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dimorphite_dl
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jdurrant
dimorphite_dl
Commits
1f8d41f2
Commit
1f8d41f2
authored
Nov 20, 2018
by
jdurrant
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Fixed Python3 compatibility.
parent
99308269
Changes
2
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2 changed files
with
13 additions
and
13 deletions
+13
-13
README.md
README.md
+6
-6
dimorphite_dl.py
dimorphite_dl.py
+7
-7
No files found.
README.md
View file @
1f8d41f2
...
...
@@ -20,7 +20,7 @@ Usage
-----
```
usage: dimorphite
-
dl.py [-h] [--min_ph MIN] [--max_ph MAX]
usage: dimorphite
_
dl.py [-h] [--min_ph MIN] [--max_ph MAX]
[--pka_precision PRE] [--smiles SMI]
[--smiles_file FILE] [--output_file FILE]
[--label_states] [--test]
...
...
@@ -47,11 +47,11 @@ Examples
--------
```
python dimorphite
-
dl.py --smiles_file sample_molecules.smi
python dimorphite
-
dl.py --smiles "CCC(=O)O" --min_ph -3.0 --max_ph -2.0
python dimorphite
-
dl.py --smiles "CCCN" --min_ph -3.0 --max_ph -2.0 --output_file output.smi
python dimorphite
-
dl.py --smiles_file sample_molecules.smi --pka_precision 2.0 --label_states
python dimorphite
-
dl.py --test
python dimorphite
_
dl.py --smiles_file sample_molecules.smi
python dimorphite
_
dl.py --smiles "CCC(=O)O" --min_ph -3.0 --max_ph -2.0
python dimorphite
_
dl.py --smiles "CCCN" --min_ph -3.0 --max_ph -2.0 --output_file output.smi
python dimorphite
_
dl.py --smiles_file sample_molecules.smi --pka_precision 2.0 --label_states
python dimorphite
_
dl.py --test
```
Authors and Contacts
...
...
dimorphite_dl.py
View file @
1f8d41f2
...
...
@@ -42,6 +42,7 @@ def main():
print
(
"
\n
PARAMETERS:
\n
"
)
for
k
in
sorted
(
args
.
keys
()):
print
(
k
.
rjust
(
13
)
+
": "
+
str
(
args
[
k
]))
print
(
""
)
if
args
[
"test"
]:
# Run tests.
...
...
@@ -82,13 +83,13 @@ class MyParser(argparse.ArgumentParser):
if
file
is
None
:
file
=
sys
.
stdout
self
.
_print_message
(
self
.
format_help
(),
file
)
print
"""
print
(
"""
examples:
python dimorphite
-
dl.py --smiles_file sample_molecules.smi
python dimorphite
-
dl.py --smiles "CCC(=O)O" --min_ph -3.0 --max_ph -2.0
python dimorphite
-
dl.py --smiles "CCCN" --min_ph -3.0 --max_ph -2.0 --output_file output.smi
python dimorphite
-
dl.py --smiles_file sample_molecules.smi --pka_precision 2.0 --label_states
python dimorphite
-dl.py --test"""
python dimorphite
_
dl.py --smiles_file sample_molecules.smi
python dimorphite
_
dl.py --smiles "CCC(=O)O" --min_ph -3.0 --max_ph -2.0
python dimorphite
_
dl.py --smiles "CCCN" --min_ph -3.0 --max_ph -2.0 --output_file output.smi
python dimorphite
_
dl.py --smiles_file sample_molecules.smi --pka_precision 2.0 --label_states
python dimorphite
_dl.py --test"""
)
print
(
""
)
def
get_args
():
...
...
@@ -703,7 +704,6 @@ def test():
average_pkas
=
{
l
.
split
()[
0
].
replace
(
"*"
,
""
):
float
(
l
.
split
()[
3
])
for
l
in
open
(
"site_substructures.smarts"
)
if
l
.
split
()[
0
]
not
in
[
"Phosphate"
,
"Phosphonate"
]}
average_pkas_phos
=
{
l
.
split
()[
0
].
replace
(
"*"
,
""
):[
float
(
l
.
split
()[
3
]),
float
(
l
.
split
()[
6
])]
for
l
in
open
(
"site_substructures.smarts"
)
if
l
.
split
()[
0
]
in
[
"Phosphate"
,
"Phosphonate"
]}
print
(
""
)
print
(
"Running Tests"
)
print
(
"============="
)
print
(
""
)
...
...
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