] >gi|2369657|emb|CAA68839.1| PAX-6 protein [Astyanax mexicanus] … 184 …protein Pax-6 isoform a [Homo sapiens] >gi|189083681|ref|NP_001121084.1| paired box protein Pax-6 … 558 >gi|33585947|gb|AAH55960.1| Pax2-A protein [Xenopus laevis] 1069 >gi|553607|gb|AAC41711.1| paired-box protein [Homo sapiens] 1345 …| paired box protein Pax-2 [Mus musculus] >gi|152012463|gb|AAI50485.1| Pax2 protein [Mus musculus]… 1647 … Full=Paired box protein Pax-2a; AltName: Full=No isthmus protein; AltName: Full=Pax[Zf-b] >gi|437… 1741 …protein Pax-5 [Xenopus laevis] >gi|82249042|sp|Q9YH95.1|PAX5_XENLA RecName: Full=Paired box protei… 1907 …24307|ref|NP_001079830.1| paired box protein Pax-2-A [Xenopus laevis] >gi|2765059|emb|CAA71207.1| … [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/ |
H A D | output.py | 73 for chain in protein.chains: 119 for chain in protein.chains: 170 str += getSummarySection(protein) 206 printPKASection(protein) 218 str = getSummarySection(protein) 232 for chain in protein.chains: 240 if protein.coupled_residues: 256 for chain in protein.chains: 283 pH, dG = protein.getPHopt() 290 dG_min, dG_max = protein.getDG80() [all …]
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/dports/science/cdk/cdk-cdk-2.3/storage/pdb/src/main/java/org/openscience/cdk/tools/ |
H A D | ProteinBuilderTool.java | 63 addAminoAcid(protein, aaToAdd, strand); in addAminoAcidAtNTerminus() 65 if (protein.getMonomerCount() == 0) { in addAminoAcidAtNTerminus() 71 return protein; in addAminoAcidAtNTerminus() 87 addAminoAcid(protein, aaToAdd, strand); in addAminoAcidAtCTerminus() 95 return protein; in addAminoAcidAtCTerminus() 149 logger.debug("protein: ", protein); in createProtein() 163 protein.addBond(bond); in createProtein() 164 return protein; in createProtein() 169 protein.addAtom(atom, aaToAdd, strand); in addAminoAcid() 171 protein.addBond(bond); in addAminoAcid() [all …]
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