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new saxs rt to cover the case of gaps in sequence
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@carlocamilloni
carlocamilloni committed May 31, 2024
1 parent ecb6587 commit 58d660f
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1 change: 1 addition & 0 deletions regtest/isdb/rt-saxs-3/Makefile
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include ../../scripts/test.make
3 changes: 3 additions & 0 deletions regtest/isdb/rt-saxs-3/config
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mpiprocs=2
type=driver
arg="--plumed plumed.dat --mf_pdb protein_rna.pdb"
10,570 changes: 10,570 additions & 0 deletions regtest/isdb/rt-saxs-3/forces.reference
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10,570 changes: 10,570 additions & 0 deletions regtest/isdb/rt-saxs-3/forces_sans.reference
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117 changes: 117 additions & 0 deletions regtest/isdb/rt-saxs-3/plumed.dat
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MOLINFO STRUCTURE=protein_rna.pdb

SAXS ...
NOPBC
ATOMS=128-3647
ATOMISTIC
LABEL=saxs
QVALUE1=0.0002
QVALUE2=0.03
QVALUE3=0.04
QVALUE4=0.05
QVALUE5=0.06
QVALUE6=0.07
QVALUE7=0.08
QVALUE8=0.09
QVALUE9=0.1
... SAXS

DUMPDERIVATIVES ARG=(saxs\.q-.*) FILE=forces FMT=%7.4f

SAXS ...
NOPBC
SERIAL
ATOMS=128-3647
ATOMISTIC
LABEL=psaxs
QVALUE1=0.0002
QVALUE2=0.03
QVALUE3=0.04
QVALUE4=0.05
QVALUE5=0.06
QVALUE6=0.07
QVALUE7=0.08
QVALUE8=0.09
QVALUE9=0.1
... SAXS

SAXS ...
NOPBC
ATOMS=128-3647
ONEBEAD
TEMPLATE=template.pdb
LABEL=psaxsoneb
QVALUE1=0.0002
QVALUE2=0.03
QVALUE3=0.04
QVALUE4=0.05
QVALUE5=0.06
QVALUE6=0.07
QVALUE7=0.08
QVALUE8=0.09
QVALUE9=0.1
... SAXS

SAXS ...
NOPBC
ATOMS=128-3647
ONEBEAD
SOLVATION_CORRECTION=0.1
TEMPLATE=template.pdb
LABEL=psaxsonebsurf
QVALUE1=0.0002
QVALUE2=0.03
QVALUE3=0.04
QVALUE4=0.05
QVALUE5=0.06
QVALUE6=0.07
QVALUE7=0.08
QVALUE8=0.09
QVALUE9=0.1
... SAXS

SANS ...
NOPBC
ATOMS=128-3647
ATOMISTIC
DEUTER_CONC=0
LABEL=sans
QVALUE1=0.0002
QVALUE2=0.03
QVALUE3=0.04
QVALUE4=0.05
QVALUE5=0.06
QVALUE6=0.07
QVALUE7=0.08
QVALUE8=0.09
QVALUE9=0.1
... SANS

SANS ...
NOPBC
ATOMS=128-3647
ONEBEAD
SOLVATION_CORRECTION=0.1
DEUTER_CONC=0
TEMPLATE=template.pdb
LABEL=psansonebsurf
QVALUE1=0.0002
QVALUE2=0.03
QVALUE3=0.04
QVALUE4=0.05
QVALUE5=0.06
QVALUE6=0.07
QVALUE7=0.08
QVALUE8=0.09
QVALUE9=0.1
... SANS

DUMPDERIVATIVES ARG=(psansonebsurf\.q-.*) FILE=forces_sans FMT=%7.4f


PRINT ARG=saxs.* FILE=saxs.dat STRIDE=1
PRINT ARG=psaxs.* FILE=psaxs.dat STRIDE=1
PRINT ARG=psaxsoneb.* FILE=psaxs_onebead.dat STRIDE=1
PRINT ARG=psaxsonebsurf.* FILE=psaxs_onebead_surf.dat STRIDE=1
PRINT ARG=sans.* FILE=sans.dat STRIDE=1
PRINT ARG=psansonebsurf.* FILE=psans_onebead_surf.dat STRIDE=1
3,711 changes: 3,711 additions & 0 deletions regtest/isdb/rt-saxs-3/protein_rna.pdb
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2 changes: 2 additions & 0 deletions regtest/isdb/rt-saxs-3/psans_onebead_surf.dat.reference
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#! FIELDS time psansonebsurf.q-0 psansonebsurf.q-1 psansonebsurf.q-2 psansonebsurf.q-3 psansonebsurf.q-4 psansonebsurf.q-5 psansonebsurf.q-6 psansonebsurf.q-7 psansonebsurf.q-8
0.000000 0.999995 0.911414 0.847796 0.772260 0.688729 0.601252 0.513703 0.429506 0.351441
2 changes: 2 additions & 0 deletions regtest/isdb/rt-saxs-3/psaxs.dat.reference
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#! FIELDS time psaxs.q-0 psaxs.q-1 psaxs.q-2 psaxs.q-3 psaxs.q-4 psaxs.q-5 psaxs.q-6 psaxs.q-7 psaxs.q-8
0.000000 0.999996 0.911483 0.847907 0.772435 0.689000 0.601656 0.514276 0.430281 0.352436
2 changes: 2 additions & 0 deletions regtest/isdb/rt-saxs-3/psaxs_onebead.dat.reference
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#! FIELDS time psaxsoneb.q-0 psaxsoneb.q-1 psaxsoneb.q-2 psaxsoneb.q-3 psaxsoneb.q-4 psaxsoneb.q-5 psaxsoneb.q-6 psaxsoneb.q-7 psaxsoneb.q-8
0.000000 0.999996 0.910966 0.847009 0.771109 0.687234 0.599474 0.511732 0.427448 0.349403
2 changes: 2 additions & 0 deletions regtest/isdb/rt-saxs-3/psaxs_onebead_surf.dat.reference
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#! FIELDS time psaxsonebsurf.q-0 psaxsonebsurf.q-1 psaxsonebsurf.q-2 psaxsonebsurf.q-3 psaxsonebsurf.q-4 psaxsonebsurf.q-5 psaxsonebsurf.q-6 psaxsonebsurf.q-7 psaxsonebsurf.q-8
0.000000 0.999996 0.902851 0.833594 0.752004 0.662673 0.570259 0.479111 0.392945 0.314630
2 changes: 2 additions & 0 deletions regtest/isdb/rt-saxs-3/sans.dat.reference
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#! FIELDS time sans.q-0 sans.q-1 sans.q-2 sans.q-3 sans.q-4 sans.q-5 sans.q-6 sans.q-7 sans.q-8
0.000000 0.999996 0.912219 0.849100 0.774086 0.691044 0.603973 0.516712 0.432673 0.354638
2 changes: 2 additions & 0 deletions regtest/isdb/rt-saxs-3/saxs.dat.reference
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#! FIELDS time saxs.q-0 saxs.q-1 saxs.q-2 saxs.q-3 saxs.q-4 saxs.q-5 saxs.q-6 saxs.q-7 saxs.q-8
0.000000 0.999996 0.911483 0.847907 0.772435 0.689000 0.601656 0.514276 0.430281 0.352436
3,521 changes: 3,521 additions & 0 deletions regtest/isdb/rt-saxs-3/template.pdb
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1 comment on commit 58d660f

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Found broken examples in automatic/ANGLES.tmp
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/CAVITY.tmp
Found broken examples in automatic/CLASSICAL_MDS.tmp
Found broken examples in automatic/CLUSTER_DIAMETER.tmp
Found broken examples in automatic/CLUSTER_DISTRIBUTION.tmp
Found broken examples in automatic/CLUSTER_PROPERTIES.tmp
Found broken examples in automatic/CONSTANT.tmp
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Found broken examples in automatic/CONTACT_MATRIX_PROPER.tmp
Found broken examples in automatic/COORDINATIONNUMBER.tmp
Found broken examples in automatic/DFSCLUSTERING.tmp
Found broken examples in automatic/DISTANCE_FROM_CONTOUR.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FIND_CONTOUR.tmp
Found broken examples in automatic/FIND_CONTOUR_SURFACE.tmp
Found broken examples in automatic/FIND_SPHERICAL_CONTOUR.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
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Found broken examples in automatic/INCLUDE.tmp
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Found broken examples in automatic/INTERPOLATE_GRID.tmp
Found broken examples in automatic/LOCAL_AVERAGE.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/MULTICOLVARDENS.tmp
Found broken examples in automatic/OUTPUT_CLUSTER.tmp
Found broken examples in automatic/PAMM.tmp
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Found broken examples in automatic/PCAVARS.tmp
Found broken examples in automatic/PIV.tmp
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Found broken examples in automatic/PYCVINTERFACE.tmp
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Found broken examples in automatic/Q3.tmp
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Found broken examples in automatic/QUATERNION.tmp
Found broken examples in automatic/SIZESHAPE_POSITION_LINEAR_PROJ.tmp
Found broken examples in automatic/SIZESHAPE_POSITION_MAHA_DIST.tmp
Found broken examples in automatic/SPRINT.tmp
Found broken examples in automatic/TETRAHEDRALPORE.tmp
Found broken examples in automatic/TORSIONS.tmp
Found broken examples in automatic/WHAM_WEIGHTS.tmp
Found broken examples in AnalysisPP.md
Found broken examples in CollectiveVariablesPP.md
Found broken examples in MiscelaneousPP.md

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