new saxs rt to cover the case of gaps in sequence

regtest/isdb/rt-saxs-3/Makefile

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+include ../../scripts/test.make

regtest/isdb/rt-saxs-3/config

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+mpiprocs=2
+type=driver
+arg="--plumed plumed.dat --mf_pdb protein_rna.pdb"

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

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

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

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

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

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

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