Release version 2024.06

.scripts/fix_smiles.py

@@ -2,6 +2,7 @@
 import sys
 import pubchempy as pcp
 
+
 def query_yes_no(question, default="yes"):
     """Ask a yes/no question via raw_input() and return their answer.
 
@@ -12,9 +13,9 @@ def query_yes_no(question, default="yes"):
 
     The "answer" return value is one of "yes" or "no".
     """
-    valid = {"yes":"yes",   "y":"yes",  "ye":"yes",
-             "no":"no",     "n":"no"}
-    if default == None:
+    valid = {"yes": "yes", "y": "yes", "ye": "yes",
+             "no": "no", "n": "no"}
+    if default is None:
         prompt = " [y/n] "
     elif default == "yes":
         prompt = " [Y/n] "
@@ -25,80 +26,93 @@ def query_yes_no(question, default="yes"):
 
     while 1:
         sys.stdout.write(question + prompt)
-        choice = raw_input().lower()
+        choice = input().lower()
         if default is not None and choice == '':
             return default
         elif choice in valid.keys():
             return valid[choice]
         else:
-            sys.stdout.write("Please respond with 'yes' or 'no' "\
-                             "(or 'y' or 'n').\n")
+            sys.stdout.write("Please respond with 'yes' or 'no' (or 'y' or 'n').\n")
 
 
 def inplace_change(filename, old_string, new_string):
     # Safely read the input filename using 'with'
     with open(filename) as f:
         s = f.read()
         if old_string not in s:
-            print '"{old_string}" not found in {filename}.'.format(**locals())
+            print('"{old_string}" not found in {filename}.'.format(**locals()))
             return
 
     # Safely write the changed content, if found in the file
     with open(filename, 'w') as f:
-        print 'Changing "{old_string}" to "{new_string}" in {filename}'.format(**locals())
+        print('Changing "{old_string}" to "{new_string}" in {filename}'.format(**locals()))
         s = s.replace(old_string, new_string)
         f.write(s)
 
-names=[]
-formula=""
-inchi=""
+
+names = []
+formula = ""
+inchi = ""
 
 for line in open(sys.argv[1]):
- if "CH$NAME" in line:
-   names.append(''.join(line.split(" ")[1:]).strip().lower())
- if "CH$FORMULA" in line:
-   formula=''.join(line.split(" ")[1:]).strip()
- if "CH$IUPAC" in line:
-   inchi=''.join(line.split(" ")[1:]).strip()
- if "CH$SMILES" in line:
-   smiles=''.join(line.split(" ")[1:]).strip()
+    if "CH$NAME" in line:
+        names.append(''.join(line.split(" ")[1:]).strip().lower())
+    if "CH$FORMULA" in line:
+        formula = ''.join(line.split(" ")[1:]).strip()
+    if "CH$IUPAC" in line:
+        inchi = ''.join(line.split(" ")[1:]).strip()
+    if "CH$SMILES" in line:
+        smiles = ''.join(line.split(" ")[1:]).strip()
 
 results = pcp.get_compounds(inchi, namespace=u'inchi')
 
+if smiles == results[0].isomeric_smiles:
+    print('Nothing to do! Exiting.')
+    sys.exit(0)
+
+#clear screen
+print(chr(27) + "[2J")
 if len(results) != 1:
-   print "#results != 1; exiting"
-   sys.exit(1)
+    print("#results != 1; exiting")
+    sys.exit(1)
 
 if results[0].molecular_formula == formula:
-   print 'Formula matches ' + '\033[92m[OK]\033[0m' 
+    print('Formula matches ' + '\033[92m[OK]\033[0m')
+    print(formula)
 else:
-   print results[0].molecular_formula
-   print formula
-   print 'Formulas different ' + '\033[93m[OK]\033[0m'
+    print(f'Formula from pubchem: {results[0].molecular_formula}')
+    print(f'Formula from file: {formula}')
+    print('Formulas different ' + '\033[93m[!!]\033[0m')
 
-synonyms=[x.encode('utf-8').lower() for x in results[0].synonyms]
+print(f'InChI : {inchi}')
 
-common_names=[]
+synonyms = []
+if results[0].synonyms is not None:
+    synonyms = [x.encode('utf-8').lower() for x in results[0].synonyms]
 
+common_names = []
+
+print()
 for name in names:
-   if name in synonyms:
-      print 'Name in synonyms ' + '\033[92m[OK]\033[0m'
-      common_names.append(name)
-   
-print synonyms
-print
-print names
-print '\033[92m'
-print common_names
-print '\033[0m'
-print
-print
+    if name in synonyms:
+        print('Name in synonyms ' + '\033[92m[OK]\033[0m')
+        common_names.append(name)
+
+print(f'Names from pubchem: {synonyms}')
+print(f'Names from file: {names}')
+if len(common_names):
+    print('\033[92m')
+    print(common_names)
+    print('\033[0m')
+print()
+print()
 if (results[0].molecular_formula == formula) and (len(common_names)):
-   inplace_change(sys.argv[1], 'CH$SMILES: '+smiles, 'CH$SMILES: '+results[0].isomeric_smiles)
+    inplace_change(sys.argv[1], 'CH$SMILES: ' + smiles, 'CH$SMILES: ' + results[0].isomeric_smiles)
 else:
-   sub=query_yes_no('Substitute \033[91m' + smiles + '\033[0m by \033[92m ' + results[0].isomeric_smiles + '\033[0m?', default="no")
-   if sub=="yes":
-      inplace_change(sys.argv[1], 'CH$SMILES: '+smiles, 'CH$SMILES: '+results[0].isomeric_smiles)
+    sub = query_yes_no(
+        'Substitute \033[91m' + smiles + '\033[0m by \033[92m ' + results[0].isomeric_smiles + '\033[0m?', default="no")
+    if sub == "yes":
+        inplace_change(sys.argv[1], 'CH$SMILES: ' + smiles, 'CH$SMILES: ' + results[0].isomeric_smiles)
 
-print 
-print
+print()
+print()

Eawag/MSBNK-Eawag-EQ00273051.txt

@@ -0,0 +1,49 @@
+ACCESSION: MSBNK-Eawag-EQ00273051
+RECORD_TITLE: N-MeFOSA; LC-ESI-QFT; MS2; CE: 15%; R=17500; [M-H]-
+DATE: 2024.05.15
+AUTHORS: B. Beck [dtc,com], J. Hollender [dtc]
+LICENSE: CC BY-SA
+COPYRIGHT: Copyright (C) Eawag 2023
+COMMENT: CONFIDENCE standard compound
+COMMENT: UCHEM_ID 2730
+CH$NAME: N-MeFOSA
+CH$NAME: Heptadecafluoro-N-methyloctanesulphonamide
+CH$NAME: 1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,8-heptadecafluoro-N-methyloctane-1-sulfonamide
+CH$COMPOUND_CLASS: N/A; Environmental Standard
+CH$FORMULA: C9H4F17NO2S
+CH$EXACT_MASS: 512.969129108
+CH$SMILES: CNS(=O)(=O)C(C(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F
+CH$IUPAC: InChI=1S/C9H4F17NO2S/c1-27-30(28,29)9(25,26)7(20,21)5(16,17)3(12,13)2(10,11)4(14,15)6(18,19)8(22,23)24/h27H,1H3
+CH$LINK: PUBCHEM CID:3034468
+CH$LINK: INCHIKEY SRMWNTGHXHOWBT-UHFFFAOYSA-N
+CH$LINK: CHEMSPIDER 2298910
+AC$INSTRUMENT: Exploris 240 Orbitrap Thermo Scientific
+AC$INSTRUMENT_TYPE: LC-ESI-QFT
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE HCD
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 15 % (nominal)
+AC$MASS_SPECTROMETRY: RESOLUTION 17500
+AC$MASS_SPECTROMETRY: MASS_RANGE_M/Z 54-543
+AC$CHROMATOGRAPHY: COLUMN_NAME XBridge C18 3.5um, 2.1x50mm, Waters
+AC$CHROMATOGRAPHY: FLOW_GRADIENT 90/10 at 0 min, 50/50 at 4 min, 5/95 at 17 min, 5/95 at 25 min, 90/10 at 25.1 min, 90/10 at 30 min
+AC$CHROMATOGRAPHY: FLOW_RATE 200 uL/min
+AC$CHROMATOGRAPHY: RETENTION_TIME 14.446 min
+MS$FOCUSED_ION: BASE_PEAK 601.9938
+MS$FOCUSED_ION: PRECURSOR_M/Z 511.9619
+MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-
+MS$DATA_PROCESSING: RECALIBRATE loess on assigned fragments and MS1
+MS$DATA_PROCESSING: REANALYZE Peaks with additional N2/O included
+MS$DATA_PROCESSING: WHOLE RMassBank 3.15.1.1
+PK$SPLASH: splash10-03di-0000090000-f58beb82ae83963dfa05
+PK$ANNOTATION: m/z tentative_formula formula_count mass error(ppm)
+  218.9871 C4F9- 3 218.9862 4.35
+  387.9821 C9F14N- 3 387.9813 2.07
+  511.9621 C9H3F17NO2S- 1 511.9619 0.53
+PK$NUM_PEAK: 3
+PK$PEAK: m/z int. rel.int.
+  218.9871 56016.6 3
+  387.9821 25188.9 1
+  511.9621 17799186 999
+//

Eawag/MSBNK-Eawag-EQ00273052.txt

@@ -0,0 +1,61 @@
+ACCESSION: MSBNK-Eawag-EQ00273052
+RECORD_TITLE: N-MeFOSA; LC-ESI-QFT; MS2; CE: 30%; R=17500; [M-H]-
+DATE: 2024.05.15
+AUTHORS: B. Beck [dtc,com], J. Hollender [dtc]
+LICENSE: CC BY-SA
+COPYRIGHT: Copyright (C) Eawag 2023
+COMMENT: CONFIDENCE standard compound
+COMMENT: UCHEM_ID 2730
+CH$NAME: N-MeFOSA
+CH$NAME: Heptadecafluoro-N-methyloctanesulphonamide
+CH$NAME: 1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,8-heptadecafluoro-N-methyloctane-1-sulfonamide
+CH$COMPOUND_CLASS: N/A; Environmental Standard
+CH$FORMULA: C9H4F17NO2S
+CH$EXACT_MASS: 512.969129108
+CH$SMILES: CNS(=O)(=O)C(C(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F
+CH$IUPAC: InChI=1S/C9H4F17NO2S/c1-27-30(28,29)9(25,26)7(20,21)5(16,17)3(12,13)2(10,11)4(14,15)6(18,19)8(22,23)24/h27H,1H3
+CH$LINK: PUBCHEM CID:3034468
+CH$LINK: INCHIKEY SRMWNTGHXHOWBT-UHFFFAOYSA-N
+CH$LINK: CHEMSPIDER 2298910
+AC$INSTRUMENT: Exploris 240 Orbitrap Thermo Scientific
+AC$INSTRUMENT_TYPE: LC-ESI-QFT
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE HCD
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 30 % (nominal)
+AC$MASS_SPECTROMETRY: RESOLUTION 17500
+AC$MASS_SPECTROMETRY: MASS_RANGE_M/Z 54-543
+AC$CHROMATOGRAPHY: COLUMN_NAME XBridge C18 3.5um, 2.1x50mm, Waters
+AC$CHROMATOGRAPHY: FLOW_GRADIENT 90/10 at 0 min, 50/50 at 4 min, 5/95 at 17 min, 5/95 at 25 min, 90/10 at 25.1 min, 90/10 at 30 min
+AC$CHROMATOGRAPHY: FLOW_RATE 200 uL/min
+AC$CHROMATOGRAPHY: RETENTION_TIME 14.446 min
+MS$FOCUSED_ION: BASE_PEAK 601.9938
+MS$FOCUSED_ION: PRECURSOR_M/Z 511.9619
+MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-
+MS$DATA_PROCESSING: RECALIBRATE loess on assigned fragments and MS1
+MS$DATA_PROCESSING: REANALYZE Peaks with additional N2/O included
+MS$DATA_PROCESSING: WHOLE RMassBank 3.15.1.1
+PK$SPLASH: splash10-03xr-1530090000-b039868553c7d505dcd7
+PK$ANNOTATION: m/z tentative_formula formula_count mass error(ppm)
+  63.9624 O2S- 1 63.9624 -1.19
+  64.9703 HO2S- 1 64.9703 0.15
+  82.9608 FO2S- 1 82.9609 -0.09
+  111.9874 CH3FNO2S- 1 111.9874 -0.12
+  118.9927 C2F5- 1 118.9926 0.81
+  168.9894 C3F7- 1 168.9894 0.23
+  218.9861 C4F9- 1 218.9862 -0.32
+  387.9801 C9F14N- 1 387.9813 -3.04
+  511.9619 C9H3F17NO2S- 1 511.9619 0.11
+PK$NUM_PEAK: 9
+PK$PEAK: m/z int. rel.int.
+  63.9624 31033.2 8
+  64.9703 380172.8 105
+  82.9608 191858.3 53
+  111.9874 379871.1 105
+  118.9927 169509.9 46
+  168.9894 1676803.9 463
+  218.9861 1243892.6 344
+  387.9801 139576.5 38
+  511.9619 3610915.2 999
+//

Eawag/MSBNK-Eawag-EQ00273053.txt

@@ -0,0 +1,57 @@
+ACCESSION: MSBNK-Eawag-EQ00273053
+RECORD_TITLE: N-MeFOSA; LC-ESI-QFT; MS2; CE: 45%; R=17500; [M-H]-
+DATE: 2024.05.15
+AUTHORS: B. Beck [dtc,com], J. Hollender [dtc]
+LICENSE: CC BY-SA
+COPYRIGHT: Copyright (C) Eawag 2023
+COMMENT: CONFIDENCE standard compound
+COMMENT: UCHEM_ID 2730
+CH$NAME: N-MeFOSA
+CH$NAME: Heptadecafluoro-N-methyloctanesulphonamide
+CH$NAME: 1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,8-heptadecafluoro-N-methyloctane-1-sulfonamide
+CH$COMPOUND_CLASS: N/A; Environmental Standard
+CH$FORMULA: C9H4F17NO2S
+CH$EXACT_MASS: 512.969129108
+CH$SMILES: CNS(=O)(=O)C(C(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F
+CH$IUPAC: InChI=1S/C9H4F17NO2S/c1-27-30(28,29)9(25,26)7(20,21)5(16,17)3(12,13)2(10,11)4(14,15)6(18,19)8(22,23)24/h27H,1H3
+CH$LINK: PUBCHEM CID:3034468
+CH$LINK: INCHIKEY SRMWNTGHXHOWBT-UHFFFAOYSA-N
+CH$LINK: CHEMSPIDER 2298910
+AC$INSTRUMENT: Exploris 240 Orbitrap Thermo Scientific
+AC$INSTRUMENT_TYPE: LC-ESI-QFT
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE HCD
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 45 % (nominal)
+AC$MASS_SPECTROMETRY: RESOLUTION 17500
+AC$MASS_SPECTROMETRY: MASS_RANGE_M/Z 54-543
+AC$CHROMATOGRAPHY: COLUMN_NAME XBridge C18 3.5um, 2.1x50mm, Waters
+AC$CHROMATOGRAPHY: FLOW_GRADIENT 90/10 at 0 min, 50/50 at 4 min, 5/95 at 17 min, 5/95 at 25 min, 90/10 at 25.1 min, 90/10 at 30 min
+AC$CHROMATOGRAPHY: FLOW_RATE 200 uL/min
+AC$CHROMATOGRAPHY: RETENTION_TIME 14.446 min
+MS$FOCUSED_ION: BASE_PEAK 601.9938
+MS$FOCUSED_ION: PRECURSOR_M/Z 511.9619
+MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-
+MS$DATA_PROCESSING: RECALIBRATE loess on assigned fragments and MS1
+MS$DATA_PROCESSING: REANALYZE Peaks with additional N2/O included
+MS$DATA_PROCESSING: WHOLE RMassBank 3.15.1.1
+PK$SPLASH: splash10-02t9-5900000000-afffac53fb15d6f6ffde
+PK$ANNOTATION: m/z tentative_formula formula_count mass error(ppm)
+  63.9626 O2S- 1 63.9624 2.92
+  64.9703 HO2S- 1 64.9703 0.85
+  82.9607 FO2S- 1 82.9609 -1.28
+  111.9872 CH3FNO2S- 1 111.9874 -1.62
+  118.9927 C2F5- 1 118.9926 1
+  168.9894 C3F7- 1 168.9894 0.05
+  218.9853 C4F9- 1 218.9862 -4.09
+PK$NUM_PEAK: 7
+PK$PEAK: m/z int. rel.int.
+  63.9626 56192.8 83
+  64.9703 451233.1 673
+  82.9607 116880.3 174
+  111.9872 136455.4 203
+  118.9927 235802 351
+  168.9894 669386.4 999
+  218.9853 109504.1 163
+//

Eawag/MSBNK-Eawag-EQ00273054.txt

@@ -0,0 +1,55 @@
+ACCESSION: MSBNK-Eawag-EQ00273054
+RECORD_TITLE: N-MeFOSA; LC-ESI-QFT; MS2; CE: 60%; R=17500; [M-H]-
+DATE: 2024.05.15
+AUTHORS: B. Beck [dtc,com], J. Hollender [dtc]
+LICENSE: CC BY-SA
+COPYRIGHT: Copyright (C) Eawag 2023
+COMMENT: CONFIDENCE standard compound
+COMMENT: UCHEM_ID 2730
+CH$NAME: N-MeFOSA
+CH$NAME: Heptadecafluoro-N-methyloctanesulphonamide
+CH$NAME: 1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,8-heptadecafluoro-N-methyloctane-1-sulfonamide
+CH$COMPOUND_CLASS: N/A; Environmental Standard
+CH$FORMULA: C9H4F17NO2S
+CH$EXACT_MASS: 512.969129108
+CH$SMILES: CNS(=O)(=O)C(C(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F
+CH$IUPAC: InChI=1S/C9H4F17NO2S/c1-27-30(28,29)9(25,26)7(20,21)5(16,17)3(12,13)2(10,11)4(14,15)6(18,19)8(22,23)24/h27H,1H3
+CH$LINK: PUBCHEM CID:3034468
+CH$LINK: INCHIKEY SRMWNTGHXHOWBT-UHFFFAOYSA-N
+CH$LINK: CHEMSPIDER 2298910
+AC$INSTRUMENT: Exploris 240 Orbitrap Thermo Scientific
+AC$INSTRUMENT_TYPE: LC-ESI-QFT
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE
+AC$MASS_SPECTROMETRY: IONIZATION ESI
+AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE HCD
+AC$MASS_SPECTROMETRY: COLLISION_ENERGY 60 % (nominal)
+AC$MASS_SPECTROMETRY: RESOLUTION 17500
+AC$MASS_SPECTROMETRY: MASS_RANGE_M/Z 54-543
+AC$CHROMATOGRAPHY: COLUMN_NAME XBridge C18 3.5um, 2.1x50mm, Waters
+AC$CHROMATOGRAPHY: FLOW_GRADIENT 90/10 at 0 min, 50/50 at 4 min, 5/95 at 17 min, 5/95 at 25 min, 90/10 at 25.1 min, 90/10 at 30 min
+AC$CHROMATOGRAPHY: FLOW_RATE 200 uL/min
+AC$CHROMATOGRAPHY: RETENTION_TIME 14.446 min
+MS$FOCUSED_ION: BASE_PEAK 601.9938
+MS$FOCUSED_ION: PRECURSOR_M/Z 511.9619
+MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-
+MS$DATA_PROCESSING: RECALIBRATE loess on assigned fragments and MS1
+MS$DATA_PROCESSING: REANALYZE Peaks with additional N2/O included
+MS$DATA_PROCESSING: WHOLE RMassBank 3.15.1.1
+PK$SPLASH: splash10-03di-9400000000-d63e8066a239a1a875b1
+PK$ANNOTATION: m/z tentative_formula formula_count mass error(ppm)
+  63.9625 O2S- 1 63.9624 1.25
+  64.9703 HO2S- 1 64.9703 0.5
+  82.9608 FO2S- 1 82.9609 -0.27
+  111.9874 CH3FNO2S- 1 111.9874 -0.33
+  118.9926 C2F5- 1 118.9926 0.68
+  168.9899 C3F7- 3 168.9894 3.39
+PK$NUM_PEAK: 6
+PK$PEAK: m/z int. rel.int.
+  63.9625 114908.7 266
+  64.9703 430633.7 999
+  82.9608 33711 78
+  111.9874 42490.1 98
+  118.9926 147210.9 341
+  168.9899 68993.2 160
+//