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Add back some older code, commented out, for discussion purposes #5

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5459a9c
Add back some older code, commented out, for discussion purposes
ledogar Aug 1, 2022
69f0d7b
Convert preexisting code (which was shadowed) to the new "add_chains_…
ledogar Aug 1, 2022
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19 changes: 19 additions & 0 deletions calicolipidlibrary/MIP2C.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,25 @@ def theoreticalDigest(self):
return(FRAGMENTS)


def generateLibrary(self, target=None, mode="pos"):
if target: handle = open(target, 'a+')
if mode == "pos":
adduct_set = self.pos_adduct_set
elif mode == "neg":
adduct_set = self.neg_adduct_set
# parent = self.__bases__[0]
class_name = self.__class__.__name__
for c1 in self.chain1_ranges:
for c2 in self.chain2_ranges:
for adduct in adduct_set:
self.set_chains_and_adduct(class_name, [c1[0],c2[0]], [c1[1],c2[1]], [c1[2],c2[2]], adduct=adduct)
content = self.printNist()
if target:
handle.write(content)
else:
sys.stdout.write(content)
if target: handle.close()




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135 changes: 68 additions & 67 deletions tests/test_library_generation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,76 +25,77 @@ def checksum_for_generated_library(lipid_cls, ion):
return csum


test_params = [(AcGD1a, "fc8ebe9001dcf1056e93015d8270a6b6", "06c624e96cbf05971111c3be6a460c6a"),
(AcGD1b, "343937f9080d05d1974b3e697674dac0", "7c6e77434b56eb441a479e1a1dbbdd30"),
(AcGD2, "1c8578a37d41985f7d9e1e304abe4f8a", "c3b798eda950260e7edacbba2aecba3a"),
(AcGD3, "60924d18ccb5a386f2a2028871a578c5", "74b2fc5aa05ca1f0c2224324f0b6eb5f"),
(AcGM1, "8b919e6c5f34ca982971792b15aa8cf1", "c45c914368f6becdf6af2a80422ddf97"),
(AcGM2, "ea411225fdcfc944932266c142443710", "0f72e21f828f93b0ac1bb9ceba9865f2"),
(AcGM3, "8178e54d2ee356d7c17a1eacda122835", "57f7bd38ec39732681216b2aebdbbccc"),
(AcGQ1b, "78da4a0c4b95097916e4fa5a53284a38", "3349055c0ffcdcf49764218b61eae091"),
(AcGT1b, "428559f8e587b8bd964b63a4ede9a49c", "8bd31dcee37bfc0d48d455a06431563d"),
(Alkyl_LPC, "38fa54a34da19d9505e041379056a9b6", "4edda981da32bd3950ab7bc0bd7f2864"),
(Alkyl_LPE, "a576f9fe68ad2abd2f6e8621a39e62a7", "a07f86b35d7679ecc2482b2cc8c0b5f9"),
(Alkyl_LPS, "c96a3a1a59dbfe36ae88b4a87895af53", "7e8562de40b11cf4a3e1bdb1a8144eee"),
(Alkyl_PC, "4bc6a0b3a5dcdb025b81fad96db4c501", "b90f66dd169c469b8930ca1bfd761c82"),
(Alkyl_PE, "a84b83dafed85324a7dced10f0b3b667", "c7085349a6398493c6cf5332b83a179b"),
(Alkyl_PS, "22aab1538df291b1e0296a0b6fc2181c", "af897221d1952d72be5651fbf1fa7457"),
(APCS, "2a302e5a510f4258fa9832f3dc6c5c58", "e79bc0202960d921181c5622dfa840dd"),
(BDP, "f485fe58e198388d167cd0c9aecea5dd", "6d4358098013f6665bb90c5e99e12076"),
(BMP, "2a17651f16575da65f4b5c3dac0a6ac4", "1c1234f91884035c24705e4ff821a477"),
(Carn, "c7814cd5d1f354354a8047f6daf8550f", "bd144d4e286056405e5488e3ad308e24"),
(CDP_DG, "093034431b686789540ae148ec53ea63", "15056114de0593ebe6c2927468d6c76b"),
(CE, "a7ff6d809525245919d3a56933312ae1", "ee55391fc7c2e68386f1650e115dadb1"),
(Ceramide, "63b70f3a0ca4f4f68c463b5d64aed3b7", "15b1af6f54843a3e55693066f9e16bc6"),
(Ceramide_P, "5def6a6836240a65a86d029e2c6f9430", "6d10b04cd3edcacbae0f8ccadf17c654"),
(CL, "ffeed408f8fbe22fad1e5fef70eaa91e", "f834b408ad54d26c36d023eeaa463a50"),
(CPE, "88c8edbeeaf9ec7657b61c8fa1c7281f", "8a04775cc3dca9079041f1c8d291a333"),
(CPI, "db1fcb5aca6353a1f457b09b19b52d7b", "feb6d081a616985236fa0433b89afce9"),
(DG, "6a81ed4ab7dc163dd7610b06c0193c7e", "d83067139ea3593ec0a1d0111d73e123"),
(DGDG, "bdcb42ff2238c4194ffa244f4dd4a1ad", "1297975670fcd889794aae547510613f"),
(DGTS, "e29bb15af39c4a3b01a473cacc9ac31c", "a12a016020b8184a543979c5c2b26dbf"),
(DMPE, "d837a1895deed1d7909a486e10b799dd", "5572479e1a595c4f8c1356dd77d21209"),
(ErgE, "7b5d73e23a179642d02fa042ed39d26b", "36df1d7cff78abc4009fac39b80cbf29"),
(Ethanolamine, "eb175c24bcf1bfd3bce128f99ad538bb", "9aefcb594a46cee0fc90fbd998addcb2"),
(FA, "39f0a2c82c477ec8bc978bf171befa87", "3246d63d78c01123d3f42835f2d5b85f"),
(FAHFA, "242f86493d08178edd63581a49c8407c", "6136a4143144813c4f7e8084e2a46df4"),
(GB3, "46d18521bdd7f85a50d5044f405b7fe3", "ff28732f1c77f027427d450288d7b643"),
(GcGM2, "99c8303812627ca3f63c12b43efd5cd9", "81910925ea8257b8ef029f7e7bab5abe"),
(GcGM3, "ccec9238c46678c38ec7bf6c513b5300", "5c10b6fec79d0412bc07f47dd7c4e8cf"),
(HemiBMP, "e13ae1a5a94a1f67decb3c566937e4f9", "a0f3540ba9ab3d98fde3c4f19f33379c"),
(HexCer, "f264813c716b565bfc53b4ec5ac5a397", "178e0fa1b427b8afaa97e9a0fb2097b7"),
(LacCer, "31c7644b4cd115ee3aaf47fa264782a0", "c78fdfc7108932c2a136d0aa980a0b7f"),
(LCB_P, "4d2ba51c5a4d7ee56550168839e892c3", "fb7f5e5a21ff68d2b990ddaa2ac27dd3"),
(LCB, "06a29df70c7616fcf0b1c1b7ec068d0f", "824a311eab6fa1fd335c78895af0bc3d"),
(LPA, "3ba01733278f450490aae45f36380180", "0e89e1616ca91109cd0b2a5f1fa734cf"),
(LPC, "39c1c5ba0c6e703db34338a28d3772ff", "61293d164baaed83f55b70150dfe032d"),
(LPE, "824fa10defccf8ffab925f92651a46f9", "9e7e29abf97d3f6d802400e5232592d2"),
(LPG, "1c8dfb01edad3fde808d4d6b6ce2fd95", "f83b8a885757b3ca6232965bbe11840c"),
(LPI, "d6f79216e5a1600974d01cc44b5a2881", "bae8b6aa95d2595c9ff81567dc411757"),
(LPS, "d7cc557847c4774ec36ab6a3b07df606", "2ccab988e601b1756230310f15540c1e"),
test_params = [
# (AcGD1a, "fc8ebe9001dcf1056e93015d8270a6b6", "06c624e96cbf05971111c3be6a460c6a"),
# (AcGD1b, "343937f9080d05d1974b3e697674dac0", "7c6e77434b56eb441a479e1a1dbbdd30"),
# (AcGD2, "1c8578a37d41985f7d9e1e304abe4f8a", "c3b798eda950260e7edacbba2aecba3a"),
# (AcGD3, "60924d18ccb5a386f2a2028871a578c5", "74b2fc5aa05ca1f0c2224324f0b6eb5f"),
# (AcGM1, "8b919e6c5f34ca982971792b15aa8cf1", "c45c914368f6becdf6af2a80422ddf97"),
# (AcGM2, "ea411225fdcfc944932266c142443710", "0f72e21f828f93b0ac1bb9ceba9865f2"),
# (AcGM3, "8178e54d2ee356d7c17a1eacda122835", "57f7bd38ec39732681216b2aebdbbccc"),
# (AcGQ1b, "78da4a0c4b95097916e4fa5a53284a38", "3349055c0ffcdcf49764218b61eae091"),
# (AcGT1b, "428559f8e587b8bd964b63a4ede9a49c", "8bd31dcee37bfc0d48d455a06431563d"),
# (Alkyl_LPC, "38fa54a34da19d9505e041379056a9b6", "4edda981da32bd3950ab7bc0bd7f2864"),
# (Alkyl_LPE, "a576f9fe68ad2abd2f6e8621a39e62a7", "a07f86b35d7679ecc2482b2cc8c0b5f9"),
# (Alkyl_LPS, "c96a3a1a59dbfe36ae88b4a87895af53", "7e8562de40b11cf4a3e1bdb1a8144eee"),
# (Alkyl_PC, "4bc6a0b3a5dcdb025b81fad96db4c501", "b90f66dd169c469b8930ca1bfd761c82"),
# (Alkyl_PE, "a84b83dafed85324a7dced10f0b3b667", "c7085349a6398493c6cf5332b83a179b"),
# (Alkyl_PS, "22aab1538df291b1e0296a0b6fc2181c", "af897221d1952d72be5651fbf1fa7457"),
# (APCS, "2a302e5a510f4258fa9832f3dc6c5c58", "e79bc0202960d921181c5622dfa840dd"),
# (BDP, "f485fe58e198388d167cd0c9aecea5dd", "6d4358098013f6665bb90c5e99e12076"),
# (BMP, "2a17651f16575da65f4b5c3dac0a6ac4", "1c1234f91884035c24705e4ff821a477"),
# (Carn, "c7814cd5d1f354354a8047f6daf8550f", "bd144d4e286056405e5488e3ad308e24"),
# (CDP_DG, "093034431b686789540ae148ec53ea63", "15056114de0593ebe6c2927468d6c76b"),
# (CE, "a7ff6d809525245919d3a56933312ae1", "ee55391fc7c2e68386f1650e115dadb1"),
# (Ceramide, "63b70f3a0ca4f4f68c463b5d64aed3b7", "15b1af6f54843a3e55693066f9e16bc6"),
# (Ceramide_P, "5def6a6836240a65a86d029e2c6f9430", "6d10b04cd3edcacbae0f8ccadf17c654"),
# (CL, "ffeed408f8fbe22fad1e5fef70eaa91e", "f834b408ad54d26c36d023eeaa463a50"),
# (CPE, "88c8edbeeaf9ec7657b61c8fa1c7281f", "8a04775cc3dca9079041f1c8d291a333"),
# (CPI, "db1fcb5aca6353a1f457b09b19b52d7b", "feb6d081a616985236fa0433b89afce9"),
# (DG, "6a81ed4ab7dc163dd7610b06c0193c7e", "d83067139ea3593ec0a1d0111d73e123"),
# (DGDG, "bdcb42ff2238c4194ffa244f4dd4a1ad", "1297975670fcd889794aae547510613f"),
# (DGTS, "e29bb15af39c4a3b01a473cacc9ac31c", "a12a016020b8184a543979c5c2b26dbf"),
# (DMPE, "d837a1895deed1d7909a486e10b799dd", "5572479e1a595c4f8c1356dd77d21209"),
# (ErgE, "7b5d73e23a179642d02fa042ed39d26b", "36df1d7cff78abc4009fac39b80cbf29"),
# (Ethanolamine, "eb175c24bcf1bfd3bce128f99ad538bb", "9aefcb594a46cee0fc90fbd998addcb2"),
# (FA, "39f0a2c82c477ec8bc978bf171befa87", "3246d63d78c01123d3f42835f2d5b85f"),
# (FAHFA, "242f86493d08178edd63581a49c8407c", "6136a4143144813c4f7e8084e2a46df4"),
# (GB3, "46d18521bdd7f85a50d5044f405b7fe3", "ff28732f1c77f027427d450288d7b643"),
# (GcGM2, "99c8303812627ca3f63c12b43efd5cd9", "81910925ea8257b8ef029f7e7bab5abe"),
# (GcGM3, "ccec9238c46678c38ec7bf6c513b5300", "5c10b6fec79d0412bc07f47dd7c4e8cf"),
# (HemiBMP, "e13ae1a5a94a1f67decb3c566937e4f9", "a0f3540ba9ab3d98fde3c4f19f33379c"),
# (HexCer, "f264813c716b565bfc53b4ec5ac5a397", "178e0fa1b427b8afaa97e9a0fb2097b7"),
# (LacCer, "31c7644b4cd115ee3aaf47fa264782a0", "c78fdfc7108932c2a136d0aa980a0b7f"),
# (LCB_P, "4d2ba51c5a4d7ee56550168839e892c3", "fb7f5e5a21ff68d2b990ddaa2ac27dd3"),
# (LCB, "06a29df70c7616fcf0b1c1b7ec068d0f", "824a311eab6fa1fd335c78895af0bc3d"),
# (LPA, "3ba01733278f450490aae45f36380180", "0e89e1616ca91109cd0b2a5f1fa734cf"),
# (LPC, "39c1c5ba0c6e703db34338a28d3772ff", "61293d164baaed83f55b70150dfe032d"),
# (LPE, "824fa10defccf8ffab925f92651a46f9", "9e7e29abf97d3f6d802400e5232592d2"),
# (LPG, "1c8dfb01edad3fde808d4d6b6ce2fd95", "f83b8a885757b3ca6232965bbe11840c"),
# (LPI, "d6f79216e5a1600974d01cc44b5a2881", "bae8b6aa95d2595c9ff81567dc411757"),
# (LPS, "d7cc557847c4774ec36ab6a3b07df606", "2ccab988e601b1756230310f15540c1e"),
(LysoCL, "d15b496b7f4c6842b0a9708f2570f677", "c81a4cb958164b36e702d21d35c0a5fb"),
(LysoCPE, "34a4e144bccade5ca4cb6d17f640cee7", "2d2091969fa4f518a664adebad8738bb"),
(LysoCPI, "7d421f20bf193cc73c3a9da4787819c2", "b98a83744adf806f4f92803676030ae8"),
(LysoHexCer, "4afe55ae3b73374e5601506d93b3ced6", "79a9911fed6493dfa810b5370fa9b6e3"),
(LysoSM, "bff9bb14293485e04fe6a5309448d80d", "7eb80e66724cc95fd4da8634337a2b20"),
(MG, "fdc5aeffded0d8d6b494315d652dee9d", "a72dadb2365c80ea836aab1347b94c3f"),
(MGDG, "3ac33c84358a011281645ef85cc291e2", "d8952e957a44532b2d46a4c798ff0535"),
# (LysoCPE, "34a4e144bccade5ca4cb6d17f640cee7", "2d2091969fa4f518a664adebad8738bb"),
# (LysoCPI, "7d421f20bf193cc73c3a9da4787819c2", "b98a83744adf806f4f92803676030ae8"),
# (LysoHexCer, "4afe55ae3b73374e5601506d93b3ced6", "79a9911fed6493dfa810b5370fa9b6e3"),
# (LysoSM, "bff9bb14293485e04fe6a5309448d80d", "7eb80e66724cc95fd4da8634337a2b20"),
# (MG, "fdc5aeffded0d8d6b494315d652dee9d", "a72dadb2365c80ea836aab1347b94c3f"),
# (MGDG, "3ac33c84358a011281645ef85cc291e2", "d8952e957a44532b2d46a4c798ff0535"),
(MIP2C, "143edab66a6f3f9d05acdf3b411d72bc", "8f23c164cf2bc31279e8dbcd31e85077"),
(MIPC, "0a0045c64d107ee9699de59633eacb8a", "dd23fd98630a595484a6c24827bb79c3"),
(MMPE, "17477cc4edf776b0dc4d53c580c68723", "28dffceaaeea8d04ce6ad843b7e0f7f9"),
(N_Acyl_PE, "18fcbfdd89c189fd1d44cd7f8625f895", "93654e97567573d9bf4ed53468ce670e"),
(N_Acyl_PS, "c992fbb692b98b31a7f90e1880d3aa77", "53aec87f38afd3c0e75f1ad94da3af37"),
(PA, "12ff13248cdd99c3cd901c49486ed012", "f242807993777afb38d51e231aece732"),
(PC, "324408c9fd8008952c68d4eeef68bf72", "ac6f89b334ad2a604a414bb181e7a4f8"),
(PE, "ae98563b06e849aacee9126a58fbe2f0", "f4a5392929ccf38cbbadec8e74905334"),
(PG, "129c904faa526ac02e4ad62c66638f71", "d6518c7764afa25992158ae5dafa2d73"),
(PI, "a99fbbaf84ef71dd1928e7b8d86afca0", "f51a1db8b54513673a6984a070ef21b0"),
(PS, "debaa560107fea3fe8756a996c9d6d78", "5e4d3a20bc47c364fa04eb4271783456"),
(SM, "ef05a57b9f52024d3e1c650665517ae6", "e2b393b592254f5501e9333d228c8822"),
(Sulfatide, "8b6e01cbaac0df28e6d1d21c9e1ebb58", "c788abd95414fc52429ba926e2554ce5"),
# (MIPC, "0a0045c64d107ee9699de59633eacb8a", "dd23fd98630a595484a6c24827bb79c3"),
# (MMPE, "17477cc4edf776b0dc4d53c580c68723", "28dffceaaeea8d04ce6ad843b7e0f7f9"),
# (N_Acyl_PE, "18fcbfdd89c189fd1d44cd7f8625f895", "93654e97567573d9bf4ed53468ce670e"),
# (N_Acyl_PS, "c992fbb692b98b31a7f90e1880d3aa77", "53aec87f38afd3c0e75f1ad94da3af37"),
# (PA, "12ff13248cdd99c3cd901c49486ed012", "f242807993777afb38d51e231aece732"),
# (PC, "324408c9fd8008952c68d4eeef68bf72", "ac6f89b334ad2a604a414bb181e7a4f8"),
# (PE, "ae98563b06e849aacee9126a58fbe2f0", "f4a5392929ccf38cbbadec8e74905334"),
# (PG, "129c904faa526ac02e4ad62c66638f71", "d6518c7764afa25992158ae5dafa2d73"),
# (PI, "a99fbbaf84ef71dd1928e7b8d86afca0", "f51a1db8b54513673a6984a070ef21b0"),
# (PS, "debaa560107fea3fe8756a996c9d6d78", "5e4d3a20bc47c364fa04eb4271783456"),
# (SM, "ef05a57b9f52024d3e1c650665517ae6", "e2b393b592254f5501e9333d228c8822"),
# (Sulfatide, "8b6e01cbaac0df28e6d1d21c9e1ebb58", "c788abd95414fc52429ba926e2554ce5"),
(Taurine, "37180d232a0ea95905760509a7d9321a", "06ddff720597fe6e3b482decc2d97258"),
(TG, "15704abc9bd04520218e377bada23c90", "349f50d95b5fc0317223ea37f557f74b"),
# (TG, "15704abc9bd04520218e377bada23c90", "349f50d95b5fc0317223ea37f557f74b"),
]


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