Changeset 5fef0d7

Timestamp:

09/02/10 10:25:36 (14 years ago)

Author:

Jan Meinke <j.meinke@…>

Branches:

master

Children:

225475c

Parents:

3fbbfbb

Message:

Changed module name from smmp to smmp_p.

Fixed conversion to residue and atom names.

Files:

• Makefile (modified) (2 diffs)
• algorithms.py (modified) (2 diffs)
• enysol_p.f (modified) (1 diff)
• protein.py (modified) (3 diffs)

Makefile

@@ -136 +136 @@
 # The following line includes the minimum set of files needed to fullfill all dependencies.
 #
-# f2py -c -m smmp basic_smmp.pyf init_molecule.f init_energy.f bldmol.f nursvr.f pdbread.f redvar.f redseq.f outvar.f redstr.f enysol.f setmvs.f mklist.f getmol.f helix.f contacts.f dihedr.f setvar.f init_lund.f90 rmsdfun.f addend.f difang.f
+# f2py -c -m smmp_p basic_smmp.pyf init_molecule.f init_energy.f bldmol.f nursvr.f pdbread.f redvar.f redseq.f outvar.f redstr.f enysol.f setmvs.f mklist.f getmol.f helix.f contacts.f dihedr.f setvar.f init_lund.f90 rmsdfun.f addend.f difang.f
 pybind: $(FILES)
         #./rmexclpoint.py $(FILES)
@@ -144 +144 @@
 # Compile bindings that include enyshe_p
 ppybind: basic_smmp.pyf init_molecule.f init_energy.f bldmol.f nursvr.f pdbread.f redvar.f redseq.f outvar.f redstr.f enysol.f setmvs.f mklist.f getmol.f helix.f contacts.f dihedr.f setvar.f init_lund.f90 rmsdfun.f addend.f difang.f energy.f enyshe_p.f enyflx.f enylun.f eninteract.f enyreg.f eyabgn.f esolan.f gradient.f twister.f opesol.f opeflx.f opereg.f opeshe.f utilities.f
-        f2py -c -m smmp basic_smmp.pyf init_molecule.f init_energy.f bldmol.f nursvr.f pdbread.f redvar.f redseq.f outvar.f redstr.f enysol.f setmvs.f mklist.f getmol.f helix.f contacts.f dihedr.f setvar.f init_lund.f90 rmsdfun.f addend.f difang.f energy.f enyshe_p.f enyflx.f enylun.f eninteract.f enyreg.f eyabgn.f esolan.f gradient.f twister.f opesol.f opeflx.f opereg.f opeshe.f utilities.f -I/usr/lib/mpi/gcc/openmpi/include -I/usr/lib/mpi/gcc/openmpi/lib -L/usr/lib/mpi/gcc/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl  -lutil -lm -ldl
+        f2py -c -m smmp_p basic_smmp.pyf init_molecule.f init_energy.f bldmol.f nursvr.f pdbread.f redvar.f redseq.f outvar.f redstr.f enysol_p.f setmvs.f mklist.f getmol.f helix.f contacts.f dihedr.f setvar.f init_lund.f90 rmsdfun.f addend.f difang.f energy.f enyshe_p.f enyflx.f enylun.f eninteract.f enyreg.f eyabgn.f esolan.f gradient.f twister.f opesol.f opeflx.f opereg.f opeshe.f utilities.f -I/usr/lib/mpi/gcc/openmpi/include -I/usr/lib/mpi/gcc/openmpi/lib -L/usr/lib/mpi/gcc/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl  -lutil -lm -ldl
 
 newbasicpybind: init_molecule.f init_energy.f energy.f utilities.f
-        f2py --overwrite-signature -h basic_smmp.pyf -m smmp init_molecule.f init_energy.f energy.f utilities.f
+        f2py --overwrite-signature -h basic_smmp.pyf -m smmp_p init_molecule.f init_energy.f energy.f utilities.f
 
 newpybind: $(FILES)

algorithms.py

@@ -6 +6 @@
 import copy
 import random
-import smmp
+import smmp_p as smmp
 from math import *
 from universe import *
@@ -58 +58 @@
         """Performs a single Monte Carlo sweep."""
         eol = self.__univ.energy()
-        eol, self.__acc = smmp.metropolis(eol, self.__acc, self.__weight)
-        #eol = self.metropolis()
+        #eol, self.__acc = smmp.metropolis(eol, self.__acc, self.__weight)
+        eol = self.metropolis()
         self.__performedSweeps += 1
         if eol < self.__minEnergy:

enysol_p.f

@@ -334 +334 @@
       call MPI_ALLREDUCE(eysl, eyslsum, 1, MPI_DOUBLE_PRECISION,
      &      MPI_SUM,my_mpi_comm, ierror)
-!       write (logString, *) 'enysol>', myrank, eysl, eyslsum
+      write (logString, *) 'enysol>', myrank, eysl, eyslsum
       tsurfres = surfres
       call MPI_ALLREDUCE(tsurfres, surfres, mxrs, MPI_DOUBLE_PRECISION,

protein.py

@@ -6 +6 @@
 #
 import sys
+import numpy as np
 import smmp_p as smmp
 from math import *
@@ -52 +53 @@
         
     def name(self):
-        return ''.join([smmp.atm_c.nmat[i][self.__id] for i in range(0,4)]).strip()
+        return ''.join(smmp.atm_c.nmat[:,0].reshape([-1,4])[self.__id]).strip()
         
     def __str__(self):
@@ -174 +175 @@
     def residues(self):
         """Returns a list of the amino acids in this protein."""
-        seq = [str(c[0]) for c in smmp.res_c.seq]
+        seq = [''.join(l) for l in np.array([str(c[0]) for c in smmp.res_c.seq]).reshape([-1, 4])]
         first = smmp.mol_i.irsml1[self.__id]- 1
         last = smmp.mol_i.irsml2[self.__id] - 1
-        return ''.join(seq).split()[first:last]
+        return seq[first:last]
         
     def id(self):