Add Python charge scripts. First example xtb GFN2 charges #998
Conversation
Read either atomic partial charges or potential at particular points Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
|
This probably still needs a bit more work, but the basics are there. |
|
This pull request introduces 1 alert when merging dcfd36b into b66a848 - view on LGTM.com new alerts:
|
![sonatype-lift[bot]](https://avatars.githubusercontent.com/in/9843?s=60&v=4){kind=small}
|
|
||
| # for now, ignore the output itself | ||
| tempdir = tempfile.mkdtemp() | ||
| output = subprocess.run([xtb, name], stdout=subprocess.PIPE, cwd=tempdir) |
There was a problem hiding this comment.
subprocess_without_shell_equals_true: subprocess call - check for execution of untrusted input.
Reply with "@sonatype-lift help" for info about LiftBot commands.
Reply with "@sonatype-lift ignore" to tell LiftBot to leave out the above finding from this PR.
Reply with "@sonatype-lift ignoreall" to tell LiftBot to leave out all the findings from this PR and from the status bar in Github.
When talking to LiftBot, you need to refresh the page to see its response. Click here to get to know more about LiftBot commands.
Was this a good recommendation?
[ 🙁 Not relevant ] - [ 😕 Won't fix ] - [ 😑 Not critical, will fix ] - [ 🙂 Critical, will fix ] - [ 😊 Critical, fixing now ]
| import os | ||
| from shutil import which | ||
| import tempfile | ||
| import subprocess |
There was a problem hiding this comment.
blacklist: Consider possible security implications associated with the subprocess module.
Reply with "@sonatype-lift help" for info about LiftBot commands.
Reply with "@sonatype-lift ignore" to tell LiftBot to leave out the above finding from this PR.
Reply with "@sonatype-lift ignoreall" to tell LiftBot to leave out all the findings from this PR and from the status bar in Github.
When talking to LiftBot, you need to refresh the page to see its response. Click here to get to know more about LiftBot commands.
Was this a good recommendation?
[ 🙁 Not relevant ] - [ 😕 Won't fix ] - [ 😑 Not critical, will fix ] - [ 🙂 Critical, will fix ] - [ 😊 Critical, fixing now ]
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
There was a problem hiding this comment.
Found 11 potential problems in the proposed changes. Check the Files changed tab for more details.
There was a problem hiding this comment.
Found 12 potential problems in the proposed changes. Check the Files changed tab for more details.
|
Here are the build results |
| import os | ||
| from shutil import which | ||
| import tempfile | ||
| import subprocess |
Check notice
Code scanning
Consider possible security implications associated with subprocess module.
Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
|
This pull request introduces 3 alerts when merging 9730314 into b66a848 - view on LGTM.com new alerts:
|
| for filename in os.listdir(tempdir): | ||
| try: | ||
| os.remove(tempdir + "/" + filename) | ||
| except: |
Check notice
Code scanning
Try, Except, Continue detected.
|
|
||
| # for now, ignore the output itself | ||
| tempdir = tempfile.mkdtemp() | ||
| output = subprocess.run( |
Check notice
Code scanning
subprocess call - check for execution of untrusted input.
| # and try to cleanup the directory | ||
| try: | ||
| os.rmdir(tempdir) | ||
| except: |
Check notice
Code scanning
Try, Except, Pass detected.
There was a problem hiding this comment.
Found 11 potential problems in the proposed changes. Check the Files changed tab for more details.
There was a problem hiding this comment.
Found 13 potential problems in the proposed changes. Check the Files changed tab for more details.
| for filename in os.listdir(tempdir): | ||
| try: | ||
| os.remove(tempdir + "/" + filename) | ||
| except: |
Check notice
Code scanning
No exception type(s) specified (bare-except)
|
|
||
| # for now, ignore the output itself | ||
| tempdir = tempfile.mkdtemp() | ||
| output = subprocess.run( |
Check notice
Code scanning
Unused variable 'output' (unused-variable)
| # and try to cleanup the directory | ||
| try: | ||
| os.rmdir(tempdir) | ||
| except: |
Check notice
Code scanning
No exception type(s) specified (bare-except)
|
Here are the build results |
|
Here are the build results |
Read either atomic partial charges or potential at particular points
Signed-off-by: Geoff Hutchison geoff.hutchison@gmail.com
Developer Certificate of Origin
Version 1.1
Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
1 Letterman Drive
Suite D4700
San Francisco, CA, 94129
Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.
Developer's Certificate of Origin 1.1
By making a contribution to this project, I certify that:
(a) The contribution was created in whole or in part by me and I
have the right to submit it under the open source license
indicated in the file; or
(b) The contribution is based upon previous work that, to the best
of my knowledge, is covered under an appropriate open source
license and I have the right under that license to submit that
work with modifications, whether created in whole or in part
by me, under the same open source license (unless I am
permitted to submit under a different license), as indicated
in the file; or
(c) The contribution was provided directly to me by some other
person who certified (a), (b) or (c) and I have not modified
it.
(d) I understand and agree that this project and the contribution
are public and that a record of the contribution (including all
personal information I submit with it, including my sign-off) is
maintained indefinitely and may be redistributed consistent with
this project or the open source license(s) involved.