# HG changeset patch
# User bgruening
# Date 1368306754 14400
# Node ID 18617b9fc70ee4a50ef4a36b403fe7132a74fdb6
# Parent d241ff83e485497312a927a3bef42b69ff2ac3e5
Uploaded
diff -r d241ff83e485 -r 18617b9fc70e chemfp_mol2fps/mol2fps.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/mol2fps.xml Sat May 11 17:12:34 2013 -0400
@@ -0,0 +1,239 @@
+
+ with different fingerprint types
+
+
+ chemfp
+ rdkit
+
+
+ #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
+ ## Open Babel fingerprints
+ ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&1
+ #else:
+ ## RDKit fingerprints
+ rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}"
+ #if $fp_opts.fp_opts_selector=="--RDK":
+ --RDK
+ --fpSize $fp_opts.fpSize
+ --minPath $fp_opts.minPath
+ --maxPath $fp_opts.maxPath
+ --nBitsPerHash $fp_opts.nBitsPerHash
+ $fp_opts.useHs
+ #elif $fp_opts.fp_opts_selector=="--torsions":
+ --torsions
+ --fpSize $fp_opts.fpSize
+ --targetSize $fp_opts.targetSize
+ #elif $fp_opts.fp_opts_selector=="--morgan":
+ --morgan
+ --fpSize $fp_opts.fpSize
+ --radius $fp_opts.radius
+ $fp_opts.useFeatures
+ $fp_opts.useChirality
+ $fp_opts.useBondTypes
+ #elif $fp_opts.fp_opts_selector=="--pairs":
+ --paris
+ --fpSize $fp_opts.fpSize
+ --minLength $fp_opts.minLength
+ --maxLength $fp_opts.maxLength
+ #elif $fp_opts.fp_opts_selector=="--maccs166":
+ --maccs166
+ #elif $fp_opts.fp_opts_selector=="--substruct":
+ --substruct
+ #endif
+ --errors report 2>&1
+ #endif
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+**What it does**
+
+Generate fingerprints using OpenBabel
+
+-----
+
+**Example**
+
+* input::
+
+ - SDF File
+
+ 28434379
+ -OEChem-02031205132D
+
+ 37 39 0 0 0 0 0 0 0999 V2000
+ 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.3704 0.9433 0.0000 C 0 0 0 0
+ ......
+ 1 15 1 0 0 0 0
+ 1 35 1 0 0 0 0
+ 2 5 1 0 0 0 0
+ 2 11 1 0 0 0 0
+ 2 12 1 0 0 0 0
+ 3 12 2 0 0 0 0
+ 3 13 1 0 0 0 0
+ 4 18 1 0 0 0 0
+ ......
+
+ >PUBCHEM_COMPOUND_CID<
+ 28434379
+
+ > <PUBCHEM_COMPOUND_CANONICALIZED>
+ 1
+
+ > <PUBCHEM_CACTVS_COMPLEXITY>
+ 280
+
+ > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
+ 2
+
+ > <PUBCHEM_CACTVS_HBOND_DONOR>
+ 2
+
+ > <PUBCHEM_CACTVS_ROTATABLE_BOND>
+ 2
+
+ > <PUBCHEM_CACTVS_SUBSKEYS>
+ AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
+
+ >
+
+ - type : FP2
+
+* output::
+
+ #FPS1
+ #num_bits=1021
+ #type=OpenBabel-FP2/1
+ #software=OpenBabel/2.3.0
+ #source=/tmp/dataset_409.dat.sdf
+ #date=2012-02-03T11:13:39
+ c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
+ 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
+ 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379
+
+
+
+
diff -r d241ff83e485 -r 18617b9fc70e chemfp_mol2fps/ob2fps.xml
--- a/chemfp_mol2fps/ob2fps.xml Fri Apr 26 11:07:08 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,239 +0,0 @@
-
- with different fingerprint types
-
-
- chemfp
- rdkit
-
-
- #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
- ## Open Babel fingerprints
- ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&1
- #else:
- ## RDKit fingerprints
- rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}"
- #if $fp_opts.fp_opts_selector=="--RDK":
- --RDK
- --fpSize $fp_opts.fpSize
- --minPath $fp_opts.minPath
- --maxPath $fp_opts.maxPath
- --nBitsPerHash $fp_opts.nBitsPerHash
- $fp_opts.useHs
- #elif $fp_opts.fp_opts_selector=="--torsions":
- --torsions
- --fpSize $fp_opts.fpSize
- --targetSize $fp_opts.targetSize
- #elif $fp_opts.fp_opts_selector=="--morgan":
- --morgan
- --fpSize $fp_opts.fpSize
- --radius $fp_opts.radius
- $fp_opts.useFeatures
- $fp_opts.useChirality
- $fp_opts.useBondTypes
- #elif $fp_opts.fp_opts_selector=="--pairs":
- --paris
- --fpSize $fp_opts.fpSize
- --minLength $fp_opts.minLength
- --maxLength $fp_opts.maxLength
- #elif $fp_opts.fp_opts_selector=="--maccs166":
- --maccs166
- #elif $fp_opts.fp_opts_selector=="--substruct":
- --substruct
- #endif
- --errors report 2>&1
- #endif
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-**What it does**
-
-Generate fingerprints using OpenBabel
-
------
-
-**Example**
-
-* input::
-
- - SDF File
-
- 28434379
- -OEChem-02031205132D
-
- 37 39 0 0 0 0 0 0 0999 V2000
- 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
- 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
- 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
- 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
- 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
- 7.3704 0.9433 0.0000 C 0 0 0 0
- ......
- 1 15 1 0 0 0 0
- 1 35 1 0 0 0 0
- 2 5 1 0 0 0 0
- 2 11 1 0 0 0 0
- 2 12 1 0 0 0 0
- 3 12 2 0 0 0 0
- 3 13 1 0 0 0 0
- 4 18 1 0 0 0 0
- ......
-
- >PUBCHEM_COMPOUND_CID<
- 28434379
-
- > <PUBCHEM_COMPOUND_CANONICALIZED>
- 1
-
- > <PUBCHEM_CACTVS_COMPLEXITY>
- 280
-
- > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
- 2
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- > <PUBCHEM_CACTVS_HBOND_DONOR>
- 2
-
- > <PUBCHEM_CACTVS_ROTATABLE_BOND>
- 2
-
- > <PUBCHEM_CACTVS_SUBSKEYS>
- AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
-
- >
-
- - type : FP2
-
-* output::
-
- #FPS1
- #num_bits=1021
- #type=OpenBabel-FP2/1
- #software=OpenBabel/2.3.0
- #source=/tmp/dataset_409.dat.sdf
- #date=2012-02-03T11:13:39
- c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
- 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
- 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379
-
-
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diff -r d241ff83e485 -r 18617b9fc70e repository_dependencies.xml
--- a/repository_dependencies.xml Fri Apr 26 11:07:08 2013 -0400
+++ b/repository_dependencies.xml Sat May 11 17:12:34 2013 -0400
@@ -1,5 +1,5 @@
-
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+
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diff -r d241ff83e485 -r 18617b9fc70e tool_dependencies.xml
--- a/tool_dependencies.xml Fri Apr 26 11:07:08 2013 -0400
+++ b/tool_dependencies.xml Sat May 11 17:12:34 2013 -0400
@@ -1,12 +1,12 @@
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