SOFTWARES, FREEWARES
© Michel Petitjean (retired since Jan 1st, 2023)
Author's most recent professional address:
INSERM ERL U1133 (BFA, CNRS UMR 8251), Université Paris Cité
35 rue Hélène Brion, 75205 Paris Cedex 13, France.
Formerly (2010-2018): MTi, INSERM UMR-S 973, Université Paris 7.
Formerly (2007-2009): CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), Saclay, France.
Formerly (1987-2006): ITODYS, CNRS UMR 7086, Université Paris 7.
Contact: petitjean.chiral@gmail.com
DISCLAIMER: all data, sources, scripts, and codes are provided as is, without any warranty.
Binaries can be generated from their f77 sources at https://hal.archives-ouvertes.fr/hal-03798049
Some people unfamiliar with calling binaries from unix scripts may look at the following example:
# script: begin
cat << eof | some_executable_binary
data line as read from keyboard
data line as read from keyboard
data line as read from keyboard
eof
# script: end
Then the result of the execution of the script can be directed to an output file.
All binaries below can be called by an appropriate unix script.
Most recent update of this page: 23 December 2023.
- ARMS: Spatial Alignment with the RMS (Root Mean Square) method, fixed pairwise correspondence.
THEORY (Procrustes Methods, Shape Recognition, Similarity and Docking)
Simplified user guide (with references)
- ASV: Analytical calculation of van der Waals surfaces and volumes (or any union of spheres).
THEORY
Simplified user guide (with references)
- CCCPP: Computes Cavites, Channels, Pores and Pockets in proteins.
Simplified user guide (with references)
- CONE: Smallest enclosing cone. Best fit cone. Conicity index.
Simplified user guide (with references)
- CONICA: Largest enclosed cone.
Simplified user guide (with references)
- CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules (pairwise correspondence computed).
THEORY (Procrustes Methods, Shape Recognition, Similarity and Docking)
Simplified user guide (with references)
- CYL: Minimal radius enclosing cylinder. Minimal radius circumscribed cylinders.
Simplified user guide (with references)
- DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers.
THEORY (Data Mining in Chemical Databases)
Simplified user guide (with references)
- DOG: Docking Geometrically two molecules (fixed pairwise correspondence).
THEORY (Procrustes Methods, Shape Recognition, Similarity and Docking)
Simplified user guide (with references)
- GRD: Computation of the Radius and Diameter of a molecular graph. Computes also the topological shape index.
Simplified user guide (with references)
- MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces. The number of classes is computed.
THEORY (Classification: Computing an Optimal Partition)
Simplified user guide (with references)
- PCI: Pocket Convexity Index. Pocket Sphericity Index. Best fit sphere. Distributional Sphericity Coefficient
Simplified user guide (with references)
- POP: Optimal Partition (classification): categorical variables. The number of classes is computed.
THEORY (Classification: Computing an Optimal Partition)
Simplified user guide (with references)
- POSE: Computes the RMSD between two ligand poses. No rotation and no translation is performed.
Simplified user guide (with references)
- PPIC: Computes the interface protein-protein or protein-ligand. Three methods are implemented, two being parameter free.
Simplified user guide (with references)
- QCM: Quantitative Chirality Measure of a conformer.
(graph automorphisms enumeration included)
THEORY (The Mathematical Theory of Chirality)
(see also: Symmetry, Chirality, Symmetry Measures and Chirality Measures: General Definitions)
(and also: An Asymmetry Coefficient for Multivariate Distributions)
Simplified user guide (with references)
- RADI: Computation of the RAdius and DIameter of a spatial set, plus various geometric descriptors.
Simplified user guide (with references)
- RESISTDIAG: Rapid evaluation of HIV drugs resistances (with database).
Data and software have migrated elsewhere: please contact anne.vanet@u-paris.fr.
- VIRAPOPS: A forward simulator dedicated to rapidly evolved viral populations.
Simplified user guide (with references)