{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# AbNumber Usage Examples"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from abnumber import Chain\n",
"import pandas as pd\n",
"\n",
"pd.options.display.max_columns = 200"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Creating a chain"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^^^^^^^^ "
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"seq = 'EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSSAKTTAPSVYPLA'\n",
"chain = Chain(seq, scheme='imgt')\n",
"chain"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 12 \n",
"1234567891234567890123456789056789012345678901234567892345678901245678901234567890123456789012345678901112223456789012345678\n",
" ABBA \n",
"EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^^^^^^^^ \n"
]
}
],
"source": [
"chain.print(numbering=True)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS'"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.seq"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'AKTTAPSVYPLA'"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.tail"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'ARYYSEDDERGHYCLDY'"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.cdr3_seq"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" H1 E CDR1 H27 G CDR2 H56 I H84 S CDR3 H109 S\n",
" H2 V CDR1 H28 Y CDR2 H57 N H85 S CDR3 H110 E\n",
" H3 Q CDR1 H29 T CDR2 H58 P H86 T CDR3 H111 D\n",
" H4 L CDR1 H30 F CDR2 H59 S H87 A CDR3 H111A D\n",
" H5 Q CDR1 H35 T CDR2 H62 R H88 Y CDR3 H111B E\n",
" H6 Q CDR1 H36 R CDR2 H63 G H89 M CDR3 H112B R\n",
" H7 S CDR1 H37 Y CDR2 H64 Y H90 Q CDR3 H112A G\n",
" H8 G CDR1 H38 T CDR2 H65 T H91 L CDR3 H112 H\n",
" H9 A H39 M H66 N H92 S CDR3 H113 Y\n",
" H11 E H40 H H67 Y H93 S CDR3 H114 C\n",
" H12 L H41 W H68 N H94 L CDR3 H115 L\n",
" H13 A H42 V H69 Q H95 T CDR3 H116 D\n",
" H14 R H43 K H70 K H96 S CDR3 H117 Y\n",
" H15 P H44 Q H71 F H97 E H118 W\n",
" H16 G H45 R H72 K H98 D H119 G\n",
" H17 A H46 P H74 D H99 S H120 Q\n",
" H18 S H47 G H75 K H100 A H121 G\n",
" H19 V H48 Q H76 A H101 V H122 T\n",
" H20 K H49 G H77 T H102 Y H123 T\n",
" H21 M H50 L H78 L H103 Y H124 L\n",
" H22 S H51 E H79 T H104 C H125 T\n",
" H23 C H52 W H80 T CDR3 H105 A H126 V\n",
" H24 K H53 I H81 D CDR3 H106 R H127 S\n",
" H25 A H54 G H82 K CDR3 H107 Y H128 S\n",
" H26 S H55 Y H83 S CDR3 H108 Y\n"
]
}
],
"source": [
"chain.print_tall()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Separate CDR definitions"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^ ^^^^^^ ^^^^^^^^^^^^^^^ "
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chain(seq, scheme='imgt', cdr_definition='chothia')"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^^^^^^^^ "
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chain(seq, scheme='imgt', cdr_definition='north')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Renumbering"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" H1 E H22 C H43 Q H63 F H82B S CDR3 H100B R\n",
" H2 V H23 K H44 G H64 K H82C L CDR3 H100C G\n",
" H3 Q H24 A H45 L H65 D H83 T CDR3 H100D H\n",
" H4 L H25 S H46 E H66 K H84 S CDR3 H100E Y\n",
" H5 Q CDR1 H26 G H47 W H67 A H85 E CDR3 H100F C\n",
" H6 Q CDR1 H27 Y H48 I H68 T H86 D CDR3 H100G L\n",
" H7 S CDR1 H28 T H49 G H69 L H87 S CDR3 H101 D\n",
" H8 G CDR1 H29 F H50 Y H70 T H88 A CDR3 H102 Y\n",
" H9 A CDR1 H30 T CDR2 H51 I H71 T H89 V H103 W\n",
" H10 E CDR1 H31 R CDR2 H52 N H72 D H90 Y H104 G\n",
" H11 L CDR1 H32 Y CDR2 H52A P H73 K H91 Y H105 Q\n",
" H12 A CDR1 H33 T CDR2 H53 S H74 S H92 C H106 G\n",
" H13 R H34 M CDR2 H54 R H75 S CDR3 H93 A H107 T\n",
" H14 P H35 H CDR2 H55 G H76 S CDR3 H94 R H108 T\n",
" H15 G H36 W CDR2 H56 Y H77 T CDR3 H95 Y H109 L\n",
" H16 A H37 V CDR2 H57 T H78 A CDR3 H96 Y H110 T\n",
" H17 S H38 K H58 N H79 Y CDR3 H97 S H111 V\n",
" H18 V H39 Q H59 Y H80 M CDR3 H98 E H112 S\n",
" H19 K H40 R H60 N H81 Q CDR3 H99 D H113 S\n",
" H20 M H41 P H61 Q H82 L CDR3 H100 D\n",
" H21 S H42 G H62 K H82A S CDR3 H100A E\n"
]
}
],
"source": [
"# Use Chothia numbering and CDR definitions\n",
"chain.renumber('chothia').print_tall(6)"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" H1 E H23 C H48 Q H71 F H93 S CDR3 H112B R\n",
" H2 V H24 K H49 G H72 K H94 L CDR3 H112A G\n",
" H3 Q H25 A H50 L H74 D H95 T CDR3 H112 H\n",
" H4 L H26 S H51 E H75 K H96 S CDR3 H113 Y\n",
" H5 Q CDR1 H27 G H52 W H76 A H97 E CDR3 H114 C\n",
" H6 Q CDR1 H28 Y H53 I H77 T H98 D CDR3 H115 L\n",
" H7 S CDR1 H29 T H54 G H78 L H99 S CDR3 H116 D\n",
" H8 G CDR1 H30 F H55 Y H79 T H100 A CDR3 H117 Y\n",
" H9 A CDR1 H35 T H56 I H80 T H101 V H118 W\n",
" H11 E CDR1 H36 R CDR2 H57 N H81 D H102 Y H119 G\n",
" H12 L CDR1 H37 Y CDR2 H58 P H82 K H103 Y H120 Q\n",
" H13 A H38 T CDR2 H59 S H83 S H104 C H121 G\n",
" H14 R H39 M CDR2 H62 R H84 S H105 A H122 T\n",
" H15 P H40 H CDR2 H63 G H85 S H106 R H123 T\n",
" H16 G H41 W CDR2 H64 Y H86 T CDR3 H107 Y H124 L\n",
" H17 A H42 V H65 T H87 A CDR3 H108 Y H125 T\n",
" H18 S H43 K H66 N H88 Y CDR3 H109 S H126 V\n",
" H19 V H44 Q H67 Y H89 M CDR3 H110 E H127 S\n",
" H20 K H45 R H68 N H90 Q CDR3 H111 D H128 S\n",
" H21 M H46 P H69 Q H91 L CDR3 H111A D\n",
" H22 S H47 G H70 K H92 S CDR3 H111B E\n"
]
}
],
"source": [
"# Keep IMGT numbering, use Chothia CDR definitions\n",
"chain.renumber(cdr_definition='chothia').print_tall(6)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Chain properties"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'imgt'"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.scheme"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'H'"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.chain_type"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.is_heavy_chain()"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"124"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"len(chain)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Chain indexing and slicing"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'H'"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain['112']"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'Y'"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.raw[112]"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"EVQLQQSGAELARPGASVKMSCKASGYTF\n",
" ^^^^"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain[:'30']"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"QGTTLTVSS\n",
" "
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain['120':]"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"GQGTTLTVSS\n",
" "
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.raw[114:]"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"GQGTTLTVSS\n",
" "
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.raw[-10:]"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"GQGTTLTVSS\n",
" "
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"chain.raw[-10:]"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CDR3 H111A D CDR3 H111B E CDR3 H112B R CDR3 H112A G\n"
]
}
],
"source": [
"chain['111A':'112A'].print_tall()"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"H111A D\n",
"H111B E\n",
"H112B R\n",
"H112A G\n"
]
}
],
"source": [
"for pos, aa in chain['111A':'112A']:\n",
" print(pos, aa)"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"H1 E\n",
"H2 V\n",
"H3 Q\n",
"H4 L\n",
"H5 Q\n",
"H6 Q\n",
"H7 S\n",
"H8 G\n",
"H9 A\n",
"H11 E\n"
]
}
],
"source": [
"for pos, aa in chain.raw[:10]:\n",
" print(pos, aa)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Alignment"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"QVQLVQSGAELDRPGATVKMSCKASGYTTTRYTMHWVKQRPGQGLDWIGYINPSDRSYTNYNQKFKDKATLTTDKSSSTAYMQKTSLTSEDSAVYYCARYYDDERYDYLDRWGQGTTLTVSS\n",
" ^^^^^^^^ ^^^^^^^^^ ^^^^^^^^^^^^^^ "
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"seq2 = 'QVQLVQSGAELDRPGATVKMSCKASGYTTTRYTMHWVKQRPGQGLDWIGYINPSDRSYTNYNQKFKDKATLTTDKSSSTAYMQKTSLTSEDSAVYYCARYYDDERYDYLDRWGQGTTLTVSSAKTTAP'\n",
"chain2 = Chain(seq2, scheme='imgt')\n",
"chain2"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPS-RGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
"+|||.||||||.||||+|||||||||||.||||||||||||||||+||||||||.|.||||||||||||||||||||||||||.+||||||||||||||||.++....+..||.|||||||||||\n",
"QVQLVQSGAELDRPGATVKMSCKASGYTTTRYTMHWVKQRPGQGLDWIGYINPSDRSYTNYNQKFKDKATLTTDKSSSTAYMQKTSLTSEDSAVYYCARYYDDE---RYDYLDRWGQGTTLTVSS\n",
" ^^^^^^^^ ^^^^^^^^^ ^^^^^^^^^^^^^^^^^ "
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"alignment = chain.align(chain2)\n",
"alignment"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Alignment indexing and slicing"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"G R\n"
]
}
],
"source": [
"aa, bb = alignment['112A']\n",
"print(aa, bb)"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"('L', 'L')"
]
},
"execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"aa, bb = alignment.raw[10]\n",
"aa, bb"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"H108 Y Y\n",
"H109 S D\n",
"H110 E D\n",
"H111 D E\n",
"H111A D -\n",
"H111B E -\n",
"H112B R -\n",
"H112A G R\n"
]
}
],
"source": [
"for pos, (aa, bb) in alignment['108':'112A']:\n",
" print(pos, aa, bb)"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"H1 E Q\n",
"H2 V V\n",
"H3 Q Q\n",
"H4 L L\n",
"H5 Q V\n",
"H6 Q Q\n",
"H7 S S\n",
"H8 G G\n",
"H9 A A\n",
"H11 E E\n"
]
}
],
"source": [
"for pos, (aa, bb) in alignment.raw[:10]:\n",
" print(pos, aa, bb)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## CDR grafting"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPS-RGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
"+|||.||||||.||||+|||||||||||.||||||||||||||||+||||||||.|.||||||||||||||||||||||||||.+||||||||||||||||.++....+..||.|||||||||||\n",
"QVQLVQSGAELDRPGATVKMSCKASGYTTTRYTMHWVKQRPGQGLDWIGYINPSDRSYTNYNQKFKDKATLTTDKSSSTAYMQKTSLTSEDSAVYYCARYYDDE---RYDYLDRWGQGTTLTVSS\n",
" ^^^^^^^^ ^^^^^^^^^ ^^^^^^^^^^^^^^^^^ "
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"alignment"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"QVQLVQSGAELDRPGATVKMSCKASGYTFTRYTMHWVKQRPGQGLDWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQKTSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^^^^^^^^ \n"
]
}
],
"source": [
"chain.graft_cdrs_onto(chain2).print()"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"EVQLQQSGAELARPGASVKMSCKASGYTTTRYTMHWVKQRPGQGLEWIGYINPSDRSYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDERYDYLDRWGQGTTLTVSS\n",
" ^^^^^^^^ ^^^^^^^^^ ^^^^^^^^^^^^^^ \n"
]
}
],
"source": [
"chain2.graft_cdrs_onto(chain).print()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Different numbering schemes"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {},
"outputs": [],
"source": [
"from IPython.display import display, HTML"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {},
"outputs": [],
"source": [
"EXAMPLES = [\n",
" 'EVQLQQSGAELARPGASVKMSCKASGYTFTSRRYTMHWVKQRPGQGLEWIGYINPSDERGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSSAKTTAPSVYPLA',\n",
" 'EIVLTQSPATLSLSPGERATLSCRASKGVSTDLSGYSYLHWYQQKPGQAPRLLIYLGYASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDGTLPLTFGGGTKVEIK',\n",
" 'QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVHWYQQLPGTAPKLLIYSDNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGVFGGGTKLTVL'\n",
"]"
]
},
{
"cell_type": "code",
"execution_count": 37,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"H imgt
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 12 \n",
"12345678912345678901234567890145678901234567890123456789012345678901245678901234567890123456789012345678901112223456789012345678\n",
" ABBA \n",
"EVQLQQSGAELARPGASVKMSCKASGYTFTSRRYTMHWVKQRPGQGLEWIGYINPSDERGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"H chothia
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 \n",
"12345678901234567890123456789011123456789012345678901222234567890123456789012345678901222234567890123456789000000001234567890123\n",
" AB ABC ABC ABCDEFG \n",
"EVQLQQSGAELARPGASVKMSCKASGYTFTSRRYTMHWVKQRPGQGLEWIGYINPSDERGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"H kabat
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 \n",
"12345678901234567890123456789012345556789012345678901222234567890123456789012345678901222234567890123456789000000001234567890123\n",
" AB ABC ABC ABCDEFG \n",
"EVQLQQSGAELARPGASVKMSCKASGYTFTSRRYTMHWVKQRPGQGLEWIGYINPSDERGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^ ^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"H chothia-north
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 \n",
"12345678901234567890123456789011123456789012345678901222234567890123456789012345678901222234567890123456789000000001234567890123\n",
" AB ABC ABC ABCDEFG \n",
"EVQLQQSGAELARPGASVKMSCKASGYTFTSRRYTMHWVKQRPGQGLEWIGYINPSDERGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^^^^^^^^^ ^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"H aho-north
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 13 14 \n",
"12345679012345678901234567901234890123456789012345678901245678901234567890123456789012345678901234567890123451234567890123456789\n",
"EVQLQQSGAELARPGASVKMSCKASGYTFTSRRYTMHWVKQRPGQGLEWIGYINPSDERGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS\n",
" ^^^^^^^^^^^^^^^ ^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"K imgt
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 12 \n",
"123456789012345678901234567890123456789012345678901234567845678901245678903456789012345678901234567890345678901234567\n",
"EIVLTQSPATLSLSPGERATLSCRASKGVSTDLSGYSYLHWYQQKPGQAPRLLIYLGYASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDGTLPLTFGGGTKVEIK\n",
" ^^^^^^^^^^^^ ^^^^^ ^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"K chothia
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 \n",
"123456789012345678901234567890000000123456789012345678901222345678901234567890123456789012345678901234555678901234567\n",
" ABCDEF AB AB \n",
"EIVLTQSPATLSLSPGERATLSCRASKGVSTDLSGYSYLHWYQQKPGQAPRLLIYLGYASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDGTLPLTFGGGTKVEIK\n",
" ^^^^^^^^^^^^^^^^^ ^^^^^^^^^ ^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"K kabat
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 \n",
"123456789012345678901234567777777890123456789012345678901222345678901234567890123456789012345678901234555678901234567\n",
" ABCDEF AB AB \n",
"EIVLTQSPATLSLSPGERATLSCRASKGVSTDLSGYSYLHWYQQKPGQAPRLLIYLGYASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDGTLPLTFGGGTKVEIK\n",
" ^^^^^^^^^^^^^^^^^ ^^^^^^^^^ ^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"K chothia-north
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 \n",
"123456789012345678901234567890000000123456789012345678901222345678901234567890123456789012345678901234555678901234567\n",
" ABCDEF AB AB \n",
"EIVLTQSPATLSLSPGERATLSCRASKGVSTDLSGYSYLHWYQQKPGQAPRLLIYLGYASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDGTLPLTFGGGTKVEIK\n",
" ^^^^^^^^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"K aho-north
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 13 14 \n",
"123456789012345678901234569012345678901234567890123456789678901234567890123478901234567890123456789012456789012345678\n",
"EIVLTQSPATLSLSPGERATLSCRASKGVSTDLSGYSYLHWYQQKPGQAPRLLIYLGYASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDGTLPLTFGGGTKVEIK\n",
" ^^^^^^^^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"L imgt
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 12 \n",
"1234567891234567890123456789056789012345678901234567567890124567890345678901234567890123456789345678901234567\n",
"QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVHWYQQLPGTAPKLLIYSDNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGVFGGGTKLTVL\n",
" ^^^^^^^^ ^^^ ^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"L chothia
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 \n",
"1234567891234567890123456789000123456789012345678901234567890123456789012345678901234567890123455678901234567\n",
" AB A \n",
"QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVHWYQQLPGTAPKLLIYSDNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGVFGGGTKLTVL\n",
" ^^^^^^^^^^^^^ ^^^^^^^ ^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"L kabat
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 \n",
"1234567891234567890123456777890123456789012345678901234567890123456789012345678901234567890123455678901234567\n",
" AB A \n",
"QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVHWYQQLPGTAPKLLIYSDNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGVFGGGTKLTVL\n",
" ^^^^^^^^^^^^^ ^^^^^^^ ^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"L chothia-north
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 \n",
"1234567891234567890123456789000123456789012345678901234567890123456789012345678901234567890123455678901234567\n",
" AB A \n",
"QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVHWYQQLPGTAPKLLIYSDNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGVFGGGTKLTVL\n",
" ^^^^^^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^ \n"
]
},
{
"data": {
"text/html": [
"L aho-north
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1 2 3 4 5 6 7 8 9 10 11 13 14 \n",
"1234567901234567890123456790123901234567890123456787890123456789012347890123456789012345678901256789012345678\n",
"QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVHWYQQLPGTAPKLLIYSDNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGVFGGGTKLTVL\n",
" ^^^^^^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^ \n"
]
}
],
"source": [
"for chain_seq in EXAMPLES:\n",
" for scheme, cdr_definition in [('imgt', 'imgt'), ('chothia','chothia'), ('kabat','kabat'), ('chothia','north'), ('aho','north')]:\n",
" chain = Chain(chain_seq, scheme=scheme, cdr_definition=cdr_definition)\n",
" scheme_label = scheme + ('-'+cdr_definition if cdr_definition != scheme else '')\n",
" display(HTML(f'{chain.chain_type} {scheme_label}
'))\n",
" print(chain.format(numbering=True))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.11"
}
},
"nbformat": 4,
"nbformat_minor": 4
}