| 1 | # Process with autom4te to create an -*- Autotest -*- test suite.
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| 2 |
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| 3 |
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| 4 | AT_INIT([Molecular Builder])
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| 5 |
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| 6 | # Checking if command line options are parsed correctly
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| 7 | AT_BANNER([MoleCuilder - standard options])
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| 8 | AT_SETUP([Standard Options])
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| 9 | AT_CHECK([pwd],[ignore],[ignore])
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| 10 | AT_CHECK([../../molecuilder -v], 0, [stdout], [ignore])
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| 11 | AT_CHECK([fgrep molecuilder stdout], 0, [ignore], [ignore])
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| 12 | AT_CHECK([../../molecuilder -h], 0, [stdout], [ignore])
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| 13 | AT_CHECK([fgrep "Give this help screen" stdout], 0, [ignore], [ignore])
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| 14 | AT_CLEANUP
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| 15 |
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| 16 | AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
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| 17 | AT_SETUP([Simple configuration])
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| 18 | # 1. create a fake element database with the only element we need
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| 19 | AT_DATA([elements.db],[# Covalent radius of each element in Angstroem from CSD (binding is: [Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t] with t = 0.4A
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| 20 | #Element Name Symbol Period Group Block Atomic Number AtomicWeight Covalent Radius vdW Radius
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| 21 | Hydrogen H 1 1 s 1 1.008 0.23 1.09
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| 22 | ])
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| 23 | # 2. create some simplest molecular geometry
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| 24 | AT_DATA([test.xyz], [[1
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| 25 | # test configuration, created by molecuilder test suite
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| 26 | H 10. 10. 10.
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| 27 | ]])
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| 28 | # 3. make sure config is empty and not remnant from last test with broken dirs
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| 29 | AT_DATA([test.conf], [])
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| 30 | AT_CHECK([../../molecuilder test.conf -e ./ -p test.xyz], 0, [ignore], [ignore])
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| 31 | AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1 10.000000000 10.000000000 10.000000000 0 # Number in molecule 0
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| 32 | ], [ignore])
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| 33 | AT_CHECK([cp test.conf main_pcp_linux], 0, [ignore], [ignore])
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| 34 | AT_DATA([input], [aa 10. 10. 10. 1
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| 35 | s
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| 36 | q
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| 37 | ])
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| 38 | AT_CHECK([../../molecuilder -e ./ <input], 0, [ignore], [ignore])
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| 39 | AT_CHECK([diff main_pcp_linux test.conf], 0, [ignore], [ignore])
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| 40 | AT_CLEANUP
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| 41 |
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| 42 | AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
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| 43 | AT_SETUP([Fragmentation])
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| 44 | # 1. create a fake element database with the only two elements we need
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| 45 | AT_DATA([elements.db],[# Covalent radius of each element in Angstroem from CSD (binding is: [Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t] with t = 0.4A
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| 46 | #Element Name Symbol Period Group Block Atomic Number AtomicWeight Covalent Radius vdW Radius
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| 47 | Hydrogen H 1 1 s 1 1.008 0.23 1.09
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| 48 | Carbon C 2 14 p 6 12.011 0.68 1.70
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| 49 | ])
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| 50 | # 2. create molecular geometry
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| 51 | AT_DATA([test.xyz], [[11
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| 52 | # test configuration, created by molecuilder test suite
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| 53 | C 9.782085945 3.275186040 3.535886037
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| 54 | C 8.532785963 4.158586027 3.535886037
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| 55 | C 7.283585982 3.275186040 3.535886037
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| 56 | H 9.782085945 2.645886050 2.645886050
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| 57 | H 9.782085945 2.645886050 4.425886024
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| 58 | H 10.672039608 3.904536878 3.535886037
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| 59 | H 8.532785963 4.787886018 2.645886050
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| 60 | H 8.532785963 4.787886018 4.425886024
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| 61 | H 6.393632318 3.904536877 3.535886037
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| 62 | H 7.283585982 2.645886050 2.645886050
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| 63 | H 7.283585982 2.645886050 4.425886024
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| 64 | ]])
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| 65 | # 3. make sure config is empty and not remnant from last test with broken dirs
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| 66 | AT_DATA([test.conf], [])
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| 67 | # 4. create the config and check it
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| 68 | AT_CHECK([../../molecuilder test.conf -e ./ -p test.xyz], 0, [ignore], [ignore])
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| 69 | AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4 8.532785963 4.787886018 2.645886050 0 # Number in molecule 6
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| 70 | ], [ignore])
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| 71 | AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
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| 72 | # 5. fragment the molecule and check the number of configs
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| 73 | AT_CHECK([../../molecuilder test.conf -e ./ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
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| 74 | AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
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| 75 | AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
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| 76 | ], [ignore])
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| 77 | # 3a. check whether parsing of BondFragment files and re-rwriting config files is working (exit code is 2 as we don't need to continue wrt to ...OrderAtSite)
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| 78 | AT_CHECK([../../molecuilder test.conf -e ./ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
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| 79 | AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
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| 80 | # 6. compare both dirs by diff'ing
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| 81 | AT_CHECK([diff -I '.*Created by molecuilder.*' std/ new/], 0, [], [])
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| 82 | AT_CLEANUP
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| 83 |
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