leeyang/drfold

drfold's Issues

Issues with Terminal Output from Test Command

My environment seems to be set up successfully. Then, I ran the test command you provided:

bash DRfold.sh test/seq.fasta test/DRfold_out

The terminal output is as follows, always displaying messages like Bad direction ... and Line search cannot locate an adequate point after MAXLS. Are these normal outputs?

No module named 'rigid' in DRfold/PotentialFold/Fold.py

ModuleNotFoundError
No module named 'rigid'
File ".../DRfold/PotentialFold/Fold.py", line 13, in
import a2b,rigid
ModuleNotFoundError: No module named 'rigid'

Questions about installing PETfold

Dear Yang,

I hope this message finds you well. I am reaching out to express my admiration for your work on DRfold. It is quite remarkable and has greatly piqued my interest.

I have been diligently trying to get DRfold up and running; however, I've encountered a snag and would sincerely appreciate your guidance.

In line with your remarks in a specific issue, I understood that you utilized PETfold v2.0 and it functioned as expected. Following the same path, I installed PETfold v2.0. The installation guide asked for specific settings related to 'HPATH' and 'LPATH' within the 'Makefile', directing them to the locations of certain Vienna RNA Package files:

PETfold needs the Vienna RNA Package (see [2]) installed on your
computer. You have to edit the variables 'HPATH' and 'LPATH' at the
top of the 'Makefile' in the 'src' subfolder by setting them to the
location of the Vienna RNA Package header files and the libRNA.a file.
The source code of Pfold is part of the PETfold program (thanks to
Bjarne Knudsen) and is compiled together with it.

$ cd src
$ make clean
$ make

If you don't start PETfold directly from the bin folder then you have
to set the environment variable PETFOLDBIN to the path of Pfold
grammar files scfg.rate and article.grm:
$ export PETFOLDBIN='<PATH>/bin'

Initially, the 'Makefile' had these defaults:

HPATH = /opt/ViennaRNA/2.0.7/include/ViennaRNA/
LPATH = /opt/ViennaRNA/2.0.7/lib/libRNA.a

Considering I have ViennaRNA v2.6.4 installed (the most recent version provided officially), the file directory structure notably differs from the default version, v2.0.7. Here are my speculative adjustments for the paths:

HPATH = /${mypath}/ViennaRNA/2.0.7/include/ViennaRNA/
LPATH = /${mypath}/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a

Upon executing make clean and make, the latter operation unfortunately resulted in an error. Here’s a part of the log close to the end for your reference:

/mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1330: undefined reference to
 `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1329: undefined
 reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o): in function `SVC_Q::S
VC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278: undefined reference to
 `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277: undefined
 reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278: undefined
 reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277: undefined
 reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.ro._ZTI7QMa
trix[_ZTI7QMatrix]+0x0): undefined reference to `vtable for __cxxabiv1::__class_type_info'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.ro._ZTI6Ker
nel[_ZTI6Kernel]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.ro._ZTI6Sol
ver[_ZTI6Solver]+0x0): undefined reference to `vtable for __cxxabiv1::__class_type_info'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.ro._ZTI9Sol
ver_NU[_ZTI9Solver_NU]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.ro._ZTI5SVC
_Q[_ZTI5SVC_Q]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.ro._ZTI11ON
E_CLASS_Q[_ZTI11ONE_CLASS_Q]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.ro._ZTI5SVR
_Q[_ZTI5SVR_Q]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.ro._ZTV6Ker
nel[_ZTV6Kernel]+0x10): undefined reference to `__cxa_pure_virtual'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.ro._ZTV6Ker
nel[_ZTV6Kernel]+0x18): undefined reference to `__cxa_pure_virtual'
/usr/bin/ld: /mnt/nas2/home/yangnianzu/DRfold/ViennaRNA-2.6.4/src/ViennaRNA/libRNA.a(svm.o):(.data.rel.local.DW.re
f.__gxx_personality_v0[DW.ref.__gxx_personality_v0]+0x0): undefined reference to `__gxx_personality_v0'
collect2: error: ld returned 1 exit status
make: *** [Makefile:15: ../bin/PETfold] Error 1

At this juncture, I am kindly seeking your advice. Could you please specify which version of ViennaRNA was in your use? Also, how did you determine the settings for LPATH and HPATH?

Thank you in advance for your time and assistance. I am looking forward to your valuable guidance.

Best regards,
Nianzu Yang

Installation of PETfold in the readme is misdirecting

Hi,
Thanks for your good work on the RNA structure prediction.
However, I found some problems installing the PETfold package.
On the homepage, you suggest

2. How to install the DRfold?
1) Third-party softwares
1. PETfold (https://rth.dk/resources/petfold/download.html)
2. The ViennaRNA Package (https://www.tbi.univie.ac.at/RNA/)
3. Arena (https://github.com/pylelab/Arena)# If bin/Arena does not work, try to compile from thsi source

The mentioned version of the PETfold was 1.0 in 2008.
Your shell script will fail because there is no option PETfold -r in version 1.0.

You should use the version 2.0/2.1 here:
version 2.1

and

export PETFOLDBIN=#Your PETFOLDBIN path here#

Hope you can update the tutorial.

what's the base.npy?

I want to know what features are in the base.npy. Anyone can tell me?