[med-svn] [Git][med-team/autodock-vina][master] Add autopkgtest
Liubov Chuprikova
gitlab at salsa.debian.org
Sat Jul 7 14:00:23 BST 2018
Liubov Chuprikova pushed to branch master at Debian Med / autodock-vina
Commits:
b99652e5 by Liubov Chuprikova at 2018-07-07T15:38:45+03:00
Add autopkgtest
- - - - -
9 changed files:
- + debian/README.test
- debian/changelog
- debian/copyright
- + debian/docs
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/tests/test-data/conf.txt
- + debian/tests/test-data/ligand.pdbqt
- + debian/tests/test-data/protein.pdbqt
Changes:
=====================================
debian/README.test
=====================================
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+_______________________________________
+
+This package can be tested by execution
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+autodock-vina (1.1.2-5) UNRELEASED; urgency=low
+
+ * Team upload.
+ * Add autopkgtest
+ Closes: #890785
+
+ -- Liubov Chuprikova <chuprikovalv at gmail.com> Sat, 07 Jul 2018 14:30:23 +0300
+
autodock-vina (1.1.2-4) unstable; urgency=low
[ Steffen Moeller ]
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -30,3 +30,10 @@ Copyright: © 2010 Yask Gupta <yask.gupta87 at gmail.com>
© 2011 Andreas Tille <tille at debian.org>
License: Apache License, Version 2.0
Same license as program itself.
+
+Files: debian/tests/test-data/*
+Copyright: © 2018 Liubov Chuprikova <chuprikovalv at gmail.com>
+License: Apache License, Version 2.0
+ Same license as program itself.
+Comment: Test data files were generated as it is discribed in Vina Video
+ Tutorial: http://vina.scripps.edu/tutorial.html
=====================================
debian/docs
=====================================
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+debian/tests/test-data
+debian/tests/run-unit-test
+debian/README.test
=====================================
debian/tests/control
=====================================
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,2 @@
+Tests: run-unit-test
+Depends: @
=====================================
debian/tests/run-unit-test
=====================================
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,20 @@
+#!/bin/sh -e
+
+pkg="autodock-vina"
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd $AUTOPKGTEST_TMP
+cp /usr/share/doc/${pkg}/test-data/* .
+gunzip *.gz
+
+echo "Testing vina...\n"
+vina --config conf.txt --log log.txt
+
+echo "\nTesting vina_split...\n"
+vina_split --input out.pdbqt
+
+echo "\nPASS"
=====================================
debian/tests/test-data/conf.txt
=====================================
--- /dev/null
+++ b/debian/tests/test-data/conf.txt
@@ -0,0 +1,14 @@
+receptor = protein.pdbqt
+ligand = ligand.pdbqt
+
+out = out.pdbqt
+
+center_x = 11
+center_y = 90.5
+center_z = 57.5
+
+size_x = 22
+size_y = 24
+size_z = 28
+
+exhaustiveness = 4
=====================================
debian/tests/test-data/ligand.pdbqt
=====================================
--- /dev/null
+++ b/debian/tests/test-data/ligand.pdbqt
@@ -0,0 +1,66 @@
+REMARK 7 active torsions:
+REMARK status: ('A' for Active; 'I' for Inactive)
+REMARK 1 A between atoms: C5_5 and C7_7
+REMARK 2 A between atoms: C9_9 and N13_13
+REMARK 3 A between atoms: N13_13 and C14_14
+REMARK 4 A between atoms: C16_16 and N21_21
+REMARK I between atoms: N21_21 and C22_22
+REMARK 5 A between atoms: C22_22 and C23_23
+REMARK 6 A between atoms: C27_26 and C46_30
+REMARK 7 A between atoms: C46_30 and N48_31
+ROOT
+HETATM 1 C1 STI 202 15.290 78.984 63.105 1.00 0.00 -0.001 A
+HETATM 2 C2 STI 202 14.162 78.322 62.514 1.00 0.00 0.095 A
+HETATM 3 N3 STI 202 14.348 77.405 61.475 1.00 0.00 -0.243 NA
+HETATM 4 C4 STI 202 15.604 77.088 60.967 1.00 0.00 0.097 A
+HETATM 5 C5 STI 202 16.790 77.718 61.516 1.00 0.00 0.020 A
+HETATM 6 C6 STI 202 16.610 78.678 62.599 1.00 0.00 0.057 A
+ENDROOT
+BRANCH 5 7
+HETATM 7 C7 STI 202 18.135 77.365 60.950 1.00 0.00 0.099 A
+HETATM 8 N8 STI 202 18.991 76.649 61.763 1.00 0.00 -0.061 NA
+HETATM 9 C9 STI 202 20.233 76.272 61.350 1.00 0.00 0.728 A
+HETATM 10 N10 STI 202 20.667 76.608 60.078 1.00 0.00 -0.059 NA
+HETATM 11 C11 STI 202 19.854 77.325 59.216 1.00 0.00 0.119 A
+HETATM 12 C12 STI 202 18.556 77.729 59.622 1.00 0.00 0.041 A
+BRANCH 9 13
+HETATM 13 N13 STI 202 21.026 75.546 62.243 1.00 0.00 -0.190 N
+HETATM 14 H STI 202 20.822 74.493 62.382 1.00 0.00 0.184 HD
+BRANCH 13 15
+HETATM 15 C14 STI 202 22.078 76.132 62.968 1.00 0.00 0.052 A
+HETATM 16 C15 STI 202 21.784 76.754 64.221 1.00 0.00 0.087 A
+HETATM 17 C16 STI 202 22.842 77.373 65.022 1.00 0.00 0.042 A
+HETATM 18 C17 STI 202 24.173 77.343 64.522 1.00 0.00 0.013 A
+HETATM 19 C18 STI 202 24.483 76.718 63.261 1.00 0.00 -0.002 A
+HETATM 20 C19 STI 202 23.455 76.105 62.465 1.00 0.00 -0.009 A
+HETATM 21 C20 STI 202 23.868 75.449 61.126 1.00 0.00 0.032 C
+BRANCH 17 22
+HETATM 22 N21 STI 202 22.625 78.015 66.297 1.00 0.00 -0.325 N
+HETATM 23 C22 STI 202 21.459 78.556 66.802 1.00 0.00 0.253 C
+HETATM 24 O29 STI 202 20.459 78.777 66.146 1.00 0.00 -0.268 OA
+HETATM 25 H STI 202 23.491 78.080 66.943 1.00 0.00 0.169 HD
+BRANCH 23 26
+HETATM 26 C23 STI 202 21.395 78.922 68.248 1.00 0.00 0.034 A
+HETATM 27 C25 STI 202 22.608 78.977 69.064 1.00 0.00 0.036 A
+HETATM 28 C26 STI 202 22.516 79.314 70.461 1.00 0.00 0.029 A
+HETATM 29 C27 STI 202 21.216 79.597 71.045 1.00 0.00 -0.011 A
+HETATM 30 C28 STI 202 20.031 79.541 70.215 1.00 0.00 -0.007 A
+HETATM 31 C29 STI 202 20.112 79.211 68.845 1.00 0.00 -0.000 A
+BRANCH 29 32
+HETATM 32 C46 STI 202 21.035 79.941 72.527 1.00 0.00 0.273 C
+BRANCH 32 33
+HETATM 33 N48 STI 202 21.864 81.048 73.091 1.00 0.00 0.145 N
+HETATM 34 C49 STI 202 23.277 80.579 73.421 1.00 0.00 0.286 C
+HETATM 35 C50 STI 202 24.142 81.743 73.995 1.00 0.00 0.286 C
+HETATM 36 N51 STI 202 23.461 82.314 75.230 1.00 0.00 0.143 N
+HETATM 37 C52 STI 202 22.054 82.791 74.907 1.00 0.00 0.286 C
+HETATM 38 C54 STI 202 24.311 83.368 75.810 1.00 0.00 0.285 C
+HETATM 39 C53 STI 202 21.211 81.634 74.310 1.00 0.00 0.286 C
+ENDBRANCH 32 33
+ENDBRANCH 29 32
+ENDBRANCH 23 26
+ENDBRANCH 17 22
+ENDBRANCH 13 15
+ENDBRANCH 9 13
+ENDBRANCH 5 7
+TORSDOF 7
=====================================
debian/tests/test-data/protein.pdbqt
=====================================
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View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/commit/b99652e56a5a542b76936549455be98c56558b03
--
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