NO_JIRA Updated and moved some conformer analysis scripts from confid… by CRingroseCCDC · Pull Request #92 · ccdc-opensource/csd-python-api-scripts

CRingroseCCDC · 2026-02-05T11:43:12Z

…ential.

github-actions · 2026-02-05T11:43:40Z

scripts/conformer_filter_density/ReadMe.md

+
+CCDC Python API Licence required, minimum version: 3.0.15
+
+Script can be run with any multimolecule file e.g. sdf. 


[markdownlint] _{reported by reviewdog 🐶}
MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1]

github-actions · 2026-02-05T11:43:40Z

scripts/conformer_filter_density/ReadMe.md

+Input file (single- or multi-molecule file)
+
+options:
+* -h, --help; Show this help message and exit


[markdownlint] _{reported by reviewdog 🐶}
MD032/blanks-around-lists Lists should be surrounded by blank lines [Context: "* -h, --help; Show this help m..."]

github-actions · 2026-02-05T11:43:41Z

scripts/conformer_filter_density/ReadMe.md

+
+options:
+* -h, --help; Show this help message and exit
+* -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on 


[markdownlint] _{reported by reviewdog 🐶}
MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1]

github-actions · 2026-02-05T11:43:41Z

scripts/conformer_filter_density/ReadMe.md

+options:
+* -h, --help; Show this help message and exit
+* -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on 
+molecule with fewest unusual torsions). WARNING: Relative mode may behave unexpectedly with conformers from 


[markdownlint] _{reported by reviewdog 🐶}
MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1]

github-actions · 2026-02-05T11:43:41Z

scripts/conformer_filter_density/ReadMe.md

+* --failurefn; Output file for molecules that fail the filter (default: failures.mol)
+* -u, --unusual-torsions; Output CSV file for unusual torsion details (default: unusual_torsions.csv)
+
+


[markdownlint] _{reported by reviewdog 🐶}
MD012/no-multiple-blanks Multiple consecutive blank lines [Expected: 1; Actual: 2]

github-actions · 2026-02-05T11:43:41Z

scripts/filter_poses/ReadMe.md

@@ -0,0 +1,23 @@
+# Filter Poses
+
+This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities. 


[markdownlint] _{reported by reviewdog 🐶}
MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1]

github-actions · 2026-02-05T11:43:41Z

scripts/filter_poses/ReadMe.md

+## Instructions on Running
+
+positional arguments:
+* input file; Input file (multi-molecule file).


[markdownlint] _{reported by reviewdog 🐶}
MD032/blanks-around-lists Lists should be surrounded by blank lines [Context: "* input file; Input file (mult..."]

github-actions · 2026-02-05T11:43:41Z

scripts/filter_poses/ReadMe.md

+* input file; Input file (multi-molecule file).
+
+options:
+* -h, --help; Show this help message and exit.


[markdownlint] _{reported by reviewdog 🐶}
MD032/blanks-around-lists Lists should be surrounded by blank lines [Context: "* -h, --help; Show this help m..."]

github-actions · 2026-02-05T11:43:44Z

scripts/conformer_filter_density/ReadMe.md

+
+CCDC Python API Licence required, minimum version: 3.0.15
+
+Script can be run with any multimolecule file e.g. sdf. 


[markdownlint-fix] _{reported by reviewdog 🐶}

Suggested change

Script can be run with any multimolecule file e.g. sdf.

Script can be run with any multimolecule file e.g. sdf.

github-actions · 2026-02-05T11:43:44Z

scripts/conformer_filter_density/ReadMe.md

+Input file (single- or multi-molecule file)
+
+options:
+* -h, --help; Show this help message and exit


[markdownlint-fix] _{reported by reviewdog 🐶}

Suggested change

* -h, --help; Show this help message and exit

* -h, --help; Show this help message and exit

github-actions · 2026-02-05T11:43:44Z

scripts/conformer_filter_density/ReadMe.md

+* -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on 
+molecule with fewest unusual torsions). WARNING: Relative mode may behave unexpectedly with conformers from 


[markdownlint-fix] _{reported by reviewdog 🐶}

Suggested change

* -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on

molecule with fewest unusual torsions). WARNING: Relative mode may behave unexpectedly with conformers from

* -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on

molecule with fewest unusual torsions). WARNING: Relative mode may behave unexpectedly with conformers from

github-actions · 2026-02-05T11:43:44Z

scripts/conformer_filter_density/ReadMe.md

+* --failurefn; Output file for molecules that fail the filter (default: failures.mol)
+* -u, --unusual-torsions; Output CSV file for unusual torsion details (default: unusual_torsions.csv)
+
+


[markdownlint-fix] _{reported by reviewdog 🐶}

Suggested change

github-actions · 2026-02-05T11:43:44Z

scripts/conformer_filter_density/ReadMe.md

+Updated by Chris Ringrose
+
+    For feedback or to report any issues please contact support@ccdc.cam.ac.uk
+


[markdownlint-fix] _{reported by reviewdog 🐶}

Suggested change

github-actions · 2026-02-05T11:43:44Z

scripts/filter_poses/ReadMe.md

@@ -0,0 +1,23 @@
+# Filter Poses
+
+This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities. 


[markdownlint-fix] _{reported by reviewdog 🐶}

Suggested change

This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities.

This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities.

github-actions · 2026-02-05T11:43:44Z

scripts/filter_poses/ReadMe.md

+## Instructions on Running
+
+positional arguments:
+* input file; Input file (multi-molecule file).


[markdownlint-fix] _{reported by reviewdog 🐶}

Suggested change

* input file; Input file (multi-molecule file).

* input file; Input file (multi-molecule file).

github-actions · 2026-02-05T11:43:44Z

scripts/filter_poses/ReadMe.md

+* input file; Input file (multi-molecule file).
+
+options:
+* -h, --help; Show this help message and exit.


[markdownlint-fix] _{reported by reviewdog 🐶}

Suggested change

* -h, --help; Show this help message and exit.

* -h, --help; Show this help message and exit.

github-actions · 2026-02-05T11:43:44Z

scripts/filter_poses/ReadMe.md

+Updated by Chris Ringrose
+
+    For feedback or to report any issues please contact support@ccdc.cam.ac.uk
+


[markdownlint-fix] _{reported by reviewdog 🐶}

Suggested change

Alex-AMC

Thanks for adding the extra info :) Sorry about the reviewdog flood 😅

sonarqubecloud · 2026-02-05T12:05:15Z

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

NO_JIRA Updated and moved some conformer analysis scripts from confid…

84ac1a7

…ential.

github-actions bot reviewed Feb 5, 2026

View reviewed changes

CRingroseCCDC requested a review from Alex-AMC February 5, 2026 11:44

Alex-AMC approved these changes Feb 5, 2026

View reviewed changes

NO_JIRA Updated ReadMe to include new scripts

a751692

CRingroseCCDC merged commit f2c0bbe into main Feb 5, 2026
6 checks passed

CRingroseCCDC deleted the conformer_scripts branch February 5, 2026 12:16


		CCDC Python API Licence required, minimum version: 3.0.15

		Script can be run with any multimolecule file e.g. sdf.

		* --failurefn; Output file for molecules that fail the filter (default: failures.mol)
		* -u, --unusual-torsions; Output CSV file for unusual torsion details (default: unusual_torsions.csv)

		@@ -0,0 +1,23 @@
		# Filter Poses

		This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities.

	* -h, --help; Show this help message and exit

	* -h, --help; Show this help message and exit

		* -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on
		molecule with fewest unusual torsions). WARNING: Relative mode may behave unexpectedly with conformers from

		Updated by Chris Ringrose

		For feedback or to report any issues please contact support@ccdc.cam.ac.uk

	* input file; Input file (multi-molecule file).

	* input file; Input file (multi-molecule file).

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