Michel Petitjean / softwares / freewares
Author's professional address:
MTi, INSERM UMR-S 973, Université Paris 7
35 rue Hélène Brion, 75205 Paris Cedex 13, France.
michel.petitjean@univ-paris-diderot.fr, or
petitjean.chiral@gmail.com
Formerly: CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), Saclay, France
(and formerly: ITODYS, UMR 7086, CNRS, Université Paris 7).
Due to minor corrections in the input data modules (e.g. the names of the molecules were sometimes truncated),
all the freewares have been recompiled the 13 April 2010 and then the 26 October 2010 on the following platforms:
Intel linux 32 bits, Intel linux 64 bits, and Mac OS X.
Some subsequent recompilations occurred, mainly to increase buffer sizes.
Binaries for other platforms are no longer maintained.
Increased versions numbers in the filenames of the binaries indicate further changes (see the associated documentations).
The corrections do NOT affect the algorithms and the calculations.
The binaries are now provided directly in executable form: neither decoding nor installation procedure is required.
Eventually, mark the binary as executable with the chmod command if not already done after download.
Personal remark for developpers and users: I recommend to work on linux systems and I do not recommend to work on Windows systems.
- ARMS:
Spatial Alignment with the RMS (Root Mean Square) method.
(fixed pairwise correspondence)
- ASV:
Analytical calculation of van der Waals surfaces and volumes.
(or any union of spheres)
- CSR:
The Combined SDM/RMS Algorithm for spatial alignment of two molecules.
(pairwise correspondence computed)
- CYL:
Minimal radius enclosing cylinder. Minimal radius circumscribed cylinder.
- DIVCF:
Selects by clustering major conformations of a molecule in a set of its conformers.
- DOG:
Docking Geometrically two molecules.
(fixed pairwise correspondence)
- GRD:
Computation of the Radius and Diameter of a molecular graph.
(computes also the topological shape index)
- MCG:
Optimal Partition (classification): numerical variables and non-euclidean spaces.
The number of classes is computed.
- POP:
Optimal Partition (classification): categorical variables.
The number of classes is computed.
- POSE:
Computes the RMSD between two ligand poses.
No rotation translation is performed.
- QCM:
Quantitative Chirality Measure of a conformer
(graph automorphisms enumeration included)
- RADI:
Computation of the Radius and Diameter of a spatial set.
(computes also various other geometrical parameters)
Theories:
- ARMS: Spatial Alignment with the RMS (Root Mean Square) method.
THEORY
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- ASV: Analytical calculation of van der Waals surfaces and volumes (union of spheres).
THEORY
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
download f77 source for surfaces (only Monte-Carlo) (input data module not included)
download f77 source for volumes (only Monte-Carlo) (input data module not included)
download f77 portable random generator (parametrized)
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules.
THEORY
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
- CYL: Minimal radius enclosing cylinder. Circumscribed cylinders.
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers.
THEORY
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- DOG: Docking Geometrically two molecules.
(enhanced version 2.*: see the documentation)
THEORY
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- GRD: Computation of the Radius and Diameter of a molecular graph.
(computes also the topological shape index)
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces.
(MCG2 corresponds to version 2.*:see the documentation)
THEORY
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
download f77 source for ascending hierarchical clustering (with stop criterion)
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- POP: Optimal Partition (classification): categorical variables.
THEORY
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
download f77 source (3 subroutines; input data module not included)
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- POSE: Computes the RMSD between two ligand poses.
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- QCM: Quantitative Chirality Measure of a conformer.
(graph automorphisms enumeration included)
THEORY
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X
- RADI: Computation of the RAdius and DIameter of a spatial set, plus various geometric descriptors.
View and/or download documentation (with references)
Hotline: michel.petitjean@univ-paris-diderot.fr,
petitjean.chiral@gmail.com
- download binary for linux Intel 32 bits
- download binary for linux Intel 64 bits
- download binary for Mac OS X