From ragno@serifos.caspur.it Tue Apr 16 03:47:01 1996 Received: from serifos.caspur.it for ragno@serifos.caspur.it by www.ccl.net (8.7.1/950822.1) id DAA23164; Tue, 16 Apr 1996 03:43:31 -0400 (EDT) Received: by serifos.caspur.it; id AA22696; Tue, 16 Apr 1996 09:43:15 +0200 Date: Tue, 16 Apr 1996 09:43:15 +0200 (MET DST) From: Gianluca Sbardella To: chemistry@www.ccl.net Subject: CCL: other mail-lists (Summary) Message-Id: Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="0-2024729160-829640595=:22411" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --0-2024729160-829640595=:22411 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, in the attachment file you'll find an overview over most of the chemical mailing lists. I hope you'll find as useful as I did. Thanks to everyone who answered my question. Bye, gianluca ***************************************************************** * * * Dr. Gianluca Sbardella E-mail: ragno@kea.caspur.it * * Dip. Studi Farmaceutici ragno@serifos.caspur.it * * Universita' "La Sapienza" Phone: 39-6-49913814 * * P.le A. Moro, 5 Fax: 39-6-491491 * * 00185 Roma * * ITALY * ***************************************************************** --0-2024729160-829640595=:22411 Content-Type: TEXT/PLAIN; charset=US-ASCII; name="listserv.txt" Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: TGlzdHNlcnZlcywgRGlzY3Vzc2lvbiBMaXN0cywgYW5kIE5ld3Nncm91cHMg Zm9yIENoZW1pc3RyeQ0KDQpVcGRhdGVkIDI1IE5vdmVtYmVyIDE5OTUNCi0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0NCg0KRS1NYWlsIFNlcnZl cnMgQmFzZWQgb24gTElTVFNFUlYgYW5kIENvbXBhcmFibGUgU29mdHdhcmUN Cg0KTkI6IFRoZSBMaXN0V2ViYmVyIHNvZnR3YXJlIGNhbiBiZSB1c2VkIHRv IGNvbmR1Y3Qgc2VhcmNoZXMgb2YgbGlzdHMgdGhhdA0KYXJlIGJhc2VkIG9u IHRoZSBMSVNUU0VSViBzb2Z0d2FyZS4NCg0KQU1CRVIgaXMgYSBtYWlsIHJl ZmxlY3RvciBmb3IgdGhlIG1vbGVjdWxhciBtZWNoYW5pY3MgcHJvZ3JhbSBv ZiB0aGUgc2FtZQ0KbmFtZS4gVG8gc3Vic2NyaWJlLCBzZW5kIGEgcmVxdWVz dCB0bzogYW1iZXItcmVxdWVzdEBjZ2wudWNzZi5lZHUgb3INCmFtYmVyLXJl 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ckBpYy5hYy51ayBUaGVyZSBpcyBhbHNvIGFuIGFzc29jaWF0ZWQNCldvcmxk LVdpZGUgV2ViIHNlcnZlciwgd2hpY2ggY2FuIGJlIGFjY2Vzc2VkIGFzOg0K aHR0cDovL3d3dy5jaC5pYy5hYy51ay93YXRvYy5odG1sDQoNClhQTE9SLUws IERpc2N1c3Npb25zIG9mIFhwbG9yIFVzZXJzLiBNb2xlY3VsYXIgU2ltdWxh dGlvbnMgSW5jLidzIFgtUExPUiBpcw0KdGhlIHRvcGljIG9mIHRoZSBsaXN0 LiBUbyBzdWJzY3JpYmUsIHNlbmQgYSByZXF1ZXN0IHRvOiBsaXN0cHJvY0Bt c2kuY29tDQo= --0-2024729160-829640595=:22411-- From golb@osi.lanet.lv Tue Apr 16 05:46:57 1996 Received: from lnx.osi.lanet.lv for golb@osi.lanet.lv by www.ccl.net (8.7.1/950822.1) id EAA24241; Tue, 16 Apr 1996 04:54:52 -0400 (EDT) Received: from localhost (golb@localhost) by lnx.osi.lanet.lv (8.7.5/8.7.3) with SMTP id LAA20395; Tue, 16 Apr 1996 11:50:50 +0300 (DST) Date: Tue, 16 Apr 1996 11:50:50 +0300 (DST) From: Alexander Golbraikh Reply-To: Alexander Golbraikh To: Robert Fraczkiewicz cc: chemistry@www.ccl.net Subject: Re: CCL:Inside or outside of a polyhedron In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 15 Apr 1996, Robert Fraczkiewicz wrote: > > Dear Netters, > > Suppose you have given N arbitrary points (in 3D space) that are vertices > of a polyhedron: (x1,y1,z1),.....,(xN,yN,zN). What is the fastest > algorithm for determining if a given point (x,y,z) is inside or outside of > this polyhedron? (Calculating distances to every vertex is not a good > idea). I will post summary to the net. > > Best regards, > > Robert Fraczkiewicz > UT Medical Branch > > Take any ray beginning at the given point. Count the number of points of intersection of this ray with polyhedron surface. If it is even, then the point is outside the polyhedron, if it is odd, then inside. One precaution: the ray may slide on some edges of the polyhedron. Best regards, Alexander Golbraikh ------------------------------------------------------------------------ Dr. Alexander Golbraikh e-mail: golb@osi.lanet.lv Latvian Institute of Organic Synthesis Aizkraukles st. 21 Phone: +(371)-7-552-354 Riga, LV-1006 FAX: +(371)-7-821-038 LATVIA ------------------------------------------------------------------------ From brian@bert.chem.wsu.edu Tue Apr 16 11:47:08 1996 Received: from cheetah.it.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.7.1/950822.1) id LAA02042; Tue, 16 Apr 1996 11:41:33 -0400 (EDT) Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.6.13/WSUit-1.1) with SMTP id IAA25464; Tue, 16 Apr 1996 08:41:20 -0700 Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA22114; Tue, 16 Apr 1996 08:35:45 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9604161535.AA22114@bert.chem.wsu.edu> Subject: Re: CCL:Inside or outside of a polyhedron To: golb@osi.lanet.lv Date: Tue, 16 Apr 1996 08:35:45 -0700 (PDT) Cc: chemistry@www.ccl.net In-Reply-To: from "Alexander Golbraikh" at Apr 16, 96 11:50:50 am X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Alexander Golbraikh wrote: : : : : Take any ray beginning at the given point. Count the number of : points of intersection of this ray with polyhedron surface. If it is : even, then the point is outside the polyhedron, if it is odd, then inside. : One precaution: the ray may slide on some edges of the polyhedron. : : Best regards, : Alexander Golbraikh : : ^ / |/ < As you say, the ray may slide. The "o" point at the left is |\ outside the "polyhedron" yet passes through the polyhedron | \ surface only once if you send the ray only through the vertices o \ defined by... say the Calphas of a protein. -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | || Biochem/Biophysics | brian@bert.chem.wsu.edu | || \\ WSU || Washington St. Univ| brian_beck@wsu.edu | |\ - *|| 206 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA, USA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= From ragno@serifos.caspur.it Tue Apr 16 12:47:06 1996 Received: from serifos.caspur.it for ragno@serifos.caspur.it by www.ccl.net (8.7.1/950822.1) id MAA02682; Tue, 16 Apr 1996 12:16:16 -0400 (EDT) Received: by serifos.caspur.it; id AA24480; Tue, 16 Apr 1996 18:15:59 +0200 Date: Tue, 16 Apr 1996 18:15:59 +0200 (MET DST) From: Gianluca Sbardella To: chemistry@www.ccl.net Subject: CCL: MAILIG LISTS (again ?!) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi again, I already sent a CCL message with the list in ASCII format. Anyway, if anybody didn't receive it, please write me back and I'll send him (or her) again. What can I say? I'M REALLY SORRY !! bye, Gianluca ***************************************************************** * * * Dr. Gianluca Sbardella E-mail: ragno@kea.caspur.it * * Dip. Studi Farmaceutici ragno@serifos.caspur.it * * Universita' "La Sapienza" Phone: 39-6-49913814 * * P.le A. Moro, 5 Fax: 39-6-491491 * * 00185 Roma * * ITALY * ***************************************************************** From owner-chemistry@ccl.net Tue Apr 16 13:47:01 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id NAA04301; Tue, 16 Apr 1996 13:26:42 -0400 (EDT) Received: from MOLENG.UCSC.EDU for wipke@SECS.UCSC.EDU by bedrock.ccl.net (8.7.1/950822.1) id NAA01109; Tue, 16 Apr 1996 13:26:36 -0400 (EDT) Received: by SECS.UCSC.EDU (MX V3.1C) id 11292; Tue, 16 Apr 1996 10:24:42 PDT Date: Tue, 16 Apr 1996 10:24:37 PDT From: "W. Todd Wipke" To: chemistry@ccl.net Message-ID: <009A0F07.60966DE0.11292@SECS.UCSC.EDU> Subject: CCL:Inside or outside of a polyhedron There are a few quick checks: If the x coords of all vertices are all less than or all greater than the x coord of the pt, then the point must be outside. Similarly for y and z. Find the center of an enclosing sphere for the polyhedron. If the point is outside the enclosing sphere, then it is outside the polyhedron. Find the center of a maximal enclosed sphere for the polyhedron. If the point is inside the enclosed sphere, then it must be inside the polyhedron. There is also the scheme of shooting out a ray from the point. If it crosses the polyhedron surface an odd number of times, then it is inside, if an even number of times, then it is outside. -Todd Wipke Molecular Engineering Laboratory University of California Santa Cruz, CA wipke@chemistry.ucsc.edu From pueyo@pinon.ccu.uniovi.es Tue Apr 16 14:47:01 1996 Received: from opalo.etsiig.uniovi.es for pueyo@pinon.ccu.uniovi.es by www.ccl.net (8.7.1/950822.1) id OAA05581; Tue, 16 Apr 1996 14:42:02 -0400 (EDT) Received: from pinon.ccu.uniovi.es (pinon.ccu.uniovi.es) by etsiig.uniovi.es (PMDF V5.0-7 #4541) id <01I3LXEK0B3M985FSU@etsiig.uniovi.es>; Tue, 16 Apr 1996 12:07:15 +0100 (GMT) Received: by pinon.ccu.uniovi.es (1.39.111.2/16.2) id AA202359582; Tue, 16 Apr 1996 12:13:02 +0200 Date: Tue, 16 Apr 1996 12:13:02 +0200 From: pueyo@pinon.ccu.uniovi.es (Lorenzo Pueyo) Subject: Re: CCL:Inside or outside of a polyhedron To: chemistry-request@www.ccl.net, chemistry@www.ccl.net Message-id: <01I3LXELDC3O985FSU@etsiig.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=X-iso88591 Content-transfer-encoding: 7bit Robert Fraczkiewicz wrote: >Dear Netters, >Suppose you have given N arbitrary points (in 3D space) that are vertices >of a polyhedron: (x1,y1,z1),.....,(xN,yN,zN). What is the fastest >algorithm for determining if a given point (x,y,z) is inside or outside of >this polyhedron? (Calculating distances to every vertex is not a good >idea). I will post summary to the net. You can find a long answer in the comp.graphics.algorithm FAQ archived at: http://www.cis.ohio-state.edu/hypertext/faq/usenet/graphics/algorithms-faq/faq.html In any case: 1) If your polyhedron is convex, it is very efficient to have determined the Ax+By+Cz+D=0 plane equation for each face with the sign convention, for instance, that all points lying in the 'inside' hemi-space are positive (i.e. A x0 + B y0 + C z0 + D > 0). In that case, checking if a new point is inside or outside is just a question of substituting the cartesian coordinates of the point in the plane equations of every face and testing whether all signs are positive or there is one or more negative. 2) No matter if your polyhedron is convex or not, an inside point is such that every ray that begins in the point will intersect the polyhedron faces an odd number of times. Given a new point, you can always decide an arbitrary direction and check for the intersections of the line with the polyhedron faces. If there is zero or an even number of intersections, your point is outside the polyhedron, otherwise it is inside. Hope this helps you. Sincerely, Victor Lua~na -- HomePage http://www.uniovi.es/~quimica.fisica/qcg/vlc/luana.html +--------------------------------------------+ +---^---/ / ! Victor Lua~na ! | ~ / Just in case ! Departamento de Quimica Fisica y Analitica ! | | you don't ! Universidad de Oviedo, 33006-Oviedo, Spain ! < / remember ! e-mail: victor@carbono.quimica.uniovi.es ! | / where Oviedo ! phone: (34)-8-5103491 ! |____ ___/ is ;-) ! fax: (34)-8-5103125 ! \/ +--------------------------------------------+ From owner-chemistry@ccl.net Tue Apr 16 16:47:02 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id QAA06941; Tue, 16 Apr 1996 16:32:41 -0400 (EDT) Received: from che.udel.edu for kotelyan@che.udel.edu by bedrock.ccl.net (8.7.1/950822.1) id QAA05963; Tue, 16 Apr 1996 16:32:37 -0400 (EDT) Received: by che.udel.edu (AIX 3.2/UCB 5.64/4.03) id AA66725; Tue, 16 Apr 1996 16:32:17 -0400 Date: Tue, 16 Apr 1996 16:19:44 +22305133 (EDT) From: Michael Kotelyanskii Subject: Re: CCL:Inside or outside of a polyhedron To: "W. Todd Wipke" Cc: chemistry@ccl.net In-Reply-To: <009A0F07.60966DE0.11292@SECS.UCSC.EDU> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII OK, here is another one: 1) Make a Delone tesselation for the polyhedron vortices. If it is convex, all Delone simplexes (tetrahedra) are inside the polyhedron. In this case if your point is inside of any of the simplexes (simplex is a tetrahedron - so check is simple (center of tetrahedron is always inside, connect center with your point and see wether the border is crossed) it is inside polyhedron. If polyhedron is not convex, there will be Delone simplexes connecting vortices which are entirely outside the polyhedron, and they can be excluded I believe it should work Mike Michael Kotelyanskii PhD Department of Chemical Engineering University of Delaware kotelyan@che.udel.edu Newark DE 19716 From owner-chemistry@ccl.net Tue Apr 16 17:47:04 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id QAA07102; Tue, 16 Apr 1996 16:53:09 -0400 (EDT) Received: from cbdcom.apgea.army.mil for grfamini@cbdcom.apgea.army.mil by bedrock.ccl.net (8.7.1/950822.1) id QAA06186; Tue, 16 Apr 1996 16:52:08 -0400 (EDT) Received: by cbdcom.apgea.army.mil id aa16328; 16 Apr 96 16:44 EDT Date: Tue, 16 Apr 96 15:11:37 EDT From: George R Famini To: chemistry@ccl.net Subject: COMP Abstracts due Organization: Division of Computers in Chemistry Priority: Urgent!!! Message-ID: <9604161511.aa16001@cbdcom.apgea.army.mil> This is a gentle reminder to all those people planning to submit abstracts to the Division of Computers in Chemistry for the upcoming American Chemical Society Meeting in Orlando. Abstracts are due to the symposia organizers or to me (for posters and general oral) by 19 April. Although I do have some leeway programmed in, there is not that much, so if you are planning to submit an abstract, please do so now. As always, abstracts submitted after the deadline may or may not be accepted (although I make every effort to accept, there are instances where this is just not possible). Plus, submitting close to my deadline to ACS places an enormous burden on the Program Chair (me). So, please get your abstracts to me this week if at all possible. I prefer abstracts fedexed, but if this creates a problem please contact me by email or fax (do not send the abstract that way, in either case it will require retyping by my overworked secretary). George R. Famini COMP Program Chair From jkl@ccl.net Tue Apr 16 22:47:23 1996 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.7.1/950822.1) id WAA10749; Tue, 16 Apr 1996 22:28:31 -0400 (EDT) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.7.1/950822.1) id WAA10165; Tue, 16 Apr 1996 22:28:23 -0400 (EDT) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id WAA02519; Tue, 16 Apr 1996 22:28:19 -0400 Date: Tue, 16 Apr 1996 22:28:19 -0400 Message-Id: <199604170228.WAA02519@krakow.ccl.net> To: chemistry@www.ccl.net Subject: List of Electronic lists Cc: jkl@ccl.net Dear Netters, In the CCL archives I keep a list of electronic lists (as an update to the one published in Steven Bachrach's "The Internet. A Guide for Chemists") I also saved there a list of lists sent in MIME encoded format by Dr. Gianluca Sbardella under listserv.lists There are also pointers to other lists there. To access this information use Web/gopher/ftp: gopher://www.ccl.net:73/11/info/electronic-lists ftp://www.ccl.net/pub/chemistry/info/electronic-lists or you can retrieve files by e-mail. Start from sending: select chemistry cd info/electronic-lists dir help quit to MAILSERV@www.ccl.net Jan Labanowski jkl@ccl.net >From owner-chemistry@ccl.net Mon Apr 15 10:14 EDT 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id KAA12637; Mon, 15 Apr 1996 10:14:46 -0400 (EDT) Received: from infoc3.icas.ac.cn for guojx@infoc3.icas.ac.cn by bedrock.ccl.net (8.7.1/950822.1) id KAA07856; Mon, 15 Apr 1996 10:14:42 -0400 (EDT) Received: (from guojx@localhost) by infoc3.icas.ac.cn (8.6.9/8.6.9) id WAA02724; Mon, 15 Apr 1996 22:01:58 +0900 Date: Mon, 15 Apr 1996 22:01:58 +0900 From: Guo Jian-xin Subject: Get the mm2(3) free software To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 305 Status: RO Dear Netters, I am sorry that I maybe give a old question on the list. I would like to do some work which need the opt. structure of the MM2 (or MM3). I need to know how and where can i get the free software? any suggestion will be appraciated highly, thanks in advances, Sincerely, Guo, Jian-xin >From siroiss@CHIMCN.UMontreal.CA Tue Apr 16 20:43 EDT 1996 Received: from harfang.CC.UMontreal.CA for siroiss@CHIMCN.UMontreal.CA by www.ccl.net (8.7.1/950822.1) id UAA09086; Tue, 16 Apr 1996 20:43:11 -0400 (EDT) Received: from chims1.CHIMCN.UMontreal.CA (chims1.CHIMCN.UMontreal.CA [132.204.11.106]) by harfang.CC.UMontreal.CA with ESMTP id UAA23935 (8.6.11/IDA-1.6 for ); Tue, 16 Apr 1996 20:41:40 -0400 Received: by chims1.CHIMCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id UAA22683; Tue, 16 Apr 1996 20:44:06 -0400 From: siroiss@CHIMCN.UMontreal.CA (Sirois Suzanne) Message-Id: <199604170044.UAA22683@chims1.CHIMCN.UMontreal.CA> Subject: cyclodextrin complexes To: CHEMISTRY@www.ccl.net Date: Tue, 16 Apr 1996 20:44:06 -0400 (EDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Content-Length: 233 Status: R Dear Netters, I'm looking for crystal structures of alpha-Cyclodextrin complexes. Is anyone can give relevant information where I can find them free. Thank's in advance, S Sirois e-mail: siroiss@chimcn.umontreal.ca >From thomas_w@btm2x2.mat.uni-bayreuth.de Tue Apr 16 03:12 EDT 1996 Received: from btr0x1.hrz.uni-bayreuth.de for thomas_w@btm2x2.mat.uni-bayreuth.de by www.ccl.net (8.7.1/950822.1) id DAA22986; Tue, 16 Apr 1996 03:12:05 -0400 (EDT) Received: from btm2x2.mat.uni-bayreuth.de by btr0x1.hrz.uni-bayreuth.de (4.1/btr0x1 (UBTGW/btr0x1-2.4.7)) id AA11010; Tue, 16 Apr 96 09:11:54 +0200 Received: by btm2x2.mat.uni-bayreuth.de (4.1/SMI-4.1) id AA04233; Tue, 16 Apr 96 09:07:41 +0200 Date: Tue, 16 Apr 96 09:07:41 +0200 From: thomas_w@btm2x2.mat.uni-bayreuth.de (Thomas Wieland) Message-Id: <9604160707.AA04233@btm2x2.mat.uni-bayreuth.de> To: chemistry@www.ccl.net Subject: Detection of ring penetrations Content-Type: text Content-Length: 1394 Status: R Dear list subscribers, I would like to ask you for your help on the following topic: Given a three-dimensional representation of a molecule (e.g. cartesian coordinates), we want to determine if there are penetrations, i.e. bonds (or paths of bonds) that go through a ring of the molecule such that two rings are linked to each other or a ligand chain penetrates a ring. Does anybody know anything about some literature on this problem or are there even programs or code fragments (preferably with free source code) out there which can compute it? Any help is appreciated. I know that this rather geometrical problem is not too difficult -but I don't have the time to figure it out myself so that I have to pass it to a student who - as usual - needs to know the whole story before he is willing to commence. Many thanks and best regards, T. Wieland ----------------------------------------------------------------------------- Thomas Wieland Dipl. Math. 95440 Bayreuth, Germany Lehrstuhl II f. Mathematik Tel. +49 (921) 553386 Universitaet Bayreuth Fax +49 (921) 553385 ----------------------------------------------------------------------------- **** Do you know MOLGEN? **** http://btm2xd.mat.uni-bayreuth.de/molgen ****