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Updates:

Apr 18, 2017:
The ArbAlign paper and code is published at JCIM.

Dec 15, 2016:
An updated version of ArbAlign and documentation is posted here.

Nov 01, 2016:
An updated version of ArbAlign is made available here. Please send in any questions, comments and suggestions.



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Coordinates Here are some Cartesian coordinates one can use for testing or other purposes.
├── coordinates/Acenaphtene+Water
│   ├── coordinates/Acenaphtene+Water/dftb-0-1701-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/dftb-1-1438-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/dftb-15-1988-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/dftb-16-1218-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/dftb-19-1279-pw91-dftb-4-744-pw91.py"
│   ├── coordinates/Acenaphtene+Water/dftb-19-1279-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/dftb-22-1877-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/dftb-26-1673-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/dftb-35-1944-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/dftb-4-744-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/dftb-6-1391-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/list"
│   ├── coordinates/Acenaphtene+Water/pm7-46-7-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/pm7-47-6-pw91.xyz"
│   ├── coordinates/Acenaphtene+Water/temp"
├── coordinates/LJ-clusters
│   ├── coordinates/LJ-clusters/1000-1.xyz"
│   ├── coordinates/LJ-clusters/1000-2.xyz"
│   ├── coordinates/LJ-clusters/100-1.xyz"
│   ├── coordinates/LJ-clusters/100-2.xyz"
│   ├── coordinates/LJ-clusters/10-1.xyz"
│   ├── coordinates/LJ-clusters/10-2.xyz"
│   ├── coordinates/LJ-clusters/150-1.xyz"
│   ├── coordinates/LJ-clusters/150-2.xyz"
│   ├── coordinates/LJ-clusters/200-1.xyz"
│   ├── coordinates/LJ-clusters/200-2.xyz"
│   ├── coordinates/LJ-clusters/300-1.xyz"
│   ├── coordinates/LJ-clusters/300-2.xyz"
│   ├── coordinates/LJ-clusters/500-1.xyz"
│   ├── coordinates/LJ-clusters/500-2.xyz"
│   ├── coordinates/LJ-clusters/50-1.xyz"
│   ├── coordinates/LJ-clusters/50-2.xyz"
├── coordinates/Peptides
│   ├── coordinates/Peptides/FGG"
│   │   ├── coordinates/Peptides/FGG/252_FGG55-258_FGG224.py"
│   │   ├── coordinates/Peptides/FGG/252_FGG55.xyz"
│   │   ├── coordinates/Peptides/FGG/253_FGG99.xyz"
│   │   ├── coordinates/Peptides/FGG/254_FGG300.xyz"
│   │   ├── coordinates/Peptides/FGG/255_FGG252.xyz"
│   │   ├── coordinates/Peptides/FGG/256_FGG366.xyz"
│   │   ├── coordinates/Peptides/FGG/257_FGG215.xyz"
│   │   ├── coordinates/Peptides/FGG/258_FGG224.xyz"
│   │   ├── coordinates/Peptides/FGG/259_FGG380.xyz"
│   │   ├── coordinates/Peptides/FGG/260_FGG412.xyz"
│   │   ├── coordinates/Peptides/FGG/261_FGG444.xyz"
│   │   ├── coordinates/Peptides/FGG/262_FGG470.xyz"
│   │   ├── coordinates/Peptides/FGG/263_FGG80.xyz"
│   │   ├── coordinates/Peptides/FGG/264_FGG114.xyz"
│   │   ├── coordinates/Peptides/FGG/265_FGG357.xyz"
│   │   ├── coordinates/Peptides/FGG/266_FGG691.xyz"
│   │   ├── coordinates/Peptides/FGG/list"
│   │   ├── coordinates/Peptides/FGG/RMSD-all.gnu"
│   │   ├── coordinates/Peptides/FGG/temp"
│   ├── coordinates/Peptides/GFA"
│   │   ├── coordinates/Peptides/GFA/236_GFA15.xyz"
│   │   ├── coordinates/Peptides/GFA/237_GFA07.xyz"
│   │   ├── coordinates/Peptides/GFA/238_GFA10.xyz"
│   │   ├── coordinates/Peptides/GFA/239_GFA02.xyz"
│   │   ├── coordinates/Peptides/GFA/240_GFA11.xyz"
│   │   ├── coordinates/Peptides/GFA/241_GFA09.xyz"
│   │   ├── coordinates/Peptides/GFA/242_GFA08.xyz"
│   │   ├── coordinates/Peptides/GFA/243_GFA13.xyz"
│   │   ├── coordinates/Peptides/GFA/244_GFA12.xyz"
│   │   ├── coordinates/Peptides/GFA/245_GFA06.xyz"
│   │   ├── coordinates/Peptides/GFA/246_GFA16.xyz"
│   │   ├── coordinates/Peptides/GFA/247_GFA03.xyz"
│   │   ├── coordinates/Peptides/GFA/248_GFA01.xyz"
│   │   ├── coordinates/Peptides/GFA/249_GFA14.xyz"
│   │   ├── coordinates/Peptides/GFA/250_GFA05.xyz"
│   │   ├── coordinates/Peptides/GFA/251_GFA04.xyz"
│   │   ├── coordinates/Peptides/GFA/list"
│   │   └── coordinates/Peptides/GFA/temp"
│   ├── coordinates/Peptides/GGF"
│   │   ├── coordinates/Peptides/GGF/221_GGF14.xyz"
│   │   ├── coordinates/Peptides/GGF/222_GGF13.xyz"
│   │   ├── coordinates/Peptides/GGF/223_GGF07.xyz"
│   │   ├── coordinates/Peptides/GGF/224_GGF12.xyz"
│   │   ├── coordinates/Peptides/GGF/225_GGF10.xyz"
│   │   ├── coordinates/Peptides/GGF/226_GGF15.xyz"
│   │   ├── coordinates/Peptides/GGF/227_GGF04.xyz"
│   │   ├── coordinates/Peptides/GGF/228_GGF08.xyz"
│   │   ├── coordinates/Peptides/GGF/229_GGF11.xyz"
│   │   ├── coordinates/Peptides/GGF/230_GGF09.xyz"
│   │   ├── coordinates/Peptides/GGF/231_GGF01.xyz"
│   │   ├── coordinates/Peptides/GGF/232_GGF06.xyz"
│   │   ├── coordinates/Peptides/GGF/233_GGF03.xyz"
│   │   ├── coordinates/Peptides/GGF/234_GGF02.xyz"
│   │   ├── coordinates/Peptides/GGF/235_GGF05.xyz"
│   │   ├── coordinates/Peptides/GGF/list"
│   │   └── coordinates/Peptides/GGF/temp"
│   ├── coordinates/Peptides/WG"
│   │   ├── coordinates/Peptides/WG/191_WG03-199_WG15.py"
│   │   ├── coordinates/Peptides/WG/191_WG03.xyz"
│   │   ├── coordinates/Peptides/WG/192_WG10.xyz"
│   │   ├── coordinates/Peptides/WG/193_WG06.xyz"
│   │   ├── coordinates/Peptides/WG/194_WG02.xyz"
│   │   ├── coordinates/Peptides/WG/195_WG01.xyz"
│   │   ├── coordinates/Peptides/WG/196_WG14.xyz"
│   │   ├── coordinates/Peptides/WG/197_WG07.xyz"
│   │   ├── coordinates/Peptides/WG/198_WG09.xyz"
│   │   ├── coordinates/Peptides/WG/199_WG15.xyz"
│   │   ├── coordinates/Peptides/WG/200_WG13.xyz"
│   │   ├── coordinates/Peptides/WG/201_WG12.xyz"
│   │   ├── coordinates/Peptides/WG/202_WG08.xyz"
│   │   ├── coordinates/Peptides/WG/203_WG11.xyz"
│   │   ├── coordinates/Peptides/WG/204_WG04.xyz"
│   │   ├── coordinates/Peptides/WG/205_WG05.xyz"
│   │   ├── coordinates/Peptides/WG/list"
│   │   ├── coordinates/Peptides/WG/temp"
│   └── coordinates/Peptides/WGG"
│   ├── coordinates/Peptides/WGG/206_WGG06.xyz"
│   ├── coordinates/Peptides/WGG/207_WGG08.xyz"
│   ├── coordinates/Peptides/WGG/208_WGG04.xyz"
│   ├── coordinates/Peptides/WGG/209_WGG03.xyz"
│   ├── coordinates/Peptides/WGG/210_WGG05.xyz"
│   ├── coordinates/Peptides/WGG/211_WGG02.xyz"
│   ├── coordinates/Peptides/WGG/212_WGG14.xyz"
│   ├── coordinates/Peptides/WGG/213_WGG15.xyz"
│   ├── coordinates/Peptides/WGG/214_WGG01.xyz"
│   ├── coordinates/Peptides/WGG/215_WGG07.xyz"
│   ├── coordinates/Peptides/WGG/216_WGG11.xyz"
│   ├── coordinates/Peptides/WGG/217_WGG09.xyz"
│   ├── coordinates/Peptides/WGG/218_WGG13.xyz"
│   ├── coordinates/Peptides/WGG/219_WGG10.xyz"
│   ├── coordinates/Peptides/WGG/220_WGG12.xyz"
│   ├── coordinates/Peptides/WGG/list"
│   ├── coordinates/Peptides/WGG/temp"
│   └── coordinates/Peptides/WGG/temp.py"
├── coordinates/s1-ma-w1
│   ├── coordinates/s1-ma-w1/list"
│   ├── coordinates/s1-ma-w1/n-s1maw1-1.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-10.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-11.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-12.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-13.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-14.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-15.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-16.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-17.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-18.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-19.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-1-s1maw1-20.py"
│   ├── coordinates/s1-ma-w1/s1maw1-1.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-20.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-2.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-3.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-4.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-5.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-6.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-7.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-8.xyz"
│   ├── coordinates/s1-ma-w1/s1maw1-9.xyz"
│   ├── coordinates/s1-ma-w1/temp"
│   └── coordinates/s1-ma-w1/t-s1maw1-1.xyz"
├── coordinates/s2-dma-a
│   ├── coordinates/s2-dma-a/list"
│   ├── coordinates/s2-dma-a/odftb-100-3373-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/odftb-114-2924-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/odftb-164-4945-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/odftb-200-5226-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/odftb-209-1929-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/odftb-223-3792-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/odftb-22-3553-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/odftb-244-3955-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/odftb-47-2656-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-2-6168-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-31-474-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-36-14976-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-102-3384-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-112-15190-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-118-8240-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-119-14564-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-125-15140-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-126-3094-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-127-3570-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-134-1705-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-135-13545-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-148-4339-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-153-16850-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-157-13530-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-158-18993-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-172-4742-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-186-720-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-189-17813-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-192-16132-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-193-19084-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-196-6179-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-198-18987-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-202-11432-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-208-19591-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-211-7033-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-214-9797-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-225-17457-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-236-19399-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-244-19538-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-30-12682-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-D-83-15684-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-S-230-14918-wb97xd.xyz"
│   ├── coordinates/s2-dma-a/opm7-S-245-9312-wb97xd.xyz"
│   └── coordinates/s2-dma-a/temp"
└── coordinates/WaterClusters
├── coordinates/WaterClusters/100-1.xyz"
├── coordinates/WaterClusters/100-2.xyz"
├── coordinates/WaterClusters/100-3.xyz"
├── coordinates/WaterClusters/10-PP1.xyz"
├── coordinates/WaterClusters/10-PP2.xyz"
├── coordinates/WaterClusters/11-551A-1.xyz"
├── coordinates/WaterClusters/11-551A-4.xyz"
├── coordinates/WaterClusters/12-D2d-1-L.xyz"
├── coordinates/WaterClusters/12-D2d-1-R.xyz"
├── coordinates/WaterClusters/13-TIP4P.xyz"
├── coordinates/WaterClusters/13-TIP5P.xyz"
├── coordinates/WaterClusters/14-1.xyz"
├── coordinates/WaterClusters/14-2.xyz"
├── coordinates/WaterClusters/15-1.xyz"
├── coordinates/WaterClusters/15-2.xyz"
├── coordinates/WaterClusters/16-TIP4P.xyz"
├── coordinates/WaterClusters/16-TIP5P.xyz"
├── coordinates/WaterClusters/17-TIP4P.xyz"
├── coordinates/WaterClusters/17-TIP5P.xyz"
├── coordinates/WaterClusters/18-TIP4P.xyz"
├── coordinates/WaterClusters/18-TIP5P.xyz"
├── coordinates/WaterClusters/19-TIP4P.xyz"
├── coordinates/WaterClusters/19-TIP5P.xyz"
├── coordinates/WaterClusters/20-TIP4P.xyz"
├── coordinates/WaterClusters/20-TIP5P.xyz"
├── coordinates/WaterClusters/21-TIP4P.xyz"
├── coordinates/WaterClusters/21-TIP5P.xyz"
├── coordinates/WaterClusters/25-1-25-2.xyz"
├── coordinates/WaterClusters/25-1.xyz"
├── coordinates/WaterClusters/25-2.xyz"
├── coordinates/WaterClusters/287-1.xyz"
├── coordinates/WaterClusters/287-2.xyz"
├── coordinates/WaterClusters/2-Cs-1.xyz"
├── coordinates/WaterClusters/2-Cs-2-matched.xyz"
├── coordinates/WaterClusters/2-Cs-2.xyz"
├── coordinates/WaterClusters/2-Cs.xyz"
├── coordinates/WaterClusters/2-OpenC1.xyz"
├── coordinates/WaterClusters/3-UUD.xyz"
├── coordinates/WaterClusters/3-UUU.xyz"
├── coordinates/WaterClusters/40-a.xyz"
├── coordinates/WaterClusters/40-b.xyz"
├── coordinates/WaterClusters/4-Ci.xyz"
├── coordinates/WaterClusters/4-S4.xyz"
├── coordinates/WaterClusters/5-CA-A.xyz"
├── coordinates/WaterClusters/5-CA-B.xyz"
├── coordinates/WaterClusters/5-CA-C.xyz"
├── coordinates/WaterClusters/5-CYC.xyz"
├── coordinates/WaterClusters/5-FR-A.xyz"
├── coordinates/WaterClusters/5-FR-B.xyz"
├── coordinates/WaterClusters/5-FR-C.xyz"
├── coordinates/WaterClusters/60-1.xyz"
├── coordinates/WaterClusters/60-2.xyz"
├── coordinates/WaterClusters/6-BAG.xyz"
├── coordinates/WaterClusters/6-BK-1.xyz"
├── coordinates/WaterClusters/6-BK-2.xyz"
├── coordinates/WaterClusters/6-CA.xyz"
├── coordinates/WaterClusters/6-CB-1.xyz"
├── coordinates/WaterClusters/6-CB-2.xyz"
├── coordinates/WaterClusters/6-CC.xyz"
├── coordinates/WaterClusters/6-PR.xyz"
├── coordinates/WaterClusters/7-BI1.xyz"
├── coordinates/WaterClusters/7-BI2.xyz"
├── coordinates/WaterClusters/7-CA1.xyz"
├── coordinates/WaterClusters/7-CA2.xyz"
├── coordinates/WaterClusters/7-CH1.xyz"
├── coordinates/WaterClusters/7-CH2.xyz"
├── coordinates/WaterClusters/7-CH3.xyz"
├── coordinates/WaterClusters/7-HM1.xyz"
├── coordinates/WaterClusters/7-PR1.xyz"
├── coordinates/WaterClusters/7-PR2.xyz"
├── coordinates/WaterClusters/7-PR3.xyz"
├── coordinates/WaterClusters/8-D2d.xyz"
├── coordinates/WaterClusters/8-S4.xyz"
├── coordinates/WaterClusters/9-D2dDD.xyz"
├── coordinates/WaterClusters/9-S4DA.xyz"
├── coordinates/WaterClusters/a"
├── coordinates/WaterClusters/list"
├── coordinates/WaterClusters/list-test"