Mercurial > repos > bgruening > chemfp

changeset 21:7c84cfa515e0

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Sat, 01 Jun 2013 20:03:04 +0200
parents 21d29a7f13d8
children 6c496b524b41
files chemfp_clustering/butina_clustering.xml chemfp_clustering/nxn_clustering.py chemfp_clustering/nxn_clustering.xml chemfp_sdf2fps/sdf2fps.xml tool_dependencies.xml
diffstat 5 files changed, 17 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/chemfp_clustering/butina_clustering.xml	Fri May 31 22:31:45 2013 +0200
+++ b/chemfp_clustering/butina_clustering.xml	Sat Jun 01 20:03:04 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.1">
+<tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.1">
     <description>of molecular fingerprints</description>
     <requirements>
         <requirement type="package" version="1.1p1">chemfp</requirement>
--- a/chemfp_clustering/nxn_clustering.py	Fri May 31 22:31:45 2013 +0200
+++ b/chemfp_clustering/nxn_clustering.py	Sat Jun 01 20:03:04 2013 +0200
@@ -12,6 +12,7 @@
 import scipy.cluster.hierarchy as hcluster
 import pylab
 import numpy
+import tempfile
 
 
 def distance_matrix(arena, tanimoto_threshold = 0.0):
@@ -63,8 +64,13 @@
 
     args = parser.parse_args()
 
+    # make sure that the file ending is fps
+    temp_file = tempfile.NamedTemporaryFile()
+    temp_link = "%s.%s" % (temp_file.name, 'fps')
+    temp_file.close()
+    os.symlink(args.input_path, temp_link)
 
-    arena = chemfp.load_fingerprints( args.input_path )
+    arena = chemfp.load_fingerprints( temp_link )
     distances  = distance_matrix( arena, args.tanimoto_threshold )
     linkage = hcluster.linkage( distances, method="single", metric="euclidean" )
 
--- a/chemfp_clustering/nxn_clustering.xml	Fri May 31 22:31:45 2013 +0200
+++ b/chemfp_clustering/nxn_clustering.xml	Sat Jun 01 20:03:04 2013 +0200
@@ -1,10 +1,10 @@
-<tool id="chemfp_nxn_clustering" name="NxN Clustering" version="0.1">
+<tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.1">
     <description>of molecular fingerprints</description>
     <requirements>
         <requirement type="package" version="1.7.0">numpy</requirement>
         <requirement type="package" version="1.1p1">chemfp</requirement>
         <requirement type="package" version="1.2.1">matplotlib</requirement>
-        <requirement type="package" version="0.12">scipy</requirement>
+        <requirement type="package" version="0.12.0">scipy</requirement>
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter='python'>
--- a/chemfp_sdf2fps/sdf2fps.xml	Fri May 31 22:31:45 2013 +0200
+++ b/chemfp_sdf2fps/sdf2fps.xml	Sat Jun 01 20:03:04 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="sdf2fps" name="SDF to Fingerprint" version="0.1.1">
+<tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="0.1.1">
     <description>extract fingerprints from sdf files metadata</description>
     <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
     <requirements>
--- a/tool_dependencies.xml	Fri May 31 22:31:45 2013 +0200
+++ b/tool_dependencies.xml	Sat Jun 01 20:03:04 2013 +0200
@@ -1,21 +1,21 @@
 <?xml version='1.0' encoding='utf-8'?>
 <tool_dependency>
     <package name="rdkit" version="2012_12_1">
-        <repository changeset_revision="5b30ea84ba25" name="package_rdkit_2012_12" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="5b30ea84ba25" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="44e09779f3e2" name="package_matplotlib_1_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="c888aa8ed318" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="chemfp" version="1.1p1">
-        <repository changeset_revision="3e3356b13281" name="package_chemfp_1_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="3e3356b13281" name="package_chemfp_1_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="096765cc084f" name="package_scipy_0_12" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="e4f395310680" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="openbabel" version="2.3.2">
-        <repository changeset_revision="3a993ff17df5" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="3a993ff17df5" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
 </tool_dependency>
\ No newline at end of file