changeset 2:7fac8e7a12d5 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1"
author bgruening
date Wed, 03 Jun 2020 12:56:49 -0400
parents 583dcdbdbf42
children 0848d3b1a46f
files rbcavity.xml rbdock.py rxdock_macros.xml
diffstat 3 files changed, 2 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/rbcavity.xml	Sat Apr 25 08:58:47 2020 -0400
+++ b/rbcavity.xml	Wed Jun 03 12:56:49 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="rxdock_rbcavity" name="rxDock cavity definition" version="0.1">
+<tool id="rxdock_rbcavity" name="rxDock cavity definition" version="0.1.5">
     <description>- generate the active site definition needed for rxDock docking</description>
     <macros>
         <import>rxdock_macros.xml</import>
--- a/rbdock.py	Sat Apr 25 08:58:47 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-import subprocess
-import argparse
-
-def main():
-    parser = argparse.ArgumentParser(description='Simple wrapper for rbdock')
-    parser.add_argument('-n', '--num', type=int, help='Number of docking poses to generate')
-    parser.add_argument('-s', '--seed', type=int, help='Random seed')
-    args = parser.parse_args()
-
-    cmd = ['rbdock', '-i', 'ligands.sdf', '-r', 'receptor.prm', '-p', 'dock.prm', '-n', str(args.num), '-o', 'rdock_output']
-    if args.seed != None:
-        cmd += ['-s', str(args.seed)]
-
-    ps = subprocess.Popen(cmd, stdout=subprocess.PIPE)
-
-    error_counter = 0
-    for stdout_line in iter(ps.stdout.readline, ''):
-        if 'RBT_DOCKING_ERROR' in str(stdout_line):
-                error_counter += 1
-                if error_counter == 10:
-                    print(ps.stdout)
-                    exit(23)
-        if ps.poll() != None:
-            print(ps.stdout)
-            exit(int(ps.poll()))
-
-if __name__ == "__main__":
-    main()
--- a/rxdock_macros.xml	Sat Apr 25 08:58:47 2020 -0400
+++ b/rxdock_macros.xml	Wed Jun 03 12:56:49 2020 -0400
@@ -6,7 +6,7 @@
     </xml>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2013.1.0_b93747f3">rxdock</requirement>
+            <requirement type="package" version="2013.1.1_148c5bd1">rxdock</requirement>
         </requirements>
     </xml>
 </macros>