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From: Luis F. <ld...@mi...> - 2007-05-31 08:34:49
|
Hello,
I'm using Open Babel 2.1.0 to convert the structure of molecules in cml
format to inchi or to smi in order to cross-check information. I started
to write a simple script in Perl (Perl 5.8.8) to read a file containing
the structures of several compounds and convert them to inchi. But I
got a "Segmentation fault" error message after running the script using
as input a file containing a single structure. Then I tried to convert
the structure inside this file using babel command and it worked good,
without any error.
After some debugging process I did not find the solution for this
problem and I decided to move to Python (Python 2.5). Then I wrote a
simple script to do the same thing:
# #!/usr/bin/python
#
# import openbabel
# import sys
# import re
#
# file = sys.argv[1]
# infile = open(file,"r")
#
# while infile:
# line = infile.readline()
# if re.search("<molecule",line):
# molecule = line
# elif re.search("</molecule",line):
# molecule += line
# obConversion = openbabel.OBConversion()
# obConversion.SetInAndOutFormats("cml", "inchi")
# mol = openbabel.OBMol()
# obConversion.ReadString(mol, molecule)
# outMDL = obConversion.WriteString(mol)
# print outMDL
# break
# elif len (molecule) > 1:
# molecule += line
But the result is the same a "Segmentation fault" error. I can get the
right conversion as in Perl but the script breaks after one conversion.
I can convert everything using a temporary file and convert it using the
command line, though it would be a brute force approach that I want to
avoid.
Best greetings
Luís Figueiredo
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From: Noel O'B. <bao...@gm...> - 2007-05-30 10:13:18
|
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From: Jurgens de B. <deb...@gm...> - 2007-05-30 10:04:16
|
SGkKCkkgd2FzIHdvbmRlcmluZyBpZiBpdCB3b3VsZCBiZSBwb3NzaWJsZSB0byBkZXRlcm1pbmUg dGhlIG51bWJlciBvZiByaW5ncyBpbgphIG1vbGVjdWxlIHdpdGhpbiBhIHB5dGhvbiBzY3JpcHRz LgoKVGhhbngKCi0tIApSZWdhcmRzL0dyb2V0ZS9NaXQgZnJldW5kbGljaGVuIEdyw7zDn2VuL3Jl Y3VlcmRvcy9tZWlsbGV1cmVzIHNhbHV0YXRpb25zLwpkaXN0aW50aSBzYWx1dGkvc2lvbmcvZHXD rCB5w7ov0L/RgNC40LLQtdGCCgpKdXJnZW5zIGRlIEJydWluCg== |
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From: Noel O'B. <bao...@gm...> - 2007-05-28 08:17:32
|
SnVzdCBsb29rZWQgYXQgdGhlIGRvY3VtZW50YXRpb24sIGFuZCBJIHNlZSB0aGUgZXJyb3IgdGhh dCBjYXVzZWQgdGhlCmNvbmZ1c2lvbi4gSXQncyBub3cgZml4ZWQuIFNvcnJ5IQoKT24gMjgvMDUv MDcsIE5vZWwgTydCb3lsZSA8YmFvaWxsZWFjaEBnbWFpbC5jb20+IHdyb3RlOgo+IFB5YmVsIGNo YW5nZXMKPiAgICBPQk1vbC5HZXRNb2xXdCgpICAgIyBub3RlIHRoZSAoKQo+ICB0bwo+ICAgIHB5 bW9sLm1vbHd0ICAgICAgICAgICAgICMgbm90ZS4uLnRoZXJlIGlzIG5vICgpCj4KPiBJZiB5b3Ug d2VyZSBjb25mdXNlZCwgaXQncyBwcm9iYWJseSBiZWNhdXNlIHRoZSBkb2N1bWVudGF0aW9uIGlz IG5vdAo+IGNsZWFyIGVub3VnaC4gUGxlYXNlIGFzayB3aGF0ZXZlciBxdWVzdGlvbnMgeW91IGhh dmUuCj4KPiBOb2VsCj4KPiBPbiAyOC8wNS8wNywgSnVyZ2VucyBkZSBCcnVpbiA8ZGVicnVpbmpq QGdtYWlsLmNvbT4gd3JvdGU6Cj4gPiBIaSB0byBhbGwKPiA+Cj4gPiBUaGlzIG1heSBiZSBhIHNp bGx5IHF1ZXN0aW9uIGJ1dCBpdCBpcyBnaXZpbmcgbWUgbXVjaCBncmllZi4gIEkgYW0gdHJ5aW5n IHRvCj4gPiBjYWxjdWxhdGUgdGhlIG1vbGVjdWxhciB3ZWlnaHQgb2YgYSBtb2xlY3VsZSBhcyBm b2xsb3dzOgo+ID4KPiA+ID5tb2wgPSBweWJlbC5yZWFkc3RyaW5nKCJzbWkiLCJ0aGVzbWlsZSIp Cj4gPiA+bW9sbXcgPSBtb2wubW9sd3QoKQo+ID4gPnByaW50ID4gbW9sbXcKPiA+Cj4gPiBCdXQg SSBnZXQgdGhlIGZvbGxvd2luZyBlcnJvcgo+ID4KPiA+ICJUeXBlRXJyb3I6ICdmbG9hdCBvYmpl Y3QgaXMgbm90IGNhbGxhYmxlIgo+ID4KPiA+IEkga25vdyB0aGlzIHNob3VsZCBiZSBlYXN5IGJ1 dCBJIGhhdmUga25vdyBpZGVlLgo+ID4KPiA+Cj4gPiAtLQo+ID4gUmVnYXJkcy9Hcm9ldGUvTWl0 IGZyZXVuZGxpY2hlbiBHcsO8w59lbi9yZWN1ZXJkb3MvbWVpbGxldXJlcyBzYWx1dGF0aW9ucy8K PiA+IGRpc3RpbnRpIHNhbHV0aS9zaW9uZy9kdcOsIHnDui/Qv9GA0LjQstC10YIKPiA+Cj4gPiBK dXJnZW5zIGRlIEJydWluCj4gPiAtLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tCj4gPiBUaGlzIFNGLm5ldCBlbWFp bCBpcyBzcG9uc29yZWQgYnkgREIyIEV4cHJlc3MKPiA+IERvd25sb2FkIERCMiBFeHByZXNzIEMg LSB0aGUgRlJFRSB2ZXJzaW9uIG9mIERCMiBleHByZXNzIGFuZCB0YWtlCj4gPiBjb250cm9sIG9m IHlvdXIgWE1MLiBObyBsaW1pdHMuIEp1c3QgZGF0YS4gQ2xpY2sgdG8gZ2V0IGl0IG5vdy4KPiA+ IGh0dHA6Ly9zb3VyY2Vmb3JnZS5uZXQvcG93ZXJiYXIvZGIyLwo+ID4gX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX18KPiA+IE9wZW5CYWJlbC1zY3JpcHRpbmcg bWFpbGluZyBsaXN0Cj4gPiBPcGVuQmFiZWwtc2NyaXB0aW5nQGxpc3RzLnNvdXJjZWZvcmdlLm5l dAo+ID4gaHR0cHM6Ly9saXN0cy5zb3VyY2Vmb3JnZS5uZXQvbGlzdHMvbGlzdGluZm8vb3BlbmJh YmVsLXNjcmlwdGluZwo+ID4KPiA+Cj4K |
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From: Noel O'B. <bao...@gm...> - 2007-05-28 08:14:11
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UHliZWwgY2hhbmdlcwogICBPQk1vbC5HZXRNb2xXdCgpICAgIyBub3RlIHRoZSAoKQogdG8KICAg cHltb2wubW9sd3QgICAgICAgICAgICAgIyBub3RlLi4udGhlcmUgaXMgbm8gKCkKCklmIHlvdSB3 ZXJlIGNvbmZ1c2VkLCBpdCdzIHByb2JhYmx5IGJlY2F1c2UgdGhlIGRvY3VtZW50YXRpb24gaXMg bm90CmNsZWFyIGVub3VnaC4gUGxlYXNlIGFzayB3aGF0ZXZlciBxdWVzdGlvbnMgeW91IGhhdmUu CgpOb2VsCgpPbiAyOC8wNS8wNywgSnVyZ2VucyBkZSBCcnVpbiA8ZGVicnVpbmpqQGdtYWlsLmNv bT4gd3JvdGU6Cj4gSGkgdG8gYWxsCj4KPiBUaGlzIG1heSBiZSBhIHNpbGx5IHF1ZXN0aW9uIGJ1 dCBpdCBpcyBnaXZpbmcgbWUgbXVjaCBncmllZi4gIEkgYW0gdHJ5aW5nIHRvCj4gY2FsY3VsYXRl IHRoZSBtb2xlY3VsYXIgd2VpZ2h0IG9mIGEgbW9sZWN1bGUgYXMgZm9sbG93czoKPgo+ID5tb2wg PSBweWJlbC5yZWFkc3RyaW5nKCJzbWkiLCJ0aGVzbWlsZSIpCj4gPm1vbG13ID0gbW9sLm1vbHd0 KCkKPiA+cHJpbnQgPiBtb2xtdwo+Cj4gQnV0IEkgZ2V0IHRoZSBmb2xsb3dpbmcgZXJyb3IKPgo+ ICJUeXBlRXJyb3I6ICdmbG9hdCBvYmplY3QgaXMgbm90IGNhbGxhYmxlIgo+Cj4gSSBrbm93IHRo aXMgc2hvdWxkIGJlIGVhc3kgYnV0IEkgaGF2ZSBrbm93IGlkZWUuCj4KPgo+IC0tCj4gUmVnYXJk cy9Hcm9ldGUvTWl0IGZyZXVuZGxpY2hlbiBHcsO8w59lbi9yZWN1ZXJkb3MvbWVpbGxldXJlcyBz YWx1dGF0aW9ucy8KPiBkaXN0aW50aSBzYWx1dGkvc2lvbmcvZHXDrCB5w7ov0L/RgNC40LLQtdGC Cj4KPiBKdXJnZW5zIGRlIEJydWluCj4gLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLQo+IFRoaXMgU0YubmV0IGVt YWlsIGlzIHNwb25zb3JlZCBieSBEQjIgRXhwcmVzcwo+IERvd25sb2FkIERCMiBFeHByZXNzIEMg LSB0aGUgRlJFRSB2ZXJzaW9uIG9mIERCMiBleHByZXNzIGFuZCB0YWtlCj4gY29udHJvbCBvZiB5 b3VyIFhNTC4gTm8gbGltaXRzLiBKdXN0IGRhdGEuIENsaWNrIHRvIGdldCBpdCBub3cuCj4gaHR0 cDovL3NvdXJjZWZvcmdlLm5ldC9wb3dlcmJhci9kYjIvCj4gX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX18KPiBPcGVuQmFiZWwtc2NyaXB0aW5nIG1haWxpbmcg bGlzdAo+IE9wZW5CYWJlbC1zY3JpcHRpbmdAbGlzdHMuc291cmNlZm9yZ2UubmV0Cj4gaHR0cHM6 Ly9saXN0cy5zb3VyY2Vmb3JnZS5uZXQvbGlzdHMvbGlzdGluZm8vb3BlbmJhYmVsLXNjcmlwdGlu Zwo+Cj4K |
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From: Jurgens de B. <deb...@gm...> - 2007-05-28 07:53:26
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SGkgdG8gYWxsCgpUaGlzIG1heSBiZSBhIHNpbGx5IHF1ZXN0aW9uIGJ1dCBpdCBpcyBnaXZpbmcg bWUgbXVjaCBncmllZi4gIEkgYW0gdHJ5aW5nIHRvCmNhbGN1bGF0ZSB0aGUgbW9sZWN1bGFyIHdl aWdodCBvZiBhIG1vbGVjdWxlIGFzIGZvbGxvd3M6Cgo+bW9sID0gcHliZWwucmVhZHN0cmluZygi c21pIiwidGhlc21pbGUiKQo+bW9sbXcgPSBtb2wubW9sd3QoKQo+cHJpbnQgPiBtb2xtdwoKQnV0 IEkgZ2V0IHRoZSBmb2xsb3dpbmcgZXJyb3IKCiJUeXBlRXJyb3I6ICdmbG9hdCBvYmplY3QgaXMg bm90IGNhbGxhYmxlIgoKSSBrbm93IHRoaXMgc2hvdWxkIGJlIGVhc3kgYnV0IEkgaGF2ZSBrbm93 IGlkZWUuCgoKLS0gClJlZ2FyZHMvR3JvZXRlL01pdCBmcmV1bmRsaWNoZW4gR3LDvMOfZW4vcmVj dWVyZG9zL21laWxsZXVyZXMgc2FsdXRhdGlvbnMvCmRpc3RpbnRpIHNhbHV0aS9zaW9uZy9kdcOs IHnDui/Qv9GA0LjQstC10YIKCkp1cmdlbnMgZGUgQnJ1aW4K |
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From: Noel O'B. <bao...@gm...> - 2007-05-23 06:37:10
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VGhlcmUgaXMgbm8gcHJvYmxlbSBjYWxjdWxhdGluZyBmaW5nZXJwcmludHMgYW5kIFRhbmltb3Rv IGNvZWZmaWNpZW50cwpmcm9tIFB5dGhvbiAoc2VlIHRoZSBQeWJlbCBtb2R1bGUgZm9yIGV4YW1w bGUpLiBIb3dldmVyLCB5b3Ugd2lsbCBoYXZlCnRvIHdyaXRlIHlvdXIgb3duIGluZGV4aW5nIGFs Z29yaXRobSB5b3Vyc2VsZi4gRm9yIGV4YW1wbGUsIHlvdSBtaWdodAp3YW50IHRvIHJlYXJyYW5n ZSBlYWNoIGZpbmdlcnByaW50IHNvIHRoYXQgdGhlIGJpdCB3aXRoIHRoZSBoaWdoZXN0Ckdpbmkg aW5kZXggd2FzIGZpcnN0LCBhbmQgc28gb24gKHlvdSBtYXkgd2FudCB0byByZWFkIGFib3V0IGJp bmFyeQp0cmVlcyksIG9yIHN0b3JlIHRoZSBtb2xlY3VsZXMgaW4gYSBNeVNRTCBkYXRhYmFzZSB1 c2luZyB0aGUKZmluZ2VycHJpbnQgYXMgYSBrZXkuCgpOb2VsCgpPbiAyMy8wNS8wNywgSnVyZ2Vu cyBkZSBCcnVpbiA8ZGVicnVpbmpqQGdtYWlsLmNvbT4gd3JvdGU6Cj4gVG8gYWxsCj4KPiBJIGFt IGludGVyZXN0ZWQgaW4gZG9pbmcgc29tZSBzaW1pbGFyaXR5IHNlYXJjaGVzIGFuZCBtZWFzdXJl cyBhbmQgY2FtZQo+IGFsb25nIHRoZSBUdXRvcmlhbDpGaW5nZXJwcmludHMuIFdoYXQgSSB3YXMg d29uZGVyaW5nIGlzIHdvdWxkIGl0IGJlCj4gcG9zc2libGUgdG8gZm9sbG93IHRoaXMgYXBwcm9h Y2ggd2l0aGluIGEgIHB5dGhvbiBzY3JpcHQsIEkgYW0gc3BlY2lhbGx5Cj4gaW50ZXJlc3RlZCBp biB0aGUgcGFydCBvbiBidWlsZGluZyBhbiBpbmRleCBhbmQgd291bGQgdGhpcyB3b3JrIHdpdGgg U01JTEVTLgo+Cj4gSSBkb24ndCB3YW50IHRvIGJlIGRpZmZpY3VsdCBidXQgSSB3b3VsZCBwcmVm ZXIgbm90IHRvIHBhc3Mgc3lzdGVtIGNvbW1hbmRzCj4gdG8gdGhlIGNvbnNvbGUgZnJvbSB0aGUg cHl0aG9uIHNjcmlwdC4KPgo+IFRoYW54IGFnYWluIGZvciBhbGwgdGhlIGhlbHAuCj4KPiAtLQo+ IFJlZ2FyZHMvR3JvZXRlL01pdCBmcmV1bmRsaWNoZW4gR3LDvMOfZW4vcmVjdWVyZG9zL21laWxs ZXVyZXMgc2FsdXRhdGlvbnMvCj4gZGlzdGludGkgc2FsdXRpL3Npb25nL2R1w6wgecO6L9C/0YDQ uNCy0LXRggo+Cj4gSnVyZ2VucyBkZSBCcnVpbgo+IC0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0KPiBUaGlzIFNG Lm5ldCBlbWFpbCBpcyBzcG9uc29yZWQgYnkgREIyIEV4cHJlc3MKPiBEb3dubG9hZCBEQjIgRXhw cmVzcyBDIC0gdGhlIEZSRUUgdmVyc2lvbiBvZiBEQjIgZXhwcmVzcyBhbmQgdGFrZQo+IGNvbnRy b2wgb2YgeW91ciBYTUwuIE5vIGxpbWl0cy4gSnVzdCBkYXRhLiBDbGljayB0byBnZXQgaXQgbm93 Lgo+IGh0dHA6Ly9zb3VyY2Vmb3JnZS5uZXQvcG93ZXJiYXIvZGIyLwo+IF9fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fCj4gT3BlbkJhYmVsLXNjcmlwdGluZyBt YWlsaW5nIGxpc3QKPiBPcGVuQmFiZWwtc2NyaXB0aW5nQGxpc3RzLnNvdXJjZWZvcmdlLm5ldAo+ IGh0dHBzOi8vbGlzdHMuc291cmNlZm9yZ2UubmV0L2xpc3RzL2xpc3RpbmZvL29wZW5iYWJlbC1z Y3JpcHRpbmcKPgo+Cg== |
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From: Jurgens de B. <deb...@gm...> - 2007-05-23 05:30:42
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VG8gYWxsCgpJIGFtIGludGVyZXN0ZWQgaW4gZG9pbmcgc29tZSBzaW1pbGFyaXR5IHNlYXJjaGVz IGFuZCBtZWFzdXJlcyBhbmQgY2FtZQphbG9uZyB0aGUgVHV0b3JpYWw6RmluZ2VycHJpbnRzLiBX aGF0IEkgd2FzIHdvbmRlcmluZyBpcyB3b3VsZCBpdCBiZQpwb3NzaWJsZSB0byBmb2xsb3cgdGhp cyBhcHByb2FjaCB3aXRoaW4gYSAgcHl0aG9uIHNjcmlwdCwgSSBhbSBzcGVjaWFsbHkKaW50ZXJl c3RlZCBpbiB0aGUgcGFydCBvbiBidWlsZGluZyBhbiBpbmRleCBhbmQgd291bGQgdGhpcyB3b3Jr IHdpdGggU01JTEVTLgoKCkkgZG9uJ3Qgd2FudCB0byBiZSBkaWZmaWN1bHQgYnV0IEkgd291bGQg cHJlZmVyIG5vdCB0byBwYXNzIHN5c3RlbSBjb21tYW5kcwp0byB0aGUgY29uc29sZSBmcm9tIHRo ZSBweXRob24gc2NyaXB0LgoKVGhhbnggYWdhaW4gZm9yIGFsbCB0aGUgaGVscC4KCi0tIApSZWdh cmRzL0dyb2V0ZS9NaXQgZnJldW5kbGljaGVuIEdyw7zDn2VuL3JlY3VlcmRvcy9tZWlsbGV1cmVz IHNhbHV0YXRpb25zLwpkaXN0aW50aSBzYWx1dGkvc2lvbmcvZHXDrCB5w7ov0L/RgNC40LLQtdGC CgpKdXJnZW5zIGRlIEJydWluCg== |
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From: Jurgens de B. <deb...@gm...> - 2007-05-23 05:18:59
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VGhhbnggdG8gYWxsIGZvciByZXBseSBpdCBpcyBtdWNoIGFwcHJlY2lhdGUuCgpJIGhhdmUgaW5z dGFsbCBPQiBvbiBhIDY0Yml0IFN1c2UgbWFjaGluZSB0aGUgZm9sbG93aW5nIGxpbmsgaGVscCBh IGxvdDoKCmh0dHA6Ly9zb3VyY2Vmb3JnZS5uZXQvbWFpbGFyY2hpdmUvbWVzc2FnZS5waHA/bXNn X2lkPTIwMDYxMTA1MTYxMzUwLjExNzYucW1haWwlNDB3ZWIzNDIwNS5tYWlsLm11ZC55YWhvby5j b20KClRoZW4gY29weSBsaWJvcGVuYmFiZWwuc28uMSBmcm9tIC91c3IvbG9jYWwvbGliIHRvIC91 c3IvbGliNjQKCnRoYW54IGFnYWluISEhCgoKT24gNS8yMi8wNywgQW5kcmV3IENvbGFzYW50aSA8 IGFjb2xhc2FudGlAZ21haWwuY29tPiB3cm90ZToKPgo+IEkgd2FzIGFibGUgdG8gaW5zdGFsbCBP cGVuYmFiZWwgMi4xIG9uIGEgQU1ELTY0IHVuZGVyIFJIRUw0LiAgV2hhdAo+IHByb2JsZW1zIGFy ZSB5b3UgaGF2aW5nLgo+Cj4gQW5kcmV3Cj4KPgo+IE9uIDUvMjIvMDcsIE5vZWwgTydCb3lsZSA8 YmFvaWxsZWFjaEBnbWFpbC5jb20+IHdyb3RlOgo+ID4gV2hpY2ggdmVyc2lvbiBvZiBPQiBhcmUg eW91IHRyeWluZyB0byBjb21waWxlIGFuZCBvbiB3aGF0IG9wZXJhdGluZwo+ID4gc3lzdGVtPyBB bHNvLCBjb3VsZCB5b3UgcGxlYXNlIHBvc3QgdGhlIGZpcnN0IGZldyBidWlsZCBlcnJvcgo+ID4g bWVzc2FnZXMuCj4gPgo+ID4gTm9lbAo+ID4KPiA+IE9uIDIyLzA1LzA3LCBKdXJnZW5zIGRlIEJy dWluIDxkZWJydWluampAZ21haWwuY29tPiB3cm90ZToKPiA+ID4gVG8gd2hvbSBpdCBtYXkgY29u Y2VybjoKPiA+ID4KPiA+ID4gSSB3b3VsZCBsaWtlIHRvIGluc3RhbGwgT3BlbmJhYmVsIGFuZCBw eWJlbCBvbiA2NGJpdCBtYWNoaW5lcyBidXQgSQo+IGVuZCB1cAo+ID4gPiBnZXR0aW5nIGEgYnVp bGQgZXJyb3IgaXMgdGhlaXIgYSB3YXkgYXJvdW5kIHRoaXMuCj4gPiA+Cj4gPiA+IFRoYW54Cj4g PiA+Cj4gPiA+IC0tCj4gPiA+IFJlZ2FyZHMvR3JvZXRlL01pdCBmcmV1bmRsaWNoZW4gR3LDvMOf ZW4vcmVjdWVyZG9zL21laWxsZXVyZXMKPiBzYWx1dGF0aW9ucy8KPiA+ID4gZGlzdGludGkgc2Fs dXRpL3Npb25nL2R1w6wgecO6L9C/0YDQuNCy0LXRggo+ID4gPgo+ID4gPiBKdXJnZW5zIGRlIEJy dWluCj4gPiA+Cj4gLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLQo+ID4gPiBUaGlzIFNGLm5ldCBlbWFpbCBpcyBz cG9uc29yZWQgYnkgREIyIEV4cHJlc3MKPiA+ID4gRG93bmxvYWQgREIyIEV4cHJlc3MgQyAtIHRo ZSBGUkVFIHZlcnNpb24gb2YgREIyIGV4cHJlc3MgYW5kIHRha2UKPiA+ID4gY29udHJvbCBvZiB5 b3VyIFhNTC4gTm8gbGltaXRzLiBKdXN0IGRhdGEuIENsaWNrIHRvIGdldCBpdCBub3cuCj4gPiA+ IGh0dHA6Ly9zb3VyY2Vmb3JnZS5uZXQvcG93ZXJiYXIvZGIyLwo+ID4gPiBfX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fXwo+ID4gPiBPcGVuQmFiZWwtc2NyaXB0 aW5nIG1haWxpbmcgbGlzdAo+ID4gPiBPcGVuQmFiZWwtc2NyaXB0aW5nQGxpc3RzLnNvdXJjZWZv cmdlLm5ldAo+ID4gPiBodHRwczovL2xpc3RzLnNvdXJjZWZvcmdlLm5ldC9saXN0cy9saXN0aW5m by9vcGVuYmFiZWwtc2NyaXB0aW5nCj4gPiA+Cj4gPiA+Cj4gPgo+IC0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0K PiA+IFRoaXMgU0YubmV0IGVtYWlsIGlzIHNwb25zb3JlZCBieSBEQjIgRXhwcmVzcwo+ID4gRG93 bmxvYWQgREIyIEV4cHJlc3MgQyAtIHRoZSBGUkVFIHZlcnNpb24gb2YgREIyIGV4cHJlc3MgYW5k IHRha2UKPiA+IGNvbnRyb2wgb2YgeW91ciBYTUwuIE5vIGxpbWl0cy4gSnVzdCBkYXRhLiBDbGlj ayB0byBnZXQgaXQgbm93Lgo+ID4gaHR0cDovL3NvdXJjZWZvcmdlLm5ldC9wb3dlcmJhci9kYjIv Cj4gPiBfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fXwo+ID4g T3BlbkJhYmVsLXNjcmlwdGluZyBtYWlsaW5nIGxpc3QKPiA+IE9wZW5CYWJlbC1zY3JpcHRpbmdA bGlzdHMuc291cmNlZm9yZ2UubmV0Cj4gPiBodHRwczovL2xpc3RzLnNvdXJjZWZvcmdlLm5ldC9s aXN0cy9saXN0aW5mby9vcGVuYmFiZWwtc2NyaXB0aW5nCj4gPgo+IC0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0K PiBUaGlzIFNGLm5ldCBlbWFpbCBpcyBzcG9uc29yZWQgYnkgREIyIEV4cHJlc3MKPiBEb3dubG9h ZCBEQjIgRXhwcmVzcyBDIC0gdGhlIEZSRUUgdmVyc2lvbiBvZiBEQjIgZXhwcmVzcyBhbmQgdGFr ZQo+IGNvbnRyb2wgb2YgeW91ciBYTUwuIE5vIGxpbWl0cy4gSnVzdCBkYXRhLiBDbGljayB0byBn ZXQgaXQgbm93Lgo+IGh0dHA6Ly9zb3VyY2Vmb3JnZS5uZXQvcG93ZXJiYXIvZGIyLwo+IF9fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fCj4gT3BlbkJhYmVsLXNj cmlwdGluZyBtYWlsaW5nIGxpc3QKPiBPcGVuQmFiZWwtc2NyaXB0aW5nQGxpc3RzLnNvdXJjZWZv cmdlLm5ldAo+IGh0dHBzOi8vbGlzdHMuc291cmNlZm9yZ2UubmV0L2xpc3RzL2xpc3RpbmZvL29w ZW5iYWJlbC1zY3JpcHRpbmcKPgoKCgotLSAKUmVnYXJkcy9Hcm9ldGUvTWl0IGZyZXVuZGxpY2hl biBHcsO8w59lbi9yZWN1ZXJkb3MvbWVpbGxldXJlcyBzYWx1dGF0aW9ucy8KZGlzdGludGkgc2Fs dXRpL3Npb25nL2R1w6wgecO6L9C/0YDQuNCy0LXRggoKSnVyZ2VucyBkZSBCcnVpbgo= |
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From: Andrew C. <aco...@gm...> - 2007-05-22 16:29:03
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SSB3YXMgYWJsZSB0byBpbnN0YWxsIE9wZW5iYWJlbCAyLjEgb24gYSBBTUQtNjQgdW5kZXIgUkhF TDQuICBXaGF0CnByb2JsZW1zIGFyZSB5b3UgaGF2aW5nLgoKQW5kcmV3CgoKT24gNS8yMi8wNywg Tm9lbCBPJ0JveWxlIDxiYW9pbGxlYWNoQGdtYWlsLmNvbT4gd3JvdGU6Cj4gV2hpY2ggdmVyc2lv biBvZiBPQiBhcmUgeW91IHRyeWluZyB0byBjb21waWxlIGFuZCBvbiB3aGF0IG9wZXJhdGluZwo+ IHN5c3RlbT8gQWxzbywgY291bGQgeW91IHBsZWFzZSBwb3N0IHRoZSBmaXJzdCBmZXcgYnVpbGQg ZXJyb3IKPiBtZXNzYWdlcy4KPgo+IE5vZWwKPgo+IE9uIDIyLzA1LzA3LCBKdXJnZW5zIGRlIEJy dWluIDxkZWJydWluampAZ21haWwuY29tPiB3cm90ZToKPiA+IFRvIHdob20gaXQgbWF5IGNvbmNl cm46Cj4gPgo+ID4gSSB3b3VsZCBsaWtlIHRvIGluc3RhbGwgT3BlbmJhYmVsIGFuZCBweWJlbCBv biA2NGJpdCBtYWNoaW5lcyBidXQgSSBlbmQgdXAKPiA+IGdldHRpbmcgYSBidWlsZCBlcnJvciBp cyB0aGVpciBhIHdheSBhcm91bmQgdGhpcy4KPiA+Cj4gPiBUaGFueAo+ID4KPiA+IC0tCj4gPiBS ZWdhcmRzL0dyb2V0ZS9NaXQgZnJldW5kbGljaGVuIEdyw7zDn2VuL3JlY3VlcmRvcy9tZWlsbGV1 cmVzIHNhbHV0YXRpb25zLwo+ID4gZGlzdGludGkgc2FsdXRpL3Npb25nL2R1w6wgecO6L9C/0YDQ uNCy0LXRggo+ID4KPiA+IEp1cmdlbnMgZGUgQnJ1aW4KPiA+IC0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0KPiA+ IFRoaXMgU0YubmV0IGVtYWlsIGlzIHNwb25zb3JlZCBieSBEQjIgRXhwcmVzcwo+ID4gRG93bmxv YWQgREIyIEV4cHJlc3MgQyAtIHRoZSBGUkVFIHZlcnNpb24gb2YgREIyIGV4cHJlc3MgYW5kIHRh a2UKPiA+IGNvbnRyb2wgb2YgeW91ciBYTUwuIE5vIGxpbWl0cy4gSnVzdCBkYXRhLiBDbGljayB0 byBnZXQgaXQgbm93Lgo+ID4gaHR0cDovL3NvdXJjZWZvcmdlLm5ldC9wb3dlcmJhci9kYjIvCj4g PiBfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fXwo+ID4gT3Bl bkJhYmVsLXNjcmlwdGluZyBtYWlsaW5nIGxpc3QKPiA+IE9wZW5CYWJlbC1zY3JpcHRpbmdAbGlz dHMuc291cmNlZm9yZ2UubmV0Cj4gPiBodHRwczovL2xpc3RzLnNvdXJjZWZvcmdlLm5ldC9saXN0 cy9saXN0aW5mby9vcGVuYmFiZWwtc2NyaXB0aW5nCj4gPgo+ID4KPiAtLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t Cj4gVGhpcyBTRi5uZXQgZW1haWwgaXMgc3BvbnNvcmVkIGJ5IERCMiBFeHByZXNzCj4gRG93bmxv YWQgREIyIEV4cHJlc3MgQyAtIHRoZSBGUkVFIHZlcnNpb24gb2YgREIyIGV4cHJlc3MgYW5kIHRh a2UKPiBjb250cm9sIG9mIHlvdXIgWE1MLiBObyBsaW1pdHMuIEp1c3QgZGF0YS4gQ2xpY2sgdG8g Z2V0IGl0IG5vdy4KPiBodHRwOi8vc291cmNlZm9yZ2UubmV0L3Bvd2VyYmFyL2RiMi8KPiBfX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fXwo+IE9wZW5CYWJlbC1z Y3JpcHRpbmcgbWFpbGluZyBsaXN0Cj4gT3BlbkJhYmVsLXNjcmlwdGluZ0BsaXN0cy5zb3VyY2Vm b3JnZS5uZXQKPiBodHRwczovL2xpc3RzLnNvdXJjZWZvcmdlLm5ldC9saXN0cy9saXN0aW5mby9v cGVuYmFiZWwtc2NyaXB0aW5nCj4K |
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From: Noel O'B. <bao...@gm...> - 2007-05-22 15:54:14
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V2hpY2ggdmVyc2lvbiBvZiBPQiBhcmUgeW91IHRyeWluZyB0byBjb21waWxlIGFuZCBvbiB3aGF0 IG9wZXJhdGluZwpzeXN0ZW0/IEFsc28sIGNvdWxkIHlvdSBwbGVhc2UgcG9zdCB0aGUgZmlyc3Qg ZmV3IGJ1aWxkIGVycm9yCm1lc3NhZ2VzLgoKTm9lbAoKT24gMjIvMDUvMDcsIEp1cmdlbnMgZGUg QnJ1aW4gPGRlYnJ1aW5qakBnbWFpbC5jb20+IHdyb3RlOgo+IFRvIHdob20gaXQgbWF5IGNvbmNl cm46Cj4KPiBJIHdvdWxkIGxpa2UgdG8gaW5zdGFsbCBPcGVuYmFiZWwgYW5kIHB5YmVsIG9uIDY0 Yml0IG1hY2hpbmVzIGJ1dCBJIGVuZCB1cAo+IGdldHRpbmcgYSBidWlsZCBlcnJvciBpcyB0aGVp ciBhIHdheSBhcm91bmQgdGhpcy4KPgo+IFRoYW54Cj4KPiAtLQo+IFJlZ2FyZHMvR3JvZXRlL01p dCBmcmV1bmRsaWNoZW4gR3LDvMOfZW4vcmVjdWVyZG9zL21laWxsZXVyZXMgc2FsdXRhdGlvbnMv Cj4gZGlzdGludGkgc2FsdXRpL3Npb25nL2R1w6wgecO6L9C/0YDQuNCy0LXRggo+Cj4gSnVyZ2Vu cyBkZSBCcnVpbgo+IC0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0KPiBUaGlzIFNGLm5ldCBlbWFpbCBpcyBzcG9u c29yZWQgYnkgREIyIEV4cHJlc3MKPiBEb3dubG9hZCBEQjIgRXhwcmVzcyBDIC0gdGhlIEZSRUUg dmVyc2lvbiBvZiBEQjIgZXhwcmVzcyBhbmQgdGFrZQo+IGNvbnRyb2wgb2YgeW91ciBYTUwuIE5v IGxpbWl0cy4gSnVzdCBkYXRhLiBDbGljayB0byBnZXQgaXQgbm93Lgo+IGh0dHA6Ly9zb3VyY2Vm b3JnZS5uZXQvcG93ZXJiYXIvZGIyLwo+IF9fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fCj4gT3BlbkJhYmVsLXNjcmlwdGluZyBtYWlsaW5nIGxpc3QKPiBPcGVu QmFiZWwtc2NyaXB0aW5nQGxpc3RzLnNvdXJjZWZvcmdlLm5ldAo+IGh0dHBzOi8vbGlzdHMuc291 cmNlZm9yZ2UubmV0L2xpc3RzL2xpc3RpbmZvL29wZW5iYWJlbC1zY3JpcHRpbmcKPgo+Cg== |
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From: Jurgens de B. <deb...@gm...> - 2007-05-22 15:47:41
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VG8gd2hvbSBpdCBtYXkgY29uY2VybjoKCkkgd291bGQgbGlrZSB0byBpbnN0YWxsIE9wZW5iYWJl bCBhbmQgcHliZWwgb24gNjRiaXQgbWFjaGluZXMgYnV0IEkgZW5kIHVwCmdldHRpbmcgYSBidWls ZCBlcnJvciBpcyB0aGVpciBhIHdheSBhcm91bmQgdGhpcy4KClRoYW54CgotLSAKUmVnYXJkcy9H cm9ldGUvTWl0IGZyZXVuZGxpY2hlbiBHcsO8w59lbi9yZWN1ZXJkb3MvbWVpbGxldXJlcyBzYWx1 dGF0aW9ucy8KZGlzdGludGkgc2FsdXRpL3Npb25nL2R1w6wgecO6L9C/0YDQuNCy0LXRggoKSnVy Z2VucyBkZSBCcnVpbgo= |
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From: Geoffrey H. <ge...@ge...> - 2007-05-21 04:04:43
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On May 20, 2007, at 2:49 PM, Kieron Taylor wrote: >> I convert SMI string into MOL (or MDL) format on Perl. The convertion >> runs normally, but in result mol-format all coordinates (x, y and z) >> of all atoms are (0,0,0). Why? > > The process of turning a smiles string into anything else requires > some > form of geometry optimisation. OpenBabel doesn't do this by default > and > I am do not believe it can do it at all, since that was not its > purpose. I'd say it's not so much an issue of "purpose," but more that generating coordinates for SMILES is a difficult problem. For example, if you request 3D coordinates for a SMILES string with unspecified chirality, what do you do? As Keiron mentioned, there are other programs which can generate coordinates for SMILES strings -- but Open Babel will eventually have support for this in the future. We're laying the groundwork now. Cheers, -Geoff |
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From: Kieron T. <kr...@so...> - 2007-05-20 18:49:53
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Yesipenko A. wrote: > I convert SMI string into MOL (or MDL) format on Perl. The convertion > runs normally, but in result mol-format all coordinates (x, y and z) > of all atoms are (0,0,0). Why? The process of turning a smiles string into anything else requires some form of geometry optimisation. OpenBabel doesn't do this by default and I am do not believe it can do it at all, since that was not its purpose. It is meant for recognising connectivity. Other programs such as Marvin have limited capabilities for creating a 3d geometry, you might like to look into them. Kieron |
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From: Jens T. <j.m...@dl...> - 2007-05-18 15:24:20
|
Hello,
I've hit what I think is a bug with the readers for NWChem and Gaussian
output files, although it manifests itself through my using pybel.
At least I think it's a bug - I could of course just be using the python
interface incorrectly, in which case I'd appreciate any pointers on the
correct way to use it!
I've been using the pybel readfile method to extract geometries from the
output files for various quantum chemistry codes. Unfortunately, when
looking at the output files, readfile just hung.
The problem seems to be that these readers (e.g
NWChemOutputFormat::ReadMolecule) never return "false". They just
trundle through the output looking for the coordinates block and
replacing the old molecule with the new one until they hit the end of
the file. Hence if you call the OBConversion ReadFile method on them,
you just get the final geometry and a return state of "true".
Subsequent calls to the OBConversion Read method just return an empty
molecule and the reader returns a state of "true". Hence the following
block of code in pybel:
obmol = ob.OBMol()
notatend = obconversion.ReadFile(obmol,filename)
while notatend:
yield Molecule(obmol)
obmol = ob.OBMol()
notatend = obconversion.Read(obmol)
just keeps looping forever.
I can get this to work for me by calling NumAtoms() on the returned
molecule and breaking if this is None.
I've included a block of code below that demonstrates what I mean and
have also attached a zipped NWChem output file that I used for testing this.
Best wishes,
Jens
import sys
import openbabel as ob
filename = 'optim_c6h6.nwo' # NWChem output file
#filename = '3d.head.sdf' # Sample SDF file where the original
method works
obconversion = ob.OBConversion()
format = obconversion.FormatFromExt( filename )
formatok = obconversion.SetInFormat(format)
if not formatok:
raise ValueError,"%s is not a recognised OpenBabel format" % format
obmol = ob.OBMol()
notatend = obconversion.ReadFile(obmol,filename)
i=0
while notatend:
# Need to check natoms or we go on forever.
natoms = obmol.NumAtoms()
if not natoms:
print "Molecule has no atoms!"
break
atom = obmol.GetFirstAtom()
print "Got 1st coords ",atom.x(),atom.y(), atom.z()
obmol = ob.OBMol()
notatend = obconversion.Read(obmol)
i+=1
print "Found %s molecules" % i
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From: Noel O'B. <bao...@gm...> - 2007-05-17 11:46:12
|
On 17/05/07, Jens Thomas <j.m...@dl...> wrote: > Hi Noel, > > I've just worked out that the problem arose because I hadn't installed > anything and was running it directly from the build directory. I assume > it looks in a set directory for the files to dynamically configure the > supported formats. Can this be changed with an environment variable? The answer is yes.You need to set LD_LIBRARY_PATH to point to the directory containing libopenbabel.so, etc. You still need to run "make install" beforehand, though, to install all the formats to the correct location. I describe both "local" and "global" intalls on the wiki page. > Anyway, it's not important as once I'd installed everything into a > directory structure it then worked fine. > I should probably mention that I hit problems with the default version > of SWIG on Ubuntu wasn't able to handle the "-naturalvar" flag, so I had > to install swig 1.3.31 to get the build to work. I will add this to the install notes. > Many thanks for your help. > > Jens > > Noel O'Boyle wrote: > > The good news is that all the Python stuff seems to be working fine > > (no initialisation necessary). The bad news is that the C++ stuff > > isn't working properly. > > > > I'm betting that if you try "babel -H" and look under "The following > > file formats are recognized", you will see nothing there. Which is > > what you're also seeing in python. To verify, try to convert a file > > using babel. This is because the file formats are loaded dynamically > > as plugins, so there can be problems if you compile with particular > > settings. > > > > How exactly are you compiling the software? Did you follow the > > instructions on the web exactly (see > > http://openbabel.sourceforge.net/wiki/Install_%28source_code%29), or > > are you doing something different? I'm using an old version of Ubuntu > > myself, so there's no reason we can't get it to work. > > > > Regards > > Noel > > > > On 15/05/07, Jens Thomas <j.m...@dl...> wrote: > >> Hello! > >> > >> It's taken me a little while to grind through all the usual little > >> hiccups that come when building an unfamiliar code straight out of the > >> repository, but I've now got what (I think) is the correct version. > >> > >> I checked out the code at r1954 and patched with r1958 as suggested > >> by Noel. > >> > >> However, I'm not getting anything from pybel.informats or > >> OBConversion.GetSupportedInputFormats as shown below: > >> > >> > >> Python 2.4.3 (#2, Oct 6 2006, 07:52:30) > >> [GCC 4.0.3 (Ubuntu 4.0.3-1ubuntu5)] on linux2 > >> Type "help", "copyright", "credits" or "license" for more information. > >> >>> import pybel > >> >>> pybel.informats > >> {} > >> >>> pybel.outformats > >> {} > >> >>> import openbabel > >> >>> obc = openbabel.OBConversion() > >> >>> i= obc.GetSupportedInputFormat() > >> >>> print i > >> () > >> >>> dir(i) > >> ['__add__', '__class__', '__contains__', '__delattr__', '__doc__', > >> '__eq__', '__ge__', '__getattribute__', '__getitem__', '__getnewargs__', > >> '__getslice__', '__gt__', '__hash__', '__init__', '__iter__', '__le__', > >> '__len__', '__lt__', '__mul__', '__ne__', '__new__', '__reduce__', > >> '__reduce_ex__', '__repr__', '__rmul__', '__setattr__', '__str__'] > >> > >> > >> Is there some sort of initialisation I need to do to get the dictionary > >> populated? > >> > >> Many thanks, > >> > >> Jens > >> > >> Noel O'Boyle wrote: > >> > I've already noticed that the latest SVN is not compatible with SWIG > >> > due to changes introducted at r1954. You'll need to check out r1953, > >> > and use "svn merge -r 1957:1958" to patch with r1958. > >> > > >> > Noel > >> > > >> > On 14/05/07, Jens Thomas <j.m...@dl...> wrote: > >> >> Hi Noel, Jerome and Chris, > >> >> > >> >> Firstly, many thanks for the quick response and warm welcome to the > >> >> list! Please accept my apologies for not replying sooner, but I've > >> been > >> >> away without access to email. > >> >> > >> >> I've tried checking out the latest version of openbabel from SVN > >> onto my > >> >> Ubuntu box (Dapper on a Pentium 4) so that I can try some of the > >> changes > >> >> you've committed. I ran a normal configure (./configure), but the > >> make > >> >> currently fails with: > >> >> > >> >> make[2]: Leaving directory `/home/jmht/openbabel/test/cmltest' > >> >> make[2]: Entering directory `/home/jmht/openbabel/test' > >> >> g++ -DHAVE_CONFIG_H -I. -I../src -I../include > >> >> -DTESTDATADIR="\"../test/files/\"" -g -O2 -MT roundtrip.o -MD > >> -MP -MF > >> >> .deps/roundtrip.Tpo -c -o roundtrip.o roundtrip.cpp > >> >> mv -f .deps/roundtrip.Tpo .deps/roundtrip.Po > >> >> /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -o roundtrip > >> >> roundtrip.o ../src/libopenbabel.la -ldl -lm > >> >> mkdir .libs > >> >> g++ -g -O2 -o .libs/roundtrip roundtrip.o > >> ../src/.libs/libopenbabel.so > >> >> -ldl -lm -Wl,--rpath -Wl,/usr/local/lib > >> >> ../src/.libs/libopenbabel.so: undefined reference to > >> >> `OpenBabel::OBFormat::FormatFromMIME(char const*)' > >> >> ../src/.libs/libopenbabel.so: undefined reference to > >> >> `OpenBabel::OBPlugin::Display(std::basic_string<char, > >> >> std::char_traits<char>, std::allocator<char> >&, char const*, char > >> >> const*)' > >> >> ../src/.libs/libopenbabel.so: undefined reference to `vtable for > >> >> OpenBabel::OBDescriptor' > >> >> ../src/.libs/libopenbabel.so: undefined reference to > >> >> `OpenBabel::OBDescriptor::Compare(OpenBabel::OBBase*, > >> >> std::basic_istream<char, std::char_traits<char> >&, bool)' > >> >> ../src/.libs/libopenbabel.so: undefined reference to `vtable for > >> >> OpenBabel::OBPlugin' > >> >> ../src/.libs/libopenbabel.so: undefined reference to > >> >> `OpenBabel::OBPlugin::ListAsVector(char const*, char const*, > >> >> std::vector<std::basic_string<char, std::char_traits<char>, > >> >> std::allocator<char> >, std::allocator<std::basic_string<char, > >> >> std::char_traits<char>, std::allocator<char> > > >&)' > >> >> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for > >> >> OpenBabel::OBPlugin' > >> >> ../src/.libs/libopenbabel.so: undefined reference to > >> >> `OpenBabel::OBDescriptor::AddProperties(OpenBabel::OBBase*, > >> >> std::basic_string<char, std::char_traits<char>, > >> std::allocator<char> > > >> >> const&)' > >> >> ../src/.libs/libopenbabel.so: undefined reference to > >> >> `OpenBabel::OBDescriptor::GetStringValue(OpenBabel::OBBase*, > >> >> std::basic_string<char, std::char_traits<char>, std::allocator<char> > >> >> >&)' > >> >> ../src/.libs/libopenbabel.so: undefined reference to > >> >> `OpenBabel::OBDescriptor::FilterCompare(OpenBabel::OBBase*, > >> >> std::basic_istream<char, std::char_traits<char> >&, bool)' > >> >> ../src/.libs/libopenbabel.so: undefined reference to > >> >> `OpenBabel::OBFormat::RegisterFormat(char const*, char const*)' > >> >> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for > >> >> OpenBabel::OBDescriptor' > >> >> ../src/.libs/libopenbabel.so: undefined reference to > >> >> `OpenBabel::OBDescriptor::DeleteProperties(OpenBabel::OBBase*, > >> >> std::basic_string<char, std::char_traits<char>, > >> std::allocator<char> > > >> >> const&)' > >> >> collect2: ld returned 1 exit status > >> >> make[2]: *** [roundtrip] Error 1 > >> >> > >> >> I'm not that familiar with C++ and so am bit stuck as to how to sort > >> >> this one out. > >> >> > >> >> Do you have any suggestions? > >> >> > >> >> Best wishes, > >> >> > >> >> Jens > >> >> > >> >> > >> >> Noel O'Boyle wrote: > >> >> > On 12/05/07, Chris Morley <c.m...@ds...> wrote: > >> >> > > >> >> >> In the revamped code for formats (and other plugins) recently > >> >> committed > >> >> >> to SVN HEAD (for the next OB version) I tried to maintain backward > >> >> >> compatibility as far as possible. So > >> >> OBConversion::SupportedInputFormat() > >> >> >> works as before but, you'll be pleased to hear, without the > >> >> '[Read-only]'. > >> >> >> > >> >> > Sounds good but SWIG doesn't like the new code. When I try to > >> compile > >> >> > openbabel_python.cpp, I get: > >> >> > > >> >> > ../../include/openbabel/fingerprint.h:48: error: 'static > >> >> > std::map<const char*, OpenBabel::OBPlugin*, > >> >> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const > >> char* > >> >> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()' > >> >> > cannot be overloaded > >> >> > ../../include/openbabel/fingerprint.h:43: error: with 'static > >> >> > std::map<const char*, OpenBabel::OBPlugin*, > >> >> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const > >> char* > >> >> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()' > >> >> > ../../include/openbabel/fingerprint.h:53: error: 'static > >> >> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()' > >> cannot > >> >> > be overloaded > >> >> > ../../include/openbabel/fingerprint.h:43: error: with 'static > >> >> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()' > >> >> > ../../include/openbabel/fingerprint.h: In constructor > >> >> > 'OpenBabel::OBFingerprint::OBFingerprint(std::string, bool)': > >> >> > ../../include/openbabel/fingerprint.h:63: error: no match for > >> >> > 'operator[]' in 'OpenBabel::OBFingerprint::Map()[ID]' > >> >> > /usr/include/c++/4.0.2/bits/stl_map.h:331: note: candidates are: > >> _Tp& > >> >> > std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const _Key&) > >> [with > >> >> > _Key = const char*, _Tp = OpenBabel::OBPlugin*, _Compare = > >> >> > OpenBabel::OBPlugin::CharPtrLess, _Alloc = > >> >> > std::allocator<std::pair<const char* const, > >> OpenBabel::OBPlugin*> >] > >> >> > > >> >> > > >> >> >> But in an effort to provide more choice on the form of the output, > >> >> there > >> >> >> are three functions which provide a list of formats(or other > >> plugin > >> >> >> classes): OBPlugin::ListAsVector, ListAsString and List. The first > >> >> two > >> >> >> were intended to be compatible with scripting, although I need > >> some > >> >> >> advice here. ListAsString returns a (big) std::string, but > >> >> ListAsVector > >> >> >> has a parameter which is a reference to a std::vector. If this is > >> >> >> incompatible with scripting languages I should change it. > >> >> >> > >> >> > There's no problem with vectors in general; these are simply > >> >> > translated to lists by SWIG. > >> >> > > >> >> > > >> >> >> All three have a parameter which can control what is in the > >> >> output. For > >> >> >> example if it contains "verbose" it output the whole > >> description, not > >> >> >> just the first line. So it would be easy to add code (4 extra > >> >> lines) to > >> >> >> output only the IDs if that would be useful: > >> >> >> ListAsVector("formats","in/ids", stringvector) > >> >> >> > >> >> >> Post-processing in pybel I'm sure is useful, but if the C++ > >> code was > >> >> >> adequate it could serve other scripting languages as well. > >> >> >> > >> >> > I think so too. In the meanwhile, I would like to push out a > >> Windows > >> >> > Python release based on 2.1.0 with the current pybel > >> enhancements. I'm > >> >> > going to try to get this together this weekend and do some testing. > >> >> > > >> >> > Noel > >> >> > > >> >> > > >> >> >> Chris > >> >> >> > >> >> >> Noel O'Boyle wrote: > >> >> >> > >> >> >>> After looking at the C++ code, I realise that maybe returning > >> a list > >> >> >>> of strings is the only choice for SupportedInputFormat. Anyway, > >> >> in the > >> >> >>> meanwhile I've added some code to pybel, so that if you access > >> >> >>> pybel.informats or outformats, you will get a dictionary of > >> >> supported > >> >> >>> formats. > >> >> >>> > >> >> >>> On 12/05/07, Noel O'Boyle <bao...@gm...> wrote: > >> >> >>> > >> >> >>>> Actually, a vector of std::strings had not yet been > >> swigified, so I > >> >> >>>> needed to added to a line to openbabel-python.i to set it up > >> >> (not yet > >> >> >>>> checked in). However, there's an additional problem, which > >> >> Jerome may > >> >> >>>> like to address. > >> >> >>>> > >> >> >>>> The data that's returned is similar to: > >> >> >>>> ('acr -- ACR format [Read-only]', 'alc -- Alchemy format', ... ) > >> >> >>>> > >> >> >>>> whereas it would make more sense to me either to return: > >> >> >>>> ('acr', 'alc', ...) > >> >> >>>> or > >> >> >>>> a std::map (i.e. a Python dict) of ['acr' : 'ACR format', 'alc': > >> >> >>>> 'Alchemy format'] > >> >> >>>> > >> >> >>>> Note that the text [Read-only] is not really necessary in a > >> list of > >> >> >>>> supported input formats. > >> >> >>>> > >> >> >>>> Since this function was added for the benefit of scripting > >> >> interfaces, > >> >> >>>> it makes sense to make it as easy as possible to access the > >> list of > >> >> >>>> formats. > >> >> >>>> > >> >> >>>> Noel > >> >> >>>> > >> >> >>>> On 11/05/07, Noel O'Boyle <bao...@gm...> wrote: > >> >> >>>> > >> >> >>>>> Hello again Jens, > >> >> >>>>> > >> >> >>>>> Good to hear from you on this list... :-) > >> >> >>>>> > >> >> >>>>> On 10/05/07, Jens Thomas <j.m...@dl...> wrote: > >> >> >>>>> > >> >> >>>>>> Hi, > >> >> >>>>>> > >> >> >>>>>> I'm trying to enable our ccp1gui code > >> >> >>>>>> (http://sourceforge.net/projects/ccp1gui/) to use openbabel so > >> >> that we > >> >> >>>>>> no longer have to support so many formats. > >> >> >>>>>> > >> >> >>>>>> I've got most of the machinery in place, but am a bit stuck on > >> >> how to > >> >> >>>>>> dynamically determine what input formats are supported by > >> >> openbabel. > >> >> >>>>>> > >> >> >>>>>> I originally tried to use OBConversion.GetNextFormat, but ran > >> >> into the > >> >> >>>>>> ground fairly quickly. I then discovered the post at: > >> >> >>>>>> > >> >> >>>>>> > >> >> > >> http://sourceforge.net/mailarchive/forum.php?thread_name=200702191105.25888.j.pansanel%40pansanel.net&forum_name=openbabel-scripting > >> > >> >> > >> >> >>>>>> > >> >> >>>>>> which suggest that I should be able to get what I want using > >> >> >>>>>> GetSupportedInputFormat(), however, I'm currently pretty > >> >> clueless as to > >> >> >>>>>> how I extract the information from the object. I get something > >> >> back as > >> >> >>>>>> shown below, but I'd appreciated any advice on what I then > >> >> need to do > >> >> >>>>>> with it. > >> >> >>>>>> > >> >> >> > >> >> > >> ------------------------------------------------------------------------- > >> > >> >> > >> >> >> This SF.net email is sponsored by DB2 Express > >> >> >> Download DB2 Express C - the FREE version of DB2 express and take > >> >> >> control of your XML. No limits. Just data. Click to get it now. > >> >> >> http://sourceforge.net/powerbar/db2/ > >> >> >> _______________________________________________ > >> >> >> OpenBabel-scripting mailing list > >> >> >> Ope...@li... > >> >> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > >> >> >> > >> >> >> > >> >> > > >> >> > > >> >> > >> ------------------------------------------------------------------------- > >> > >> >> > >> >> > This SF.net email is sponsored by DB2 Express > >> >> > Download DB2 Express C - the FREE version of DB2 express and take > >> >> > control of your XML. No limits. Just data. Click to get it now. > >> >> > http://sourceforge.net/powerbar/db2/ > >> >> > _______________________________________________ > >> >> > OpenBabel-scripting mailing list > >> >> > Ope...@li... > >> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > >> >> > > >> >> > > >> >> > >> >> > >> > > >> > >> > > > > |
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From: Jens T. <j.m...@dl...> - 2007-05-17 11:21:02
|
Hi Noel, I've just worked out that the problem arose because I hadn't installed anything and was running it directly from the build directory. I assume it looks in a set directory for the files to dynamically configure the supported formats. Can this be changed with an environment variable? Anyway, it's not important as once I'd installed everything into a directory structure it then worked fine. I should probably mention that I hit problems with the default version of SWIG on Ubuntu wasn't able to handle the "-naturalvar" flag, so I had to install swig 1.3.31 to get the build to work. Many thanks for your help. Jens Noel O'Boyle wrote: > The good news is that all the Python stuff seems to be working fine > (no initialisation necessary). The bad news is that the C++ stuff > isn't working properly. > > I'm betting that if you try "babel -H" and look under "The following > file formats are recognized", you will see nothing there. Which is > what you're also seeing in python. To verify, try to convert a file > using babel. This is because the file formats are loaded dynamically > as plugins, so there can be problems if you compile with particular > settings. > > How exactly are you compiling the software? Did you follow the > instructions on the web exactly (see > http://openbabel.sourceforge.net/wiki/Install_%28source_code%29), or > are you doing something different? I'm using an old version of Ubuntu > myself, so there's no reason we can't get it to work. > > Regards > Noel > > On 15/05/07, Jens Thomas <j.m...@dl...> wrote: >> Hello! >> >> It's taken me a little while to grind through all the usual little >> hiccups that come when building an unfamiliar code straight out of the >> repository, but I've now got what (I think) is the correct version. >> >> I checked out the code at r1954 and patched with r1958 as suggested >> by Noel. >> >> However, I'm not getting anything from pybel.informats or >> OBConversion.GetSupportedInputFormats as shown below: >> >> >> Python 2.4.3 (#2, Oct 6 2006, 07:52:30) >> [GCC 4.0.3 (Ubuntu 4.0.3-1ubuntu5)] on linux2 >> Type "help", "copyright", "credits" or "license" for more information. >> >>> import pybel >> >>> pybel.informats >> {} >> >>> pybel.outformats >> {} >> >>> import openbabel >> >>> obc = openbabel.OBConversion() >> >>> i= obc.GetSupportedInputFormat() >> >>> print i >> () >> >>> dir(i) >> ['__add__', '__class__', '__contains__', '__delattr__', '__doc__', >> '__eq__', '__ge__', '__getattribute__', '__getitem__', '__getnewargs__', >> '__getslice__', '__gt__', '__hash__', '__init__', '__iter__', '__le__', >> '__len__', '__lt__', '__mul__', '__ne__', '__new__', '__reduce__', >> '__reduce_ex__', '__repr__', '__rmul__', '__setattr__', '__str__'] >> >> >> Is there some sort of initialisation I need to do to get the dictionary >> populated? >> >> Many thanks, >> >> Jens >> >> Noel O'Boyle wrote: >> > I've already noticed that the latest SVN is not compatible with SWIG >> > due to changes introducted at r1954. You'll need to check out r1953, >> > and use "svn merge -r 1957:1958" to patch with r1958. >> > >> > Noel >> > >> > On 14/05/07, Jens Thomas <j.m...@dl...> wrote: >> >> Hi Noel, Jerome and Chris, >> >> >> >> Firstly, many thanks for the quick response and warm welcome to the >> >> list! Please accept my apologies for not replying sooner, but I've >> been >> >> away without access to email. >> >> >> >> I've tried checking out the latest version of openbabel from SVN >> onto my >> >> Ubuntu box (Dapper on a Pentium 4) so that I can try some of the >> changes >> >> you've committed. I ran a normal configure (./configure), but the >> make >> >> currently fails with: >> >> >> >> make[2]: Leaving directory `/home/jmht/openbabel/test/cmltest' >> >> make[2]: Entering directory `/home/jmht/openbabel/test' >> >> g++ -DHAVE_CONFIG_H -I. -I../src -I../include >> >> -DTESTDATADIR="\"../test/files/\"" -g -O2 -MT roundtrip.o -MD >> -MP -MF >> >> .deps/roundtrip.Tpo -c -o roundtrip.o roundtrip.cpp >> >> mv -f .deps/roundtrip.Tpo .deps/roundtrip.Po >> >> /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -o roundtrip >> >> roundtrip.o ../src/libopenbabel.la -ldl -lm >> >> mkdir .libs >> >> g++ -g -O2 -o .libs/roundtrip roundtrip.o >> ../src/.libs/libopenbabel.so >> >> -ldl -lm -Wl,--rpath -Wl,/usr/local/lib >> >> ../src/.libs/libopenbabel.so: undefined reference to >> >> `OpenBabel::OBFormat::FormatFromMIME(char const*)' >> >> ../src/.libs/libopenbabel.so: undefined reference to >> >> `OpenBabel::OBPlugin::Display(std::basic_string<char, >> >> std::char_traits<char>, std::allocator<char> >&, char const*, char >> >> const*)' >> >> ../src/.libs/libopenbabel.so: undefined reference to `vtable for >> >> OpenBabel::OBDescriptor' >> >> ../src/.libs/libopenbabel.so: undefined reference to >> >> `OpenBabel::OBDescriptor::Compare(OpenBabel::OBBase*, >> >> std::basic_istream<char, std::char_traits<char> >&, bool)' >> >> ../src/.libs/libopenbabel.so: undefined reference to `vtable for >> >> OpenBabel::OBPlugin' >> >> ../src/.libs/libopenbabel.so: undefined reference to >> >> `OpenBabel::OBPlugin::ListAsVector(char const*, char const*, >> >> std::vector<std::basic_string<char, std::char_traits<char>, >> >> std::allocator<char> >, std::allocator<std::basic_string<char, >> >> std::char_traits<char>, std::allocator<char> > > >&)' >> >> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for >> >> OpenBabel::OBPlugin' >> >> ../src/.libs/libopenbabel.so: undefined reference to >> >> `OpenBabel::OBDescriptor::AddProperties(OpenBabel::OBBase*, >> >> std::basic_string<char, std::char_traits<char>, >> std::allocator<char> > >> >> const&)' >> >> ../src/.libs/libopenbabel.so: undefined reference to >> >> `OpenBabel::OBDescriptor::GetStringValue(OpenBabel::OBBase*, >> >> std::basic_string<char, std::char_traits<char>, std::allocator<char> >> >> >&)' >> >> ../src/.libs/libopenbabel.so: undefined reference to >> >> `OpenBabel::OBDescriptor::FilterCompare(OpenBabel::OBBase*, >> >> std::basic_istream<char, std::char_traits<char> >&, bool)' >> >> ../src/.libs/libopenbabel.so: undefined reference to >> >> `OpenBabel::OBFormat::RegisterFormat(char const*, char const*)' >> >> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for >> >> OpenBabel::OBDescriptor' >> >> ../src/.libs/libopenbabel.so: undefined reference to >> >> `OpenBabel::OBDescriptor::DeleteProperties(OpenBabel::OBBase*, >> >> std::basic_string<char, std::char_traits<char>, >> std::allocator<char> > >> >> const&)' >> >> collect2: ld returned 1 exit status >> >> make[2]: *** [roundtrip] Error 1 >> >> >> >> I'm not that familiar with C++ and so am bit stuck as to how to sort >> >> this one out. >> >> >> >> Do you have any suggestions? >> >> >> >> Best wishes, >> >> >> >> Jens >> >> >> >> >> >> Noel O'Boyle wrote: >> >> > On 12/05/07, Chris Morley <c.m...@ds...> wrote: >> >> > >> >> >> In the revamped code for formats (and other plugins) recently >> >> committed >> >> >> to SVN HEAD (for the next OB version) I tried to maintain backward >> >> >> compatibility as far as possible. So >> >> OBConversion::SupportedInputFormat() >> >> >> works as before but, you'll be pleased to hear, without the >> >> '[Read-only]'. >> >> >> >> >> > Sounds good but SWIG doesn't like the new code. When I try to >> compile >> >> > openbabel_python.cpp, I get: >> >> > >> >> > ../../include/openbabel/fingerprint.h:48: error: 'static >> >> > std::map<const char*, OpenBabel::OBPlugin*, >> >> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const >> char* >> >> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()' >> >> > cannot be overloaded >> >> > ../../include/openbabel/fingerprint.h:43: error: with 'static >> >> > std::map<const char*, OpenBabel::OBPlugin*, >> >> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const >> char* >> >> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()' >> >> > ../../include/openbabel/fingerprint.h:53: error: 'static >> >> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()' >> cannot >> >> > be overloaded >> >> > ../../include/openbabel/fingerprint.h:43: error: with 'static >> >> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()' >> >> > ../../include/openbabel/fingerprint.h: In constructor >> >> > 'OpenBabel::OBFingerprint::OBFingerprint(std::string, bool)': >> >> > ../../include/openbabel/fingerprint.h:63: error: no match for >> >> > 'operator[]' in 'OpenBabel::OBFingerprint::Map()[ID]' >> >> > /usr/include/c++/4.0.2/bits/stl_map.h:331: note: candidates are: >> _Tp& >> >> > std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const _Key&) >> [with >> >> > _Key = const char*, _Tp = OpenBabel::OBPlugin*, _Compare = >> >> > OpenBabel::OBPlugin::CharPtrLess, _Alloc = >> >> > std::allocator<std::pair<const char* const, >> OpenBabel::OBPlugin*> >] >> >> > >> >> > >> >> >> But in an effort to provide more choice on the form of the output, >> >> there >> >> >> are three functions which provide a list of formats(or other >> plugin >> >> >> classes): OBPlugin::ListAsVector, ListAsString and List. The first >> >> two >> >> >> were intended to be compatible with scripting, although I need >> some >> >> >> advice here. ListAsString returns a (big) std::string, but >> >> ListAsVector >> >> >> has a parameter which is a reference to a std::vector. If this is >> >> >> incompatible with scripting languages I should change it. >> >> >> >> >> > There's no problem with vectors in general; these are simply >> >> > translated to lists by SWIG. >> >> > >> >> > >> >> >> All three have a parameter which can control what is in the >> >> output. For >> >> >> example if it contains "verbose" it output the whole >> description, not >> >> >> just the first line. So it would be easy to add code (4 extra >> >> lines) to >> >> >> output only the IDs if that would be useful: >> >> >> ListAsVector("formats","in/ids", stringvector) >> >> >> >> >> >> Post-processing in pybel I'm sure is useful, but if the C++ >> code was >> >> >> adequate it could serve other scripting languages as well. >> >> >> >> >> > I think so too. In the meanwhile, I would like to push out a >> Windows >> >> > Python release based on 2.1.0 with the current pybel >> enhancements. I'm >> >> > going to try to get this together this weekend and do some testing. >> >> > >> >> > Noel >> >> > >> >> > >> >> >> Chris >> >> >> >> >> >> Noel O'Boyle wrote: >> >> >> >> >> >>> After looking at the C++ code, I realise that maybe returning >> a list >> >> >>> of strings is the only choice for SupportedInputFormat. Anyway, >> >> in the >> >> >>> meanwhile I've added some code to pybel, so that if you access >> >> >>> pybel.informats or outformats, you will get a dictionary of >> >> supported >> >> >>> formats. >> >> >>> >> >> >>> On 12/05/07, Noel O'Boyle <bao...@gm...> wrote: >> >> >>> >> >> >>>> Actually, a vector of std::strings had not yet been >> swigified, so I >> >> >>>> needed to added to a line to openbabel-python.i to set it up >> >> (not yet >> >> >>>> checked in). However, there's an additional problem, which >> >> Jerome may >> >> >>>> like to address. >> >> >>>> >> >> >>>> The data that's returned is similar to: >> >> >>>> ('acr -- ACR format [Read-only]', 'alc -- Alchemy format', ... ) >> >> >>>> >> >> >>>> whereas it would make more sense to me either to return: >> >> >>>> ('acr', 'alc', ...) >> >> >>>> or >> >> >>>> a std::map (i.e. a Python dict) of ['acr' : 'ACR format', 'alc': >> >> >>>> 'Alchemy format'] >> >> >>>> >> >> >>>> Note that the text [Read-only] is not really necessary in a >> list of >> >> >>>> supported input formats. >> >> >>>> >> >> >>>> Since this function was added for the benefit of scripting >> >> interfaces, >> >> >>>> it makes sense to make it as easy as possible to access the >> list of >> >> >>>> formats. >> >> >>>> >> >> >>>> Noel >> >> >>>> >> >> >>>> On 11/05/07, Noel O'Boyle <bao...@gm...> wrote: >> >> >>>> >> >> >>>>> Hello again Jens, >> >> >>>>> >> >> >>>>> Good to hear from you on this list... :-) >> >> >>>>> >> >> >>>>> On 10/05/07, Jens Thomas <j.m...@dl...> wrote: >> >> >>>>> >> >> >>>>>> Hi, >> >> >>>>>> >> >> >>>>>> I'm trying to enable our ccp1gui code >> >> >>>>>> (http://sourceforge.net/projects/ccp1gui/) to use openbabel so >> >> that we >> >> >>>>>> no longer have to support so many formats. >> >> >>>>>> >> >> >>>>>> I've got most of the machinery in place, but am a bit stuck on >> >> how to >> >> >>>>>> dynamically determine what input formats are supported by >> >> openbabel. >> >> >>>>>> >> >> >>>>>> I originally tried to use OBConversion.GetNextFormat, but ran >> >> into the >> >> >>>>>> ground fairly quickly. I then discovered the post at: >> >> >>>>>> >> >> >>>>>> >> >> >> http://sourceforge.net/mailarchive/forum.php?thread_name=200702191105.25888.j.pansanel%40pansanel.net&forum_name=openbabel-scripting >> >> >> >> >> >>>>>> >> >> >>>>>> which suggest that I should be able to get what I want using >> >> >>>>>> GetSupportedInputFormat(), however, I'm currently pretty >> >> clueless as to >> >> >>>>>> how I extract the information from the object. I get something >> >> back as >> >> >>>>>> shown below, but I'd appreciated any advice on what I then >> >> need to do >> >> >>>>>> with it. >> >> >>>>>> >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> >> >> >> >> This SF.net email is sponsored by DB2 Express >> >> >> Download DB2 Express C - the FREE version of DB2 express and take >> >> >> control of your XML. No limits. Just data. Click to get it now. >> >> >> http://sourceforge.net/powerbar/db2/ >> >> >> _______________________________________________ >> >> >> OpenBabel-scripting mailing list >> >> >> Ope...@li... >> >> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting >> >> >> >> >> >> >> >> > >> >> > >> >> >> ------------------------------------------------------------------------- >> >> >> >> >> > This SF.net email is sponsored by DB2 Express >> >> > Download DB2 Express C - the FREE version of DB2 express and take >> >> > control of your XML. No limits. Just data. Click to get it now. >> >> > http://sourceforge.net/powerbar/db2/ >> >> > _______________________________________________ >> >> > OpenBabel-scripting mailing list >> >> > Ope...@li... >> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting >> >> > >> >> > >> >> >> >> >> > >> >> > |
|
From: Yesipenko A. <esi...@if...> - 2007-05-17 09:27:21
|
I convert SMI string into MOL (or MDL) format on Perl. The convertion =
runs normally, but in result mol-format all coordinates (x, y and z) of =
all atoms are (0,0,0). Why?
Scipt:
---------
my $obMol =3D new Chemistry::OpenBabel::OBMol;
my $obConv =3D new Chemistry::OpenBabel::OBConversion;
$obConv->SetInAndOutFormats("smi","mdl");
$obConv->ReadString($obMol,$FORM{'smlout'});
$molstr =3D $obConv->WriteString($obMol);
---------
Input SMI strintg ($FORM{'smlout'}) is : C1CCC1
Output MOL format (value $molstr) is :
---------
OpenBabel0512D
4 4 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
1 4 1 0 0 0
1 2 1 0 0 0
2 3 1 0 0 0
3 4 1 0 0 0
M END
---------
Best regards,
Alex Yesipenko
esi...@if...
|
|
From: Noel O'B. <bao...@gm...> - 2007-05-16 21:01:27
|
The good news is that all the Python stuff seems to be working fine (no initialisation necessary). The bad news is that the C++ stuff isn't working properly. I'm betting that if you try "babel -H" and look under "The following file formats are recognized", you will see nothing there. Which is what you're also seeing in python. To verify, try to convert a file using babel. This is because the file formats are loaded dynamically as plugins, so there can be problems if you compile with particular settings. How exactly are you compiling the software? Did you follow the instructions on the web exactly (see http://openbabel.sourceforge.net/wiki/Install_%28source_code%29), or are you doing something different? I'm using an old version of Ubuntu myself, so there's no reason we can't get it to work. Regards Noel On 15/05/07, Jens Thomas <j.m...@dl...> wrote: > Hello! > > It's taken me a little while to grind through all the usual little > hiccups that come when building an unfamiliar code straight out of the > repository, but I've now got what (I think) is the correct version. > > I checked out the code at r1954 and patched with r1958 as suggested by Noel. > > However, I'm not getting anything from pybel.informats or > OBConversion.GetSupportedInputFormats as shown below: > > > Python 2.4.3 (#2, Oct 6 2006, 07:52:30) > [GCC 4.0.3 (Ubuntu 4.0.3-1ubuntu5)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> import pybel > >>> pybel.informats > {} > >>> pybel.outformats > {} > >>> import openbabel > >>> obc = openbabel.OBConversion() > >>> i= obc.GetSupportedInputFormat() > >>> print i > () > >>> dir(i) > ['__add__', '__class__', '__contains__', '__delattr__', '__doc__', > '__eq__', '__ge__', '__getattribute__', '__getitem__', '__getnewargs__', > '__getslice__', '__gt__', '__hash__', '__init__', '__iter__', '__le__', > '__len__', '__lt__', '__mul__', '__ne__', '__new__', '__reduce__', > '__reduce_ex__', '__repr__', '__rmul__', '__setattr__', '__str__'] > > > Is there some sort of initialisation I need to do to get the dictionary > populated? > > Many thanks, > > Jens > > Noel O'Boyle wrote: > > I've already noticed that the latest SVN is not compatible with SWIG > > due to changes introducted at r1954. You'll need to check out r1953, > > and use "svn merge -r 1957:1958" to patch with r1958. > > > > Noel > > > > On 14/05/07, Jens Thomas <j.m...@dl...> wrote: > >> Hi Noel, Jerome and Chris, > >> > >> Firstly, many thanks for the quick response and warm welcome to the > >> list! Please accept my apologies for not replying sooner, but I've been > >> away without access to email. > >> > >> I've tried checking out the latest version of openbabel from SVN onto my > >> Ubuntu box (Dapper on a Pentium 4) so that I can try some of the changes > >> you've committed. I ran a normal configure (./configure), but the make > >> currently fails with: > >> > >> make[2]: Leaving directory `/home/jmht/openbabel/test/cmltest' > >> make[2]: Entering directory `/home/jmht/openbabel/test' > >> g++ -DHAVE_CONFIG_H -I. -I../src -I../include > >> -DTESTDATADIR="\"../test/files/\"" -g -O2 -MT roundtrip.o -MD -MP -MF > >> .deps/roundtrip.Tpo -c -o roundtrip.o roundtrip.cpp > >> mv -f .deps/roundtrip.Tpo .deps/roundtrip.Po > >> /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -o roundtrip > >> roundtrip.o ../src/libopenbabel.la -ldl -lm > >> mkdir .libs > >> g++ -g -O2 -o .libs/roundtrip roundtrip.o ../src/.libs/libopenbabel.so > >> -ldl -lm -Wl,--rpath -Wl,/usr/local/lib > >> ../src/.libs/libopenbabel.so: undefined reference to > >> `OpenBabel::OBFormat::FormatFromMIME(char const*)' > >> ../src/.libs/libopenbabel.so: undefined reference to > >> `OpenBabel::OBPlugin::Display(std::basic_string<char, > >> std::char_traits<char>, std::allocator<char> >&, char const*, char > >> const*)' > >> ../src/.libs/libopenbabel.so: undefined reference to `vtable for > >> OpenBabel::OBDescriptor' > >> ../src/.libs/libopenbabel.so: undefined reference to > >> `OpenBabel::OBDescriptor::Compare(OpenBabel::OBBase*, > >> std::basic_istream<char, std::char_traits<char> >&, bool)' > >> ../src/.libs/libopenbabel.so: undefined reference to `vtable for > >> OpenBabel::OBPlugin' > >> ../src/.libs/libopenbabel.so: undefined reference to > >> `OpenBabel::OBPlugin::ListAsVector(char const*, char const*, > >> std::vector<std::basic_string<char, std::char_traits<char>, > >> std::allocator<char> >, std::allocator<std::basic_string<char, > >> std::char_traits<char>, std::allocator<char> > > >&)' > >> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for > >> OpenBabel::OBPlugin' > >> ../src/.libs/libopenbabel.so: undefined reference to > >> `OpenBabel::OBDescriptor::AddProperties(OpenBabel::OBBase*, > >> std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >> const&)' > >> ../src/.libs/libopenbabel.so: undefined reference to > >> `OpenBabel::OBDescriptor::GetStringValue(OpenBabel::OBBase*, > >> std::basic_string<char, std::char_traits<char>, std::allocator<char> > >> >&)' > >> ../src/.libs/libopenbabel.so: undefined reference to > >> `OpenBabel::OBDescriptor::FilterCompare(OpenBabel::OBBase*, > >> std::basic_istream<char, std::char_traits<char> >&, bool)' > >> ../src/.libs/libopenbabel.so: undefined reference to > >> `OpenBabel::OBFormat::RegisterFormat(char const*, char const*)' > >> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for > >> OpenBabel::OBDescriptor' > >> ../src/.libs/libopenbabel.so: undefined reference to > >> `OpenBabel::OBDescriptor::DeleteProperties(OpenBabel::OBBase*, > >> std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >> const&)' > >> collect2: ld returned 1 exit status > >> make[2]: *** [roundtrip] Error 1 > >> > >> I'm not that familiar with C++ and so am bit stuck as to how to sort > >> this one out. > >> > >> Do you have any suggestions? > >> > >> Best wishes, > >> > >> Jens > >> > >> > >> Noel O'Boyle wrote: > >> > On 12/05/07, Chris Morley <c.m...@ds...> wrote: > >> > > >> >> In the revamped code for formats (and other plugins) recently > >> committed > >> >> to SVN HEAD (for the next OB version) I tried to maintain backward > >> >> compatibility as far as possible. So > >> OBConversion::SupportedInputFormat() > >> >> works as before but, you'll be pleased to hear, without the > >> '[Read-only]'. > >> >> > >> > Sounds good but SWIG doesn't like the new code. When I try to compile > >> > openbabel_python.cpp, I get: > >> > > >> > ../../include/openbabel/fingerprint.h:48: error: 'static > >> > std::map<const char*, OpenBabel::OBPlugin*, > >> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const char* > >> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()' > >> > cannot be overloaded > >> > ../../include/openbabel/fingerprint.h:43: error: with 'static > >> > std::map<const char*, OpenBabel::OBPlugin*, > >> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const char* > >> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()' > >> > ../../include/openbabel/fingerprint.h:53: error: 'static > >> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()' cannot > >> > be overloaded > >> > ../../include/openbabel/fingerprint.h:43: error: with 'static > >> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()' > >> > ../../include/openbabel/fingerprint.h: In constructor > >> > 'OpenBabel::OBFingerprint::OBFingerprint(std::string, bool)': > >> > ../../include/openbabel/fingerprint.h:63: error: no match for > >> > 'operator[]' in 'OpenBabel::OBFingerprint::Map()[ID]' > >> > /usr/include/c++/4.0.2/bits/stl_map.h:331: note: candidates are: _Tp& > >> > std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const _Key&) [with > >> > _Key = const char*, _Tp = OpenBabel::OBPlugin*, _Compare = > >> > OpenBabel::OBPlugin::CharPtrLess, _Alloc = > >> > std::allocator<std::pair<const char* const, OpenBabel::OBPlugin*> >] > >> > > >> > > >> >> But in an effort to provide more choice on the form of the output, > >> there > >> >> are three functions which provide a list of formats(or other plugin > >> >> classes): OBPlugin::ListAsVector, ListAsString and List. The first > >> two > >> >> were intended to be compatible with scripting, although I need some > >> >> advice here. ListAsString returns a (big) std::string, but > >> ListAsVector > >> >> has a parameter which is a reference to a std::vector. If this is > >> >> incompatible with scripting languages I should change it. > >> >> > >> > There's no problem with vectors in general; these are simply > >> > translated to lists by SWIG. > >> > > >> > > >> >> All three have a parameter which can control what is in the > >> output. For > >> >> example if it contains "verbose" it output the whole description, not > >> >> just the first line. So it would be easy to add code (4 extra > >> lines) to > >> >> output only the IDs if that would be useful: > >> >> ListAsVector("formats","in/ids", stringvector) > >> >> > >> >> Post-processing in pybel I'm sure is useful, but if the C++ code was > >> >> adequate it could serve other scripting languages as well. > >> >> > >> > I think so too. In the meanwhile, I would like to push out a Windows > >> > Python release based on 2.1.0 with the current pybel enhancements. I'm > >> > going to try to get this together this weekend and do some testing. > >> > > >> > Noel > >> > > >> > > >> >> Chris > >> >> > >> >> Noel O'Boyle wrote: > >> >> > >> >>> After looking at the C++ code, I realise that maybe returning a list > >> >>> of strings is the only choice for SupportedInputFormat. Anyway, > >> in the > >> >>> meanwhile I've added some code to pybel, so that if you access > >> >>> pybel.informats or outformats, you will get a dictionary of > >> supported > >> >>> formats. > >> >>> > >> >>> On 12/05/07, Noel O'Boyle <bao...@gm...> wrote: > >> >>> > >> >>>> Actually, a vector of std::strings had not yet been swigified, so I > >> >>>> needed to added to a line to openbabel-python.i to set it up > >> (not yet > >> >>>> checked in). However, there's an additional problem, which > >> Jerome may > >> >>>> like to address. > >> >>>> > >> >>>> The data that's returned is similar to: > >> >>>> ('acr -- ACR format [Read-only]', 'alc -- Alchemy format', ... ) > >> >>>> > >> >>>> whereas it would make more sense to me either to return: > >> >>>> ('acr', 'alc', ...) > >> >>>> or > >> >>>> a std::map (i.e. a Python dict) of ['acr' : 'ACR format', 'alc': > >> >>>> 'Alchemy format'] > >> >>>> > >> >>>> Note that the text [Read-only] is not really necessary in a list of > >> >>>> supported input formats. > >> >>>> > >> >>>> Since this function was added for the benefit of scripting > >> interfaces, > >> >>>> it makes sense to make it as easy as possible to access the list of > >> >>>> formats. > >> >>>> > >> >>>> Noel > >> >>>> > >> >>>> On 11/05/07, Noel O'Boyle <bao...@gm...> wrote: > >> >>>> > >> >>>>> Hello again Jens, > >> >>>>> > >> >>>>> Good to hear from you on this list... :-) > >> >>>>> > >> >>>>> On 10/05/07, Jens Thomas <j.m...@dl...> wrote: > >> >>>>> > >> >>>>>> Hi, > >> >>>>>> > >> >>>>>> I'm trying to enable our ccp1gui code > >> >>>>>> (http://sourceforge.net/projects/ccp1gui/) to use openbabel so > >> that we > >> >>>>>> no longer have to support so many formats. > >> >>>>>> > >> >>>>>> I've got most of the machinery in place, but am a bit stuck on > >> how to > >> >>>>>> dynamically determine what input formats are supported by > >> openbabel. > >> >>>>>> > >> >>>>>> I originally tried to use OBConversion.GetNextFormat, but ran > >> into the > >> >>>>>> ground fairly quickly. I then discovered the post at: > >> >>>>>> > >> >>>>>> > >> http://sourceforge.net/mailarchive/forum.php?thread_name=200702191105.25888.j.pansanel%40pansanel.net&forum_name=openbabel-scripting > >> > >> >>>>>> > >> >>>>>> which suggest that I should be able to get what I want using > >> >>>>>> GetSupportedInputFormat(), however, I'm currently pretty > >> clueless as to > >> >>>>>> how I extract the information from the object. I get something > >> back as > >> >>>>>> shown below, but I'd appreciated any advice on what I then > >> need to do > >> >>>>>> with it. > >> >>>>>> > >> >> > >> ------------------------------------------------------------------------- > >> > >> >> This SF.net email is sponsored by DB2 Express > >> >> Download DB2 Express C - the FREE version of DB2 express and take > >> >> control of your XML. No limits. Just data. Click to get it now. > >> >> http://sourceforge.net/powerbar/db2/ > >> >> _______________________________________________ > >> >> OpenBabel-scripting mailing list > >> >> Ope...@li... > >> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > >> >> > >> >> > >> > > >> > > >> ------------------------------------------------------------------------- > >> > >> > This SF.net email is sponsored by DB2 Express > >> > Download DB2 Express C - the FREE version of DB2 express and take > >> > control of your XML. No limits. Just data. Click to get it now. > >> > http://sourceforge.net/powerbar/db2/ > >> > _______________________________________________ > >> > OpenBabel-scripting mailing list > >> > Ope...@li... > >> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > >> > > >> > > >> > >> > > > > |
|
From: Jens T. <j.m...@dl...> - 2007-05-15 17:30:26
|
Hello!
It's taken me a little while to grind through all the usual little
hiccups that come when building an unfamiliar code straight out of the
repository, but I've now got what (I think) is the correct version.
I checked out the code at r1954 and patched with r1958 as suggested by Noel.
However, I'm not getting anything from pybel.informats or
OBConversion.GetSupportedInputFormats as shown below:
Python 2.4.3 (#2, Oct 6 2006, 07:52:30)
[GCC 4.0.3 (Ubuntu 4.0.3-1ubuntu5)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
>>> pybel.informats
{}
>>> pybel.outformats
{}
>>> import openbabel
>>> obc = openbabel.OBConversion()
>>> i= obc.GetSupportedInputFormat()
>>> print i
()
>>> dir(i)
['__add__', '__class__', '__contains__', '__delattr__', '__doc__',
'__eq__', '__ge__', '__getattribute__', '__getitem__', '__getnewargs__',
'__getslice__', '__gt__', '__hash__', '__init__', '__iter__', '__le__',
'__len__', '__lt__', '__mul__', '__ne__', '__new__', '__reduce__',
'__reduce_ex__', '__repr__', '__rmul__', '__setattr__', '__str__']
Is there some sort of initialisation I need to do to get the dictionary
populated?
Many thanks,
Jens
Noel O'Boyle wrote:
> I've already noticed that the latest SVN is not compatible with SWIG
> due to changes introducted at r1954. You'll need to check out r1953,
> and use "svn merge -r 1957:1958" to patch with r1958.
>
> Noel
>
> On 14/05/07, Jens Thomas <j.m...@dl...> wrote:
>> Hi Noel, Jerome and Chris,
>>
>> Firstly, many thanks for the quick response and warm welcome to the
>> list! Please accept my apologies for not replying sooner, but I've been
>> away without access to email.
>>
>> I've tried checking out the latest version of openbabel from SVN onto my
>> Ubuntu box (Dapper on a Pentium 4) so that I can try some of the changes
>> you've committed. I ran a normal configure (./configure), but the make
>> currently fails with:
>>
>> make[2]: Leaving directory `/home/jmht/openbabel/test/cmltest'
>> make[2]: Entering directory `/home/jmht/openbabel/test'
>> g++ -DHAVE_CONFIG_H -I. -I../src -I../include
>> -DTESTDATADIR="\"../test/files/\"" -g -O2 -MT roundtrip.o -MD -MP -MF
>> .deps/roundtrip.Tpo -c -o roundtrip.o roundtrip.cpp
>> mv -f .deps/roundtrip.Tpo .deps/roundtrip.Po
>> /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -o roundtrip
>> roundtrip.o ../src/libopenbabel.la -ldl -lm
>> mkdir .libs
>> g++ -g -O2 -o .libs/roundtrip roundtrip.o ../src/.libs/libopenbabel.so
>> -ldl -lm -Wl,--rpath -Wl,/usr/local/lib
>> ../src/.libs/libopenbabel.so: undefined reference to
>> `OpenBabel::OBFormat::FormatFromMIME(char const*)'
>> ../src/.libs/libopenbabel.so: undefined reference to
>> `OpenBabel::OBPlugin::Display(std::basic_string<char,
>> std::char_traits<char>, std::allocator<char> >&, char const*, char
>> const*)'
>> ../src/.libs/libopenbabel.so: undefined reference to `vtable for
>> OpenBabel::OBDescriptor'
>> ../src/.libs/libopenbabel.so: undefined reference to
>> `OpenBabel::OBDescriptor::Compare(OpenBabel::OBBase*,
>> std::basic_istream<char, std::char_traits<char> >&, bool)'
>> ../src/.libs/libopenbabel.so: undefined reference to `vtable for
>> OpenBabel::OBPlugin'
>> ../src/.libs/libopenbabel.so: undefined reference to
>> `OpenBabel::OBPlugin::ListAsVector(char const*, char const*,
>> std::vector<std::basic_string<char, std::char_traits<char>,
>> std::allocator<char> >, std::allocator<std::basic_string<char,
>> std::char_traits<char>, std::allocator<char> > > >&)'
>> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for
>> OpenBabel::OBPlugin'
>> ../src/.libs/libopenbabel.so: undefined reference to
>> `OpenBabel::OBDescriptor::AddProperties(OpenBabel::OBBase*,
>> std::basic_string<char, std::char_traits<char>, std::allocator<char> >
>> const&)'
>> ../src/.libs/libopenbabel.so: undefined reference to
>> `OpenBabel::OBDescriptor::GetStringValue(OpenBabel::OBBase*,
>> std::basic_string<char, std::char_traits<char>, std::allocator<char>
>> >&)'
>> ../src/.libs/libopenbabel.so: undefined reference to
>> `OpenBabel::OBDescriptor::FilterCompare(OpenBabel::OBBase*,
>> std::basic_istream<char, std::char_traits<char> >&, bool)'
>> ../src/.libs/libopenbabel.so: undefined reference to
>> `OpenBabel::OBFormat::RegisterFormat(char const*, char const*)'
>> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for
>> OpenBabel::OBDescriptor'
>> ../src/.libs/libopenbabel.so: undefined reference to
>> `OpenBabel::OBDescriptor::DeleteProperties(OpenBabel::OBBase*,
>> std::basic_string<char, std::char_traits<char>, std::allocator<char> >
>> const&)'
>> collect2: ld returned 1 exit status
>> make[2]: *** [roundtrip] Error 1
>>
>> I'm not that familiar with C++ and so am bit stuck as to how to sort
>> this one out.
>>
>> Do you have any suggestions?
>>
>> Best wishes,
>>
>> Jens
>>
>>
>> Noel O'Boyle wrote:
>> > On 12/05/07, Chris Morley <c.m...@ds...> wrote:
>> >
>> >> In the revamped code for formats (and other plugins) recently
>> committed
>> >> to SVN HEAD (for the next OB version) I tried to maintain backward
>> >> compatibility as far as possible. So
>> OBConversion::SupportedInputFormat()
>> >> works as before but, you'll be pleased to hear, without the
>> '[Read-only]'.
>> >>
>> > Sounds good but SWIG doesn't like the new code. When I try to compile
>> > openbabel_python.cpp, I get:
>> >
>> > ../../include/openbabel/fingerprint.h:48: error: 'static
>> > std::map<const char*, OpenBabel::OBPlugin*,
>> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const char*
>> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()'
>> > cannot be overloaded
>> > ../../include/openbabel/fingerprint.h:43: error: with 'static
>> > std::map<const char*, OpenBabel::OBPlugin*,
>> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const char*
>> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()'
>> > ../../include/openbabel/fingerprint.h:53: error: 'static
>> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()' cannot
>> > be overloaded
>> > ../../include/openbabel/fingerprint.h:43: error: with 'static
>> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()'
>> > ../../include/openbabel/fingerprint.h: In constructor
>> > 'OpenBabel::OBFingerprint::OBFingerprint(std::string, bool)':
>> > ../../include/openbabel/fingerprint.h:63: error: no match for
>> > 'operator[]' in 'OpenBabel::OBFingerprint::Map()[ID]'
>> > /usr/include/c++/4.0.2/bits/stl_map.h:331: note: candidates are: _Tp&
>> > std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const _Key&) [with
>> > _Key = const char*, _Tp = OpenBabel::OBPlugin*, _Compare =
>> > OpenBabel::OBPlugin::CharPtrLess, _Alloc =
>> > std::allocator<std::pair<const char* const, OpenBabel::OBPlugin*> >]
>> >
>> >
>> >> But in an effort to provide more choice on the form of the output,
>> there
>> >> are three functions which provide a list of formats(or other plugin
>> >> classes): OBPlugin::ListAsVector, ListAsString and List. The first
>> two
>> >> were intended to be compatible with scripting, although I need some
>> >> advice here. ListAsString returns a (big) std::string, but
>> ListAsVector
>> >> has a parameter which is a reference to a std::vector. If this is
>> >> incompatible with scripting languages I should change it.
>> >>
>> > There's no problem with vectors in general; these are simply
>> > translated to lists by SWIG.
>> >
>> >
>> >> All three have a parameter which can control what is in the
>> output. For
>> >> example if it contains "verbose" it output the whole description, not
>> >> just the first line. So it would be easy to add code (4 extra
>> lines) to
>> >> output only the IDs if that would be useful:
>> >> ListAsVector("formats","in/ids", stringvector)
>> >>
>> >> Post-processing in pybel I'm sure is useful, but if the C++ code was
>> >> adequate it could serve other scripting languages as well.
>> >>
>> > I think so too. In the meanwhile, I would like to push out a Windows
>> > Python release based on 2.1.0 with the current pybel enhancements. I'm
>> > going to try to get this together this weekend and do some testing.
>> >
>> > Noel
>> >
>> >
>> >> Chris
>> >>
>> >> Noel O'Boyle wrote:
>> >>
>> >>> After looking at the C++ code, I realise that maybe returning a list
>> >>> of strings is the only choice for SupportedInputFormat. Anyway,
>> in the
>> >>> meanwhile I've added some code to pybel, so that if you access
>> >>> pybel.informats or outformats, you will get a dictionary of
>> supported
>> >>> formats.
>> >>>
>> >>> On 12/05/07, Noel O'Boyle <bao...@gm...> wrote:
>> >>>
>> >>>> Actually, a vector of std::strings had not yet been swigified, so I
>> >>>> needed to added to a line to openbabel-python.i to set it up
>> (not yet
>> >>>> checked in). However, there's an additional problem, which
>> Jerome may
>> >>>> like to address.
>> >>>>
>> >>>> The data that's returned is similar to:
>> >>>> ('acr -- ACR format [Read-only]', 'alc -- Alchemy format', ... )
>> >>>>
>> >>>> whereas it would make more sense to me either to return:
>> >>>> ('acr', 'alc', ...)
>> >>>> or
>> >>>> a std::map (i.e. a Python dict) of ['acr' : 'ACR format', 'alc':
>> >>>> 'Alchemy format']
>> >>>>
>> >>>> Note that the text [Read-only] is not really necessary in a list of
>> >>>> supported input formats.
>> >>>>
>> >>>> Since this function was added for the benefit of scripting
>> interfaces,
>> >>>> it makes sense to make it as easy as possible to access the list of
>> >>>> formats.
>> >>>>
>> >>>> Noel
>> >>>>
>> >>>> On 11/05/07, Noel O'Boyle <bao...@gm...> wrote:
>> >>>>
>> >>>>> Hello again Jens,
>> >>>>>
>> >>>>> Good to hear from you on this list... :-)
>> >>>>>
>> >>>>> On 10/05/07, Jens Thomas <j.m...@dl...> wrote:
>> >>>>>
>> >>>>>> Hi,
>> >>>>>>
>> >>>>>> I'm trying to enable our ccp1gui code
>> >>>>>> (http://sourceforge.net/projects/ccp1gui/) to use openbabel so
>> that we
>> >>>>>> no longer have to support so many formats.
>> >>>>>>
>> >>>>>> I've got most of the machinery in place, but am a bit stuck on
>> how to
>> >>>>>> dynamically determine what input formats are supported by
>> openbabel.
>> >>>>>>
>> >>>>>> I originally tried to use OBConversion.GetNextFormat, but ran
>> into the
>> >>>>>> ground fairly quickly. I then discovered the post at:
>> >>>>>>
>> >>>>>>
>> http://sourceforge.net/mailarchive/forum.php?thread_name=200702191105.25888.j.pansanel%40pansanel.net&forum_name=openbabel-scripting
>>
>> >>>>>>
>> >>>>>> which suggest that I should be able to get what I want using
>> >>>>>> GetSupportedInputFormat(), however, I'm currently pretty
>> clueless as to
>> >>>>>> how I extract the information from the object. I get something
>> back as
>> >>>>>> shown below, but I'd appreciated any advice on what I then
>> need to do
>> >>>>>> with it.
>> >>>>>>
>> >>
>> -------------------------------------------------------------------------
>>
>> >> This SF.net email is sponsored by DB2 Express
>> >> Download DB2 Express C - the FREE version of DB2 express and take
>> >> control of your XML. No limits. Just data. Click to get it now.
>> >> http://sourceforge.net/powerbar/db2/
>> >> _______________________________________________
>> >> OpenBabel-scripting mailing list
>> >> Ope...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> >>
>> >>
>> >
>> >
>> -------------------------------------------------------------------------
>>
>> > This SF.net email is sponsored by DB2 Express
>> > Download DB2 Express C - the FREE version of DB2 express and take
>> > control of your XML. No limits. Just data. Click to get it now.
>> > http://sourceforge.net/powerbar/db2/
>> > _______________________________________________
>> > OpenBabel-scripting mailing list
>> > Ope...@li...
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> >
>> >
>>
>>
>
|
|
From: David R. <tom...@gm...> - 2007-05-14 17:42:53
|
I obtained an older version of svn to try to exclude that as a possible explanation, and again tried configuring and making revision 1960. Outputs from configure and make are attached. Thanks again for your help. Dave. On 5/14/07, Geoffrey Hutchison <ge...@ge...> wrote: > > On May 14, 2007, at 10:30 AM, Noel O'Boyle wrote: > > > If any errors occur, please provide the first error messages rather > > than the tail end, as the real problem is usually described at the > > start. > > >> __ZN9OpenBabel8OBFormat14FormatFromMIMEEPKc > >> __ZN9OpenBabel8OBFormat14RegisterFormatEPKcS2_ > > Indeed, these are missing symbols during linking. So if there are > error messages earlier on, they'll certainly explain why these > symbols are missing. > > You may also be linking the newer SWIG code to an older libopenbabel, > which would also result in missing symbols. > > Cheers, > -Geoff > |
|
From: Chris M. <c.m...@ds...> - 2007-05-14 16:08:14
|
The new files are:
include/openbabel/descriptor.h, include/openbabel/format.h
include/openbabel/plugin.h, src/descriptor.cpp
src/filters.cpp, src/format.cpp, src/plugin.cpp
Removed file:
include/openbabel/pluginiter.h
Noel O'Boyle wrote:
> I think the Makefiles need to be updated. That is, there's been a
> pluginiter.h --> plugin.h transition. After installing automake-1.9
> and libtool, and editing a Makefile.am, it overwrites the Makefile.in,
> but the top level "make" just fails. This is possibly because the
> version of libtool I have access to is a couple of years out of date
> (1.5.6).
>
> Noel
>
> On 13/05/07, Noel O'Boyle <bao...@gm...> wrote:
>> On 12/05/07, Chris Morley <c.m...@ds...> wrote:
>> > In the revamped code for formats (and other plugins) recently committed
>> > to SVN HEAD (for the next OB version) I tried to maintain backward
>> > compatibility as far as possible. So
>> OBConversion::SupportedInputFormat()
>> > works as before but, you'll be pleased to hear, without the
>> '[Read-only]'.
>> Sounds good but SWIG doesn't like the new code. When I try to compile
>> openbabel_python.cpp, I get:
>>
>> ../../include/openbabel/fingerprint.h:48: error: 'static
>> std::map<const char*, OpenBabel::OBPlugin*,
>> OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const char*
>> const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()'
>> cannot be overloaded
>> ../../include/openbabel/fingerprint.h:43: error: with 'static
>> std::map<const char*, OpenBabel::OBPlugin*,
>> OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const char*
>> const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()'
>> ../../include/openbabel/fingerprint.h:53: error: 'static
>> OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()' cannot
>> be overloaded
>> ../../include/openbabel/fingerprint.h:43: error: with 'static
>> OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()'
>> ../../include/openbabel/fingerprint.h: In constructor
>> 'OpenBabel::OBFingerprint::OBFingerprint(std::string, bool)':
>> ../../include/openbabel/fingerprint.h:63: error: no match for
>> 'operator[]' in 'OpenBabel::OBFingerprint::Map()[ID]'
>> /usr/include/c++/4.0.2/bits/stl_map.h:331: note: candidates are: _Tp&
>> std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const _Key&) [with
>> _Key = const char*, _Tp = OpenBabel::OBPlugin*, _Compare =
>> OpenBabel::OBPlugin::CharPtrLess, _Alloc =
>> std::allocator<std::pair<const char* const, OpenBabel::OBPlugin*> >]
>>
>> > But in an effort to provide more choice on the form of the output,
>> there
>> > are three functions which provide a list of formats(or other plugin
>> > classes): OBPlugin::ListAsVector, ListAsString and List. The first two
>> > were intended to be compatible with scripting, although I need some
>> > advice here. ListAsString returns a (big) std::string, but ListAsVector
>> > has a parameter which is a reference to a std::vector. If this is
>> > incompatible with scripting languages I should change it.
>> There's no problem with vectors in general; these are simply
>> translated to lists by SWIG.
>>
>> > All three have a parameter which can control what is in the output. For
>> > example if it contains "verbose" it output the whole description, not
>> > just the first line. So it would be easy to add code (4 extra lines) to
>> > output only the IDs if that would be useful:
>> > ListAsVector("formats","in/ids", stringvector)
>> >
>> > Post-processing in pybel I'm sure is useful, but if the C++ code was
>> > adequate it could serve other scripting languages as well.
>> I think so too. In the meanwhile, I would like to push out a Windows
>> Python release based on 2.1.0 with the current pybel enhancements. I'm
>> going to try to get this together this weekend and do some testing.
>>
>> Noel
>>
>> > Chris
>> >
>> > Noel O'Boyle wrote:
>> > > After looking at the C++ code, I realise that maybe returning a list
>> > > of strings is the only choice for SupportedInputFormat. Anyway, in
>> the
>> > > meanwhile I've added some code to pybel, so that if you access
>> > > pybel.informats or outformats, you will get a dictionary of supported
>> > > formats.
>> > >
>> > > On 12/05/07, Noel O'Boyle <bao...@gm...> wrote:
>> > >> Actually, a vector of std::strings had not yet been swigified, so I
>> > >> needed to added to a line to openbabel-python.i to set it up (not
>> yet
>> > >> checked in). However, there's an additional problem, which Jerome
>> may
>> > >> like to address.
>> > >>
>> > >> The data that's returned is similar to:
>> > >> ('acr -- ACR format [Read-only]', 'alc -- Alchemy format', ... )
>> > >>
>> > >> whereas it would make more sense to me either to return:
>> > >> ('acr', 'alc', ...)
>> > >> or
>> > >> a std::map (i.e. a Python dict) of ['acr' : 'ACR format', 'alc':
>> > >> 'Alchemy format']
>> > >>
>> > >> Note that the text [Read-only] is not really necessary in a list of
>> > >> supported input formats.
>> > >>
>> > >> Since this function was added for the benefit of scripting
>> interfaces,
>> > >> it makes sense to make it as easy as possible to access the list of
>> > >> formats.
>> > >>
>> > >> Noel
>> > >>
>> > >> On 11/05/07, Noel O'Boyle <bao...@gm...> wrote:
>> > >>> Hello again Jens,
>> > >>>
>> > >>> Good to hear from you on this list... :-)
>> > >>>
>> > >>> On 10/05/07, Jens Thomas <j.m...@dl...> wrote:
>> > >>>> Hi,
>> > >>>>
>> > >>>> I'm trying to enable our ccp1gui code
>> > >>>> (http://sourceforge.net/projects/ccp1gui/) to use openbabel so
>> that we
>> > >>>> no longer have to support so many formats.
>> > >>>>
>> > >>>> I've got most of the machinery in place, but am a bit stuck on
>> how to
>> > >>>> dynamically determine what input formats are supported by
>> openbabel.
>> > >>>>
>> > >>>> I originally tried to use OBConversion.GetNextFormat, but ran
>> into the
>> > >>>> ground fairly quickly. I then discovered the post at:
>> > >>>>
>> > >>>>
>> http://sourceforge.net/mailarchive/forum.php?thread_name=200702191105.25888.j.pansanel%40pansanel.net&forum_name=openbabel-scripting
>>
>> > >>>>
>> > >>>> which suggest that I should be able to get what I want using
>> > >>>> GetSupportedInputFormat(), however, I'm currently pretty
>> clueless as to
>> > >>>> how I extract the information from the object. I get something
>> back as
>> > >>>> shown below, but I'd appreciated any advice on what I then need
>> to do
>> > >>>> with it.
>> >
>> >
>> >
>> -------------------------------------------------------------------------
>> > This SF.net email is sponsored by DB2 Express
>> > Download DB2 Express C - the FREE version of DB2 express and take
>> > control of your XML. No limits. Just data. Click to get it now.
>> > http://sourceforge.net/powerbar/db2/
>> > _______________________________________________
>> > OpenBabel-scripting mailing list
>> > Ope...@li...
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> >
>>
>
|
|
From: Noel O'B. <bao...@gm...> - 2007-05-14 15:50:23
|
I think the Makefiles need to be updated. That is, there's been a
pluginiter.h --> plugin.h transition. After installing automake-1.9
and libtool, and editing a Makefile.am, it overwrites the Makefile.in,
but the top level "make" just fails. This is possibly because the
version of libtool I have access to is a couple of years out of date
(1.5.6).
Noel
On 13/05/07, Noel O'Boyle <bao...@gm...> wrote:
> On 12/05/07, Chris Morley <c.m...@ds...> wrote:
> > In the revamped code for formats (and other plugins) recently committed
> > to SVN HEAD (for the next OB version) I tried to maintain backward
> > compatibility as far as possible. So OBConversion::SupportedInputFormat()
> > works as before but, you'll be pleased to hear, without the '[Read-only]'.
> Sounds good but SWIG doesn't like the new code. When I try to compile
> openbabel_python.cpp, I get:
>
> ../../include/openbabel/fingerprint.h:48: error: 'static
> std::map<const char*, OpenBabel::OBPlugin*,
> OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const char*
> const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()'
> cannot be overloaded
> ../../include/openbabel/fingerprint.h:43: error: with 'static
> std::map<const char*, OpenBabel::OBPlugin*,
> OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const char*
> const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()'
> ../../include/openbabel/fingerprint.h:53: error: 'static
> OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()' cannot
> be overloaded
> ../../include/openbabel/fingerprint.h:43: error: with 'static
> OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()'
> ../../include/openbabel/fingerprint.h: In constructor
> 'OpenBabel::OBFingerprint::OBFingerprint(std::string, bool)':
> ../../include/openbabel/fingerprint.h:63: error: no match for
> 'operator[]' in 'OpenBabel::OBFingerprint::Map()[ID]'
> /usr/include/c++/4.0.2/bits/stl_map.h:331: note: candidates are: _Tp&
> std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const _Key&) [with
> _Key = const char*, _Tp = OpenBabel::OBPlugin*, _Compare =
> OpenBabel::OBPlugin::CharPtrLess, _Alloc =
> std::allocator<std::pair<const char* const, OpenBabel::OBPlugin*> >]
>
> > But in an effort to provide more choice on the form of the output, there
> > are three functions which provide a list of formats(or other plugin
> > classes): OBPlugin::ListAsVector, ListAsString and List. The first two
> > were intended to be compatible with scripting, although I need some
> > advice here. ListAsString returns a (big) std::string, but ListAsVector
> > has a parameter which is a reference to a std::vector. If this is
> > incompatible with scripting languages I should change it.
> There's no problem with vectors in general; these are simply
> translated to lists by SWIG.
>
> > All three have a parameter which can control what is in the output. For
> > example if it contains "verbose" it output the whole description, not
> > just the first line. So it would be easy to add code (4 extra lines) to
> > output only the IDs if that would be useful:
> > ListAsVector("formats","in/ids", stringvector)
> >
> > Post-processing in pybel I'm sure is useful, but if the C++ code was
> > adequate it could serve other scripting languages as well.
> I think so too. In the meanwhile, I would like to push out a Windows
> Python release based on 2.1.0 with the current pybel enhancements. I'm
> going to try to get this together this weekend and do some testing.
>
> Noel
>
> > Chris
> >
> > Noel O'Boyle wrote:
> > > After looking at the C++ code, I realise that maybe returning a list
> > > of strings is the only choice for SupportedInputFormat. Anyway, in the
> > > meanwhile I've added some code to pybel, so that if you access
> > > pybel.informats or outformats, you will get a dictionary of supported
> > > formats.
> > >
> > > On 12/05/07, Noel O'Boyle <bao...@gm...> wrote:
> > >> Actually, a vector of std::strings had not yet been swigified, so I
> > >> needed to added to a line to openbabel-python.i to set it up (not yet
> > >> checked in). However, there's an additional problem, which Jerome may
> > >> like to address.
> > >>
> > >> The data that's returned is similar to:
> > >> ('acr -- ACR format [Read-only]', 'alc -- Alchemy format', ... )
> > >>
> > >> whereas it would make more sense to me either to return:
> > >> ('acr', 'alc', ...)
> > >> or
> > >> a std::map (i.e. a Python dict) of ['acr' : 'ACR format', 'alc':
> > >> 'Alchemy format']
> > >>
> > >> Note that the text [Read-only] is not really necessary in a list of
> > >> supported input formats.
> > >>
> > >> Since this function was added for the benefit of scripting interfaces,
> > >> it makes sense to make it as easy as possible to access the list of
> > >> formats.
> > >>
> > >> Noel
> > >>
> > >> On 11/05/07, Noel O'Boyle <bao...@gm...> wrote:
> > >>> Hello again Jens,
> > >>>
> > >>> Good to hear from you on this list... :-)
> > >>>
> > >>> On 10/05/07, Jens Thomas <j.m...@dl...> wrote:
> > >>>> Hi,
> > >>>>
> > >>>> I'm trying to enable our ccp1gui code
> > >>>> (http://sourceforge.net/projects/ccp1gui/) to use openbabel so that we
> > >>>> no longer have to support so many formats.
> > >>>>
> > >>>> I've got most of the machinery in place, but am a bit stuck on how to
> > >>>> dynamically determine what input formats are supported by openbabel.
> > >>>>
> > >>>> I originally tried to use OBConversion.GetNextFormat, but ran into the
> > >>>> ground fairly quickly. I then discovered the post at:
> > >>>>
> > >>>> http://sourceforge.net/mailarchive/forum.php?thread_name=200702191105.25888.j.pansanel%40pansanel.net&forum_name=openbabel-scripting
> > >>>>
> > >>>> which suggest that I should be able to get what I want using
> > >>>> GetSupportedInputFormat(), however, I'm currently pretty clueless as to
> > >>>> how I extract the information from the object. I get something back as
> > >>>> shown below, but I'd appreciated any advice on what I then need to do
> > >>>> with it.
> >
> >
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> >
>
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From: Geoffrey H. <ge...@ge...> - 2007-05-14 15:11:24
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On May 14, 2007, at 10:30 AM, Noel O'Boyle wrote: > If any errors occur, please provide the first error messages rather > than the tail end, as the real problem is usually described at the > start. >> __ZN9OpenBabel8OBFormat14FormatFromMIMEEPKc >> __ZN9OpenBabel8OBFormat14RegisterFormatEPKcS2_ Indeed, these are missing symbols during linking. So if there are error messages earlier on, they'll certainly explain why these symbols are missing. You may also be linking the newer SWIG code to an older libopenbabel, which would also result in missing symbols. Cheers, -Geoff |
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From: Noel O'B. <bao...@gm...> - 2007-05-14 14:30:14
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First of all, I've already noticed that the latest SVN is not compatible with SWIG due to changes introducted at r1954. You'll need to check out r1953 instead of the very latest one. Next, please ensure you follow the steps outlined at http://openbabel.sourceforge.net/wiki/Install_%28source_code%29 remembering to use "./configure --enable-maintainer-mode" as you will need to run SWIG yourself (which you will need to install first) to create the Python bindings. If any errors occur, please provide the first error messages rather than the tail end, as the real problem is usually described at the start. Noel On 14/05/07, David Rose <tom...@gm...> wrote: > I am having trouble getting this to work. I used SVN to get the new > version, but am unable to build it successfully; running make yields > the following error messages: > > __ZN9OpenBabel8OBFormat14FormatFromMIMEEPKc > __ZN9OpenBabel8OBFormat14RegisterFormatEPKcS2_ > __ZN9OpenBabel8OBPlugin12ListAsVectorEPKcS2_RSt6vectorISsSaISsEE > __ZN9OpenBabel12OBDescriptor13AddPropertiesEPNS_6OBBaseERKSs > __ZN9OpenBabel12OBDescriptor13FilterCompareEPNS_6OBBaseERSib > __ZN9OpenBabel12OBDescriptor16DeletePropertiesEPNS_6OBBaseERKSs > __ZN9OpenBabel12OBDescriptor14GetStringValueEPNS_6OBBaseERSs > __ZN9OpenBabel12OBDescriptor7CompareEPNS_6OBBaseERSib > __ZN9OpenBabel8OBPlugin7DisplayERSsPKcS3_ > __ZTIN9OpenBabel12OBDescriptorE > __ZTVN9OpenBabel12OBDescriptorE > __ZTVN9OpenBabel8OBPluginE > __ZTIN9OpenBabel8OBPluginE > /usr/bin/libtool: internal link edit command failed > make[3]: *** [libopenbabel.la] Error 1 > make[2]: *** [all-recursive] Error 1 > make[1]: *** [all] Error 2 > make: *** [all-recursive] Error 1 > > > I also tried (perhaps naively) just moving the new openbabel-perl.i > file to my version 2.1.0 source tree and rebuilt that, but it doesn't > seem to have worked either (no errors, but no new functionality > either). > > Can anyone offer suggestion? > > thanks, > Dave. > > > On 5/8/07, Noel O'Boyle <bao...@gm...> wrote: > > Your confusion is due to the fact that the Perl wrapper does not yet > > include a vector of OBRing*, which is what is returned by GetSSSR(). > > As a result, you currently can't do anything with the result from > > GetSSSR(). > > > > I'm just about to check in the appropriate fix to the development > > code, which is available through subversion (SVN) as described on the > > openbabel install page: > > http://openbabel.sourceforge.net/wiki/Install > > > > Once you have compiled and installed the latest code, the following > > code will work (it's in Python, but I'm sure you can figure it out): > > > > import pybel > > obmol = pybel.readstring("smi", "c1ccccc1").OBMol # Benzene > > vector_of_sssr = obmol.GetSSSR() > > print vector_of_sssr.size() # 1 > > obring = vector_of_sssr[0] > > print dir(obring) > > # GetParent, IsAromatic, IsInRing, IsMember, etc... > > > > Noel > > > > On 07/05/07, David Rose <tom...@gm...> wrote: > > > Hello: > > > > > > I am confused about the use, in Perl, of OBMol::getSSSR and OBRing. > > > I am trying to find the size of the largest ring returned by getSSSR. > > > I instantiate an OBMol, and the method getSSSR returns something, but > > > I am unsure what it is or what to do with it. I assume I can pass it > > > to OBRing->new() to get an OBRing object, and it looks like OBRing has > > > a method called 'size' which is what I want, but I wonder if anyone > > > can offer a snippet of sample code. Thanks for all the help, past and > > > future. > > > > > > David Rose. > > > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by DB2 Express > > > Download DB2 Express C - the FREE version of DB2 express and take > > > control of your XML. No limits. Just data. Click to get it now. > > > http://sourceforge.net/powerbar/db2/ > > > _______________________________________________ > > > OpenBabel-scripting mailing list > > > Ope...@li... > > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > > > > > |
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