diff --git a/docs/tutorials/databases_klifs.ipynb b/docs/tutorials/databases_klifs.ipynb
index f14abb6a..0dfb7ff6 100644
--- a/docs/tutorials/databases_klifs.ipynb
+++ b/docs/tutorials/databases_klifs.ipynb
@@ -102,16 +102,7 @@
"cell_type": "code",
"execution_count": 5,
"metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.api:Set up remote session...\n",
- "INFO:opencadd.databases.klifs.api:Remote session is ready!\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"remote = setup_remote()"
]
@@ -154,21 +145,7 @@
"cell_type": "code",
"execution_count": 7,
"metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.api:Set up local session...\n",
- "INFO:opencadd.databases.klifs.local:Load overview.csv...\n",
- "INFO:opencadd.databases.klifs.local:Load KLIFS_export.csv...\n",
- "INFO:opencadd.databases.klifs.local:Merge both csv files...\n",
- "INFO:opencadd.databases.klifs.local:Add paths to coordinate folders to structures...\n",
- "INFO:opencadd.databases.klifs.local:Add KLIFS IDs to structures (uses remote since not available locally!)...\n",
- "INFO:opencadd.databases.klifs.api:Local session is ready!\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"local = setup_local(\"../../opencadd/tests/data/klifs\")"
]
@@ -263,18 +240,18 @@
"
4 | \n",
" 0 | \n",
" 0000000000000010000001000000000000000000000000... | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 1.0 | \n",
+ " 1.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
" [BMX] | \n",
" BMX | \n",
" BMX | \n",
@@ -304,18 +281,18 @@
" 7 | \n",
" 61 | \n",
" 0000000000000000000000000000000000000000000000... | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 1.0 | \n",
+ " 1.0 | \n",
+ " 1.0 | \n",
+ " 1.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
" [BRAF] | \n",
" BRAF | \n",
" BRAF | \n",
@@ -330,163 +307,219 @@
" 509 | \n",
" \n",
" \n",
- " 2 | \n",
- " Mouse | \n",
- " 1fpu | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ "
\n",
+ " \n",
+ " 4 | \n",
+ " Human | \n",
+ " 7lht | \n",
" - | \n",
" A | \n",
- " PRC | \n",
" - | \n",
- " 0.925 | \n",
- " 2.319 | \n",
- " 8.8 | \n",
- " HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
- " 2.40 | \n",
- " 0 | \n",
- " 8 | \n",
- " 0000000000000010000000000000000000000000000000... | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
+ " ATP | \n",
+ " 10.267 | \n",
+ " 15.045 | \n",
+ " 4.0 | \n",
+ " KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK... | \n",
+ " 3.50 | \n",
" 0 | \n",
" 0 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " [Abl1, ABL1] | \n",
- " Abl1 | \n",
- " ABL1 | \n",
- " Abl | \n",
- " TK | \n",
- " N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " [LRRK2] | \n",
+ " LRRK2 | \n",
+ " LRRK2 | \n",
+ " LRRK | \n",
+ " TKL | \n",
" - | \n",
+ " ADENOSINE-5'-TRIPHOSPHATE | \n",
" out | \n",
" out | \n",
- " MOUSE/ABL1/1fpu_chainA | \n",
- " 5728 | \n",
- " 532 | \n",
+ " HUMAN/LRRK2/7lht_chainA | \n",
+ " 13623 | \n",
+ " 495 | \n",
"
\n",
" \n",
- " 3 | \n",
- " Mouse | \n",
- " 1fpu | \n",
+ " 5 | \n",
+ " Human | \n",
+ " 2ogv | \n",
" - | \n",
- " B | \n",
- " PRC | \n",
+ " A | \n",
" - | \n",
- " 0.925 | \n",
- " 2.329 | \n",
- " 9.2 | \n",
- " HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
- " 2.40 | \n",
- " 0 | \n",
- " 4 | \n",
- " 0000000000000010000000000000000000000000000000... | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
+ " - | \n",
+ " 1.043 | \n",
+ " 2.362 | \n",
+ " 6.4 | \n",
+ " KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE... | \n",
+ " 2.70 | \n",
+ " 2 | \n",
" 0 | \n",
- " [Abl1, ABL1] | \n",
- " Abl1 | \n",
- " ABL1 | \n",
- " Abl | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " [CSF1R, FMS] | \n",
+ " CSF1R | \n",
+ " FMS | \n",
+ " PDGFR | \n",
" TK | \n",
- " N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
+ " - | \n",
" - | \n",
" out | \n",
- " out | \n",
- " MOUSE/ABL1/1fpu_chainB | \n",
- " 5705 | \n",
- " 532 | \n",
+ " in | \n",
+ " HUMAN/FMS/2ogv_chainA | \n",
+ " 1243 | \n",
+ " 449 | \n",
"
\n",
" \n",
"\n",
+ "6 rows × 38 columns
\n",
""
],
"text/plain": [
- " species.klifs structure.pdb_id structure.alternate_model structure.chain \\\n",
- "0 Human 3sxr - A \n",
- "1 Human 6uuo - A \n",
- "2 Mouse 1fpu - A \n",
- "3 Mouse 1fpu - B \n",
- "\n",
- " ligand.expo_id ligand_allosteric.expo_id structure.rmsd1 structure.rmsd2 \\\n",
- "0 1N1 - 0.839 1.967 \n",
- "1 QH1 - 0.806 2.028 \n",
- "2 PRC - 0.925 2.319 \n",
- "3 PRC - 0.925 2.329 \n",
- "\n",
- " structure.qualityscore structure.pocket \\\n",
- "0 6.4 KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... \n",
- "1 5.2 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... \n",
- "2 8.8 HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... \n",
- "3 9.2 HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... \n",
- "\n",
- " structure.resolution structure.missing_residues structure.missing_atoms \\\n",
- "0 2.40 4 0 \n",
- "1 3.29 7 61 \n",
- "2 2.40 0 8 \n",
- "3 2.40 0 4 \n",
- "\n",
- " interaction.fingerprint structure.fp_i \\\n",
- "0 0000000000000010000001000000000000000000000000... 0 \n",
- "1 0000000000000000000000000000000000000000000000... 0 \n",
- "2 0000000000000010000000000000000000000000000000... 0 \n",
- "3 0000000000000010000000000000000000000000000000... 0 \n",
- "\n",
- " structure.fp_ii structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 0 1 1 0 \n",
- "1 0 1 1 1 \n",
- "2 0 1 1 0 \n",
- "3 0 0 1 0 \n",
+ " species.klifs structure.pdb_id structure.alternate_model structure.chain \\\n",
+ "0 Human 3sxr - A \n",
+ "1 Human 6uuo - A \n",
+ ".. ... ... ... ... \n",
+ "4 Human 7lht - A \n",
+ "5 Human 2ogv - A \n",
+ "\n",
+ " ligand.expo_id ligand_allosteric.expo_id structure.rmsd1 structure.rmsd2 \\\n",
+ "0 1N1 - 0.839 1.967 \n",
+ "1 QH1 - 0.806 2.028 \n",
+ ".. ... ... ... ... \n",
+ "4 - ATP 10.267 15.045 \n",
+ "5 - - 1.043 2.362 \n",
+ "\n",
+ " structure.qualityscore structure.pocket \\\n",
+ "0 6.4 KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... \n",
+ "1 5.2 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... \n",
+ ".. ... ... \n",
+ "4 4.0 KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK... \n",
+ "5 6.4 KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE... \n",
+ "\n",
+ " structure.resolution structure.missing_residues structure.missing_atoms \\\n",
+ "0 2.40 4 0 \n",
+ "1 3.29 7 61 \n",
+ ".. ... ... ... \n",
+ "4 3.50 0 0 \n",
+ "5 2.70 2 0 \n",
+ "\n",
+ " interaction.fingerprint structure.fp_i \\\n",
+ "0 0000000000000010000001000000000000000000000000... 0.0 \n",
+ "1 0000000000000000000000000000000000000000000000... 0.0 \n",
+ ".. ... ... \n",
+ "4 NaN NaN \n",
+ "5 NaN NaN \n",
"\n",
- " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 0 0 0 \n",
- "1 1 0 0 \n",
- "2 0 0 1 \n",
- "3 0 0 1 \n",
- "\n",
- " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 0 0 0 0 \n",
- "1 0 0 0 0 \n",
- "2 0 0 0 0 \n",
- "3 0 0 0 0 \n",
+ " structure.fp_ii structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
+ "0 0.0 1.0 1.0 0.0 \n",
+ "1 0.0 1.0 1.0 1.0 \n",
+ ".. ... ... ... ... \n",
+ "4 NaN NaN NaN NaN \n",
+ "5 NaN NaN NaN NaN \n",
"\n",
- " kinase.names kinase.gene_name kinase.klifs_name kinase.family kinase.group \\\n",
- "0 [BMX] BMX BMX Tec TK \n",
- "1 [BRAF] BRAF BRAF RAF TKL \n",
- "2 [Abl1, ABL1] Abl1 ABL1 Abl TK \n",
- "3 [Abl1, ABL1] Abl1 ABL1 Abl TK \n",
+ " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
+ "0 0.0 0.0 0.0 \n",
+ "1 1.0 0.0 0.0 \n",
+ ".. ... ... ... \n",
+ "4 NaN NaN NaN \n",
+ "5 NaN NaN NaN \n",
"\n",
- " ligand.name ligand_allosteric.name \\\n",
- "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... - \n",
- "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... - \n",
- "2 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... - \n",
- "3 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... - \n",
- "\n",
- " structure.dfg structure.ac_helix structure.filepath \\\n",
- "0 out-like in HUMAN/BMX/3sxr_chainA \n",
- "1 in out-like HUMAN/BRAF/6uuo_chainA \n",
- "2 out out MOUSE/ABL1/1fpu_chainA \n",
- "3 out out MOUSE/ABL1/1fpu_chainB \n",
- "\n",
- " structure.klifs_id kinase.klifs_id \n",
- "0 3482 472 \n",
- "1 12347 509 \n",
- "2 5728 532 \n",
- "3 5705 532 "
+ " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
+ "0 0.0 0.0 0.0 0.0 \n",
+ "1 0.0 0.0 0.0 0.0 \n",
+ ".. ... ... ... ... \n",
+ "4 NaN NaN NaN NaN \n",
+ "5 NaN NaN NaN NaN \n",
+ "\n",
+ " kinase.names kinase.gene_name kinase.klifs_name kinase.family \\\n",
+ "0 [BMX] BMX BMX Tec \n",
+ "1 [BRAF] BRAF BRAF RAF \n",
+ ".. ... ... ... ... \n",
+ "4 [LRRK2] LRRK2 LRRK2 LRRK \n",
+ "5 [CSF1R, FMS] CSF1R FMS PDGFR \n",
+ "\n",
+ " kinase.group ligand.name \\\n",
+ "0 TK N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
+ "1 TKL 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... \n",
+ ".. ... ... \n",
+ "4 TKL - \n",
+ "5 TK - \n",
+ "\n",
+ " ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
+ "0 - out-like in \n",
+ "1 - in out-like \n",
+ ".. ... ... ... \n",
+ "4 ADENOSINE-5'-TRIPHOSPHATE out out \n",
+ "5 - out in \n",
+ "\n",
+ " structure.filepath structure.klifs_id kinase.klifs_id \n",
+ "0 HUMAN/BMX/3sxr_chainA 3482 472 \n",
+ "1 HUMAN/BRAF/6uuo_chainA 12347 509 \n",
+ ".. ... ... ... \n",
+ "4 HUMAN/LRRK2/7lht_chainA 13623 495 \n",
+ "5 HUMAN/FMS/2ogv_chainA 1243 449 \n",
+ "\n",
+ "[6 rows x 38 columns]"
]
},
"execution_count": 8,
@@ -528,14 +561,12 @@
"|:--------------------------| - | - | - | - | - | - |\n",
"| __by_kinase_klifs_id__ | x* | x* | x* | | x | | \n",
"| __by_kinase_name__ | x* | x | x | | | |\n",
- "| __by_ligand_klifs_id__ | | x* | x | x\\* \\** | x | |\n",
- "| __by_ligand_expo_id__ | | x | x | x\\* \\** | | |\n",
+ "| __by_ligand_klifs_id__ | | x* | x | x* | x | |\n",
+ "| __by_ligand_expo_id__ | | x | x | x* | | |\n",
"| __by_structure_klifs_id__ | | | x* | | x* | x* |\n",
"| __by_structure_pdb_id__ | | | x* | | | |\n",
"\n",
- " \\* Direct use of KLIFS Swagger API.\n",
- " \n",
- " \\** KLIFS Swagger API allows only ONE input value."
+ " \\* Direct use of KLIFS Swagger API."
]
},
{
@@ -937,6 +968,14 @@
" 2 | \n",
" Abl | \n",
" \n",
+ " \n",
+ " 3 | \n",
+ " LRRK | \n",
+ "
\n",
+ " \n",
+ " 4 | \n",
+ " PDGFR | \n",
+ "
\n",
" \n",
"\n",
""
@@ -945,7 +984,9 @@
" kinase.family\n",
"0 Tec\n",
"1 RAF\n",
- "2 Abl"
+ "2 Abl\n",
+ "3 LRRK\n",
+ "4 PDGFR"
]
},
"execution_count": 14,
@@ -995,6 +1036,10 @@
" 1 | \n",
" Abl | \n",
" \n",
+ " \n",
+ " 2 | \n",
+ " PDGFR | \n",
+ "
\n",
" \n",
"\n",
""
@@ -1002,7 +1047,8 @@
"text/plain": [
" kinase.family\n",
"0 Tec\n",
- "1 Abl"
+ "1 Abl\n",
+ "2 PDGFR"
]
},
"execution_count": 15,
@@ -1351,9 +1397,9 @@
" 0 | \n",
" 472 | \n",
" BMX | \n",
- " None | \n",
+ " <NA> | \n",
" BMX | \n",
- " None | \n",
+ " <NA> | \n",
" Human | \n",
" \n",
" \n",
@@ -1362,10 +1408,10 @@
],
"text/plain": [
" kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
- "0 472 BMX None BMX \n",
+ "0 472 BMX BMX \n",
"\n",
" kinase.uniprot species.klifs \n",
- "0 None Human "
+ "0 Human "
]
},
"execution_count": 20,
@@ -1416,9 +1462,9 @@
" 0 | \n",
" 532 | \n",
" ABL1 | \n",
- " None | \n",
+ " <NA> | \n",
" Abl1 | \n",
- " None | \n",
+ " <NA> | \n",
" Mouse | \n",
" \n",
" \n",
@@ -1427,10 +1473,10 @@
],
"text/plain": [
" kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
- "0 532 ABL1 None Abl1 \n",
+ "0 532 ABL1 Abl1 \n",
"\n",
" kinase.uniprot species.klifs \n",
- "0 None Mouse "
+ "0 Mouse "
]
},
"execution_count": 21,
@@ -1508,7 +1554,7 @@
" kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
@@ -1541,11 +1587,11 @@
" kinase.full_name kinase.gene_name \\\n",
"0 v-akt murine thymoma viral oncogene homolog 1 AKT1 \n",
"\n",
- " kinase.family kinase.group kinase.class species.klifs kinase.uniprot \\\n",
- "0 Akt AGC Human P31749 \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Akt AGC Human P31749 \n",
"\n",
- " kinase.iuphar kinase.pocket \n",
- "0 1479 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... "
+ " kinase.iuphar kinase.pocket \n",
+ "0 1479 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... "
]
},
"execution_count": 23,
@@ -1589,7 +1635,7 @@
" kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
@@ -1638,13 +1684,13 @@
"0 v-akt murine thymoma viral oncogene homolog 1 AKT1 \n",
"1 v-akt murine thymoma viral oncogene homolog 2 AKT2 \n",
"\n",
- " kinase.family kinase.group kinase.class species.klifs kinase.uniprot \\\n",
- "0 Akt AGC Human P31749 \n",
- "1 Akt AGC Human P31751 \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Akt AGC Human P31749 \n",
+ "1 Akt AGC Human P31751 \n",
"\n",
- " kinase.iuphar kinase.pocket \n",
- "0 1479 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... \n",
- "1 1480 KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVME... "
+ " kinase.iuphar kinase.pocket \n",
+ "0 1479 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... \n",
+ "1 1480 KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVME... "
]
},
"execution_count": 24,
@@ -1715,7 +1761,7 @@
" kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
@@ -1727,15 +1773,15 @@
" 0 | \n",
" 472 | \n",
" BMX | \n",
- " None | \n",
+ " <NA> | \n",
" BMX | \n",
" Tec | \n",
" TK | \n",
- " None | \n",
+ " <NA> | \n",
" Human | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" \n",
" \n",
"\n",
@@ -1743,13 +1789,13 @@
],
"text/plain": [
" kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
- "0 472 BMX None BMX \n",
+ "0 472 BMX BMX \n",
"\n",
- " kinase.family kinase.group kinase.class species.klifs kinase.uniprot \\\n",
- "0 Tec TK None Human None \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Tec TK Human \n",
"\n",
" kinase.iuphar kinase.pocket \n",
- "0 None None "
+ "0 "
]
},
"execution_count": 26,
@@ -1793,7 +1839,7 @@
" kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
@@ -1805,29 +1851,29 @@
" 0 | \n",
" 472 | \n",
" BMX | \n",
- " None | \n",
+ " <NA> | \n",
" BMX | \n",
" Tec | \n",
" TK | \n",
- " None | \n",
+ " <NA> | \n",
" Human | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" \n",
" \n",
" 1 | \n",
" 509 | \n",
" BRAF | \n",
- " None | \n",
+ " <NA> | \n",
" BRAF | \n",
" RAF | \n",
" TKL | \n",
- " None | \n",
+ " <NA> | \n",
" Human | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
"
\n",
" \n",
"\n",
@@ -1835,16 +1881,16 @@
],
"text/plain": [
" kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
- "0 472 BMX None BMX \n",
- "1 509 BRAF None BRAF \n",
+ "0 472 BMX BMX \n",
+ "1 509 BRAF BRAF \n",
"\n",
- " kinase.family kinase.group kinase.class species.klifs kinase.uniprot \\\n",
- "0 Tec TK None Human None \n",
- "1 RAF TKL None Human None \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Tec TK Human \n",
+ "1 RAF TKL Human \n",
"\n",
" kinase.iuphar kinase.pocket \n",
- "0 None None \n",
- "1 None None "
+ "0 \n",
+ "1 "
]
},
"execution_count": 27,
@@ -1922,7 +1968,7 @@
" kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
@@ -1967,13 +2013,13 @@
"0 574 BMX BMX non-receptor tyrosine kinase \n",
"1 472 BMX BMX non-receptor tyrosine kinase \n",
"\n",
- " kinase.gene_name kinase.family kinase.group kinase.class species.klifs \\\n",
- "0 Bmx Tec TK Mouse \n",
- "1 BMX Tec TK Human \n",
+ " kinase.gene_name kinase.family kinase.group kinase.subfamily species.klifs \\\n",
+ "0 Bmx Tec TK Mouse \n",
+ "1 BMX Tec TK Human \n",
"\n",
- " kinase.uniprot kinase.iuphar \\\n",
- "0 P97504 0 \n",
- "1 P51813 1942 \n",
+ " kinase.uniprot kinase.iuphar \\\n",
+ "0 P97504 0 \n",
+ "1 P51813 1942 \n",
"\n",
" kinase.pocket \n",
"0 KELGNGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... \n",
@@ -2021,7 +2067,7 @@
" kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
@@ -2066,13 +2112,13 @@
"0 574 BMX BMX non-receptor tyrosine kinase \n",
"1 472 BMX BMX non-receptor tyrosine kinase \n",
"\n",
- " kinase.gene_name kinase.family kinase.group kinase.class species.klifs \\\n",
- "0 Bmx Tec TK Mouse \n",
- "1 BMX Tec TK Human \n",
+ " kinase.gene_name kinase.family kinase.group kinase.subfamily species.klifs \\\n",
+ "0 Bmx Tec TK Mouse \n",
+ "1 BMX Tec TK Human \n",
"\n",
- " kinase.uniprot kinase.iuphar \\\n",
- "0 P97504 0 \n",
- "1 P51813 1942 \n",
+ " kinase.uniprot kinase.iuphar \\\n",
+ "0 P97504 0 \n",
+ "1 P51813 1942 \n",
"\n",
" kinase.pocket \n",
"0 KELGNGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... \n",
@@ -2140,7 +2186,7 @@
" kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
@@ -2189,13 +2235,13 @@
"0 B-Raf proto-oncogene, serine/threonine kinase BRAF \n",
"1 BMX non-receptor tyrosine kinase BMX \n",
"\n",
- " kinase.family kinase.group kinase.class species.klifs kinase.uniprot \\\n",
- "0 RAF TKL RAF Human P15056 \n",
- "1 Tec TK Human P51813 \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 RAF TKL RAF Human P15056 \n",
+ "1 Tec TK Human P51813 \n",
"\n",
- " kinase.iuphar kinase.pocket \n",
- "0 1943 QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... \n",
- "1 1942 KELGSGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... "
+ " kinase.iuphar kinase.pocket \n",
+ "0 1943 QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... \n",
+ "1 1942 KELGSGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... "
]
},
"execution_count": 32,
@@ -2246,7 +2292,7 @@
" kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
@@ -2258,15 +2304,15 @@
" 0 | \n",
" 472 | \n",
" BMX | \n",
- " None | \n",
+ " <NA> | \n",
" BMX | \n",
" Tec | \n",
" TK | \n",
- " None | \n",
+ " <NA> | \n",
" Human | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" \n",
" \n",
"\n",
@@ -2274,13 +2320,13 @@
],
"text/plain": [
" kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
- "0 472 BMX None BMX \n",
+ "0 472 BMX BMX \n",
"\n",
- " kinase.family kinase.group kinase.class species.klifs kinase.uniprot \\\n",
- "0 Tec TK None Human None \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Tec TK Human \n",
"\n",
" kinase.iuphar kinase.pocket \n",
- "0 None None "
+ "0 "
]
},
"execution_count": 33,
@@ -2344,7 +2390,7 @@
" kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
@@ -2356,29 +2402,29 @@
" 0 | \n",
" 472 | \n",
" BMX | \n",
- " None | \n",
+ " <NA> | \n",
" BMX | \n",
" Tec | \n",
" TK | \n",
- " None | \n",
+ " <NA> | \n",
" Human | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" \n",
" \n",
" 1 | \n",
" 509 | \n",
" BRAF | \n",
- " None | \n",
+ " <NA> | \n",
" BRAF | \n",
" RAF | \n",
" TKL | \n",
- " None | \n",
+ " <NA> | \n",
" Human | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
"
\n",
" \n",
"\n",
@@ -2386,16 +2432,16 @@
],
"text/plain": [
" kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
- "0 472 BMX None BMX \n",
- "1 509 BRAF None BRAF \n",
+ "0 472 BMX BMX \n",
+ "1 509 BRAF BRAF \n",
"\n",
- " kinase.family kinase.group kinase.class species.klifs kinase.uniprot \\\n",
- "0 Tec TK None Human None \n",
- "1 RAF TKL None Human None \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Tec TK Human \n",
+ "1 RAF TKL Human \n",
"\n",
" kinase.iuphar kinase.pocket \n",
- "0 None None \n",
- "1 None None "
+ "0 \n",
+ "1 "
]
},
"execution_count": 35,
@@ -2595,47 +2641,58 @@
" \n",
" \n",
" 0 | \n",
- " None | \n",
+ " <NA> | \n",
" 1N1 | \n",
" N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
"
\n",
" \n",
" 1 | \n",
- " None | \n",
+ " <NA> | \n",
" QH1 | \n",
" 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
"
\n",
" \n",
" 2 | \n",
- " None | \n",
+ " <NA> | \n",
" PRC | \n",
" N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ "
\n",
+ " \n",
+ " 3 | \n",
+ " <NA> | \n",
+ " - | \n",
+ " - | \n",
+ " <NA> | \n",
+ " <NA> | \n",
"
\n",
" \n",
"\n",
""
],
"text/plain": [
- " ligand.klifs_id ligand.expo_id \\\n",
- "0 None 1N1 \n",
- "1 None QH1 \n",
- "2 None PRC \n",
+ " ligand.klifs_id ligand.expo_id \\\n",
+ "0 1N1 \n",
+ "1 QH1 \n",
+ "2 PRC \n",
+ "3 - \n",
"\n",
" ligand.name ligand.smiles \\\n",
- "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... None \n",
- "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... None \n",
- "2 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... None \n",
+ "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
+ "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... \n",
+ "2 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... \n",
+ "3 - \n",
"\n",
" ligand.inchikey \n",
- "0 None \n",
- "1 None \n",
- "2 None "
+ "0 \n",
+ "1 \n",
+ "2 \n",
+ "3 "
]
},
"execution_count": 37,
@@ -2676,7 +2733,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "aab889d91de64b29ba449882101d589d",
+ "model_id": "490e594cdbc643c9b105c4924b8e4738",
"version_major": 2,
"version_minor": 0
},
@@ -2787,7 +2844,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "2cf8023b0aef40959214b94a316c2c0e",
+ "model_id": "350de9c0c8fa42caa4a2a98a80ec17e1",
"version_major": 2,
"version_minor": 0
},
@@ -2802,9 +2859,9 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "ERROR:opencadd.databases.klifs.core:There was (were) 1/3 failed request(s).\n",
+ "There was (were) 1/3 failed request(s).\n",
"Show error messages (up to 5 messages only):\n",
- "ERROR:opencadd.databases.klifs.core:Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
+ "Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
]
},
{
@@ -2936,7 +2993,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "376df0e4170f477093f4b34e09f842b4",
+ "model_id": "00879a77d46a408984bf81abe93b1931",
"version_major": 2,
"version_minor": 0
},
@@ -2951,9 +3008,9 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "ERROR:opencadd.databases.klifs.core:There was (were) 1/1 failed request(s).\n",
+ "There was (were) 1/1 failed request(s).\n",
"Show error messages (up to 5 messages only):\n",
- "ERROR:opencadd.databases.klifs.core:Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
+ "Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
]
},
{
@@ -3015,11 +3072,11 @@
" \n",
" \n",
" 0 | \n",
- " None | \n",
+ " <NA> | \n",
" 1N1 | \n",
" N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" 472 | \n",
"
\n",
" \n",
@@ -3027,14 +3084,14 @@
""
],
"text/plain": [
- " ligand.klifs_id ligand.expo_id \\\n",
- "0 None 1N1 \n",
+ " ligand.klifs_id ligand.expo_id \\\n",
+ "0 1N1 \n",
"\n",
" ligand.name ligand.smiles \\\n",
- "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... None \n",
+ "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
"\n",
" ligand.inchikey kinase.klifs_id (query) \n",
- "0 None 472 "
+ "0 472 "
]
},
"execution_count": 41,
@@ -3083,20 +3140,20 @@
" \n",
" \n",
" 0 | \n",
- " None | \n",
+ " <NA> | \n",
" 1N1 | \n",
" N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" 472 | \n",
"
\n",
" \n",
" 1 | \n",
- " None | \n",
+ " <NA> | \n",
" QH1 | \n",
" 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" 509 | \n",
"
\n",
" \n",
@@ -3104,17 +3161,17 @@
""
],
"text/plain": [
- " ligand.klifs_id ligand.expo_id \\\n",
- "0 None 1N1 \n",
- "1 None QH1 \n",
+ " ligand.klifs_id ligand.expo_id \\\n",
+ "0 1N1 \n",
+ "1 QH1 \n",
"\n",
" ligand.name ligand.smiles \\\n",
- "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... None \n",
- "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... None \n",
+ "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
+ "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... \n",
"\n",
" ligand.inchikey kinase.klifs_id (query) \n",
- "0 None 472 \n",
- "1 None 509 "
+ "0 472 \n",
+ "1 509 "
]
},
"execution_count": 42,
@@ -3165,18 +3222,10 @@
"execution_count": 44,
"metadata": {},
"outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.remote:Fetch kinase KLIFS IDs for input kinase names...\n",
- "INFO:opencadd.databases.klifs.remote:Fetch ligands based on these KLIFS IDs...\n"
- ]
- },
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "87c1a6993fd94af795927f3cf7880ce4",
+ "model_id": "98bd8339663140a7865be50814f5490e",
"version_major": 2,
"version_minor": 0
},
@@ -3191,9 +3240,9 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "ERROR:opencadd.databases.klifs.core:There was (were) 1/4 failed request(s).\n",
+ "There was (were) 1/4 failed request(s).\n",
"Show error messages (up to 5 messages only):\n",
- "ERROR:opencadd.databases.klifs.core:Error for 574: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
+ "Error for 574: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
]
},
{
@@ -3347,13 +3396,6 @@
"execution_count": 45,
"metadata": {},
"outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.remote:Fetch kinase KLIFS IDs for input kinase names...\n"
- ]
- },
{
"name": "stdout",
"output_type": "stream",
@@ -3415,22 +3457,22 @@
" \n",
" \n",
" 0 | \n",
- " None | \n",
+ " <NA> | \n",
" 1N1 | \n",
" N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" BMX | \n",
" BMX | \n",
" Human | \n",
"
\n",
" \n",
" 1 | \n",
- " None | \n",
+ " <NA> | \n",
" PRC | \n",
" N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" ABL1 | \n",
" Abl1 | \n",
" Mouse | \n",
@@ -3440,17 +3482,17 @@
""
],
"text/plain": [
- " ligand.klifs_id ligand.expo_id \\\n",
- "0 None 1N1 \n",
- "1 None PRC \n",
+ " ligand.klifs_id ligand.expo_id \\\n",
+ "0 1N1 \n",
+ "1 PRC \n",
"\n",
" ligand.name ligand.smiles \\\n",
- "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... None \n",
- "1 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... None \n",
+ "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
+ "1 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... \n",
"\n",
" ligand.inchikey kinase.klifs_name (query) kinase.gene_name (query) \\\n",
- "0 None BMX BMX \n",
- "1 None ABL1 Abl1 \n",
+ "0 BMX BMX \n",
+ "1 ABL1 Abl1 \n",
"\n",
" species.klifs (query) \n",
"0 Human \n",
@@ -3768,25 +3810,25 @@
" \n",
" \n",
" 0 | \n",
- " None | \n",
+ " <NA> | \n",
" PRC | \n",
" N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
"
\n",
" \n",
"\n",
""
],
"text/plain": [
- " ligand.klifs_id ligand.expo_id \\\n",
- "0 None PRC \n",
+ " ligand.klifs_id ligand.expo_id \\\n",
+ "0 PRC \n",
"\n",
" ligand.name ligand.smiles \\\n",
- "0 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... None \n",
+ "0 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... \n",
"\n",
" ligand.inchikey \n",
- "0 None "
+ "0 "
]
},
"execution_count": 52,
@@ -3874,6 +3916,7 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
@@ -3891,6 +3934,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -3910,6 +3954,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
"
\n",
" \n",
" \n",
@@ -3922,15 +3967,16 @@
" Human | \n",
" 1 | \n",
" AKT1 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... | \n",
" CQW | \n",
" - | \n",
" 2147 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" in | \n",
" in | \n",
" 2.0 | \n",
@@ -3939,6 +3985,7 @@
" 0 | \n",
" 0.779 | \n",
" 2.093 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -3954,10 +4001,11 @@
" False | \n",
" False | \n",
" False | \n",
- " 17.9435 | \n",
- " 58.2835 | \n",
- " 52.7742 | \n",
- " None | \n",
+ " 17.943501 | \n",
+ " 58.283501 | \n",
+ " 52.774200 | \n",
+ " <NA> | \n",
+ " False | \n",
" \n",
" \n",
" 1 | \n",
@@ -3968,15 +4016,16 @@
" Human | \n",
" 1 | \n",
" AKT1 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... | \n",
" - | \n",
" - | \n",
" 0 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" in | \n",
" in | \n",
" 2.4 | \n",
@@ -3985,6 +4034,7 @@
" 0 | \n",
" 0.776 | \n",
" 2.091 | \n",
+ " <NA> | \n",
" False | \n",
" False | \n",
" False | \n",
@@ -4000,10 +4050,11 @@
" False | \n",
" False | \n",
" False | \n",
- " 17.9011 | \n",
- " 59.5948 | \n",
- " 60.8725 | \n",
- " None | \n",
+ " 17.901100 | \n",
+ " 59.594799 | \n",
+ " 60.872501 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" ... | \n",
@@ -4050,6 +4101,9 @@
" ... | \n",
" ... | \n",
" ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
"
\n",
" \n",
" 12519 | \n",
@@ -4060,15 +4114,16 @@
" Human | \n",
" 1096 | \n",
" PI4KA | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" _PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE... | \n",
" E4S | \n",
" - | \n",
" 2974 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" out-like | \n",
" in | \n",
" NaN | \n",
@@ -4077,6 +4132,7 @@
" 0 | \n",
" 1.704 | \n",
" 2.676 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -4092,10 +4148,11 @@
" False | \n",
" False | \n",
" False | \n",
- " 18.3243 | \n",
- " 58.9635 | \n",
- " 131.1870 | \n",
- " None | \n",
+ " 18.324301 | \n",
+ " 58.963501 | \n",
+ " 131.186996 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" 12520 | \n",
@@ -4106,15 +4163,16 @@
" Human | \n",
" 1096 | \n",
" PI4KA | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" _PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE... | \n",
" E4S | \n",
" - | \n",
" 2974 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" out-like | \n",
" in | \n",
" NaN | \n",
@@ -4123,6 +4181,7 @@
" 0 | \n",
" 1.699 | \n",
" 2.670 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" False | \n",
@@ -4138,14 +4197,15 @@
" False | \n",
" False | \n",
" False | \n",
- " 18.1686 | \n",
- " 58.6454 | \n",
- " 136.5030 | \n",
- " None | \n",
+ " 18.168600 | \n",
+ " 58.645401 | \n",
+ " 136.503006 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
"\n",
- "12521 rows × 43 columns
\n",
+ "12521 rows × 46 columns
\n",
""
],
"text/plain": [
@@ -4163,12 +4223,12 @@
"12519 A Human 1096 PI4KA \n",
"12520 E Human 1096 PI4KA \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 None None \n",
- "1 None None \n",
- "... ... ... \n",
- "12519 None None \n",
- "12520 None None \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 \n",
+ "1 \n",
+ "... ... ... ... \n",
+ "12519 \n",
+ "12520 \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... CQW \n",
@@ -4185,11 +4245,11 @@
"12520 - 2974 0 \n",
"\n",
" ligand.name ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
- "0 None None in in \n",
- "1 None None in in \n",
+ "0 in in \n",
+ "1 in in \n",
"... ... ... ... ... \n",
- "12519 None None out-like in \n",
- "12520 None None out-like in \n",
+ "12519 out-like in \n",
+ "12520 out-like in \n",
"\n",
" structure.resolution structure.qualityscore \\\n",
"0 2.0 8.0 \n",
@@ -4205,49 +4265,56 @@
"12519 2 0 1.704 \n",
"12520 2 0 1.699 \n",
"\n",
- " structure.rmsd2 structure.front structure.gate structure.back \\\n",
- "0 2.093 True False False \n",
- "1 2.091 False False False \n",
- "... ... ... ... ... \n",
- "12519 2.676 True False False \n",
- "12520 2.670 True True False \n",
- "\n",
- " structure.fp_i structure.fp_ii structure.bp_i_a structure.bp_i_b \\\n",
- "0 False False False False \n",
- "1 False False False False \n",
- "... ... ... ... ... \n",
- "12519 False False False True \n",
- "12520 False False True True \n",
- "\n",
- " structure.bp_ii_in structure.bp_ii_a_in structure.bp_ii_b_in \\\n",
- "0 False False False \n",
- "1 False False False \n",
- "... ... ... ... \n",
- "12519 False False False \n",
- "12520 False False False \n",
- "\n",
- " structure.bp_ii_out structure.bp_ii_b structure.bp_iii \\\n",
- "0 False False False \n",
- "1 False False False \n",
- "... ... ... ... \n",
- "12519 False False False \n",
- "12520 False False False \n",
- "\n",
- " structure.bp_iv structure.bp_v structure.grich_distance \\\n",
- "0 False False 17.9435 \n",
- "1 False False 17.9011 \n",
- "... ... ... ... \n",
- "12519 False False 18.3243 \n",
- "12520 False False 18.1686 \n",
- "\n",
- " structure.grich_angle structure.grich_rotation structure.filepath \n",
- "0 58.2835 52.7742 None \n",
- "1 59.5948 60.8725 None \n",
- "... ... ... ... \n",
- "12519 58.9635 131.1870 None \n",
- "12520 58.6454 136.5030 None \n",
- "\n",
- "[12521 rows x 43 columns]"
+ " structure.rmsd2 interaction.fingerprint structure.front \\\n",
+ "0 2.093 True \n",
+ "1 2.091 False \n",
+ "... ... ... ... \n",
+ "12519 2.676 True \n",
+ "12520 2.670 True \n",
+ "\n",
+ " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
+ "0 False False False False \n",
+ "1 False False False False \n",
+ "... ... ... ... ... \n",
+ "12519 False False False False \n",
+ "12520 True False False False \n",
+ "\n",
+ " structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
+ "0 False False False \n",
+ "1 False False False \n",
+ "... ... ... ... \n",
+ "12519 False True False \n",
+ "12520 True True False \n",
+ "\n",
+ " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
+ "0 False False False \n",
+ "1 False False False \n",
+ "... ... ... ... \n",
+ "12519 False False False \n",
+ "12520 False False False \n",
+ "\n",
+ " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
+ "0 False False False False \n",
+ "1 False False False False \n",
+ "... ... ... ... ... \n",
+ "12519 False False False False \n",
+ "12520 False False False False \n",
+ "\n",
+ " structure.grich_distance structure.grich_angle \\\n",
+ "0 17.943501 58.283501 \n",
+ "1 17.901100 59.594799 \n",
+ "... ... ... \n",
+ "12519 18.324301 58.963501 \n",
+ "12520 18.168600 58.645401 \n",
+ "\n",
+ " structure.grich_rotation structure.filepath structure.curation_flag \n",
+ "0 52.774200 False \n",
+ "1 60.872501 False \n",
+ "... ... ... ... \n",
+ "12519 131.186996 False \n",
+ "12520 136.503006 False \n",
+ "\n",
+ "[12521 rows x 46 columns]"
]
},
"execution_count": 54,
@@ -4301,6 +4368,7 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
@@ -4318,6 +4386,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -4337,6 +4406,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -4349,13 +4419,14 @@
" Human | \n",
" 472 | \n",
" BMX | \n",
+ " ['BMX'] | \n",
" Tec | \n",
" TK | \n",
" KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
" 1N1 | \n",
" - | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... | \n",
" - | \n",
" out-like | \n",
@@ -4366,25 +4437,27 @@
" 0 | \n",
" 0.839 | \n",
" 1.967 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " 0000000000000010000001000000000000000000000000... | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " False | \n",
+ " False | \n",
+ " True | \n",
+ " True | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
" HUMAN/BMX/3sxr_chainA | \n",
+ " <NA> | \n",
" \n",
" \n",
" 1 | \n",
@@ -4395,13 +4468,14 @@
" Human | \n",
" 509 | \n",
" BRAF | \n",
+ " ['BRAF'] | \n",
" RAF | \n",
" TKL | \n",
" QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
" QH1 | \n",
" - | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... | \n",
" - | \n",
" in | \n",
@@ -4412,212 +4486,294 @@
" 61 | \n",
" 0.806 | \n",
" 2.028 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " 0000000000000000000000000000000000000000000000... | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " False | \n",
+ " False | \n",
+ " True | \n",
+ " True | \n",
+ " True | \n",
+ " True | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
" HUMAN/BRAF/6uuo_chainA | \n",
+ " <NA> | \n",
"
\n",
" \n",
- " 2 | \n",
- " 5728 | \n",
- " 1fpu | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ "
\n",
+ " \n",
+ " 4 | \n",
+ " 13623 | \n",
+ " 7lht | \n",
" - | \n",
" A | \n",
- " Mouse | \n",
- " 532 | \n",
- " ABL1 | \n",
- " Abl | \n",
- " TK | \n",
- " HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
- " PRC | \n",
+ " Human | \n",
+ " 495 | \n",
+ " LRRK2 | \n",
+ " ['LRRK2'] | \n",
+ " LRRK | \n",
+ " TKL | \n",
+ " KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK... | \n",
" - | \n",
- " None | \n",
- " None | \n",
- " N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
+ " ATP | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" - | \n",
+ " ADENOSINE-5'-TRIPHOSPHATE | \n",
" out | \n",
" out | \n",
- " 2.40 | \n",
- " 8.8 | \n",
- " 0 | \n",
- " 8 | \n",
- " 0.925 | \n",
- " 2.319 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
+ " 3.50 | \n",
+ " 4.0 | \n",
" 0 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
- " MOUSE/ABL1/1fpu_chainA | \n",
- "
\n",
- " \n",
- " 3 | \n",
- " 5705 | \n",
- " 1fpu | \n",
- " - | \n",
- " B | \n",
- " Mouse | \n",
- " 532 | \n",
- " ABL1 | \n",
- " Abl | \n",
- " TK | \n",
- " HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
- " PRC | \n",
- " - | \n",
- " None | \n",
- " None | \n",
- " N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
+ " 10.267 | \n",
+ " 15.045 | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " HUMAN/LRRK2/7lht_chainA | \n",
+ " <NA> | \n",
+ "
\n",
+ " \n",
+ " 5 | \n",
+ " 1243 | \n",
+ " 2ogv | \n",
+ " - | \n",
+ " A | \n",
+ " Human | \n",
+ " 449 | \n",
+ " FMS | \n",
+ " ['CSF1R', 'FMS'] | \n",
+ " PDGFR | \n",
+ " TK | \n",
+ " KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE... | \n",
+ " - | \n",
+ " - | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " - | \n",
" - | \n",
" out | \n",
- " out | \n",
- " 2.40 | \n",
- " 9.2 | \n",
- " 0 | \n",
- " 4 | \n",
- " 0.925 | \n",
- " 2.329 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
+ " in | \n",
+ " 2.70 | \n",
+ " 6.4 | \n",
+ " 2 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
- " MOUSE/ABL1/1fpu_chainB | \n",
+ " 1.043 | \n",
+ " 2.362 | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " HUMAN/FMS/2ogv_chainA | \n",
+ " <NA> | \n",
"
\n",
" \n",
"\n",
+ "6 rows × 46 columns
\n",
""
],
"text/plain": [
- " structure.klifs_id structure.pdb_id structure.alternate_model \\\n",
- "0 3482 3sxr - \n",
- "1 12347 6uuo - \n",
- "2 5728 1fpu - \n",
- "3 5705 1fpu - \n",
+ " structure.klifs_id structure.pdb_id structure.alternate_model \\\n",
+ "0 3482 3sxr - \n",
+ "1 12347 6uuo - \n",
+ ".. ... ... ... \n",
+ "4 13623 7lht - \n",
+ "5 1243 2ogv - \n",
"\n",
- " structure.chain species.klifs kinase.klifs_id kinase.klifs_name \\\n",
- "0 A Human 472 BMX \n",
- "1 A Human 509 BRAF \n",
- "2 A Mouse 532 ABL1 \n",
- "3 B Mouse 532 ABL1 \n",
+ " structure.chain species.klifs kinase.klifs_id kinase.klifs_name \\\n",
+ "0 A Human 472 BMX \n",
+ "1 A Human 509 BRAF \n",
+ ".. ... ... ... ... \n",
+ "4 A Human 495 LRRK2 \n",
+ "5 A Human 449 FMS \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 Tec TK \n",
- "1 RAF TKL \n",
- "2 Abl TK \n",
- "3 Abl TK \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 ['BMX'] Tec TK \n",
+ "1 ['BRAF'] RAF TKL \n",
+ ".. ... ... ... \n",
+ "4 ['LRRK2'] LRRK TKL \n",
+ "5 ['CSF1R', 'FMS'] PDGFR TK \n",
"\n",
- " structure.pocket ligand.expo_id \\\n",
- "0 KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... 1N1 \n",
- "1 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... QH1 \n",
- "2 HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... PRC \n",
- "3 HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... PRC \n",
+ " structure.pocket ligand.expo_id \\\n",
+ "0 KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... 1N1 \n",
+ "1 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... QH1 \n",
+ ".. ... ... \n",
+ "4 KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK... - \n",
+ "5 KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE... - \n",
"\n",
- " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
- "0 - None None \n",
- "1 - None None \n",
- "2 - None None \n",
- "3 - None None \n",
+ " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
+ "0 - \n",
+ "1 - \n",
+ ".. ... ... ... \n",
+ "4 ATP \n",
+ "5 - \n",
"\n",
- " ligand.name ligand_allosteric.name \\\n",
- "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... - \n",
- "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... - \n",
- "2 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... - \n",
- "3 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... - \n",
+ " ligand.name \\\n",
+ "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
+ "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... \n",
+ ".. ... \n",
+ "4 - \n",
+ "5 - \n",
"\n",
- " structure.dfg structure.ac_helix structure.resolution \\\n",
- "0 out-like in 2.40 \n",
- "1 in out-like 3.29 \n",
- "2 out out 2.40 \n",
- "3 out out 2.40 \n",
+ " ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
+ "0 - out-like in \n",
+ "1 - in out-like \n",
+ ".. ... ... ... \n",
+ "4 ADENOSINE-5'-TRIPHOSPHATE out out \n",
+ "5 - out in \n",
"\n",
- " structure.qualityscore structure.missing_residues \\\n",
- "0 6.4 4 \n",
- "1 5.2 7 \n",
- "2 8.8 0 \n",
- "3 9.2 0 \n",
+ " structure.resolution structure.qualityscore structure.missing_residues \\\n",
+ "0 2.40 6.4 4 \n",
+ "1 3.29 5.2 7 \n",
+ ".. ... ... ... \n",
+ "4 3.50 4.0 0 \n",
+ "5 2.70 6.4 2 \n",
"\n",
- " structure.missing_atoms structure.rmsd1 structure.rmsd2 structure.front \\\n",
- "0 0 0.839 1.967 None \n",
- "1 61 0.806 2.028 None \n",
- "2 8 0.925 2.319 None \n",
- "3 4 0.925 2.329 None \n",
+ " structure.missing_atoms structure.rmsd1 structure.rmsd2 \\\n",
+ "0 0 0.839 1.967 \n",
+ "1 61 0.806 2.028 \n",
+ ".. ... ... ... \n",
+ "4 0 10.267 15.045 \n",
+ "5 0 1.043 2.362 \n",
+ "\n",
+ " interaction.fingerprint structure.front \\\n",
+ "0 0000000000000010000001000000000000000000000000... \n",
+ "1 0000000000000000000000000000000000000000000000... \n",
+ ".. ... ... \n",
+ "4 \n",
+ "5 \n",
+ "\n",
+ " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
+ "0 False False \n",
+ "1 False False \n",
+ ".. ... ... ... ... \n",
+ "4 \n",
+ "5 \n",
+ "\n",
+ " structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
+ "0 True True False \n",
+ "1 True True True \n",
+ ".. ... ... ... \n",
+ "4 \n",
+ "5 \n",
+ "\n",
+ " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
+ "0 False False False \n",
+ "1 True False False \n",
+ ".. ... ... ... \n",
+ "4 \n",
+ "5 \n",
"\n",
- " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
- "0 None None 0 0 \n",
- "1 None None 0 0 \n",
- "2 None None 0 0 \n",
- "3 None None 0 0 \n",
+ " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
+ "0 False False False False \n",
+ "1 False False False False \n",
+ ".. ... ... ... ... \n",
+ "4 \n",
+ "5 \n",
"\n",
- " structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 1 1 0 \n",
- "1 1 1 1 \n",
- "2 1 1 0 \n",
- "3 0 1 0 \n",
+ " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
+ "0 NaN NaN NaN \n",
+ "1 NaN NaN NaN \n",
+ ".. ... ... ... \n",
+ "4 NaN NaN NaN \n",
+ "5 NaN NaN NaN \n",
"\n",
- " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 0 0 0 \n",
- "1 1 0 0 \n",
- "2 0 0 1 \n",
- "3 0 0 1 \n",
+ " structure.filepath structure.curation_flag \n",
+ "0 HUMAN/BMX/3sxr_chainA \n",
+ "1 HUMAN/BRAF/6uuo_chainA \n",
+ ".. ... ... \n",
+ "4 HUMAN/LRRK2/7lht_chainA \n",
+ "5 HUMAN/FMS/2ogv_chainA \n",
"\n",
- " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 0 0 0 0 \n",
- "1 0 0 0 0 \n",
- "2 0 0 0 0 \n",
- "3 0 0 0 0 \n",
- "\n",
- " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
- "0 None None None \n",
- "1 None None None \n",
- "2 None None None \n",
- "3 None None None \n",
- "\n",
- " structure.filepath \n",
- "0 HUMAN/BMX/3sxr_chainA \n",
- "1 HUMAN/BRAF/6uuo_chainA \n",
- "2 MOUSE/ABL1/1fpu_chainA \n",
- "3 MOUSE/ABL1/1fpu_chainB "
+ "[6 rows x 46 columns]"
]
},
"execution_count": 55,
@@ -4676,6 +4832,7 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
@@ -4693,6 +4850,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -4712,6 +4870,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -4724,15 +4883,16 @@
" Human | \n",
" 509 | \n",
" BRAF | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
" QH1 | \n",
" - | \n",
" 3715 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" in | \n",
" out | \n",
" 3.29 | \n",
@@ -4741,6 +4901,7 @@
" 61 | \n",
" 0.806 | \n",
" 2.028 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" True | \n",
@@ -4759,7 +4920,8 @@
" 0.0 | \n",
" 0.0 | \n",
" 0.0 | \n",
- " None | \n",
+ " <NA> | \n",
+ " False | \n",
" \n",
" \n",
"\n",
@@ -4772,8 +4934,8 @@
" structure.chain species.klifs kinase.klifs_id kinase.klifs_name \\\n",
"0 A Human 509 BRAF \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 None None \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... QH1 \n",
@@ -4782,31 +4944,31 @@
"0 - 3715 0 \n",
"\n",
" ligand.name ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
- "0 None None in out \n",
+ "0 in out \n",
"\n",
" structure.resolution structure.qualityscore structure.missing_residues \\\n",
"0 3.29 5.2 7 \n",
"\n",
- " structure.missing_atoms structure.rmsd1 structure.rmsd2 structure.front \\\n",
- "0 61 0.806 2.028 True \n",
+ " structure.missing_atoms structure.rmsd1 structure.rmsd2 \\\n",
+ "0 61 0.806 2.028 \n",
"\n",
- " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
- "0 True True False False \n",
+ " interaction.fingerprint structure.front structure.gate structure.back \\\n",
+ "0 True True True \n",
"\n",
- " structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 True True True \n",
+ " structure.fp_i structure.fp_ii structure.bp_i_a structure.bp_i_b \\\n",
+ "0 False False True True \n",
"\n",
- " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 True False False \n",
+ " structure.bp_ii_in structure.bp_ii_a_in structure.bp_ii_b_in \\\n",
+ "0 True True False \n",
"\n",
- " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 False False False False \n",
+ " structure.bp_ii_out structure.bp_ii_b structure.bp_iii structure.bp_iv \\\n",
+ "0 False False False False \n",
"\n",
- " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
- "0 0.0 0.0 0.0 \n",
+ " structure.bp_v structure.grich_distance structure.grich_angle \\\n",
+ "0 False 0.0 0.0 \n",
"\n",
- " structure.filepath \n",
- "0 None "
+ " structure.grich_rotation structure.filepath structure.curation_flag \n",
+ "0 0.0 False "
]
},
"execution_count": 56,
@@ -4878,6 +5040,7 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
@@ -4895,6 +5058,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -4914,6 +5078,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -4926,13 +5091,14 @@
" Human | \n",
" 509 | \n",
" BRAF | \n",
+ " ['BRAF'] | \n",
" RAF | \n",
" TKL | \n",
" QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
" QH1 | \n",
" - | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... | \n",
" - | \n",
" in | \n",
@@ -4943,25 +5109,27 @@
" 61 | \n",
" 0.806 | \n",
" 2.028 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " 0000000000000000000000000000000000000000000000... | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " False | \n",
+ " False | \n",
+ " True | \n",
+ " True | \n",
+ " True | \n",
+ " True | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
" HUMAN/BRAF/6uuo_chainA | \n",
+ " <NA> | \n",
" \n",
" \n",
"\n",
@@ -4974,14 +5142,14 @@
" structure.chain species.klifs kinase.klifs_id kinase.klifs_name \\\n",
"0 A Human 509 BRAF \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 RAF TKL \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 ['BRAF'] RAF TKL \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... QH1 \n",
"\n",
- " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
- "0 - None None \n",
+ " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
+ "0 - \n",
"\n",
" ligand.name ligand_allosteric.name \\\n",
"0 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... - \n",
@@ -4992,26 +5160,29 @@
" structure.qualityscore structure.missing_residues \\\n",
"0 5.2 7 \n",
"\n",
- " structure.missing_atoms structure.rmsd1 structure.rmsd2 structure.front \\\n",
- "0 61 0.806 2.028 None \n",
+ " structure.missing_atoms structure.rmsd1 structure.rmsd2 \\\n",
+ "0 61 0.806 2.028 \n",
"\n",
- " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
- "0 None None 0 0 \n",
+ " interaction.fingerprint structure.front \\\n",
+ "0 0000000000000000000000000000000000000000000000... \n",
+ "\n",
+ " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
+ "0 False False \n",
"\n",
" structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 1 1 1 \n",
+ "0 True True True \n",
"\n",
" structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 1 0 0 \n",
+ "0 True False False \n",
"\n",
" structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 0 0 0 0 \n",
+ "0 False False False False \n",
"\n",
- " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
- "0 None None None \n",
+ " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
+ "0 NaN NaN NaN \n",
"\n",
- " structure.filepath \n",
- "0 HUMAN/BRAF/6uuo_chainA "
+ " structure.filepath structure.curation_flag \n",
+ "0 HUMAN/BRAF/6uuo_chainA "
]
},
"execution_count": 58,
@@ -5031,7 +5202,7 @@
{
"data": {
"text/plain": [
- "(1, 43)"
+ "(1, 46)"
]
},
"execution_count": 59,
@@ -5110,6 +5281,7 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
@@ -5127,6 +5299,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -5146,6 +5319,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -5158,15 +5332,16 @@
" Human | \n",
" 128 | \n",
" MELK | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" ETIGTGGFAKVKLVAIKIMRIKTEIEALKNLRQHICQLYHVFMVLE... | \n",
" KSA | \n",
" - | \n",
" 100 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" in | \n",
" in | \n",
" 1.9 | \n",
@@ -5175,6 +5350,7 @@
" 0 | \n",
" 0.775 | \n",
" 2.083 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -5191,9 +5367,10 @@
" False | \n",
" False | \n",
" 14.9753 | \n",
- " 51.0238 | \n",
- " 60.3786 | \n",
- " None | \n",
+ " 51.023800 | \n",
+ " 60.378601 | \n",
+ " <NA> | \n",
+ " False | \n",
" \n",
" \n",
" 1 | \n",
@@ -5204,15 +5381,16 @@
" Human | \n",
" 128 | \n",
" MELK | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" ETIGTGGFAKVKLVAIKIMRIKTEIEALKNLRQHICQLYHVFMVLE... | \n",
" KSA | \n",
" - | \n",
" 100 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" in | \n",
" in | \n",
" 1.9 | \n",
@@ -5221,6 +5399,7 @@
" 0 | \n",
" 0.775 | \n",
" 2.083 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -5237,9 +5416,10 @@
" False | \n",
" False | \n",
" 14.9753 | \n",
- " 51.0238 | \n",
- " 60.3786 | \n",
- " None | \n",
+ " 51.023800 | \n",
+ " 60.378601 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" ... | \n",
@@ -5286,6 +5466,9 @@
" ... | \n",
" ... | \n",
" ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
"
\n",
" \n",
" 12 | \n",
@@ -5296,15 +5479,16 @@
" Human | \n",
" 383 | \n",
" MAP2K1 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" SELGAGNGGVVFKMARKLIQIIRELQVLHECNPYIVGFYGASICME... | \n",
" KSA | \n",
" - | \n",
" 100 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" in | \n",
" out | \n",
" 2.7 | \n",
@@ -5313,6 +5497,7 @@
" 0 | \n",
" 0.816 | \n",
" 2.199 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -5329,9 +5514,10 @@
" False | \n",
" False | \n",
" 15.1080 | \n",
- " 51.2885 | \n",
- " 69.3669 | \n",
- " None | \n",
+ " 51.288502 | \n",
+ " 69.366898 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" 13 | \n",
@@ -5342,15 +5528,16 @@
" Human | \n",
" 446 | \n",
" MET | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" EVIGRGHFGCVYHCAVKSLQFLTEGIIMKDFSPNVLSLLGILVVLP... | \n",
" KSA | \n",
" - | \n",
" 100 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" in | \n",
" out | \n",
" 1.8 | \n",
@@ -5359,6 +5546,7 @@
" 0 | \n",
" 0.848 | \n",
" 2.189 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -5375,13 +5563,14 @@
" False | \n",
" False | \n",
" 20.0054 | \n",
- " 66.3494 | \n",
- " 48.1602 | \n",
- " None | \n",
+ " 66.349403 | \n",
+ " 48.160198 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
"\n",
- "14 rows × 43 columns
\n",
+ "14 rows × 46 columns
\n",
""
],
"text/plain": [
@@ -5399,12 +5588,12 @@
"12 A Human 383 MAP2K1 \n",
"13 A Human 446 MET \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 None None \n",
- "1 None None \n",
- ".. ... ... \n",
- "12 None None \n",
- "13 None None \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 \n",
+ "1 \n",
+ ".. ... ... ... \n",
+ "12 \n",
+ "13 \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 ETIGTGGFAKVKLVAIKIMRIKTEIEALKNLRQHICQLYHVFMVLE... KSA \n",
@@ -5421,11 +5610,11 @@
"13 - 100 0 \n",
"\n",
" ligand.name ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
- "0 None None in in \n",
- "1 None None in in \n",
+ "0 in in \n",
+ "1 in in \n",
".. ... ... ... ... \n",
- "12 None None in out \n",
- "13 None None in out \n",
+ "12 in out \n",
+ "13 in out \n",
"\n",
" structure.resolution structure.qualityscore structure.missing_residues \\\n",
"0 1.9 8.0 0 \n",
@@ -5441,49 +5630,49 @@
"12 0 0.816 2.199 \n",
"13 0 0.848 2.189 \n",
"\n",
- " structure.front structure.gate structure.back structure.fp_i \\\n",
- "0 True False False False \n",
- "1 True False False False \n",
- ".. ... ... ... ... \n",
- "12 True False False False \n",
- "13 True False False False \n",
- "\n",
- " structure.fp_ii structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 False False False False \n",
- "1 False False False False \n",
- ".. ... ... ... ... \n",
- "12 False False False False \n",
- "13 True False False False \n",
- "\n",
- " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 False False False \n",
- "1 False False False \n",
- ".. ... ... ... \n",
- "12 False False False \n",
- "13 False False False \n",
- "\n",
- " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 False False False False \n",
- "1 False False False False \n",
- ".. ... ... ... ... \n",
- "12 False False False False \n",
- "13 False False False False \n",
- "\n",
- " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
- "0 14.9753 51.0238 60.3786 \n",
- "1 14.9753 51.0238 60.3786 \n",
- ".. ... ... ... \n",
- "12 15.1080 51.2885 69.3669 \n",
- "13 20.0054 66.3494 48.1602 \n",
- "\n",
- " structure.filepath \n",
- "0 None \n",
- "1 None \n",
- ".. ... \n",
- "12 None \n",
- "13 None \n",
- "\n",
- "[14 rows x 43 columns]"
+ " interaction.fingerprint structure.front structure.gate structure.back \\\n",
+ "0 True False False \n",
+ "1 True False False \n",
+ ".. ... ... ... ... \n",
+ "12 True False False \n",
+ "13 True False False \n",
+ "\n",
+ " structure.fp_i structure.fp_ii structure.bp_i_a structure.bp_i_b \\\n",
+ "0 False False False False \n",
+ "1 False False False False \n",
+ ".. ... ... ... ... \n",
+ "12 False False False False \n",
+ "13 False True False False \n",
+ "\n",
+ " structure.bp_ii_in structure.bp_ii_a_in structure.bp_ii_b_in \\\n",
+ "0 False False False \n",
+ "1 False False False \n",
+ ".. ... ... ... \n",
+ "12 False False False \n",
+ "13 False False False \n",
+ "\n",
+ " structure.bp_ii_out structure.bp_ii_b structure.bp_iii structure.bp_iv \\\n",
+ "0 False False False False \n",
+ "1 False False False False \n",
+ ".. ... ... ... ... \n",
+ "12 False False False False \n",
+ "13 False False False False \n",
+ "\n",
+ " structure.bp_v structure.grich_distance structure.grich_angle \\\n",
+ "0 False 14.9753 51.023800 \n",
+ "1 False 14.9753 51.023800 \n",
+ ".. ... ... ... \n",
+ "12 False 15.1080 51.288502 \n",
+ "13 False 20.0054 66.349403 \n",
+ "\n",
+ " structure.grich_rotation structure.filepath structure.curation_flag \n",
+ "0 60.378601 False \n",
+ "1 60.378601 False \n",
+ ".. ... ... ... \n",
+ "12 69.366898 False \n",
+ "13 48.160198 False \n",
+ "\n",
+ "[14 rows x 46 columns]"
]
},
"execution_count": 61,
@@ -5571,6 +5760,7 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
@@ -5588,6 +5778,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -5607,6 +5798,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -5619,15 +5811,16 @@
" Human | \n",
" 472 | \n",
" BMX | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" KELGSGQFGVVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
" PP2 | \n",
" - | \n",
" 632 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" out-like | \n",
" in | \n",
" 1.89 | \n",
@@ -5636,6 +5829,7 @@
" 0 | \n",
" 0.834 | \n",
" 2.106 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" False | \n",
@@ -5652,9 +5846,10 @@
" False | \n",
" False | \n",
" 15.3623 | \n",
- " 50.7101 | \n",
- " 62.7444 | \n",
- " None | \n",
+ " 50.710098 | \n",
+ " 62.744400 | \n",
+ " <NA> | \n",
+ " False | \n",
" \n",
" \n",
" 1 | \n",
@@ -5665,15 +5860,16 @@
" Human | \n",
" 472 | \n",
" BMX | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" KEL______VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
" 1N1 | \n",
" - | \n",
" 281 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" out-like | \n",
" in | \n",
" 2.40 | \n",
@@ -5682,6 +5878,7 @@
" 0 | \n",
" 0.839 | \n",
" 1.946 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" False | \n",
@@ -5698,9 +5895,10 @@
" False | \n",
" False | \n",
" 0.0000 | \n",
- " 0.0000 | \n",
- " 0.0000 | \n",
- " None | \n",
+ " 0.000000 | \n",
+ " 0.000000 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" ... | \n",
@@ -5747,6 +5945,9 @@
" ... | \n",
" ... | \n",
" ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
"
\n",
" \n",
" 225 | \n",
@@ -5757,15 +5958,16 @@
" Human | \n",
" 509 | \n",
" BRAF | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
" 2VX | \n",
" - | \n",
" 945 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" in | \n",
" out | \n",
" 3.40 | \n",
@@ -5774,6 +5976,7 @@
" 0 | \n",
" 0.813 | \n",
" 2.142 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" True | \n",
@@ -5790,9 +5993,10 @@
" False | \n",
" False | \n",
" 17.1234 | \n",
- " 55.5483 | \n",
- " 31.8510 | \n",
- " None | \n",
+ " 55.548302 | \n",
+ " 31.851000 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" 226 | \n",
@@ -5803,15 +6007,16 @@
" Human | \n",
" 509 | \n",
" BRAF | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
" SM5 | \n",
" - | \n",
" 249 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" in | \n",
" in | \n",
" 2.80 | \n",
@@ -5820,6 +6025,7 @@
" 0 | \n",
" 0.779 | \n",
" 2.120 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" False | \n",
@@ -5836,13 +6042,14 @@
" False | \n",
" False | \n",
" 14.7287 | \n",
- " 49.4656 | \n",
- " 72.6044 | \n",
- " None | \n",
+ " 49.465599 | \n",
+ " 72.604401 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
"\n",
- "227 rows × 43 columns
\n",
+ "227 rows × 46 columns
\n",
""
],
"text/plain": [
@@ -5860,12 +6067,12 @@
"225 B Human 509 BRAF \n",
"226 A Human 509 BRAF \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 None None \n",
- "1 None None \n",
- ".. ... ... \n",
- "225 None None \n",
- "226 None None \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 \n",
+ "1 \n",
+ ".. ... ... ... \n",
+ "225 \n",
+ "226 \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 KELGSGQFGVVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... PP2 \n",
@@ -5882,11 +6089,11 @@
"226 - 249 0 \n",
"\n",
" ligand.name ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
- "0 None None out-like in \n",
- "1 None None out-like in \n",
+ "0 out-like in \n",
+ "1 out-like in \n",
".. ... ... ... ... \n",
- "225 None None in out \n",
- "226 None None in in \n",
+ "225 in out \n",
+ "226 in in \n",
"\n",
" structure.resolution structure.qualityscore structure.missing_residues \\\n",
"0 1.89 8.0 0 \n",
@@ -5902,49 +6109,56 @@
"225 0 0.813 2.142 \n",
"226 0 0.779 2.120 \n",
"\n",
- " structure.front structure.gate structure.back structure.fp_i \\\n",
- "0 True True False False \n",
- "1 True True False False \n",
- ".. ... ... ... ... \n",
- "225 True True True True \n",
- "226 True True False False \n",
- "\n",
- " structure.fp_ii structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 False False True False \n",
- "1 False True True False \n",
- ".. ... ... ... ... \n",
- "225 False True True True \n",
- "226 False False True False \n",
- "\n",
- " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 False False False \n",
- "1 False False False \n",
- ".. ... ... ... \n",
- "225 False False False \n",
- "226 False False False \n",
- "\n",
- " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 False False False False \n",
- "1 False False False False \n",
- ".. ... ... ... ... \n",
- "225 False False False False \n",
- "226 False False False False \n",
- "\n",
- " structure.grich_distance structure.grich_angle \\\n",
- "0 15.3623 50.7101 \n",
- "1 0.0000 0.0000 \n",
- ".. ... ... \n",
- "225 17.1234 55.5483 \n",
- "226 14.7287 49.4656 \n",
- "\n",
- " structure.grich_rotation structure.filepath \n",
- "0 62.7444 None \n",
- "1 0.0000 None \n",
- ".. ... ... \n",
- "225 31.8510 None \n",
- "226 72.6044 None \n",
- "\n",
- "[227 rows x 43 columns]"
+ " interaction.fingerprint structure.front structure.gate structure.back \\\n",
+ "0 True True False \n",
+ "1 True True False \n",
+ ".. ... ... ... ... \n",
+ "225 True True True \n",
+ "226 True True False \n",
+ "\n",
+ " structure.fp_i structure.fp_ii structure.bp_i_a structure.bp_i_b \\\n",
+ "0 False False False True \n",
+ "1 False False True True \n",
+ ".. ... ... ... ... \n",
+ "225 True False True True \n",
+ "226 False False False True \n",
+ "\n",
+ " structure.bp_ii_in structure.bp_ii_a_in structure.bp_ii_b_in \\\n",
+ "0 False False False \n",
+ "1 False False False \n",
+ ".. ... ... ... \n",
+ "225 True False False \n",
+ "226 False False False \n",
+ "\n",
+ " structure.bp_ii_out structure.bp_ii_b structure.bp_iii \\\n",
+ "0 False False False \n",
+ "1 False False False \n",
+ ".. ... ... ... \n",
+ "225 False False False \n",
+ "226 False False False \n",
+ "\n",
+ " structure.bp_iv structure.bp_v structure.grich_distance \\\n",
+ "0 False False 15.3623 \n",
+ "1 False False 0.0000 \n",
+ ".. ... ... ... \n",
+ "225 False False 17.1234 \n",
+ "226 False False 14.7287 \n",
+ "\n",
+ " structure.grich_angle structure.grich_rotation structure.filepath \\\n",
+ "0 50.710098 62.744400 \n",
+ "1 0.000000 0.000000 \n",
+ ".. ... ... ... \n",
+ "225 55.548302 31.851000 \n",
+ "226 49.465599 72.604401 \n",
+ "\n",
+ " structure.curation_flag \n",
+ "0 False \n",
+ "1 False \n",
+ ".. ... \n",
+ "225 False \n",
+ "226 False \n",
+ "\n",
+ "[227 rows x 46 columns]"
]
},
"execution_count": 63,
@@ -6016,6 +6230,7 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
@@ -6033,6 +6248,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -6052,6 +6268,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -6064,13 +6281,14 @@
" Human | \n",
" 472 | \n",
" BMX | \n",
+ " ['BMX'] | \n",
" Tec | \n",
" TK | \n",
" KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
" 1N1 | \n",
" - | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... | \n",
" - | \n",
" out-like | \n",
@@ -6081,25 +6299,27 @@
" 0 | \n",
" 0.839 | \n",
" 1.967 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " 0000000000000010000001000000000000000000000000... | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " False | \n",
+ " False | \n",
+ " True | \n",
+ " True | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
" HUMAN/BMX/3sxr_chainA | \n",
+ " <NA> | \n",
" \n",
" \n",
" 1 | \n",
@@ -6110,13 +6330,14 @@
" Human | \n",
" 509 | \n",
" BRAF | \n",
+ " ['BRAF'] | \n",
" RAF | \n",
" TKL | \n",
" QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
" QH1 | \n",
" - | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... | \n",
" - | \n",
" in | \n",
@@ -6127,25 +6348,27 @@
" 61 | \n",
" 0.806 | \n",
" 2.028 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " None | \n",
- " None | \n",
- " None | \n",
+ " 0000000000000000000000000000000000000000000000... | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " False | \n",
+ " False | \n",
+ " True | \n",
+ " True | \n",
+ " True | \n",
+ " True | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " False | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
" HUMAN/BRAF/6uuo_chainA | \n",
+ " <NA> | \n",
"
\n",
" \n",
"\n",
@@ -6160,17 +6383,17 @@
"0 A Human 472 BMX \n",
"1 A Human 509 BRAF \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 Tec TK \n",
- "1 RAF TKL \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 ['BMX'] Tec TK \n",
+ "1 ['BRAF'] RAF TKL \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... 1N1 \n",
"1 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... QH1 \n",
"\n",
- " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
- "0 - None None \n",
- "1 - None None \n",
+ " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
+ "0 - \n",
+ "1 - \n",
"\n",
" ligand.name ligand_allosteric.name \\\n",
"0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... - \n",
@@ -6184,33 +6407,37 @@
"0 6.4 4 \n",
"1 5.2 7 \n",
"\n",
- " structure.missing_atoms structure.rmsd1 structure.rmsd2 structure.front \\\n",
- "0 0 0.839 1.967 None \n",
- "1 61 0.806 2.028 None \n",
+ " structure.missing_atoms structure.rmsd1 structure.rmsd2 \\\n",
+ "0 0 0.839 1.967 \n",
+ "1 61 0.806 2.028 \n",
"\n",
- " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
- "0 None None 0 0 \n",
- "1 None None 0 0 \n",
+ " interaction.fingerprint structure.front \\\n",
+ "0 0000000000000010000001000000000000000000000000... \n",
+ "1 0000000000000000000000000000000000000000000000... \n",
+ "\n",
+ " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
+ "0 False False \n",
+ "1 False False \n",
"\n",
" structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 1 1 0 \n",
- "1 1 1 1 \n",
+ "0 True True False \n",
+ "1 True True True \n",
"\n",
" structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 0 0 0 \n",
- "1 1 0 0 \n",
+ "0 False False False \n",
+ "1 True False False \n",
"\n",
" structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 0 0 0 0 \n",
- "1 0 0 0 0 \n",
+ "0 False False False False \n",
+ "1 False False False False \n",
"\n",
- " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
- "0 None None None \n",
- "1 None None None \n",
+ " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
+ "0 NaN NaN NaN \n",
+ "1 NaN NaN NaN \n",
"\n",
- " structure.filepath \n",
- "0 HUMAN/BMX/3sxr_chainA \n",
- "1 HUMAN/BRAF/6uuo_chainA "
+ " structure.filepath structure.curation_flag \n",
+ "0 HUMAN/BMX/3sxr_chainA \n",
+ "1 HUMAN/BRAF/6uuo_chainA "
]
},
"execution_count": 65,
@@ -6289,6 +6516,7 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
@@ -6306,6 +6534,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -6325,6 +6554,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -6337,15 +6567,16 @@
" Mouse | \n",
" 532 | \n",
" ABL1 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
" PRC | \n",
" - | \n",
" 1793 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" out | \n",
" in | \n",
" 2.4 | \n",
@@ -6354,6 +6585,7 @@
" 4 | \n",
" 0.925 | \n",
" 2.329 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" True | \n",
@@ -6369,10 +6601,11 @@
" False | \n",
" False | \n",
" False | \n",
- " 15.3329 | \n",
- " 51.0939 | \n",
- " 49.2289 | \n",
- " None | \n",
+ " 15.332900 | \n",
+ " 51.093899 | \n",
+ " 49.228901 | \n",
+ " <NA> | \n",
+ " False | \n",
" \n",
" \n",
" 1 | \n",
@@ -6383,15 +6616,16 @@
" Mouse | \n",
" 532 | \n",
" ABL1 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
" PRC | \n",
" - | \n",
" 1793 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" out | \n",
" in | \n",
" 2.4 | \n",
@@ -6400,6 +6634,7 @@
" 8 | \n",
" 0.925 | \n",
" 2.319 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" True | \n",
@@ -6415,10 +6650,11 @@
" False | \n",
" False | \n",
" False | \n",
- " 16.1554 | \n",
- " 54.1402 | \n",
- " 48.7414 | \n",
- " None | \n",
+ " 16.155399 | \n",
+ " 54.140202 | \n",
+ " 48.741402 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" 2 | \n",
@@ -6429,15 +6665,16 @@
" Human | \n",
" 472 | \n",
" BMX | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" KEL______VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
" 1N1 | \n",
" - | \n",
" 281 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" out-like | \n",
" in | \n",
" 2.4 | \n",
@@ -6446,6 +6683,7 @@
" 0 | \n",
" 0.839 | \n",
" 1.946 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" False | \n",
@@ -6461,10 +6699,11 @@
" False | \n",
" False | \n",
" False | \n",
- " 0.0000 | \n",
- " 0.0000 | \n",
- " 0.0000 | \n",
- " None | \n",
+ " 0.000000 | \n",
+ " 0.000000 | \n",
+ " 0.000000 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" 3 | \n",
@@ -6475,15 +6714,16 @@
" Human | \n",
" 472 | \n",
" BMX | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
" 1N1 | \n",
" - | \n",
" 281 | \n",
" 0 | \n",
- " None | \n",
- " None | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" out-like | \n",
" in | \n",
" 2.4 | \n",
@@ -6492,6 +6732,7 @@
" 0 | \n",
" 0.839 | \n",
" 1.967 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" False | \n",
@@ -6507,10 +6748,11 @@
" False | \n",
" False | \n",
" False | \n",
- " 0.0000 | \n",
- " 0.0000 | \n",
- " 0.0000 | \n",
- " None | \n",
+ " 0.000000 | \n",
+ " 0.000000 | \n",
+ " 0.000000 | \n",
+ " <NA> | \n",
+ " False | \n",
"
\n",
" \n",
"\n",
@@ -6529,11 +6771,11 @@
"2 B Human 472 BMX \n",
"3 A Human 472 BMX \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 None None \n",
- "1 None None \n",
- "2 None None \n",
- "3 None None \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 \n",
+ "1 \n",
+ "2 \n",
+ "3 \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... PRC \n",
@@ -6548,10 +6790,10 @@
"3 - 281 0 \n",
"\n",
" ligand.name ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
- "0 None None out in \n",
- "1 None None out in \n",
- "2 None None out-like in \n",
- "3 None None out-like in \n",
+ "0 out in \n",
+ "1 out in \n",
+ "2 out-like in \n",
+ "3 out-like in \n",
"\n",
" structure.resolution structure.qualityscore structure.missing_residues \\\n",
"0 2.4 9.2 0 \n",
@@ -6559,47 +6801,47 @@
"2 2.4 5.6 6 \n",
"3 2.4 6.4 4 \n",
"\n",
- " structure.missing_atoms structure.rmsd1 structure.rmsd2 structure.front \\\n",
- "0 4 0.925 2.329 True \n",
- "1 8 0.925 2.319 True \n",
- "2 0 0.839 1.946 True \n",
- "3 0 0.839 1.967 True \n",
- "\n",
- " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
- "0 True True False False \n",
- "1 True True False False \n",
- "2 True False False False \n",
- "3 True False False False \n",
- "\n",
- " structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 False True False \n",
- "1 True True False \n",
- "2 True True False \n",
- "3 True True False \n",
- "\n",
- " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 False False True \n",
- "1 False False True \n",
- "2 False False False \n",
- "3 False False False \n",
- "\n",
- " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 False False False False \n",
- "1 False False False False \n",
- "2 False False False False \n",
- "3 False False False False \n",
- "\n",
- " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
- "0 15.3329 51.0939 49.2289 \n",
- "1 16.1554 54.1402 48.7414 \n",
- "2 0.0000 0.0000 0.0000 \n",
- "3 0.0000 0.0000 0.0000 \n",
- "\n",
- " structure.filepath \n",
- "0 None \n",
- "1 None \n",
- "2 None \n",
- "3 None "
+ " structure.missing_atoms structure.rmsd1 structure.rmsd2 \\\n",
+ "0 4 0.925 2.329 \n",
+ "1 8 0.925 2.319 \n",
+ "2 0 0.839 1.946 \n",
+ "3 0 0.839 1.967 \n",
+ "\n",
+ " interaction.fingerprint structure.front structure.gate structure.back \\\n",
+ "0 True True True \n",
+ "1 True True True \n",
+ "2 True True False \n",
+ "3 True True False \n",
+ "\n",
+ " structure.fp_i structure.fp_ii structure.bp_i_a structure.bp_i_b \\\n",
+ "0 False False False True \n",
+ "1 False False True True \n",
+ "2 False False True True \n",
+ "3 False False True True \n",
+ "\n",
+ " structure.bp_ii_in structure.bp_ii_a_in structure.bp_ii_b_in \\\n",
+ "0 False False False \n",
+ "1 False False False \n",
+ "2 False False False \n",
+ "3 False False False \n",
+ "\n",
+ " structure.bp_ii_out structure.bp_ii_b structure.bp_iii structure.bp_iv \\\n",
+ "0 True False False False \n",
+ "1 True False False False \n",
+ "2 False False False False \n",
+ "3 False False False False \n",
+ "\n",
+ " structure.bp_v structure.grich_distance structure.grich_angle \\\n",
+ "0 False 15.332900 51.093899 \n",
+ "1 False 16.155399 54.140202 \n",
+ "2 False 0.000000 0.000000 \n",
+ "3 False 0.000000 0.000000 \n",
+ "\n",
+ " structure.grich_rotation structure.filepath structure.curation_flag \n",
+ "0 49.228901 False \n",
+ "1 48.741402 False \n",
+ "2 0.000000 False \n",
+ "3 0.000000