build.rna_tools.tools.rna_x3dna.rna_x3dna.x3DNA.run_x3dna() - Code Metrics - mmagnus/rna-tools - Measure and Improve Code Quality continuously with Scrutinizer

x3DNA.run_x3dna() B
last analyzed 2025-11-03 17:23 UTC

↳ Parent: build.rna_tools.tools.rna_x3dna.rna_x3dna

Complexity

Conditions

Size

Total Lines	32
Code Lines	23

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	7
eloc	23
nop	3
dl	0
loc	32
rs	7.9279
c	0
b	0
f	0

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Python parser to 3dna <http://x3dna.org/>.

Installation::

  # install the code from http://forum.x3dna.org/downloads/3dna-download/
  Create a copy of the rna_x3dna_config_local_sample.py (remove "_sample") present in rna-tools/rna_tools/tools/rna_x3dna folder.
  Edit this line :
  BINARY_PATH = <path to your x3dna-dssr file>
  matching the path with the path of your x3dna-dssr file.
  e.g. in my case: BINARY_PATH = ~/bin/x3dna-dssr.bin

For one structure you can run this script as::

    [mm] py3dna$ git:(master) ✗ ./rna_x3dna.py test_data/1xjr.pdb
    test_data/1xjr.pdb
    >1xjr nts=47 [1xjr] -- secondary structure derived by DSSR
    gGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
    ..(((((((...((((.((((.....))..))..))).).)))))))

For multiple structures in the folder, run the script like this::

    [mm] py3dna$ git:(master) ✗ ./rna_x3dna.py test_data/*
    test_data/1xjr.pdb
    >1xjr nts=47 [1xjr] -- secondary structure derived by DSSR
    gGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
    ..(((((((...((((.((((.....))..))..))).).)))))))
    test_data/6TNA.pdb
    >6TNA nts=76 [6TNA] -- secondary structure derived by DSSR
    GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAPcUGGAGgUCcUGUGtPCGaUCCACAGAAUUCGCACCA
    (((((((..((((.....[..)))).((((.........)))).....(((((..]....))))))))))))....
    test_data/rp2_bujnicki_1_rpr.pdb
    >rp2_bujnicki_1_rpr nts=100 [rp2_bujnicki_1_rpr] -- secondary structure derived by DSSR
    CCGGAGGAACUACUG&CCGGCAGCCU&CCGGAGGAACUACUG&CCGGCAGCCU&CCGGAGGAACUACUG&CCGGCAGCCU&CCGGAGGAACUACUG&CCGGCAGCCU
    [[[[(((.....(((&{{{{))))))&(((((((.....(.(&]]]]).))))&[[[[[[......[[[&))))]]].]]&}}}}(((.....(((&]]]]))))))

.. warning:: This script should not be used in this given form with Parallel because it process output files from x3dna that are named always in the same way, e.g. dssr-torsions.txt. #TODO

"""
import re
import argparse

from subprocess import Popen, PIPE
import os
from rna_tools.rna_tools_config import X3DNA, X3DNA_FP
# x3dna-dssr-64bit


class x3DNAMissingFile(Exception):
    pass


def get_parser():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('-c', '--compact',  action='store_true')
    parser.add_argument('-x', '--rerun',  action='store_true')
    parser.add_argument('-s', '--show',  action='store_true', help="show results")
    parser.add_argument('--pymol',  action='store_true', help='get resi to color code puckers in PyMOL')
    parser.add_argument('-l', '--show-log',  action='store_true', help="show full log")
    parser.add_argument('-v', '--verbose',  action='store_true', help="show full log")
    parser.add_argument('files', help='file', nargs='+')
    return parser


class x3DNA(object):

    """
    Atributes:

     **curr_fn**
     **report**

    """

    def __init__(self, pdbfn, show_log=False):
        """Set self.curr_fn based on pdbfn"""
        self.curr_fn = pdbfn
        self.run_x3dna(show_log)
        self.clean_up()

    def __get_report(self):
        """Off right now. Run find_pair

        ..warning:: To get modification use get_modifications()
        """
        cmd = X3DNA_FP + ' ' + self.curr_fn + ' stdout | analyze stdin'  # hack
        out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True)

        stdout = out.stdout.read()
        outerr = out.stderr.read()

        text = ''
        for l in outerr.split('\n'):
            if l.startswith('Time used') or l.startswith('..') or l.startswith('handling') or l.startswith('uncommon residue'):
                continue
            if l.strip():
                text += l + '\n'
        return text.strip()

    def get_modifications(self):
        """Run find_pair to find modifications.
        """
        cmd = X3DNA_FP + ' -p ' + self.curr_fn + ' /tmp/fpout'  # hack
        out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True)

        outerr = out.stderr.read()

        text = ''
        for l in outerr.split('\n'):
            if l.startswith('uncommon residue'):
                text += l.replace('uncommon residue ', '') + '\n'
        return text.strip()

    def run_x3dna(self, show_log=False, verbose=False):
        """
        """
        cmd = X3DNA + ' -i=' + self.curr_fn
        out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True)

        stdout = str(out.stdout.read().decode())
        outerr = str(out.stderr.read().decode())

        f = open('py3dna.log', 'w')
        if verbose: print(f'cmd: {cmd}')
        f.write(cmd + '\n' + stdout)

        if show_log:
            print(stdout)
        f.close()

        if outerr.find('does not exist!') > -1:  # not very pretty
            raise x3DNAMissingFile
        if outerr.find('not found') > -1:  # not very pretty
            raise Exception('x3dna not found!')

        rx = re.compile('no. of DNA/RNA chains:\s+(?P<no_DNARNAchains>\d+)\s').search(stdout)
        if rx:
            no_of_DNARNA_chains = int(rx.group('no_DNARNAchains'))
            msg = 'py3dna::no of DNARNA chains'
            self.report = msg + '\n' + msg + '\n'  # hack!
        else:
            raise Exception('no_of_DNARNA_chains not found')

        if no_of_DNARNA_chains:
            self.report = stdout.strip()

    def get_ion_water_report(self):
        """@todo
File name: /tmp/tmp0pdNHS
    no. of DNA/RNA chains: 0 []
    no. of nucleotides:    174
    no. of waters:         793
    no. of metals:         33 [Na=29, Mg=1, K=3]
        """
        pass

    def clean_up(self, verbose=False):
        files_to_remove = [
            'dssr-helices.pdb',
            'dssr-pairs.pdb',
            'dssr-torsions.dat',
            'dssr-hairpins.pdb',
            'dssr-multiplets.pdb',
            'dssr-stems.pdb',
            'dssr-Aminors.pdb',
            'hel_regions.pdb',
            'bp_order.dat',
            'bestpairs.pdb',
        ]

        for f in files_to_remove:
            try:
                os.remove(f)
                pass
            except OSError:
                if verbose:
                    print('error: can not remove %s' % f)

    def get_seq(self):
        """Get sequence.

        Somehow 1bzt_1 x3dna	UCAGACUUUUAAPCUGA, what is P?
        P -> u
        
        """
        return self.report.split('\n')[-2].replace('P', 'u').replace('I', 'a')

    def get_secstruc(self):
        """Get secondary structure.
        """
        hits = re.search("as a whole and per chain.*?\n(?P<ss>.+?)\n\*", self.report, re.DOTALL|re.MULTILINE)
        if hits:
             return hits.group('ss').strip()
        else:
            self.report.split('\n')[-1] # tofix

    def get_torsions(self, outfn) -> str:
        """Get torsion angles into 'torsion.csv' file::

            nt,id,res,alpha,beta,gamma,delta,epsilon,zeta,e-z,chi,phase-angle,sugar-type,ssZp,Dp,splay,bpseq
            1,g,A.GTP1,nan,nan,142.1,89.5,-131.0,-78.3,-53(BI),-178.2(anti),358.6(C2'-exo),~C3'-endo,4.68,4.68,29.98,0
            2,G,A.G2,-75.8,-167.0,57.2,79.5,-143.4,-69.7,-74(BI),-169.2(anti),5.8(C3'-endo),~C3'-endo,4.68,4.76,25.61,0
        
        """
        angles = ''
        save = False

        c2pendo = []
        c3pendo = []
        if not os.path.isfile('dssr-torsions.txt'):
            
            print(f'Problem to get torsion angles for {self.curr_fn}')
            return f'Problem to get torsion angles for {self.curr_fn}'
            
        for l in open('dssr-torsions.txt'):
            if 'nt               alpha    beta' in l:
                save = True
                l = l.replace('nt',  'nt id   res   ')
            if '***************' in l and save:
                save = False
            if save:
                if "~C2'-endo" in l:
                    c2pendo.append(l.split()[0])
                if "~C3'-endo" in l:
                    c3pendo.append(l.split()[0])
                angles += l

        c2 = 'color pink, resi ' + '+'.join(c2pendo)
        c3 = 'color blue, resi ' + '+'.join(c3pendo)

        if args.pymol:

            print(c2)
            print(c3)
            return
            
        import re
        nangles = ''
        #'9 C    41',
        #'10 C     0',
        bpseq = ['bpseq'] + [x.strip().split()[2] for x in open('dssr-2ndstrs.bpseq').readlines()]
        for i, l in enumerate(angles.split('\n')):
            if l.strip():
                l = re.sub(r'\s+', ',', l, 0, re.MULTILINE)
                if bpseq[i] == '0':
                    bpseq[i] = 'no paired'
                else:
                    bpseq[i] = 'paired'
                l = l[1:] + ',' + bpseq[i] + '\n'
                nangles += l
        nangles = re.sub(r'---', 'nan', nangles, 0, re.MULTILINE)
        with open(outfn, 'w') as f:
            f.write(nangles.strip())

        if args.show:
            import pandas as pd
            df = pd.read_csv(outfn)
            print(df)
        return nangles.strip()
    
# name
if __name__ == '__main__':
    if not X3DNA:
        raise Exception(
            'Set up BINARY_PATH in rna_x3dna_config_local.py, .e.g "/Users/magnus/work/opt/x3dna/x3dna-dssr"')

    # get parser and arguments
    parser = get_parser()
    args = parser.parse_args()

    # try:
    #    compact = sys.argv[2]
    #    if compact == '-c':
    #       compact = True
    #
    # except IndexError:
    #    compact = False

    for f in args.files:
        if args.compact:
            p = x3DNA(f)
            print((f, p.get_secstruc()))
        else:
            print(f'input: {f}')
            outfn = os.path.basename(f.replace('.pdb', '')) + '-torsion-paired.csv'
            if not args.rerun:
                if os.path.isfile(outfn):
                    print(f'skip: {f}, use --rerun to run analysis again')
                    continue
            p = x3DNA(f, args.show_log, args.verbose)
            s = p.get_seq()
            print(s)
            s = p.get_secstruc()
            print(s)
            s = p.get_torsions(outfn)
            if args.verbose: print(s)
            p.clean_up(args.verbose)


1			#!/usr/bin/env python
2			# -- coding: utf-8 --
3			"""Python parser to 3dna <http://x3dna.org/>.
4
5			Installation::
6
7			# install the code from http://forum.x3dna.org/downloads/3dna-download/
8			Create a copy of the rna_x3dna_config_local_sample.py (remove "_sample") present in rna-tools/rna_tools/tools/rna_x3dna folder.
9			Edit this line :
10			BINARY_PATH = <path to your x3dna-dssr file>
11			matching the path with the path of your x3dna-dssr file.
12			e.g. in my case: BINARY_PATH = ~/bin/x3dna-dssr.bin
13
14			For one structure you can run this script as::
15
16			[mm] py3dna$ git:(master) ✗ ./rna_x3dna.py test_data/1xjr.pdb
17			test_data/1xjr.pdb
18			>1xjr nts=47 [1xjr] -- secondary structure derived by DSSR
19			gGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
20			..(((((((...((((.((((.....))..))..))).).)))))))
21
22			For multiple structures in the folder, run the script like this::
23
24			[mm] py3dna$ git:(master) ✗ ./rna_x3dna.py test_data/*
25			test_data/1xjr.pdb
26			>1xjr nts=47 [1xjr] -- secondary structure derived by DSSR
27			gGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
28			..(((((((...((((.((((.....))..))..))).).)))))))
29			test_data/6TNA.pdb
30			>6TNA nts=76 [6TNA] -- secondary structure derived by DSSR
31			GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAPcUGGAGgUCcUGUGtPCGaUCCACAGAAUUCGCACCA
32			(((((((..((((.....[..)))).((((.........)))).....(((((..]....))))))))))))....
33			test_data/rp2_bujnicki_1_rpr.pdb
34			>rp2_bujnicki_1_rpr nts=100 [rp2_bujnicki_1_rpr] -- secondary structure derived by DSSR
35			CCGGAGGAACUACUG&CCGGCAGCCU&CCGGAGGAACUACUG&CCGGCAGCCU&CCGGAGGAACUACUG&CCGGCAGCCU&CCGGAGGAACUACUG&CCGGCAGCCU
36			[[[[(((.....(((&{{{{))))))&(((((((.....(.(&]]]]).))))&[[[[[[......[[[&))))]]].]]&}}}}(((.....(((&]]]]))))))
37
38			.. warning:: This script should not be used in this given form with Parallel because it process output files from x3dna that are named always in the same way, e.g. dssr-torsions.txt. #TODO
39
40			"""
41			import re
42			import argparse
43
44			from subprocess import Popen, PIPE
45			import os
46			from rna_tools.rna_tools_config import X3DNA, X3DNA_FP
47			# x3dna-dssr-64bit
48
49
50			class x3DNAMissingFile(Exception):
51			pass
52
53
54			def get_parser():
55			parser = argparse.ArgumentParser(
56			description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
57			parser.add_argument('-c', '--compact', action='store_true')
58			parser.add_argument('-x', '--rerun', action='store_true')
59			parser.add_argument('-s', '--show', action='store_true', help="show results")
60			parser.add_argument('--pymol', action='store_true', help='get resi to color code puckers in PyMOL')
61			parser.add_argument('-l', '--show-log', action='store_true', help="show full log")
62			parser.add_argument('-v', '--verbose', action='store_true', help="show full log")
63			parser.add_argument('files', help='file', nargs='+')
64			return parser
65
66
67			class x3DNA(object):
68
69			"""
70			Atributes:
71
72			curr_fn
73			report
74
75			"""
76
77			def __init__(self, pdbfn, show_log=False):
78			"""Set self.curr_fn based on pdbfn"""
79			self.curr_fn = pdbfn
80			self.run_x3dna(show_log)
81			self.clean_up()
82
83			def __get_report(self):
84			"""Off right now. Run find_pair
85
86			..warning:: To get modification use get_modifications()
87			"""
88			cmd = X3DNA_FP + ' ' + self.curr_fn + ' stdout \| analyze stdin' # hack
89			out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True)
90
91			stdout = out.stdout.read()
92			outerr = out.stderr.read()
93
94			text = ''
95			for l in outerr.split('\n'):
96			if l.startswith('Time used') or l.startswith('..') or l.startswith('handling') or l.startswith('uncommon residue'):
97			continue
98			if l.strip():
99			text += l + '\n'
100			return text.strip()
101
102			def get_modifications(self):
103			"""Run find_pair to find modifications.
104			"""
105			cmd = X3DNA_FP + ' -p ' + self.curr_fn + ' /tmp/fpout' # hack
106			out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True)
107
108			outerr = out.stderr.read()
109
110			text = ''
111			for l in outerr.split('\n'):
112			if l.startswith('uncommon residue'):
113			text += l.replace('uncommon residue ', '') + '\n'
114			return text.strip()
115
116			def run_x3dna(self, show_log=False, verbose=False):
117			"""
118			"""
119			cmd = X3DNA + ' -i=' + self.curr_fn
120			out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True)
121
122			stdout = str(out.stdout.read().decode())
123			outerr = str(out.stderr.read().decode())
124
125			f = open('py3dna.log', 'w')
126			if verbose: print(f'cmd: {cmd}')
127			f.write(cmd + '\n' + stdout)
128
129			if show_log:
130			print(stdout)
131			f.close()
132
133			if outerr.find('does not exist!') > -1: # not very pretty
134			raise x3DNAMissingFile
135			if outerr.find('not found') > -1: # not very pretty
136			raise Exception('x3dna not found!')
137
138			rx = re.compile('no. of DNA/RNA chains:\s+(?P<no_DNARNAchains>\d+)\s').search(stdout)
139			if rx:
140			no_of_DNARNA_chains = int(rx.group('no_DNARNAchains'))
141			msg = 'py3dna::no of DNARNA chains'
142			self.report = msg + '\n' + msg + '\n' # hack!
143			else:
144			raise Exception('no_of_DNARNA_chains not found')
145
146			if no_of_DNARNA_chains:
147			self.report = stdout.strip()
148
149			def get_ion_water_report(self):
150			"""@todo
151			File name: /tmp/tmp0pdNHS
152			no. of DNA/RNA chains: 0 []
153			no. of nucleotides: 174
154			no. of waters: 793
155			no. of metals: 33 [Na=29, Mg=1, K=3]
156			"""
157			pass
158
159			def clean_up(self, verbose=False):
160			files_to_remove = [
161			'dssr-helices.pdb',
162			'dssr-pairs.pdb',
163			'dssr-torsions.dat',
164			'dssr-hairpins.pdb',
165			'dssr-multiplets.pdb',
166			'dssr-stems.pdb',
167			'dssr-Aminors.pdb',
168			'hel_regions.pdb',
169			'bp_order.dat',
170			'bestpairs.pdb',
171			]
172
173			for f in files_to_remove:
174			try:
175			os.remove(f)
176			pass
177			except OSError:
178			if verbose:
179			print('error: can not remove %s' % f)
180
181			def get_seq(self):
182			"""Get sequence.
183
184			Somehow 1bzt_1 x3dna UCAGACUUUUAAPCUGA, what is P?
185			P -> u
186
187			"""
188			return self.report.split('\n')[-2].replace('P', 'u').replace('I', 'a')
189
190			def get_secstruc(self):
191			"""Get secondary structure.
192			"""
193			hits = re.search("as a whole and per chain.?\n(?P<ss>.+?)\n\", self.report, re.DOTALL\|re.MULTILINE)
194			if hits:
195			return hits.group('ss').strip()
196			else:
197			self.report.split('\n')[-1] # tofix
198
199			def get_torsions(self, outfn) -> str:
200			"""Get torsion angles into 'torsion.csv' file::
201
202			nt,id,res,alpha,beta,gamma,delta,epsilon,zeta,e-z,chi,phase-angle,sugar-type,ssZp,Dp,splay,bpseq
203			1,g,A.GTP1,nan,nan,142.1,89.5,-131.0,-78.3,-53(BI),-178.2(anti),358.6(C2'-exo),~C3'-endo,4.68,4.68,29.98,0
204			2,G,A.G2,-75.8,-167.0,57.2,79.5,-143.4,-69.7,-74(BI),-169.2(anti),5.8(C3'-endo),~C3'-endo,4.68,4.76,25.61,0
205
206			"""
207			angles = ''
208			save = False
209
210			c2pendo = []
211			c3pendo = []
212			if not os.path.isfile('dssr-torsions.txt'):
213
214			print(f'Problem to get torsion angles for {self.curr_fn}')
215			return f'Problem to get torsion angles for {self.curr_fn}'
216
217			for l in open('dssr-torsions.txt'):
218			if 'nt alpha beta' in l:
219			save = True
220			l = l.replace('nt', 'nt id res ')
221			if '***************' in l and save:
222			save = False
223			if save:
224			if "~C2'-endo" in l:
225			c2pendo.append(l.split()[0])
226			if "~C3'-endo" in l:
227			c3pendo.append(l.split()[0])
228			angles += l
229
230			c2 = 'color pink, resi ' + '+'.join(c2pendo)
231			c3 = 'color blue, resi ' + '+'.join(c3pendo)
232
233			if args.pymol:
			0 ignored issues – show introduced 2024-04-16 18:55 UTC by Report Bug Copy Issue Report The variable `args` does not seem to be defined in case `__name__ == '__main__'` on line `263` is `False`. Are you sure this can never be the case? Loading history...
234			print(c2)
235			print(c3)
236			return
237
238			import re
239			nangles = ''
240			#'9 C 41',
241			#'10 C 0',
242			bpseq = ['bpseq'] + [x.strip().split()[2] for x in open('dssr-2ndstrs.bpseq').readlines()]
243			for i, l in enumerate(angles.split('\n')):
244			if l.strip():
245			l = re.sub(r'\s+', ',', l, 0, re.MULTILINE)
246			if bpseq[i] == '0':
247			bpseq[i] = 'no paired'
248			else:
249			bpseq[i] = 'paired'
250			l = l[1:] + ',' + bpseq[i] + '\n'
251			nangles += l
252			nangles = re.sub(r'---', 'nan', nangles, 0, re.MULTILINE)
253			with open(outfn, 'w') as f:
254			f.write(nangles.strip())
255
256			if args.show:
257			import pandas as pd
258			df = pd.read_csv(outfn)
259			print(df)
260			return nangles.strip()
261
262			# name
263			if __name__ == '__main__':
264			if not X3DNA:
265			raise Exception(
266			'Set up BINARY_PATH in rna_x3dna_config_local.py, .e.g "/Users/magnus/work/opt/x3dna/x3dna-dssr"')
267
268			# get parser and arguments
269			parser = get_parser()
270			args = parser.parse_args()
271
272			# try:
273			# compact = sys.argv[2]
274			# if compact == '-c':
275			# compact = True
276			#
277			# except IndexError:
278			# compact = False
279
280			for f in args.files:
281			if args.compact:
282			p = x3DNA(f)
283			print((f, p.get_secstruc()))
284			else:
285			print(f'input: {f}')
286			outfn = os.path.basename(f.replace('.pdb', '')) + '-torsion-paired.csv'
287			if not args.rerun:
288			if os.path.isfile(outfn):
289			print(f'skip: {f}, use --rerun to run analysis again')
290			continue
291			p = x3DNA(f, args.show_log, args.verbose)
292			s = p.get_seq()
293			print(s)
294			s = p.get_secstruc()
295			print(s)
296			s = p.get_torsions(outfn)
297			if args.verbose: print(s)
298			p.clean_up(args.verbose)
299

mmagnus / rna-tools

x3DNA.run_x3dna() B last analyzed 2025-11-03 17:23 UTC

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x3DNA.run_x3dna() B
last analyzed 2025-11-03 17:23 UTC